=>> Building biology/artemis build started at Fri Mar 13 14:46:28 EDT 2026 port directory: /usr/ports/biology/artemis package name: artemis-17.0.1.11_1 building for: FreeBSD pkg.DaveG.ca 14.4-RELEASE FreeBSD 14.4-RELEASE 1404000 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1431 Mar 6 20:23 /usr/ports/biology/artemis/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: 2baaf1637579 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 07 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE 1404000 UNAME_r=14.4-RELEASE BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_4_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/artemis/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/artemis/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/artemis/work/.cache HOME=/wrkdirs/usr/ports/biology/artemis/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/artemis/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/artemis/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/artemis/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/artemis/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/artemis/work/.cache HOME=/wrkdirs/usr/ports/biology/artemis/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/artemis/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/artemis/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTVERSION="17.0.1.11" JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=14.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/artemis" EXAMPLESDIR="share/examples/artemis" DATADIR="share/artemis" WWWDIR="www/artemis" ETCDIR="etc/artemis" --End PLIST_SUB-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/artemis DOCSDIR=/usr/local/share/doc/artemis EXAMPLESDIR=/usr/local/share/examples/artemis WWWDIR=/usr/local/www/artemis ETCDIR=/usr/local/etc/artemis --End SUB_LIST-- ---Begin make.conf--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 8192 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> artemis-17.0.1.11_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> artemis-17.0.1.11_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of artemis-17.0.1.11_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by artemis-17.0.1.11_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by artemis-17.0.1.11_1 for building => SHA256 Checksum OK for sanger-pathogens-artemis-v17.0.1-11-g3e43d27e_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by artemis-17.0.1.11_1 for building ===> Extracting for artemis-17.0.1.11_1 => SHA256 Checksum OK for sanger-pathogens-artemis-v17.0.1-11-g3e43d27e_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for artemis-17.0.1.11_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> artemis-17.0.1.11_1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> artemis-17.0.1.11_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of artemis-17.0.1.11_1 ===> artemis-17.0.1.11_1 depends on file: /usr/local/openjdk21/bin/java - not found ===> Installing existing package /packages/All/openjdk21-21.0.10+7.1_1.pkg [pkg.DaveG.ca] Installing openjdk21-21.0.10+7.1_1... [pkg.DaveG.ca] `-- Installing alsa-lib-1.2.15.3... [pkg.DaveG.ca] `-- Extracting alsa-lib-1.2.15.3: .......... done [pkg.DaveG.ca] `-- Installing fontconfig-2.17.1,1... [pkg.DaveG.ca] | `-- Installing expat-2.7.4... [pkg.DaveG.ca] | `-- Extracting expat-2.7.4: .......... done [pkg.DaveG.ca] | `-- Installing freetype2-2.14.1... [pkg.DaveG.ca] | | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | | `-- Installing png-1.6.55... [pkg.DaveG.ca] | | `-- Extracting png-1.6.55: .......... done [pkg.DaveG.ca] | `-- Extracting freetype2-2.14.1: .......... done [pkg.DaveG.ca] `-- Extracting fontconfig-2.17.1,1: .......... done [pkg.DaveG.ca] `-- Installing giflib-5.2.2... [pkg.DaveG.ca] `-- Extracting giflib-5.2.2: .......... done [pkg.DaveG.ca] `-- Installing harfbuzz-12.3.2... [pkg.DaveG.ca] | `-- Installing glib-2.84.4,2... [pkg.DaveG.ca] | | `-- Installing libffi-3.5.1... [pkg.DaveG.ca] | | `-- Extracting libffi-3.5.1: .......... done [pkg.DaveG.ca] | | `-- Installing libiconv-1.18_1... [pkg.DaveG.ca] | | `-- Extracting libiconv-1.18_1: .......... done [pkg.DaveG.ca] | | `-- Installing libinotify-20240724_3... [pkg.DaveG.ca] | | `-- Extracting libinotify-20240724_3: .......... done [pkg.DaveG.ca] | | `-- Installing pcre2-10.47_1... [pkg.DaveG.ca] | | `-- Extracting pcre2-10.47_1: .......... done [pkg.DaveG.ca] | | `-- Installing py311-packaging-26.0... [pkg.DaveG.ca] | | `-- Installing python311-3.11.15... [pkg.DaveG.ca] | | | `-- Installing mpdecimal-4.0.1... [pkg.DaveG.ca] | | | `-- Extracting mpdecimal-4.0.1: .......... done [pkg.DaveG.ca] | | | `-- Installing readline-8.3.3... [pkg.DaveG.ca] | | | `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] | | `-- Extracting python311-3.11.15: .......... done [pkg.DaveG.ca] | | `-- Extracting py311-packaging-26.0: .......... done [pkg.DaveG.ca] | `-- Extracting glib-2.84.4,2: .......... done [pkg.DaveG.ca] | `-- Installing graphite2-1.3.14... [pkg.DaveG.ca] | `-- Extracting graphite2-1.3.14: .......... done [pkg.DaveG.ca] `-- Extracting harfbuzz-12.3.2: .......... done [pkg.DaveG.ca] `-- Installing javavmwrapper-2.7.10_1... [pkg.DaveG.ca] `-- Extracting javavmwrapper-2.7.10_1: .......... done [pkg.DaveG.ca] `-- Installing jpeg-turbo-3.1.3... [pkg.DaveG.ca] `-- Extracting jpeg-turbo-3.1.3: .......... done [pkg.DaveG.ca] `-- Installing lcms2-2.18... [pkg.DaveG.ca] | `-- Installing tiff-4.7.1... [pkg.DaveG.ca] | | `-- Installing jbigkit-2.1_3... [pkg.DaveG.ca] | | `-- Extracting jbigkit-2.1_3: .......... done [pkg.DaveG.ca] | | `-- Installing lerc-4.0.0... [pkg.DaveG.ca] | | `-- Extracting lerc-4.0.0: ..... done [pkg.DaveG.ca] | | `-- Installing libdeflate-1.25... [pkg.DaveG.ca] | | `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | `-- Extracting tiff-4.7.1: .......... done [pkg.DaveG.ca] `-- Extracting lcms2-2.18: .......... done [pkg.DaveG.ca] `-- Installing libX11-1.8.12,1... [pkg.DaveG.ca] | `-- Installing libxcb-1.17.0... [pkg.DaveG.ca] | | `-- Installing libXau-1.0.12... [pkg.DaveG.ca] | | `-- Extracting libXau-1.0.12: .......... done [pkg.DaveG.ca] | | `-- Installing libXdmcp-1.1.5... [pkg.DaveG.ca] | | `-- Installing xorgproto-2024.1... [pkg.DaveG.ca] | | `-- Extracting xorgproto-2024.1: .......... done [pkg.DaveG.ca] | | `-- Extracting libXdmcp-1.1.5: ...... done [pkg.DaveG.ca] | `-- Extracting libxcb-1.17.0: .......... done [pkg.DaveG.ca] `-- Extracting libX11-1.8.12,1: .......... done [pkg.DaveG.ca] `-- Installing libXext-1.3.6,1... [pkg.DaveG.ca] `-- Extracting libXext-1.3.6,1: .......... done [pkg.DaveG.ca] `-- Installing libXi-1.8.2,1... [pkg.DaveG.ca] | `-- Installing libXfixes-6.0.1... [pkg.DaveG.ca] | `-- Extracting libXfixes-6.0.1: ....... done [pkg.DaveG.ca] `-- Extracting libXi-1.8.2,1: .......... done [pkg.DaveG.ca] `-- Installing libXrandr-1.5.4... [pkg.DaveG.ca] | `-- Installing libXrender-0.9.12... [pkg.DaveG.ca] | `-- Extracting libXrender-0.9.12: ....... done [pkg.DaveG.ca] `-- Extracting libXrandr-1.5.4: .......... done [pkg.DaveG.ca] `-- Installing libXt-1.3.0,1... [pkg.DaveG.ca] | `-- Installing libICE-1.1.2,1... [pkg.DaveG.ca] | `-- Extracting libICE-1.1.2,1: .......... done [pkg.DaveG.ca] | `-- Installing libSM-1.2.6,1... [pkg.DaveG.ca] | `-- Extracting libSM-1.2.6,1: ........ done [pkg.DaveG.ca] `-- Extracting libXt-1.3.0,1: .......... done [pkg.DaveG.ca] `-- Installing libXtst-1.2.5... [pkg.DaveG.ca] `-- Extracting libXtst-1.2.5: .......... done [pkg.DaveG.ca] `-- Installing xorg-fonts-truetype-7.7_1... [pkg.DaveG.ca] | `-- Installing dejavu-2.37_4... [pkg.DaveG.ca] | | `-- Installing mkfontscale-1.2.3... [pkg.DaveG.ca] | | `-- Installing libfontenc-1.1.8... [pkg.DaveG.ca] | | `-- Extracting libfontenc-1.1.8: ...... done [pkg.DaveG.ca] | | `-- Extracting mkfontscale-1.2.3: .... done [pkg.DaveG.ca] | `-- Extracting dejavu-2.37_4: .......... done [pkg.DaveG.ca] | `-- Installing encodings-1.1.0,1... [pkg.DaveG.ca] | `-- Extracting encodings-1.1.0,1: .......... done [pkg.DaveG.ca] | `-- Installing font-bh-ttf-1.0.3_5... [pkg.DaveG.ca] | `-- Extracting font-bh-ttf-1.0.3_5: .......... done [pkg.DaveG.ca] | `-- Installing font-misc-ethiopic-1.0.4... [pkg.DaveG.ca] | `-- Extracting font-misc-ethiopic-1.0.4: ... done [pkg.DaveG.ca] | `-- Installing font-misc-meltho-1.0.3_5... [pkg.DaveG.ca] | `-- Extracting font-misc-meltho-1.0.3_5: .......... done [pkg.DaveG.ca] Extracting openjdk21-21.0.10+7.1_1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ==> Running trigger: gio-modules.ucl Generating GIO modules cache ==> Running trigger: glib-schemas.ucl Compiling glib schemas No schema files found: doing nothing. ===== Message from freetype2-2.14.1: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===== Message from libinotify-20240724_3: -- You might want to consider increasing the kern.maxfiles tunable if you plan to use this library for applications that need to monitor activity of a lot of files. ===== Message from python311-3.11.15: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===== Message from openjdk21-21.0.10+7.1_1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===> artemis-17.0.1.11_1 depends on file: /usr/local/openjdk21/bin/java - found ===> Returning to build of artemis-17.0.1.11_1 ===> artemis-17.0.1.11_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> artemis-17.0.1.11_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of artemis-17.0.1.11_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for artemis-17.0.1.11_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for artemis-17.0.1.11_1 CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Action.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ActionController.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ActionVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/AlignMatch.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/AlignMatchVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/AlignmentSelectionChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/AlignmentSelectionChangeListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/BlastM8ComparisonData.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ChangeEventVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ChangeListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ClipBoard.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ComparisonData.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ComparisonDataFactory.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ComparisonDataParseException.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Entry.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntryChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntryChangeListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntryGroup.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntryGroupChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntryGroupChangeListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntrySource.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntrySourceVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntryVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgram.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramException.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramMonitor.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramThread.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Feature.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureChangeListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureEnumeration.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureFromVectorPredicate.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureKeyPredicate.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureKeyQualifierPredicate.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeaturePatternPredicate.