=>> Building biology/artemis build started at Fri Mar 13 06:58:18 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: 06 ---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/06/.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 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 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 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/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 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 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 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. 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 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/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 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/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 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] 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 Note: Annotation processing is enabled because one or more processors were found 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. 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] 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] bootstrap class path not set in conjunction with -source 8 warning: [options] target 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] To suppress warnings about obsolete options, use -Xlint:-options. 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] 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] 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. 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. 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. 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 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 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] 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. 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. 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] 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] 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. 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] 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] 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. 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] 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] 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. 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 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] 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] 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] 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. 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. 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 4 warnings 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 4 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); ^ 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/SimpleExternalProgramMonitor.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/SimpleGotoEventSource.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/ChangeEventVector.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 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/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 ./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. 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/chado/ChadoDemo.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. 11 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/ChadoTransaction.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/ChadoTransactionManager.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/ClusterLazyQualifierValue.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); ^ 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 ./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); ^ 4 warnings ./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. Note: ./uk/ac/sanger/artemis/util/FastVector.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 5 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)); ^ 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 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 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. 5 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/FeatureLocLazyQualifierValue.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/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 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 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. 4 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 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/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 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. 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. 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 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 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. 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. 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] 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. 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. 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: 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 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/circular/EmbossCirdnaReader.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. ./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 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/Feature.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); ^ 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. 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. 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/GCSkewGraph.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/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. 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. 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. ./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/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/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/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:72: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ 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/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/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/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: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/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/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/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/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/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: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/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/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/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: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); ^ 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/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/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/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/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/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: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:172: 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: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/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); ^ ./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/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/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: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: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/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 ./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()); ^ 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/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: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: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 ./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); ^ 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/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: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/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/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: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 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/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/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: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/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/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/circular/TrackManager.java:68: error: cannot access RangeVector import uk.ac.sanger.artemis.io.RangeVector; ^ bad class file: ./uk/ac/sanger/artemis/io/RangeVector.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/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/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/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/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: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/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/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: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/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: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/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/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/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: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/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/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: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/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/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/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/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/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/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: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/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: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: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: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/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: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:875: warning: [removal] Integer(int) in Integer 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.setPhase(new Integer(0)); return new Character (current_char); ^ ./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: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: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/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: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: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/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); ^ ./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: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: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/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); ^ ^ ./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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ warning: [options] bootstrap class path not set in conjunction with -source 8 ./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)); ^ 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 ./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: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/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 () { ^ warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. ./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/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/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/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/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/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); ^ ./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/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/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/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/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: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: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/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:193: 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/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: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/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/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: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/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/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/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/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/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/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/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/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: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/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/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: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/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/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: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/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: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/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:837: 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/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/FeatureVector.java:29: 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/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); ^ 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: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/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: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: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/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/FeatureVector.java:165: error: cannot find symbol private FastVector vector = new FastVector (); ^ symbol: class FastVector location: class FeatureVector ./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: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/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/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/FeatureSegmentVector.java:46: error: cannot find symbol private FastVector vector = new FastVector (); ^ symbol: class FastVector location: class FeatureSegmentVector ./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: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/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/KeyVector.java:37: error: cannot find symbol public class KeyVector extends FastVector ^ symbol: class FastVector ./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: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: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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./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/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/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/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/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/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); ^ ./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: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/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: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: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: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: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/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/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/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/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/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/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: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: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: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/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)); ^ 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/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 ./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/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/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/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()); ^ 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 ./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(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/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/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: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/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/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 ./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/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: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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ 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 () { ^ ./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: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/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/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/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/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/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/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: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/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: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: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/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/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/ChadoTransaction.java:205: error: cannot access CvTerm 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/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/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/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:103: error: cannot find symbol private static Hashtable cvterms; ^ 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 CvTerm location: class DatabaseDocument ./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/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: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/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/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/chado/Graph.java:94: error: cannot find symbol } ^ 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 ./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/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: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: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/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/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:113: error: cannot find symbol CvTerm cvTerm, boolean not); ^ symbol: class CvTerm location: interface SequenceDaoI ./org/gmod/schema/dao/SequenceDaoI.java:146: error: cannot find symbol public Synonym getSynonymByNameAndCvTerm(String name, CvTerm type); ^ symbol: class CvTerm location: interface SequenceDaoI ./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/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: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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./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 ./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/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: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/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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./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/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 ./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); ^ (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 read_succeeded = new Boolean(false); ^ ./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/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/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: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/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ 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/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: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/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/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/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/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/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/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: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: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/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:495: error: cannot find symbol private CvTerm getCvTermFromCache(final Hashtable cvTermCache, ^ symbol: class CvTerm location: class GFFDocumentEntry ./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: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 ./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:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ 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/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/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/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/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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean 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/sequence/Marker.java:193: warning: [removal] finalize() in Object 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/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ 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/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/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)); ^ 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()); ^ public void finalize () { ^ ./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/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: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/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/genebuilder/cv/GoBox.java:241: error: cannot find symbol public static CvTerm getGOCvTerm(String term) ^ symbol: class CvTerm location: class GoBox ./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/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/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/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:259: error: incompatible types: RangeVector cannot be converted to Vector Vector ranges = f.getLocation().getRanges(); ^ ./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: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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./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: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: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/ArtemisUtils.java:703: error: cannot find symbol private static CvTerm getCvTerm(String cvTermName) ^ symbol: class CvTerm location: class ArtemisUtils ./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/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/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/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/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/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: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/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/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/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/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: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/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: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/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/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: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/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/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:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./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:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./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)); ./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: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/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: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: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/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: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/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: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: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/genebuilder/cv/CVPanel.java:624: error: cannot find symbol private void addCvTermQualifier(CvTerm cvterm, ^ symbol: class CvTerm location: class CVPanel ./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/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: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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./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/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: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: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/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: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/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: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: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/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: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/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/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/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: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/cv/CvTermsComparator.java:31: error: cannot find symbol 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/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: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: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/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: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/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/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/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: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 ./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/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/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/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()); ^ 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: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/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)); ^ 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/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short 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/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: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: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: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: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))); ^ 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: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: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/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: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: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: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/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: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/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: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: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/components/filetree/RemoteFileNode.java:91: 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 this.file_length = new Integer(fat.getSize().intValue()); featureloc.setPhase(new Integer(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/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: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/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: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: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: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: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: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: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: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/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 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: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/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/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: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: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))); ^ 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/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/util/DatabaseDocument.java:2140: 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: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 ./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 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 ./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()); ^ return new Character (current_char); ^ ./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: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 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: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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ 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/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/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: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/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: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 ./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/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/chado/ChadoTransactionManager.java:771: error: cannot find symbol CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm("part_of", "relationship"); ^ symbol: class CvTerm location: class ChadoTransactionManager 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: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: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: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: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()); ^ Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./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/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: 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/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: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)); ^ featureloc.setPhase(new Integer(2)); ^ ./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: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:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:797: error: cannot find symbol CvTerm cvterm = new CvTerm(); ^ ./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))); ^ symbol: class CvTerm ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal location: class ChadoTransactionManager 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:797: error: cannot find symbol CvTerm cvterm = new CvTerm(); ^ symbol: class CvTerm location: class ChadoTransactionManager ./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/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/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: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/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: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: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/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: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/chado/ChadoTransactionManager.java:2192: 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/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:933: 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); ^ 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: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: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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ 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/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/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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./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: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: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/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: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 ./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/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/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: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/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/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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(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)); ^ featureloc.setPhase(new Integer(2)); ^ ./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:903: error: cannot find symbol CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm("part_of", "relationship"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short 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/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/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ 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/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/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/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/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: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: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: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: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/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/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/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/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: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/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/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: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:954: error: cannot find symbol CvTerm cvterm = getCvTerm(key, "sequence"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./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/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: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: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/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: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/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/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/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: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: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/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: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: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: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/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/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:1071: error: cannot find symbol CvTerm cvTerm = DatabaseDocument.getCvTermByCvAndCvTerm(featureKey, "sequence"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./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/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/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/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/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: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:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ./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/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/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/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:972: 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/ChadoTransactionManager.java:689: 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 feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ 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: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: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: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/FeatureSegmentVector.java:155: error: cannot find symbol return_vector.vector = (FastVector) vector.clone (); ^ symbol: class FastVector location: class FeatureSegmentVector ./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/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/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: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/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: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/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/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/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:1167: error: cannot find symbol final CvTerm cvTerm = DatabaseDocument.getCvTermByCvTermName(name); ^ 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: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: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())); ^ 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/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/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: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/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer 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)); ^ ./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: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: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/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/io/QualifierInfo.java:131: error: cannot find symbol return required_keys.contains (key); ^ symbol: method contains(Key) location: variable required_keys of type KeyVector Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().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/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/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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 fasta_header_positions.remove(new Integer(nbase)); ^ ./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/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/KeyVector.java:85: error: cannot find symbol setElementAt (get(smallest), i); ^ symbol: method get(int) location: class KeyVector ./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/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/JdbcDAO.java:2074: 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( ^ ./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:1285: error: cannot find symbol CvTerm cvTerm = getCvTerm(key, "sequence"); ^ symbol: class CvTerm location: class ChadoTransactionManager ^ ./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 ./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:1354: error: cannot find symbol CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm(name, "feature_property"); ^ symbol: class CvTerm location: class ChadoTransactionManager ./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/KeyVector.java:86: error: cannot find symbol setElementAt (tmp, smallest); ^ symbol: method setElementAt(Key,int) location: class KeyVector ./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: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()); ^ 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)); ^ 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: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:1426: error: cannot find symbol CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm(name, "feature_property"); ^ symbol: class CvTerm location: class ChadoTransactionManager 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/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/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/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: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())); ^ 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: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/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/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/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: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: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/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/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: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/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/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/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: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: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: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:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./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: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/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: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: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: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: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/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/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: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/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: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/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: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: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: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: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: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/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/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 ./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/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())); ^ !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: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:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./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: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: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: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: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/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: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: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: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: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: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:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = 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: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: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:1383: 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/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: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:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ 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/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: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: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: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 ./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: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/chado/ChadoTransactionManager.java:274: 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 ./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/chado/JdbcDAO.java:952: 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 featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ 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/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/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: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: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)); ^ 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:2192: 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"))); ^ featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./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: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: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: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: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/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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./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:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = 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: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: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())); ^ return cvterms.get(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/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: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: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: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: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/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: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 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 ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ 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/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:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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())); ^ featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./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 ./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: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: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/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/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()); ^ ./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()); ^ featureloc.setPhase(new Integer(2)); ^ ./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: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: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: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( ^ featureCvTermDbXRefId = 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/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: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:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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/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/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: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/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: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: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 ./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() ); ^ 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/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/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: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: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/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: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/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: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:2401: error: cannot find symbol CvTerm cvTerm = getCvTerm( DatabaseDocument.getCvTermByCvTermId( ^ symbol: class CvTerm location: class ChadoTransactionManager ./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: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())); ^ 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 ./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: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/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ return cvterms.get(new Integer(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/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: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/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: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/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: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 Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./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: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: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: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: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: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/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: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: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: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: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/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: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: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: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/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/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/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/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/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: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: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: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/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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/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: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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./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 ./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: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: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 ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./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: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/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/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/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); ^ 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/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: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/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/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))); ^ return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./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: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/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: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: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/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: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: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: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/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:2583: error: cannot find symbol CvTerm cvTerm = new CvTerm(); ./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/RawStreamSequence.java:310: 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/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: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 ./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))); ^ ^ 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 uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2612: error: cannot find symbol final CvTerm cvTerm = getCvTerm(cvTermName, cvName, null, dbName); ^ symbol: class CvTerm location: class ChadoTransactionManager 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:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ 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: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/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: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:2650: error: cannot find symbol CvTerm cvTerm = null; ^ symbol: class CvTerm location: class ChadoTransactionManager ./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:1825: 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 return cvterms.get(new Integer(id)); ^ 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: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/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/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: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: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: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: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: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/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/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: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/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)); ^ 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: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: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: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: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: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: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:807: 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)); ^ featureId = new Integer(alias.