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeaturePredicate.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeaturePredicateConjunction.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeaturePredicateVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureSegment.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureSegmentVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FilteredEntryGroup.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/GotoEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/GotoEventSource.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/GotoListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/LastSegmentException.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Logger.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/MSPcrunchComparisonData.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/MUMmerComparisonData.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/MegaBlastComparisonData.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/OptionChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/OptionChangeListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Options.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ProcessMonitor.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/SSAHAComparisonData.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Selectable.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Selection.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/SelectionChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/SelectionChangeListener.java warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/SimpleComparisonData.java warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] target value 8 is obsolete and will be removed in a future release Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/SimpleEntryGroup.java ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ 4 warnings ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 11 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/SimpleExternalProgramMonitor.java warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/SimpleGotoEventSource.java 4 warnings 4 warnings 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/ArtemisUtils.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/ChadoCvTermView.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/ChadoDAO.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/ChadoDemo.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/ChadoTransaction.java ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ 4 warnings ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. Note: ./uk/ac/sanger/artemis/util/FastVector.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 11 warnings 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/ChadoTransactionManager.java ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/CommitFrame.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/DbSqlConfig.java ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/FeatureForUpdatingResidues.java warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. Note: ./uk/ac/sanger/artemis/util/FastVector.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 11 warnings ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. Note: ./uk/ac/sanger/artemis/util/FastVector.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 11 warnings warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. Note: ./uk/ac/sanger/artemis/SimpleExternalProgramMonitor.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 5 warnings 4 warnings warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/GmodDAO.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/Graph.java Note: uk/ac/sanger/artemis/ChangeEventVector.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/IBatisDAO.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/JdbcDAO.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/Block.java warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/BlockComparator.java warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: uk/ac/sanger/artemis/SimpleExternalProgramMonitor.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/DNADraw.java 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 6 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/Feature.java warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/GCGraph.java warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/GCSkewGraph.java Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/GeneticMarker.java Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:69: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:69: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:70: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(null); ^ uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:72: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:146: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal Integer bstart = new Integer((String)stok.nextElement()); ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:147: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal Integer bend = new Integer((String)stok.nextElement()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:160: warning: [removal] Float(float) in Float has been deprecated and marked for removal marker.add(new Float(10.f)); ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:161: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal marker.add(new Boolean(false)); ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:162: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal marker.add(new Boolean(false)); ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:170: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal Integer pos = new Integer((String)stok.nextElement()); ^ ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ Note: uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 14 warnings ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/Graph.java ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/FeatureVector.java:167: error: cannot access ExternalProgramException bad class file: ./uk/ac/sanger/artemis/ExternalProgramException.class class file truncated at offset 0 Please remove or make sure it appears in the correct subdirectory of the classpath. ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:174: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(0)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:175: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ lineAttr.put("end",new Integer(4000)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:177: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(true)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:724: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:739: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal majorTicks.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/FeatureSegmentVector.java:31: error: cannot access FastVector import uk.ac.sanger.artemis.util.FastVector; ^ bad class file: ./uk/ac/sanger/artemis/util/FastVector.class class file truncated at offset 0 Please remove or make sure it appears in the correct subdirectory of the classpath. ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/FeatureVector.java:165: error: cannot find symbol private FastVector vector = new FastVector (); ^ symbol: class FastVector location: class FeatureVector ./uk/ac/sanger/artemis/FeatureSegmentVector.java:46: error: cannot find symbol private FastVector vector = new FastVector (); ^ symbol: class FastVector location: class FeatureSegmentVector ./uk/ac/sanger/artemis/io/KeyVector.java:37: error: cannot find symbol public class KeyVector extends FastVector ^ symbol: class FastVector ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); return new Character (current_char); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ featureloc.setPhase(new Integer(1)); ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal ^ read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java:40: error: cannot access CvTerm import java.util.Enumeration; ^ bad class file: ./org/gmod/schema/cv/CvTerm.class class file truncated at offset 9 Please remove or make sure it appears in the correct subdirectory of the classpath. final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransaction.java:205: error: cannot find symbol symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransaction.java:205: error: cannot find symbol symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransaction.java:205: error: cannot find symbol symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:103: error: cannot find symbol private static Hashtable cvterms; ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); fasta_header_positions.remove(new Integer(nbase)); ^ ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1816: error: cannot find symbol private static CvTerm getCvTerm(final int id, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1833: error: cannot find symbol public static CvTerm getCvTermByCvTermName(final String cvterm_name) ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1851: error: cannot find symbol public static CvTerm getCvTermByCvTermId(final int cvTermId, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1889: error: cannot find symbol public static CvTerm getCvTermByCvAndCvTerm(final String cvterm_name, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1911: error: cannot find symbol public static CvTerm getCvTermByCvPartAndCvTerm(final String cvterm_name, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1929: error: cannot find symbol private static Hashtable getCvterms(final GmodDAO dao) ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2006: error: cannot find symbol public static Vector getCvterms(final String search_str, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2035: error: cannot find symbol public static CvTerm getCvtermFromGoId(final String goId) ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2135: error: cannot find symbol public void insertCvTerm(CvTerm cvTerm) ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:174: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:372: error: cannot find symbol CvTerm cvTerm, boolean not) ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/IBatisDAO.java:400: error: cannot find symbol String name, CvTerm type) ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/IBatisDAO.java:674: error: cannot find symbol public CvTerm getCvTermByNameAndCvName(String cvTermName, String name) ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/IBatisDAO.java:686: error: cannot find symbol public CvTerm getCvTermById(final int cvTermId) ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1162: error: cannot find symbol private void insertCvTerm(final CvTerm cvTerm) ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:345: error: cannot find symbol CvTerm cvTerm, boolean not) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:493: error: cannot find symbol String name, CvTerm cvTerm) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:903: error: cannot find symbol final CvTerm cvTerm) ^ symbol: class CvTerm location: class JdbcDAO return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:1223: error: cannot find symbol public CvTerm getCvTermByNameAndCvName(String cvTermName, String name) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:1228: error: cannot find symbol public CvTerm getCvTermById(final int cvTermId) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:218: error: cannot find symbol public List getPossibleMatches(String arg0, CvTerm arg1, int arg2) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:307: error: cannot find symbol public CvTerm getCvTermByDbXRef(DbXRef arg0) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:351: error: cannot find symbol public CvTerm getGoCvTermByAcc(String value) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:363: error: cannot find symbol public CvTerm getGoCvTermByAccViaDb(final String id) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:369: error: cannot find symbol public List getFeatureCvTermsByFeatureAndCvTermAndNot(Feature arg0, CvTerm arg1, boolean arg2) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/circular/DNADraw.java:175: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(4000)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:177: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(true)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/GmodDAO.java:414: error: cannot find symbol public List getPubPropByPubAndCvTerm(Pub arg0, CvTerm arg1) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./org/gmod/schema/organism/Organism.java:5: error: cannot access PhylonodeOrganism return_object = new Integer(start_value); import org.gmod.schema.phylogeny.PhylonodeOrganism; ^ bad class file: ./org/gmod/schema/phylogeny/PhylonodeOrganism.class class file truncated at offset 718 Please remove or make sure it appears in the correct subdirectory of the classpath. ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./org/gmod/schema/dao/SequenceDaoI.java:113: error: cannot find symbol CvTerm cvTerm, boolean not); ^ symbol: class CvTerm location: interface SequenceDaoI ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./org/gmod/schema/dao/SequenceDaoI.java:146: error: cannot find symbol public Synonym getSynonymByNameAndCvTerm(String name, CvTerm type); ^ symbol: class CvTerm location: interface SequenceDaoI ./org/gmod/schema/dao/SequenceDaoI.java:230: error: cannot find symbol public List getPossibleMatches(String name,CvTerm cvTerm, int limit); ^ symbol: class CvTerm location: interface SequenceDaoI ./org/gmod/schema/dao/CvDaoI.java:55: error: cannot find symbol public abstract CvTerm getCvTermById(int id); ^ symbol: class CvTerm location: interface CvDaoI ./org/gmod/schema/dao/CvDaoI.java:66: error: cannot find symbol public abstract List getCvTermByNameInCv(String cvTermName, Cv cv); ^ symbol: class CvTerm location: interface CvDaoI ./org/gmod/schema/dao/CvDaoI.java:75: error: cannot find symbol public abstract CvTerm getGoCvTermByAcc(String value); ^ symbol: class CvTerm location: interface CvDaoI ./org/gmod/schema/dao/CvDaoI.java:84: error: cannot find symbol public abstract CvTerm getGoCvTermByAccViaDb(final String id); ^ symbol: class CvTerm location: interface CvDaoI ./org/gmod/schema/dao/CvDaoI.java:91: error: cannot find symbol public abstract List getCvTerms(); ^ symbol: class CvTerm location: interface CvDaoI ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./org/gmod/schema/dao/CvDaoI.java:100: error: cannot find symbol public abstract CvTerm getCvTermByNameAndCvName(String cvTermName, String name); ^ symbol: class CvTerm location: interface CvDaoI ./org/gmod/schema/dao/CvDaoI.java:108: error: cannot find symbol public abstract CvTerm getCvTermByDbXRef(DbXRef dbXRef); ^ symbol: class CvTerm location: interface CvDaoI ./org/gmod/schema/dao/PubDaoI.java:64: error: cannot find symbol public abstract List getPubPropByPubAndCvTerm(Pub pub,CvTerm cvTerm); ^ symbol: class CvTerm location: interface PubDaoI ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:495: error: cannot find symbol private CvTerm getCvTermFromCache(final Hashtable cvTermCache, ^ symbol: class CvTerm location: class GFFDocumentEntry ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/components/Splash.java:42: error: cannot access CvTerm import java.lang.management.ManagementFactory; ^ bad class file: ./org/gmod/schema/cv/CvTerm.class class file truncated at offset 0 Please remove or make sure it appears in the correct subdirectory of the classpath. ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./org/gmod/schema/organism/Organism.java:25: error: cannot find symbol private Set phylonodeOrganisms = new HashSet(0); ^ symbol: class PhylonodeOrganism location: class Organism ./org/gmod/schema/organism/Organism.java:27: error: cannot find symbol public Set getPhylonodeOrganisms() { ^ symbol: class PhylonodeOrganism location: class Organism ./org/gmod/schema/organism/Organism.java:31: error: cannot find symbol public void setPhylonodeOrganisms(Set phylonodeOrganisms) { ^ symbol: class PhylonodeOrganism location: class Organism ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:496: error: cannot access Feature final org.gmod.schema.sequence.Feature matchFeature, ^ bad class file: ./org/gmod/schema/sequence/Feature.class class file truncated at offset 0 Please remove or make sure it appears in the correct subdirectory of the classpath. ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:495: error: cannot find symbol private CvTerm getCvTermFromCache(final Hashtable cvTermCache, ^ symbol: class CvTerm location: class GFFDocumentEntry ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:103: error: cannot find symbol private static Hashtable cvterms; ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ uk/ac/sanger/artemis/circular/GeneticMarker.java:510: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal arow.add(new Integer(b.getBstart())); ^ uk/ac/sanger/artemis/circular/GeneticMarker.java:511: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal arow.add(new Integer(b.getBend())); ^ uk/ac/sanger/artemis/circular/GeneticMarker.java:513: warning: [removal] Float(float) in Float has been deprecated and marked for removal arow.add(new Float(b.getStrokeSize())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ uk/ac/sanger/artemis/circular/GeneticMarker.java:514: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal arow.add(new Boolean(b.isArrowHead())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ uk/ac/sanger/artemis/circular/GeneticMarker.java:515: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal arow.add(new Boolean(b.isArrowTail())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ 1 error 4 warnings ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/ByteBuffer.java:120: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/LargeObjectDocument.java:122: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/util/LargeObjectDocument.java:122: error: cannot find symbol symbol: class Feature location: class DatabaseDocument ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/SqlMapClientWrapper.java:154: error: cannot find symbol } ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ !seen.contains(new Integer(j))) ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/Graph.java:94: error: cannot find symbol } ^ symbol: class Feature location: class IBatisDAO ./uk/ac/sanger/artemis/chado/Graph.java:94: error: cannot find symbol } ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:111: error: cannot find symbol public Feature getLazyFeatureNoResiduesById(final Integer featureId) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:140: error: cannot find symbol public List getFeatureDbXRefsBySrcFeature(Feature srcFeature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:146: error: cannot find symbol public List getFeatureSynonymsBySrcFeature(Feature srcFeature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:178: error: cannot find symbol public List getFeaturePubsBySrcFeature(Feature srcFeature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:184: error: cannot find symbol public List getFeaturePubsByFeature(final Feature feature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:199: error: cannot find symbol public List getFeatureCvTermDbXRefBySrcFeature(Feature srcFeature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:205: error: cannot find symbol public List getFeatureCvTermPubBySrcFeature(Feature srcFeature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:211: error: cannot find symbol public List getFeatureCvTermsBySrcFeature(Feature srcFeature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:239: error: cannot find symbol public Feature getFeatureById(int id) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:252: error: cannot find symbol public Feature getFeatureByUniqueName(final String uniquename, final String featureType) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:328: error: cannot find symbol public List getFeaturesByLocatedOnFeature(final Feature feature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:344: error: cannot find symbol Feature feature, ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:345: error: cannot find symbol CvTerm cvTerm, boolean not) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:350: error: cannot find symbol public List getFeatureCvTermsByFeature(Feature feature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:493: error: cannot find symbol String name, CvTerm cvTerm) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:528: error: cannot find symbol Feature feature, Synonym synonym) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ^ file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:541: error: cannot find symbol ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Feature feature, Synonym synonym) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:777: error: cannot find symbol public List getFeatureCvTermDbXRefByFeature(Feature feature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:827: error: cannot find symbol public List getFeatureCvTermPubByFeature(Feature feature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:883: error: cannot find symbol private Feature getLazyFeature(final Feature feature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:883: error: cannot find symbol private Feature getLazyFeature(final Feature feature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:903: error: cannot find symbol final CvTerm cvTerm) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ./uk/ac/sanger/artemis/chado/JdbcDAO.java:1223: error: cannot find symbol public CvTerm getCvTermByNameAndCvName(String cvTermName, String name) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:1228: error: cannot find symbol public CvTerm getCvTermById(final int cvTermId) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:1434: error: cannot find symbol private void updateFeature(Feature feature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/FeatureForUpdatingResidues.java:29: error: cannot find symbol public class FeatureForUpdatingResidues extends Feature ^ symbol: class Feature ./uk/ac/sanger/artemis/chado/JdbcDAO.java:1625: error: cannot find symbol (final Feature feature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:1742: error: cannot find symbol (final Feature feature) ^ symbol: class Feature location: class JdbcDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:65: error: cannot find symbol public abstract Feature getLazyFeatureNoResiduesById(final Integer featureId); ^ symbol: class Feature location: class GmodDAO ./uk/ac/sanger/artemis/circular/DNADraw.java:724: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:739: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal majorTicks.