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/chado/ChadoTransactionManager.java:689: 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 ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: 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( ^ featureloc.setStrand(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: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: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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ 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/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: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)); ^ ./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/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/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:901: 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 featureCvTermDbXRefId = new Integer( ^ ./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); ^ 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/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: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/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/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/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/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/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/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: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: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/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: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: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: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/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: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)); ^ ./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 ./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: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/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: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: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()); ^ 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/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: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: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: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: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: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: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: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: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: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/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: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/chado/ChadoTransactionManager.java:2221: 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( ^ ./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: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/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/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:2074: 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/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/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: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/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: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: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: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/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/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/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:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ 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/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/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/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: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/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/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: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/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/IBatisDAO.java:339: 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.setFmin(new Integer(min)); ^ ^ ./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: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/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: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/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/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/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/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: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: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: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: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/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: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/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: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: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: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: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: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: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: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: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: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: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: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: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: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: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/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/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: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/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: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: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: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/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: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/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/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: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 ./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: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: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 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: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: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: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: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: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/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)); ^ featureloc.setFmin(new Integer(rs.getInt("fmin"))); ./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: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/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/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:1249: 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/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/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/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/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/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/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: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/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ final Integer featureId = new Integer(feat.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:1280: 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: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: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:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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: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( ^ ./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:274: 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 chadoFeature.setSeqLen(new Integer( 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/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/IBatisDAO.java:339: 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/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/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: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: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: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: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 ./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/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/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()); ^ 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() ); ^ 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()); ^ featureId = new Integer(featurePub.getFeature().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:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ 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: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/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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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/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)); ^ featureCvTermDbXRefId = new Integer( ^ ./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:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = 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/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: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: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: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: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 ./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: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: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: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/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: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: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/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: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/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: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: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: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: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/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: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/IBatisDAO.java:339: 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/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:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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() ); ^ fasta_header_positions.remove(new Integer(nbase)); ^ ./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: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() ); ^ chadoFeature.setSeqLen(new Integer( ^ 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/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:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().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/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/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/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: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: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/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: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: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/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/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: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: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/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/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: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/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: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: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: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: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/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/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 8 Please remove or make sure it appears in the correct subdirectory of the classpath. ./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/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/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/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:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./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: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/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 ./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/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")); ^ 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/circular/TrackManager.java:55: error: cannot access Entry import uk.ac.sanger.artemis.Entry; ^ bad class file: ./uk/ac/sanger/artemis/Entry.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/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: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: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/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/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: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: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)); ^ ./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: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/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: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: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/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:675: error: cannot find symbol CvTerm cvTerm; ^ symbol: class CvTerm location: class DatabaseDocument ./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: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/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: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: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/IBatisDAO.java:1383: 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/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: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/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/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: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/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: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: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: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: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: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/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/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/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() ); ^ ./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:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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: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: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( ^ cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./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/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: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: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/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/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: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: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: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/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/io/IndexedGFFDocumentEntry.java:59: error: cannot find symbol private TabixReader reader; ^ symbol: class TabixReader location: class IndexedGFFDocumentEntry ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:283: error: package TabixReader does not exist final TabixReader.Iterator tabixIterator, ^ ./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/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: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: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/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: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/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/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 ./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: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/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: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)); ^ 