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/AbstractCvBox.java:177: error: cannot find symbol } ^ symbol: class CvTerm location: class CVPanel ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/GmodDAO.java:134: error: cannot find symbol public abstract List getFeatureCvTermsBySrcFeature(Feature srcFeature); ^ symbol: class Feature location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:141: error: cannot find symbol public abstract List getFeatureCvTermDbXRefBySrcFeature(Feature srcFeature); ^ symbol: class Feature location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:148: error: cannot find symbol public abstract List getFeatureCvTermPubBySrcFeature(Feature srcFeature); ^ symbol: class Feature location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:155: error: cannot find symbol public abstract List getFeaturePubsBySrcFeature(Feature srcFeature); ^ symbol: class Feature location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:162: error: cannot find symbol public abstract List getFeaturePubsByFeature(Feature feature); ^ symbol: class Feature location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:169: error: cannot find symbol public abstract List getFeatureSynonymsBySrcFeature(Feature srcFeature); ^ symbol: class Feature location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:210: error: cannot find symbol public abstract List getFeatureDbXRefsBySrcFeature(Feature srcFeature); ^ symbol: class Feature location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:218: error: cannot find symbol public List getPossibleMatches(String arg0, CvTerm arg1, int arg2) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:224: error: cannot find symbol public AnalysisFeature getAnalysisFeatureFromFeature(Feature arg0) ^ symbol: class Feature location: class GmodDAO ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/GmodDAO.java:307: error: cannot find symbol public CvTerm getCvTermByDbXRef(DbXRef arg0) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/GmodDAO.java:351: error: cannot find symbol public CvTerm getGoCvTermByAcc(String value) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:363: error: cannot find symbol public CvTerm getGoCvTermByAccViaDb(final String id) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:369: error: cannot find symbol public List getFeatureCvTermsByFeatureAndCvTermAndNot(Feature arg0, CvTerm arg1, boolean arg2) ^ symbol: class Feature location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:369: error: cannot find symbol public List getFeatureCvTermsByFeatureAndCvTermAndNot(Feature arg0, CvTerm arg1, boolean arg2) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:376: error: cannot find symbol public FeatureDbXRef getFeatureDbXRefByFeatureAndDbXRef(Feature arg0, DbXRef arg1) ^ symbol: class Feature location: class GmodDAO ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/GmodDAO.java:414: error: cannot find symbol public List getPubPropByPubAndCvTerm(Pub arg0, CvTerm arg1) ^ symbol: class CvTerm location: class GmodDAO ./org/gmod/schema/dao/SequenceDaoI.java:45: error: cannot find symbol public Feature getFeatureById(int id); ^ symbol: class Feature parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ location: interface SequenceDaoI ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.class] Error 1 gmake: *** Waiting for unfinished jobs.... ./uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:241: error: cannot find symbol public static CvTerm getGOCvTerm(String term) ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ^ symbol: class CvTerm location: class GoBox ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:311: error: cannot find symbol protected static Vector getCvTerms() ^ symbol: class CvTerm location: class HistoryBox ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:328: error: cannot find symbol public static CvTerm getDefaultTerm() ^ symbol: class CvTerm location: class HistoryBox ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:703: error: cannot find symbol private static CvTerm getCvTerm(String cvTermName) ^ symbol: class CvTerm location: class ArtemisUtils ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermsComparator.java:31: error: cannot find symbol ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ public class CvTermsComparator implements Comparator ^ symbol: class CvTerm ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermsComparator.java:33: error: cannot find symbol public int compare(CvTerm cvTerm1, CvTerm cvTerm2) ^ symbol: class CvTerm location: class CvTermsComparator ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermsComparator.java:33: error: cannot find symbol public int compare(CvTerm cvTerm1, CvTerm cvTerm2) ^ symbol: class CvTerm location: class CvTermsComparator ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:174: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(0)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:175: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(4000)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/circular/DNADraw.java:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:177: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(true)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:724: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:739: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal majorTicks.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:174: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(0)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:175: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(4000)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:177: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(true)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:724: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:739: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ featureIds.add(new Integer(thisFeature.getFeatureId())); ./uk/ac/sanger/artemis/circular/DNADraw.java:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal majorTicks.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./org/gmod/schema/organism/Organism.java:25: error: cannot find symbol private Set phylonodeOrganisms = new HashSet(0); ^ symbol: class PhylonodeOrganism location: class Organism ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:47: error: cannot access TabixReader import uk.ac.sanger.artemis.components.variant.TabixReader; ^ bad class file: ./uk/ac/sanger/artemis/components/variant/TabixReader.class class file truncated at offset 0 Please remove or make sure it appears in the correct subdirectory of the classpath. ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:59: error: cannot find symbol ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ private TabixReader reader; ^ symbol: class TabixReader location: class IndexedGFFDocumentEntry return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:283: error: package TabixReader does not exist final TabixReader.Iterator tabixIterator, ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/circular/DNADraw.java:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ dbxref_id = new Integer(rs.getInt("dbxref_id")); ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/FeatureSegmentVector.java:46: error: cannot find symbol ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ private FastVector vector = new FastVector (); ^ symbol: class FastVector location: class FeatureSegmentVector ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/FeatureSegmentVector.java:155: error: cannot find symbol return_vector.vector = (FastVector) vector.clone (); ^ symbol: class FastVector location: class FeatureSegmentVector ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/FeatureVector.java:145: error: cannot find symbol return_vector.vector = (FastVector) vector.clone (); ^ symbol: class FastVector location: class FeatureVector ./uk/ac/sanger/artemis/FeatureVector.java:165: error: cannot find symbol private FastVector vector = new FastVector (); ^ symbol: class FastVector location: class FeatureVector ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/io/QualifierInfo.java:119: error: cannot find symbol return keys.contains (key); ^ symbol: method contains(Key) location: variable keys of type KeyVector ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/QualifierInfo.java:131: error: cannot find symbol return required_keys.contains (key); ^ symbol: method contains(Key) location: variable required_keys of type KeyVector ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/KeyVector.java:51: error: cannot find symbol add (new_key); ^ symbol: method add(Key) location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:59: error: cannot find symbol final KeyVector new_key_vector = (KeyVector)clone(); ^ symbol: method clone() location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:72: error: cannot find symbol for (int i = 0; i < size (); ++i) ^ symbol: method size() location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:76: error: cannot find symbol for(int j = i + 1 ; j < size () ; ++j) ^ symbol: method size() location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:78: error: cannot find symbol if(((Key)get(j)).compareTo( (Key)get(smallest)) < 0) ^ symbol: method get(int) location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:78: error: cannot find symbol if(((Key)get(j)).compareTo( (Key)get(smallest)) < 0) ^ symbol: method get(int) location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:84: error: cannot find symbol final Key tmp = (Key)get(i); ^ symbol: method get(int) location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:85: error: cannot find symbol setElementAt (get(smallest), i); ^ symbol: method get(int) location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:86: error: cannot find symbol setElementAt (tmp, smallest); ^ symbol: method setElementAt(Key,int) location: class KeyVector ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/Options.java:1433: error: cannot find symbol valid_keys.add(current_key); ^ symbol: method add(Key) location: variable valid_keys of type KeyVector ./uk/ac/sanger/artemis/Options.java:1438: error: cannot find symbol valid_keys.add(current_key); ^ symbol: method add(Key) location: variable valid_keys of type KeyVector ./uk/ac/sanger/artemis/Options.java:1439: error: cannot find symbol required_keys.add(current_key); ^ symbol: method add(Key) location: variable required_keys of type KeyVector ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java:438: error: cannot find symbol for(int i=0; i'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:174: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:175: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(4000)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:177: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(true)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:428: error: cannot find symbol final CvTerm cvTerm = getCvTermFromCache(cvTermCache, matchFeature, f); ^ symbol: class CvTerm location: class GFFDocumentEntry ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:500: error: cannot find symbol final CvTerm cvTerm; ^ symbol: class CvTerm location: class GFFDocumentEntry ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:503: error: cannot find symbol cvTerm = (CvTerm) cvTermCache.get(cvTermId); ^ symbol: class CvTerm location: class GFFDocumentEntry ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:668: error: cannot find symbol CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm("part_of", "relationship"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:771: error: cannot find symbol CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm("part_of", "relationship"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:797: error: cannot find symbol CvTerm cvterm = new CvTerm(); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:797: error: cannot find symbol CvTerm cvterm = new CvTerm(); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:820: error: cannot find symbol CvTerm cvTerm = DatabaseDocument.getCvTermByCvAndCvTerm(key, "sequence"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ file_length = new Integer(fat.getSize().intValue()); ^ lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:903: error: cannot find symbol CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm("part_of", "relationship"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:931: error: cannot find symbol CvTerm cvterm = new CvTerm(); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:931: error: cannot find symbol CvTerm cvterm = new CvTerm(); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:954: error: cannot find symbol CvTerm cvterm = getCvTerm(key, "sequence"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:1071: error: cannot find symbol CvTerm cvTerm = DatabaseDocument.getCvTermByCvAndCvTerm(featureKey, "sequence"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:1167: error: cannot find symbol final CvTerm cvTerm = DatabaseDocument.getCvTermByCvTermName(name); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:1285: error: cannot find symbol CvTerm cvTerm = getCvTerm(key, "sequence"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:1354: error: cannot find symbol CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm(name, "feature_property"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:1426: error: cannot find symbol CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm(name, "feature_property"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2269: error: cannot find symbol CvTerm cvterm = new CvTerm(); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2269: error: cannot find symbol CvTerm cvterm = new CvTerm(); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2307: error: cannot find symbol CvTerm cvterm = new CvTerm(); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2307: error: cannot find symbol CvTerm cvterm = new CvTerm(); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2401: error: cannot find symbol CvTerm cvTerm = getCvTerm( DatabaseDocument.getCvTermByCvTermId( ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2439: error: cannot find symbol CvTerm cvTerm; ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2504: error: cannot find symbol CvTerm cvTerm; ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2548: error: cannot find symbol CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm(qualifierName, "sequence"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2583: error: cannot find symbol CvTerm cvTerm = new CvTerm(); ^ symbol: class CvTerm location: class ChadoTransactionManager featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:724: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:739: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal majorTicks.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( this.file_length = new Integer(fat.getSize().intValue()); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ uk/ac/sanger/artemis/circular/DNADraw.java:174: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ lineAttr.put("start",new Integer(0)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ uk/ac/sanger/artemis/circular/DNADraw.java:175: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(4000)); ^ uk/ac/sanger/artemis/circular/DNADraw.java:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ uk/ac/sanger/artemis/circular/DNADraw.java:177: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(true)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ final Integer featureId = new Integer(feat.getFeatureId()); ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ uk/ac/sanger/artemis/circular/DNADraw.java:724: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ uk/ac/sanger/artemis/circular/DNADraw.java:739: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ uk/ac/sanger/artemis/circular/DNADraw.java:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal majorTicks.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ uk/ac/sanger/artemis/circular/DNADraw.java:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:341: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize", new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:342: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular", new Boolean(true)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:343: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start", new Integer(0)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:344: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end", new Integer(sequenceLength)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:350: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal lineAttr.put("lsize", new Integer(lineAttrStr[i+1])); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:352: warning: [removal] Boolean(String) in Boolean has been deprecated and marked for removal lineAttr.put("circular", new Boolean(lineAttrStr[i+1])); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ uk/ac/sanger/artemis/circular/DNADraw.java:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:708: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize", new Integer(1)); ^ matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:709: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular", new Boolean(true)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:710: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start", new Integer(0)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:711: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end", new Integer(entry.getBases().getLength())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:199: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(null); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/BasePlotGroup.java:63: error: cannot access BaseAlgorithm private final Vector plot_value_producers = new Vector (); ^ bad class file: ./uk/ac/sanger/artemis/plot/BaseAlgorithm.class class file truncated at offset 8 Please remove or make sure it appears in the correct subdirectory of the classpath. ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/BasePlotGroup.java:261: error: cannot find symbol public BasePlot addAlgorithm(final BaseAlgorithm algorithm) ^ symbol: class BaseAlgorithm location: class BasePlotGroup ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:174: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/BasePlotGroup.java:288: error: cannot find symbol public BaseAlgorithm[] getPlotAlgorithms() ^ symbol: class BaseAlgorithm location: class BasePlotGroup ./uk/ac/sanger/artemis/components/BasePlotGroup.java:379: error: cannot find symbol private BasePlot makePlot(BaseAlgorithm algorithm, ^ symbol: class BaseAlgorithm location: class BasePlotGroup ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:175: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(4000)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:177: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(true)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/components/BasePlot.java:172: error: cannot find symbol public BasePlot(final BaseAlgorithm algorithm, ^ symbol: class BaseAlgorithm location: class BasePlot ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/BasePlot.java:314: error: cannot find symbol public BaseAlgorithm getBaseAlgorithm() ^ symbol: class BaseAlgorithm location: class BasePlot ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ public void finalize () { ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:724: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:739: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal majorTicks.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ return new Integer (24); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ featureloc.setStrand(new Short((short)-1)); ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:341: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ lineAttr.put("lsize", new Integer(1)); ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ^ ./uk/ac/sanger/artemis/circular/Wizard.java:342: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular", new Boolean(true)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:343: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start", new Integer(0)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:344: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end", new Integer(sequenceLength)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:350: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal lineAttr.put("lsize", new Integer(lineAttrStr[i+1])); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:352: warning: [removal] Boolean(String) in Boolean has been deprecated and marked for removal lineAttr.put("circular", new Boolean(lineAttrStr[i+1])); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:708: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize", new Integer(1)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:709: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular", new Boolean(true)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:710: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start", new Integer(0)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:711: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end", new Integer(entry.getBases().getLength())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:199: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(null); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:199: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(null); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:199: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(null); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:199: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(null); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:341: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize", new Integer(1)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:342: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular", new Boolean(true)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:343: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start", new Integer(0)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:344: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end", new Integer(sequenceLength)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:350: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal lineAttr.put("lsize", new Integer(lineAttrStr[i+1])); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:352: warning: [removal] Boolean(String) in Boolean has been deprecated and marked for removal lineAttr.put("circular", new Boolean(lineAttrStr[i+1])); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ^ featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:708: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize", new Integer(1)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:709: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular", new Boolean(true)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:710: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start", new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:711: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end", new Integer(entry.getBases().getLength())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:99: error: cannot find symbol ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ reader = new TabixReader(gffFile.getAbsolutePath()); ^ symbol: class TabixReader location: class IndexedGFFDocumentEntry ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1681: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal removals.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1684: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matches_to_split.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:252: error: package TabixReader does not exist TabixReader.Iterator tabixIterator = null; ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1868: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal removals.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1897: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal removals.