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/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: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/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/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/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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/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: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: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/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 ./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)); ^ parent = dao.getLazyFeatureNoResiduesById(new Integer(src_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)); ^ 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: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/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/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/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/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: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:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./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/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:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ 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/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/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: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: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/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: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: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: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: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: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: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: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: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: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/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/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/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: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: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: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: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: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:1512: error: cannot find symbol CvTerm cvterm = getCvTerm( feature_cvterm.getCvTerm().getCvTermId(), dao, gene_builder); ^ symbol: class CvTerm location: class DatabaseDocument ./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: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: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: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: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/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: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/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/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/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: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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = 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:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = 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: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: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 ./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: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/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/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/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: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: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: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:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ progress.setValue((new Long(bytesSoFar)).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/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: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: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: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:1351: 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/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:1835: error: cannot find symbol Enumeration enum_cvterm = cvterms.elements(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1838: error: cannot find symbol CvTerm cvterm = enum_cvterm.nextElement(); ^ symbol: class CvTerm location: class DatabaseDocument 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/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/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: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: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/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: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() ); ^ ./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: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:1872: error: cannot find symbol Enumeration enum_cvterm = cvterms.elements(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1875: error: cannot find symbol CvTerm cvterm = enum_cvterm.nextElement(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1892: error: cannot find symbol final Enumeration enum_cvterm = cvterms.elements(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1895: error: cannot find symbol final CvTerm cvterm = enum_cvterm.nextElement(); ^ symbol: class CvTerm location: class DatabaseDocument ./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/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: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: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: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/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/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ featureloc.setPhase(new Integer(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/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: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: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: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: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/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 ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ 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/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: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/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:1914: error: cannot find symbol Enumeration enum_cvterm = cvterms.elements(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1917: error: cannot find symbol CvTerm cvterm = enum_cvterm.nextElement(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1933: error: cannot find symbol final List cvterm_list = dao.getCvTerms(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1934: error: cannot find symbol final Iterator it = cvterm_list.iterator(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1935: error: cannot find symbol cvterms = new Hashtable(cvterm_list.size()); ^ 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/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:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1939: error: cannot find symbol if(strand.equals( new Short((short)-1)) ) // strand ^ final CvTerm cvterm = it.next(); ^ symbol: class CvTerm location: class DatabaseDocument ./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/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: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/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:2010: error: cannot find symbol final Vector cvterm_match = new Vector(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2010: error: cannot find symbol final Vector cvterm_match = new Vector(); ^ symbol: class CvTerm location: class DatabaseDocument ./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:2015: error: cannot find symbol CvTerm cvterm = cvterms.get(key); ^ return cvterms.get(new Integer(id)); ^ ./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: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: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)); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2041: error: cannot find symbol CvTerm cvTerm = cvterms.get(key); ^ symbol: class CvTerm location: class DatabaseDocument ./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/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: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:2083: error: cannot find symbol final Enumeration enum_cvterm = cvterms.elements(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2086: error: cannot find symbol final CvTerm cvTerm = enum_cvterm.nextElement(); ^ symbol: class CvTerm location: class DatabaseDocument ./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/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: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: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:2111: error: cannot find symbol ./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); ^ List synonymCvTerms = doc.getDAO().getCvTermByNameInCv(null, cv); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2123: error: cannot find symbol Enumeration cvterm_enum = cvterms.elements(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2126: error: cannot find symbol CvTerm cvterm = cvterm_enum.nextElement(); ^ symbol: class CvTerm location: class DatabaseDocument ./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: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)); ^ ./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: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/sequence/Marker.java:193: warning: [removal] finalize() in Object 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"))); ^ public void finalize () { ./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/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/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: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: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: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: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: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: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 ./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: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/IBatisDAO.java:688: 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 return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./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/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: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/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() ); ^ 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: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); ^ 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 ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./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: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/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/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: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: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: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)); ^ ./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/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/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/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/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: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/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/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: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/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: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/GmodDAO.java:473: error: cannot find symbol CvTerm cvTerm; ^ symbol: class CvTerm location: class GmodDAO ./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: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/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: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/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:258: error: cannot find symbol CvTerm cvTerm = new CvTerm(); ^ symbol: class CvTerm location: class JdbcDAO ./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/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ./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/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/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/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/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: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: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 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/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/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/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: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: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: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: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 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: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/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/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/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: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/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: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/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/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/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: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/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/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/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/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/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/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: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/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/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: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/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/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/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/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/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/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: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:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(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/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: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 ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ db_id = new Integer(rs.getInt("db_id")); ^ ./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/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/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: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: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: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:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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)); ^ 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/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/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: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/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/circular/DNADraw.java:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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)); ^ 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/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/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/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/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/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/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/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/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/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/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: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/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: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/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/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: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: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: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/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/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./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/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: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: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/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: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/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/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: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/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: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: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: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: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: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:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./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); ^ ./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/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/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/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: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/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/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/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: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/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: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/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: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: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/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 ./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); ^ 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: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/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: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: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/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/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/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/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/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/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/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/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: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/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/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/Location.java:850: 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())); ^ return_object = new Integer(start_value); ^ ./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/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/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/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/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/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: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/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: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: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: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/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: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/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/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/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/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/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: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:274: warning: [removal] Integer(int) in Integer 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/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)); ^ chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/circular/Track.java:50: error: cannot find symbol private Entry entry; ^ symbol: class Entry location: class Track ./uk/ac/sanger/artemis/circular/Track.java:53: error: cannot find symbol public Track(double position, Entry entry) ^ symbol: class Entry location: class Track ./uk/ac/sanger/artemis/circular/Track.java:65: error: cannot find symbol Entry entry) ^ symbol: class Entry location: class Track ./uk/ac/sanger/artemis/circular/Track.java:94: error: cannot find symbol Entry entry) ^ symbol: class Entry location: class Track ./uk/ac/sanger/artemis/circular/Track.java:225: error: cannot find symbol public Entry getEntry() ^ symbol: class Entry location: class Track ./uk/ac/sanger/artemis/circular/Track.java:230: error: cannot find symbol public void setEntry(Entry entry) ^ symbol: class Entry location: class Track ./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:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java:319: error: cannot find symbol public static void lazyLoadAll(final Entry entry, final JFrame parent) ^ symbol: class Entry location: class GeneUtils ./uk/ac/sanger/artemis/components/DisplayComponent.java:52: error: cannot find symbol symbol: class Entry location: class EditMenu ./uk/ac/sanger/artemis/components/DisplayComponent.java:52: error: cannot find symbol symbol: class Entry location: class EditMenu ./uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java:372: error: cannot find symbol symbol: class Entry location: class GeneBuilderFrame ./uk/ac/sanger/artemis/components/QualifierTextArea.java:145: error: cannot find symbol Style style = addStyle("Blue", null); ^ symbol: class Entry location: class FeatureEdit ./uk/ac/sanger/artemis/components/UserDefinedQualifiers.java:868: error: cannot find symbol } ^ symbol: class Entry location: class FeatureEdit ./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/UserDefinedQualifiers.java:868: error: cannot find symbol } ^ symbol: class Entry location: class FeatureEdit ./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/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/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/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 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/database/DatabaseEntrySource.java:96: error: cannot find symbol public Entry getEntry(final Bases bases, final boolean show_progress) ^ symbol: class Entry location: class DatabaseEntrySource ./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/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: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/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: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/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/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:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/components/database/DatabaseEntrySource.java:102: error: cannot find symbol public Entry getEntry(final boolean show_progress) ^ symbol: class Entry location: class DatabaseEntrySource ./uk/ac/sanger/artemis/components/database/DatabaseEntrySource.java:120: error: cannot find symbol public Entry getEntry(String id, String schema, ^ symbol: class Entry location: class DatabaseEntrySource ./uk/ac/sanger/artemis/components/database/DatabaseEntrySource.java:127: error: cannot find symbol public Entry getEntry(String id, String schema, ^ symbol: class Entry location: class DatabaseEntrySource ./uk/ac/sanger/artemis/components/database/DatabaseEntrySource.java:235: error: cannot find symbol private Entry makeFromID(final Bases bases, final String id, ^ symbol: class Entry location: class DatabaseEntrySource ./uk/ac/sanger/artemis/components/genebuilder/BasicGeneBuilderFrame.java:655: error: cannot find symbol private Entry getEntry() ^ symbol: class Entry location: class BasicGeneBuilderFrame ./uk/ac/sanger/artemis/components/SelectionInfoDisplay.java:488: error: cannot find symbol symbol: class Entry location: class EntryEdit ./uk/ac/sanger/artemis/components/SelectionInfoDisplay.java:488: error: cannot find symbol symbol: class Entry location: class EntryEdit ./uk/ac/sanger/artemis/components/SelectionInfoDisplay.java:488: error: cannot find symbol symbol: class Entry location: class EntryEdit ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:178: error: cannot find symbol symbol: class Entry location: class BamView ./uk/ac/sanger/artemis/components/EntryGroupDisplay.java:187: error: cannot find symbol private void add(final Entry entry) ^ symbol: class Entry location: class EntryGroupDisplay ./uk/ac/sanger/artemis/components/EntryGroupDisplay.java:285: error: cannot find symbol private void setEntryHighlight(final Entry entry, ^ symbol: class Entry location: class EntryGroupDisplay ./uk/ac/sanger/artemis/components/ArtemisMain.java:699: error: cannot find symbol public static EntryEdit makeEntryEdit(final Entry entry) ^ symbol: class Entry location: class ArtemisMain ./uk/ac/sanger/artemis/components/EntryEdit.java:2413: error: cannot find symbol final Entry destination_entry) ^ symbol: class Entry location: class ReadFeaturesActionListener ./uk/ac/sanger/artemis/components/EntryActionListener.java:45: error: cannot find symbol final Entry entry) { ^ symbol: class Entry location: class EntryActionListener ./uk/ac/sanger/artemis/components/EntryActionListener.java:52: error: cannot find symbol public Entry getEntry () { ^ symbol: class Entry location: class EntryActionListener ./uk/ac/sanger/artemis/components/EntryActionListener.java:60: error: cannot find symbol final private Entry entry; ^ symbol: class Entry location: class EntryActionListener ./uk/ac/sanger/artemis/components/EntryEdit.java:2491: error: cannot find symbol final Entry entry) ^ symbol: class Entry location: class SaveEntryActionListener ./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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./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)); ^ progress.setValue((new Long(bytesSoFar)).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/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: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: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/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/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: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/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: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: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/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/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/EntryEdit.java:2510: error: cannot find symbol final Entry entry) ^ symbol: class Entry location: class SaveEntryAsActionListener ./uk/ac/sanger/artemis/components/EntryEdit.java:2529: error: cannot find symbol final Entry entry) ^ symbol: class Entry location: class SaveEntryAsEMBLActionListener ./uk/ac/sanger/artemis/components/EntryEdit.java:2548: error: cannot find symbol final Entry entry) ^ symbol: class Entry location: class SaveEntryAsGenbankActionListener ./uk/ac/sanger/artemis/components/EntryEdit.java:2568: error: cannot find symbol final Entry entry) ^ symbol: class Entry location: class SaveEntryAsGFFActionListener ./uk/ac/sanger/artemis/components/EntryEdit.java:2587: error: cannot find symbol final Entry entry) ^ symbol: class Entry location: class SaveEntryAsSubmissionActionListener 37 errors 4 warnings ./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/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/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: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); ^ 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: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: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/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/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: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/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: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: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: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/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/TrackManager.java:649: error: cannot find symbol RangeVector ranges = f.getLocation().getRanges(); ^ symbol: class RangeVector location: class TrackManager ./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/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/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: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: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: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:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./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: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 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: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/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:193: warning: [removal] Character(char) in Character 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( ^ ./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/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:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./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: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: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/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/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()); ^ 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/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)); ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/circular/GCGraph.class] Error 1 gmake: *** Waiting for unfinished jobs.... ./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 ./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/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: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/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/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: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)); ^ 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 ^ ./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: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: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: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/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 () { ^ 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/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/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/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/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: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:314: 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/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/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: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: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: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/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/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: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: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())); ^ 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/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 ./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: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: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: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/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: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: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: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/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/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/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: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: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: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: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: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: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: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: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/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: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: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/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/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/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/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/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal ./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/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/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/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/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/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:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./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/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: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/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: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: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: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: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:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(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/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/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./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: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/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/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/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/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: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/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: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/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/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: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/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: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/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/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/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/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/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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./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: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/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: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/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: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/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/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: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/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/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: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: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/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/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/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/chado/ChadoTransactionManager.java:2192: 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/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: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/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/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)); ^ 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/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/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/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/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/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/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/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ^ 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/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/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: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); ^ lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./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/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: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/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/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 ./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/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/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"))); ^ chadoFeature.setSeqLen(new Integer( ^ ./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: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: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: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/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: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/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/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/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: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/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/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/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: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: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: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/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/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: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: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: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/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/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: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/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/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/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/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/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/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/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/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/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: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:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./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/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/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 ./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/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: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: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)); ^ 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/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/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/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 ./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:1825: 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()); ^ 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:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ 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/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/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: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: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: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/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: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/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/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ 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/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: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/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/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:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(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/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: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: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/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/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/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:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: 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/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: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: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: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: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() ); ^ 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/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/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: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/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 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/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/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/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: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/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: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/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: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/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/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/IBatisDAO.java:1383: 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/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/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/util/DatabaseDocument.java:2140: 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/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/circular/Wizard.java:580: error: cannot find symbol final RangeVector ranges = new RangeVector(); ^ symbol: class RangeVector location: class Wizard 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)); ^ Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:580: error: cannot find symbol final RangeVector ranges = new RangeVector(); ^ symbol: class RangeVector location: class Wizard ./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: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: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: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: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: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/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: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/GFFDocumentEntry.java:664: 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/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)); ^ 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/plot/CodonUsageAlgorithm.java:183: 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 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: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)); ^ return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./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/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/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/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/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/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/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/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/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/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: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:309: 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 ./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/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)); ^ 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)); ^ 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/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:1078: 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: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)); ^ 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/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/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/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/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: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/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/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/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/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/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/circular/Wizard.java:719: error: cannot find symbol RangeVector ranges = f.getLocation().getRanges(); ^ symbol: class RangeVector location: class Wizard ./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/circular/Wizard.java:833: error: cannot find symbol RangeVector ranges = f.getLocation().getRanges(); ^ symbol: class RangeVector location: class Wizard ./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/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/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/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/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:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./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/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/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/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./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/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new 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/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/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: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/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"))); ^ 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/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: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/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/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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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: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: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 ./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/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.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())); ^ 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: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/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/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: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/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/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/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 ./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/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/EntryFileDialog.java:199: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(null); ^ ./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/components/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ 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/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: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: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/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: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); ^ 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/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/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:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)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/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/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/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/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./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/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: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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./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/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/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: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/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: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: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/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/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: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/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/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/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/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/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/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: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:289: 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/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); 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:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./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/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: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/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: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/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()); ^ ./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)); ^ 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/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/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())); ^ 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./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/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: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/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: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/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/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/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/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/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/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: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/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/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: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/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/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/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/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/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/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/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 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/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/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/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/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/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/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/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/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/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/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/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/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 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/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/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/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/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./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/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ./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: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/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/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: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/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/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/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: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/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/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal ./uk/ac/sanger/artemis/circular/Wizard.java:711: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); lineAttr.put("end", new Integer(entry.getBases().getLength())); ^ ./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/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/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/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: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: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: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:837: 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); ^ dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./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: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/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/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/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/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/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/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/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/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: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:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./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/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/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/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/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 ./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/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/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/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/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/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ featureId = new Integer(featurePub.getFeature().