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:199: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(null); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:898: error: package TabixReader does not exist TabixReader.Iterator tabixIterator = reader.query(r); ^ ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:955: error: package TabixReader does not exist TabixReader.Iterator tabixIterator = reader.query(r); ^ ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:1024: error: package TabixReader does not exist TabixReader.Iterator tabixIterator = reader.query(r); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:211: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:897: error: cannot find symbol private TabixReader reader; ^ symbol: class TabixReader location: class UserDataAlgorithm.TabixIdxGraph ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:174: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(0)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:175: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(4000)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:177: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(true)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:724: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:739: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal majorTicks.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/editor/HitInfo.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(startQuery)); ^ ./uk/ac/sanger/artemis/editor/HitInfo.java:275: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(endQuery)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/GraphMenu.java:298: error: cannot find symbol private JCheckBoxMenuItem addAlgorithm (final BaseAlgorithm algorithm, ^ symbol: class BaseAlgorithm location: class GraphMenu ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/BasePlotGroup.java:63: error: cannot find symbol private final Vector plot_value_producers = new Vector (); ^ symbol: class BaseAlgorithm location: class BasePlotGroup ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:211: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ./uk/ac/sanger/artemis/components/BasePlotGroup.java:222: error: incompatible types: Algorithm cannot be converted to UserDataAlgorithm if(alg instanceof UserDataAlgorithm && ^ ./uk/ac/sanger/artemis/components/BasePlotGroup.java:223: error: incompatible types: Algorithm cannot be converted to UserDataAlgorithm ((UserDataAlgorithm)alg).FORMAT != UserDataAlgorithm.TABIX_INDEXED_FORMAT && ^ ./uk/ac/sanger/artemis/components/BasePlotGroup.java:276: error: cannot find symbol final BaseAlgorithm this_algorithm = plot_value_producers.elementAt(i); ^ symbol: class BaseAlgorithm location: class BasePlotGroup ./uk/ac/sanger/artemis/components/BasePlotGroup.java:290: error: cannot find symbol final BaseAlgorithm[] return_array = ^ symbol: class BaseAlgorithm location: class BasePlotGroup ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/components/BasePlotGroup.java:291: error: cannot find symbol new BaseAlgorithm[plot_value_producers.size ()]; ^ symbol: class BaseAlgorithm location: class BasePlotGroup ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/components/BasePlotGroup.java:295: error: cannot find symbol final BaseAlgorithm this_algorithm = plot_value_producers.elementAt (i); ^ symbol: class BaseAlgorithm location: class BasePlotGroup ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/UI.java:74: warning: [removal] stop() in Thread has been deprecated and marked for removal mask.stop(); ^ ./uk/ac/sanger/artemis/components/Plot.java:398: error: cannot find symbol if(numPlots == 1 && getAlgorithm() instanceof BaseAlgorithm) ^ symbol: class BaseAlgorithm ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/Plot.java:701: error: cannot find symbol if(lines == null && getAlgorithm() instanceof BaseAlgorithm) ^ symbol: class BaseAlgorithm location: class Plot ./uk/ac/sanger/artemis/components/Plot.java:704: error: cannot find symbol ((BaseAlgorithm)getAlgorithm()).getValueCount(); ^ symbol: class BaseAlgorithm location: class Plot ./uk/ac/sanger/artemis/components/Plot.java:706: error: incompatible types: Algorithm cannot be converted to UserDataAlgorithm if(getAlgorithm() instanceof UserDataAlgorithm) ^ ./uk/ac/sanger/artemis/components/Plot.java:707: error: incompatible types: Algorithm cannot be converted to UserDataAlgorithm lines = ((UserDataAlgorithm)getAlgorithm()).getLineAttributes(); ^ ./uk/ac/sanger/artemis/components/Plot.java:855: error: incompatible types: Algorithm cannot be converted to UserDataAlgorithm int span = ((UserDataAlgorithm)getAlgorithm()).getWiggleSpan(value_index); ^ ./uk/ac/sanger/artemis/components/Plot.java:1040: error: cannot find symbol ((BaseAlgorithm)getAlgorithm()).drawLegend(g,font_height, ^ symbol: class BaseAlgorithm location: class Plot ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/components/BasePlot.java:316: error: cannot find symbol return (BaseAlgorithm)super.getAlgorithm(); ^ symbol: class BaseAlgorithm location: class BasePlot ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/BasePlot.java:725: error: incompatible types: Algorithm cannot be converted to UserDataAlgorithm if( getAlgorithm() instanceof UserDataAlgorithm && ^ ./uk/ac/sanger/artemis/components/BasePlot.java:726: error: incompatible types: Algorithm cannot be converted to UserDataAlgorithm ((UserDataAlgorithm)getAlgorithm()).FORMAT == UserDataAlgorithm.TABIX_INDEXED_FORMAT) ^ ./uk/ac/sanger/artemis/components/BasePlot.java:728: error: incompatible types: Algorithm cannot be converted to UserDataAlgorithm ((UserDataAlgorithm) getAlgorithm()).readIndexValues(recalculate_flag, ^ ./uk/ac/sanger/artemis/components/BasePlot.java:750: error: incompatible types: Algorithm cannot be converted to UserDataAlgorithm if(getAlgorithm() instanceof UserDataAlgorithm) ^ ./uk/ac/sanger/artemis/components/BasePlot.java:752: error: incompatible types: Algorithm cannot be converted to UserDataAlgorithm int format = ((UserDataAlgorithm)getAlgorithm()).FORMAT; ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/io/UI.java:74: warning: [removal] stop() in Thread has been deprecated and marked for removal mask.stop(); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/editor/HitInfo.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(startQuery)); ^ ./uk/ac/sanger/artemis/editor/HitInfo.java:275: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(endQuery)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 5 errors 100 warnings ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/chado/GmodDAO.class] Error 1 ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:510: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal arow.add(new Integer(b.getBstart())); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:511: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal arow.add(new Integer(b.getBend())); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/editor/HitInfo.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(startQuery)); ^ ./uk/ac/sanger/artemis/editor/HitInfo.java:275: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(endQuery)); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:513: warning: [removal] Float(float) in Float has been deprecated and marked for removal arow.add(new Float(b.getStrokeSize())); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:514: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal arow.add(new Boolean(b.isArrowHead())); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:515: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal arow.add(new Boolean(b.isArrowTail())); ^ ./uk/ac/sanger/artemis/circular/RestrictionEnzyme.java:119: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal re.add(new Integer(pos.getValue())); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:61: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_default = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:62: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_remote = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:63: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_listFile = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:64: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(jcirc.isSelected())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:75: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(jcirc.isSelected())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:83: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(draw.isCircular())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:98: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(s)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:125: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(e)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:151: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lsize)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:510: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal arow.add(new Integer(b.getBstart())); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:511: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal arow.add(new Integer(b.getBend())); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:513: warning: [removal] Float(float) in Float has been deprecated and marked for removal arow.add(new Float(b.getStrokeSize())); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:514: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal arow.add(new Boolean(b.isArrowHead())); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:515: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal arow.add(new Boolean(b.isArrowTail())); ^ ./uk/ac/sanger/artemis/circular/RestrictionEnzyme.java:119: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal re.add(new Integer(pos.getValue())); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:61: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_default = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:62: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_remote = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:63: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_listFile = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:64: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(jcirc.isSelected())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:75: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(jcirc.isSelected())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:83: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(draw.isCircular())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:98: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(s)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:125: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(e)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:151: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lsize)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:168: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(size)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:184: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(size)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:226: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start.getValue())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:227: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end.getValue())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:228: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize.getValue())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/io/UI.java:74: warning: [removal] stop() in Thread has been deprecated and marked for removal mask.stop(); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1681: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal removals.add(new Integer(i)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1684: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matches_to_split.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1868: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal removals.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1897: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal removals.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1982: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[0] = new Integer(start); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1983: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[1] = new Integer(this_start-1); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:2026: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[0] = new Integer(start+1); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:2027: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[1] = new Integer(next_start-1); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:2036: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[0] = new Integer(start+1); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:2037: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[1] = new Integer(length); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:906: error: cannot find symbol this.reader = new TabixReader(fName); ^ symbol: class TabixReader location: class UserDataAlgorithm.TabixIdxGraph ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:991: error: package TabixReader does not exist final TabixReader.Iterator tbxIt = reader.query(r); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 errors 100 warnings only showing the first 100 errors, of 445 total; use -Xmaxerrs if you would like to see more ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/chado/CommitFrame.class] Error 1 Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 errors 100 warnings only showing the first 100 errors, of 222 total; use -Xmaxerrs if you would like to see more gmake: *** [Makefile:47: uk/ac/sanger/artemis/SimpleGotoEventSource.class] Error 1 Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/AddMenu.java:417: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[0] = new Integer(istart); ^ ./uk/ac/sanger/artemis/components/AddMenu.java:418: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[1] = new Integer(jend); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/GraphMenu.java:121: error: cannot find symbol final BaseAlgorithm [] orig_algorithms = ^ symbol: class BaseAlgorithm location: class GraphMenu ./uk/ac/sanger/artemis/components/GraphMenu.java:129: error: cannot find symbol final BaseAlgorithm [] current_algorithms = ^ symbol: class BaseAlgorithm ./uk/ac/sanger/artemis/components/GraphMenu.java:134: error: cannot find symbol final BaseAlgorithm this_algorithm = current_algorithms[i]; ^ symbol: class BaseAlgorithm ./uk/ac/sanger/artemis/components/GraphMenu.java:217: error: cannot find symbol final BaseAlgorithm this_algorithm = orig_algorithms[i]; ^ symbol: class BaseAlgorithm location: class GraphMenu ./uk/ac/sanger/artemis/components/GraphMenu.java:335: error: cannot find symbol final BaseAlgorithm [] current_algorithms = ^ symbol: class BaseAlgorithm location: class GraphMenu ./uk/ac/sanger/artemis/editor/HitInfo.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(startQuery)); ^ ./uk/ac/sanger/artemis/editor/HitInfo.java:275: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(endQuery)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/components/GraphMenu.java:462: error: incompatible types: CodonUsageAlgorithm cannot be converted to Algorithm base_plot_group.setVisibleByAlgorithm (codon_usage_algorithm, is_visible); ^ ./uk/ac/sanger/artemis/components/GraphMenu.java:518: error: incompatible types: UserDataAlgorithm cannot be converted to Algorithm base_plot_group.setVisibleByAlgorithm(new_algorithm, true); ^ ./uk/ac/sanger/artemis/components/GraphMenu.java:612: error: incompatible types: UserDataAlgorithm cannot be converted to Algorithm base_plot_group.setVisibleByAlgorithm (new_algorithm, true); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:127: error: cannot find symbol setAlgorithmName( ^ symbol: method setAlgorithmName(logTransfo[...]ame()) location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:188: error: cannot find symbol max_min_disabled = Options.getOptions ().getPropertyTruthValue( ^ symbol: variable max_min_disabled location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:189: error: cannot find symbol getAlgorithmShortName () + "_scaling_on"); ^ symbol: method getAlgorithmShortName() location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:191: error: cannot find symbol String propStr = getAlgorithmShortName () + "_data_max"; ^ symbol: method getAlgorithmShortName() location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:195: error: cannot find symbol propStr = getAlgorithmShortName () + "_data_min"; ^ symbol: method getAlgorithmShortName() location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:224: error: cannot find symbol final int seqLength = getStrand ().getSequenceLength (); ^ symbol: method getStrand() location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:228: error: cannot find symbol Options.getOptions ().getIntegerProperty (getAlgorithmShortName () + ^ symbol: method getAlgorithmShortName() location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:231: error: cannot find symbol default_window_size = Options.getOptions ().getIntegerProperty (getAlgorithmShortName () + ^ symbol: method getAlgorithmShortName() location: class UserDataAlgorithm Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:315: error: cannot find symbol final int seqLength = getStrand ().getSequenceLength (); ^ symbol: method getStrand() location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:405: error: cannot find symbol final int seqLength = getStrand ().getSequenceLength (); ^ symbol: method getStrand() location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:538: error: cannot find symbol if(getStrand ().getDirection() == Bases.REVERSE) ^ symbol: method getStrand() location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:542: error: cannot find symbol end = getStrand().getBases().getComplementPosition(tstart); ^ symbol: method getStrand() location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:543: error: cannot find symbol start = getStrand().getBases().getComplementPosition(tend); ^ symbol: method getStrand() location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:795: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (default_window_size); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:805: error: cannot find symbol if(Options.getOptions ().getIntegerProperty (getAlgorithmShortName () + ^ symbol: method getAlgorithmShortName() location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (100); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:809: error: cannot find symbol return super.getDefaultMaxWindowSize (); ^ symbol: variable super location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:819: error: cannot find symbol if(Options.getOptions ().getIntegerProperty (getAlgorithmShortName () + ^ symbol: method getAlgorithmShortName() location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:821: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (1); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:823: error: cannot find symbol return super.getDefaultMinWindowSize(); ^ symbol: variable super location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:834: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 10); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:844: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (data_max); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:852: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (data_min); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:860: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (average_value); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 11 errors 100 warnings Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:51: error: cannot find symbol setScalingFlag (true); ^ symbol: method setScalingFlag(boolean) location: class GCWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:65: error: cannot find symbol sequence = getStrand ().getSubSequence (new Range (start, end)); ^ symbol: method getStrand() location: class GCWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:100: error: cannot find symbol final Integer super_window_size = super.getDefaultWindowSize (); ^ symbol: variable super location: class GCWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:106: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:115: error: cannot find symbol final Integer super_max_window_size = super.getDefaultMaxWindowSize (); ^ symbol: variable super location: class GCWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:121: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:130: error: cannot find symbol final Integer super_min_window_size = super.getDefaultMinWindowSize (); ^ symbol: variable super location: class GCWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:136: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:146: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 10); ^ ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:157: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (100); ^ ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:165: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:174: error: cannot find symbol return new Float (getStrand ().getBases ().getAverageGCPercent ()); ^ symbol: method getStrand() location: class GCWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:53: error: cannot find symbol setScalingFlag (false); ^ symbol: method setScalingFlag(boolean) location: class GCSDWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:88: error: cannot find symbol sequence = getStrand ().getSubSequence (new Range (start, end)); ^ symbol: method getStrand() location: class GCSDWindowAlgorithm Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:107: error: cannot find symbol ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ getStrand ().getBases ().getAverageGCPercent (); ^ symbol: method getStrand() location: class GCSDWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:123: error: cannot find symbol final int sequence_length = getStrand ().getBases ().getLength (); ^ symbol: method getStrand() location: class GCSDWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:125: error: cannot find symbol final String bases = getStrand ().getBases ().toString (); ^ symbol: method getStrand() location: class GCSDWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:197: error: cannot find symbol final Integer super_window_size = super.getDefaultWindowSize (); ^ symbol: variable super location: class GCSDWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (1000); ^ ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:212: error: cannot find symbol final Integer super_max_window_size = super.getDefaultMaxWindowSize (); ^ symbol: variable super location: class GCSDWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:218: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (5000); ^ ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:227: error: cannot find symbol final Integer super_min_window_size = super.getDefaultMinWindowSize (); ^ symbol: variable super location: class GCSDWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:233: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (100); ^ ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:242: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (1); ^ ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:251: error: cannot find symbol return new Float (getStrand ().getBases ().getAverageGCPercent ()); ^ symbol: method getStrand() location: class GCSDWindowAlgorithm ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:259: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (100); ^ ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:267: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:51: error: cannot find symbol setScalingFlag (true); ^ symbol: method setScalingFlag(boolean) location: class AGWindowAlgorithm ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:65: error: cannot find symbol sequence = getStrand ().getSubSequence (new Range (start, end)); ^ symbol: method getStrand() location: class AGWindowAlgorithm ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:100: error: cannot find symbol final Integer super_window_size = super.getDefaultWindowSize (); ^ symbol: variable super location: class AGWindowAlgorithm ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:106: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:115: error: cannot find symbol final Integer super_max_window_size = super.getDefaultMaxWindowSize (); ^ symbol: variable super location: class AGWindowAlgorithm ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:121: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:130: error: cannot find symbol final Integer super_min_window_size = super.getDefaultMinWindowSize (); ^ symbol: variable super location: class AGWindowAlgorithm ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:136: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:144: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (100); ^ ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:152: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:162: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 10); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:174: error: cannot find symbol Note: Some input files use or override a deprecated API. return new Float (getStrand ().getBases ().getAverageAGPercent ()); ^ symbol: method getStrand() location: class AGWindowAlgorithm Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:52: error: cannot find symbol setScalingFlag(true); ^ symbol: method setScalingFlag(boolean) location: class GCFrameAlgorithm ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:74: error: cannot find symbol if(isRevCompDisplay()) ^ symbol: method isRevCompDisplay() location: class GCFrameAlgorithm ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:77: error: cannot find symbol getStrand().getBases().getComplementPosition(start); ^ symbol: method getStrand() location: class GCFrameAlgorithm ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:79: error: cannot find symbol getStrand().getBases().getComplementPosition(end); ^ symbol: method getStrand() location: class GCFrameAlgorithm ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:86: error: cannot find symbol if(getStrand().isForwardStrand()) ^ symbol: method getStrand() location: class GCFrameAlgorithm ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:98: error: cannot find symbol sub_sequence = getStrand().getRawSubSequenceC(new Range(start, end)); ^ symbol: method getStrand() location: class GCFrameAlgorithm ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:107: error: cannot find symbol if(getStrand().isForwardStrand()) ^ symbol: method getStrand() location: class GCFrameAlgorithm ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:122: error: cannot find symbol final int whole_sequence_length = getStrand().getSequenceLength(); ^ symbol: method getStrand() location: class GCFrameAlgorithm ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:170: error: cannot find symbol final Integer super_window_size = super.getDefaultWindowSize(); ^ symbol: variable super location: class GCFrameAlgorithm ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:177: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(120); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:187: error: cannot find symbol final Integer super_max_window_size = super.getDefaultMaxWindowSize(); ^ symbol: variable super location: class GCFrameAlgorithm ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(500); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:204: error: cannot find symbol final Integer super_min_window_size = super.getDefaultMinWindowSize(); ^ symbol: variable super location: class GCFrameAlgorithm ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:211: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(24); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:222: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(window_size / 8); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:233: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float(100); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float(0); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:252: error: cannot find symbol return new Float(getStrand().getBases().getAverageGCPercent()); ^ symbol: method getStrand() location: class GCFrameAlgorithm ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:52: error: cannot find symbol setScalingFlag(true); ^ symbol: method setScalingFlag(boolean) location: class Codon12CorrelationAlgorithm ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:87: error: cannot find symbol if(isRevCompDisplay()) ^ symbol: method isRevCompDisplay() location: class Codon12CorrelationAlgorithm ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:90: error: cannot find symbol getStrand().getBases().getComplementPosition(start); ^ symbol: method getStrand() location: class Codon12CorrelationAlgorithm ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:92: error: cannot find symbol getStrand().getBases().getComplementPosition(end); ^ symbol: method getStrand() location: class Codon12CorrelationAlgorithm ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:99: error: cannot find symbol if(getStrand().isForwardStrand()) ^ symbol: method getStrand() location: class Codon12CorrelationAlgorithm ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:108: error: cannot find symbol sub_sequence_raw = getStrand().getRawSubSequenceC(new Range(start, end)); ^ symbol: method getStrand() location: class Codon12CorrelationAlgorithm Note: Some input files use or override a deprecated API. ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:121: error: cannot find symbol if(getStrand().isForwardStrand()) ^ symbol: method getStrand() location: class Codon12CorrelationAlgorithm Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:146: error: cannot find symbol final int whole_sequence_length = getStrand().getSequenceLength(); ^ symbol: method getStrand() location: class Codon12CorrelationAlgorithm ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:182: error: cannot find symbol if(getStrand().isForwardStrand()) ^ symbol: method getStrand() location: class Codon12CorrelationAlgorithm ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:217: error: cannot find symbol final Integer super_window_size = super.getDefaultWindowSize(); ^ symbol: variable super location: class Codon12CorrelationAlgorithm ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:224: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(240); ^ ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:234: error: cannot find symbol final Integer super_max_window_size = super.getDefaultMaxWindowSize(); ^ symbol: variable super location: class Codon12CorrelationAlgorithm ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:241: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(600); ^ ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:251: error: cannot find symbol final Integer super_min_window_size = super.getDefaultMinWindowSize(); ^ symbol: variable super location: class Codon12CorrelationAlgorithm ./uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.java:50: error: cannot find symbol setScalingFlag (true); ^ symbol: method setScalingFlag(boolean) location: class GCDeviationAlgorithm ./uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.java:65: error: cannot find symbol sequence = getStrand ().getSubSequence (new Range (start, end)); ^ symbol: method getStrand() location: class GCDeviationAlgorithm ./uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.java:109: error: cannot find symbol final Integer super_window_size = super.getDefaultWindowSize (); ^ symbol: variable super location: class GCDeviationAlgorithm ./uk/ac/sanger/artemis/components/ViewMenu.java:1447: error: cannot access FeatureFromVectorPredicate new FeatureFromVectorPredicate (selection.getAllFeatures ()); ^ bad class file: ./uk/ac/sanger/artemis/FeatureFromVectorPredicate.class class file truncated at offset 8 Please remove or make sure it appears in the correct subdirectory of the classpath. Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more gmake: *** [Makefile:47: uk/ac/sanger/artemis/circular/GCSkewGraph.class] Error 1 Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/circular/RestrictionEnzyme.java:119: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal re.add(new Integer(pos.getValue())); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/circular/SequenceData.java:61: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_default = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:62: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_remote = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:63: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_listFile = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:64: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(jcirc.isSelected())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:75: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(jcirc.isSelected())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:83: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(draw.isCircular())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:98: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(s)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:125: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(e)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:151: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lsize)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:168: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(size)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:184: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(size)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/circular/LineAttribute.java:226: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start.getValue())); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/EditMenu.java:2696: error: cannot find symbol new FeatureFromVectorPredicate (bad_features); ^ symbol: class FeatureFromVectorPredicate location: class EditMenu Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:211: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. Note: Some messages have been simplified; recompile with -Xdiags:verbose to get full output 100 errors 100 warnings only showing the first 100 errors, of 195 total; use -Xmaxerrs if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more gmake: *** [Makefile:47: uk/ac/sanger/artemis/circular/Graph.class] Error 1 Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/Selector.java:469: error: cannot find symbol new FeatureFromVectorPredicate(getSelected()); ^ symbol: class FeatureFromVectorPredicate Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 3 errors 100 warnings Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more gmake: *** [Makefile:47: uk/ac/sanger/artemis/circular/GeneticMarker.class] Error 1 Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped making "build" in /usr/ports/biology/artemis =>> Cleaning up wrkdir ===> Cleaning for artemis-17.0.1.11_1 build of biology/artemis | artemis-17.0.1.11_1 ended at Fri Mar 13 14:54:38 EDT 2026 build time: 00:08:19 !!! build failure encountered !!!