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/util/DatabaseDocument.java:867: 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 featureId = new Integer(feature_cvterm.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/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = 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/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/FeatureLocLazyQualifierValue.java:97: 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/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) 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/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/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: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/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); ^ 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)); ^ final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./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/chado/JdbcDAO.java:2074: 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)); ^ 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/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/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()); ^ 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/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/ChadoTransactionManager.java:274: 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/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/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/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: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() ); ^ 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 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 ^ ./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/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/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/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/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: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/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/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/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float 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/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)); 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/FeatureLocLazyQualifierValue.java:97: 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/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 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: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: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/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: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/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/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: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: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/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 ./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/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: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: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/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/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)); ^ this.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/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/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); ^ 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/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: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: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/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)); ^ return new Float (0); ^ ./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/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: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/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/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/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/ChadoTransactionManager.java:274: 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: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)) ) ^ chadoFeature.setSeqLen(new Integer( ^ ./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/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/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/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/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/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/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 final Vector v = (Vector)hash.get(new Integer(clusterFeature.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/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:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./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/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/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/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: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: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: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: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/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/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/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/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: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/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: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/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: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:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ 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/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/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/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/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer 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 final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ 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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer 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 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: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:181: 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/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./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:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./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/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/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()); ^ 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 !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/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/GeneUtils.java:438: error: cannot find symbol for(int i=0; i sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./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/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/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/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/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/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/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: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); ^ 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/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/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/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/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/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: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: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: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/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/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/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/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/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/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/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: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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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: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: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/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: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 final Vector v = (Vector)hash.get(new Integer(clusterFeature.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/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/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/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/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: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/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/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/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/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/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/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/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/components/filetree/RemoteFileNode.java:91: 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/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/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/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); 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/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/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: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/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/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/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/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/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/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/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/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/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./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/SimpleEntryInformation.java:74: error: cannot find symbol if (user_keys != null && user_keys.contains (key)) { ^ symbol: method contains(Key) location: variable user_keys of type KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:82: error: cannot find symbol user_keys.add (key); ^ symbol: method add(Key) location: variable user_keys of type KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:124: error: cannot find symbol for (int i = 0 ; i < qualifier_valid_keys.size () ; ++i) { ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) 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())); ^ ./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)); ^ symbol: method size() location: variable qualifier_valid_keys of type KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:125: error: cannot find symbol final Key this_key = (Key)qualifier_valid_keys.get(i); ^ symbol: method get(int) location: variable qualifier_valid_keys of type KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:127: error: cannot find symbol if (valid_keys != null && valid_keys.contains (this_key)) { ^ symbol: method contains(Key) location: variable valid_keys of type KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:135: error: cannot find symbol valid_keys.add (this_key); ^ symbol: method add(Key) location: variable valid_keys of type KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:156: error: cannot find symbol for (int i = 0 ; i < user_keys.size () ; ++i) { ^ symbol: method size() location: variable user_keys of type KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:157: error: cannot find symbol if (!return_keys.contains ((Key)user_keys.get (i))) { ^ symbol: method get(int) location: variable user_keys of type KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:157: error: cannot find symbol if (!return_keys.contains ((Key)user_keys.get (i))) { ^ symbol: method contains(Key) location: variable return_keys of type KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:158: error: cannot find symbol return_keys.add ((Key)user_keys.get (i)); ^ symbol: method get(int) location: variable user_keys of type KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:158: error: cannot find symbol return_keys.add ((Key)user_keys.get (i)); ^ symbol: method add(Key) location: variable return_keys of type KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:195: error: cannot find symbol return (Key)getValidKeys ().get (0); ^ symbol: method get(int) location: class KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:282: error: cannot find symbol if (getUserKeys () != null && getUserKeys ().contains (key)) { ^ symbol: method contains(Key) location: class KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:307: error: cannot find symbol if (getUserKeys () != null && getUserKeys ().contains (key)) { ^ symbol: method contains(Key) location: class KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:334: error: cannot find symbol if (valid_keys.contains (key)) { ^ symbol: method contains(Key) location: variable valid_keys of type KeyVector ./uk/ac/sanger/artemis/io/SimpleEntryInformation.java:337: error: cannot find symbol if (getUserKeys () != null && getUserKeys ().contains (key)) { ^ symbol: method contains(Key) location: class KeyVector ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: 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()); ^ 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: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/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/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/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/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/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/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/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/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/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/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/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/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 final Vector v = (Vector)hash.get(new Integer(clusterFeature.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/components/AlignmentViewer.java:320: error: cannot find symbol public void selectFromSubjectRanges(final RangeVector select_ranges) ^ symbol: class RangeVector location: class AlignmentViewer ./uk/ac/sanger/artemis/components/AlignmentViewer.java:387: error: cannot find symbol public void selectFromQueryRanges(final RangeVector select_ranges) ^ symbol: class RangeVector location: class AlignmentViewer ./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/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/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/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/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/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/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/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/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/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/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: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/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/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/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/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/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/KeyChoice.java:142: error: cannot find symbol keys.add (Key.CDS); ^ symbol: method add(Key) location: variable keys of type KeyVector ./uk/ac/sanger/artemis/components/KeyChoice.java:145: error: cannot find symbol for (int i = 0 ; i < keys.size () ; ++i) ^ symbol: method size() location: variable keys of type KeyVector ./uk/ac/sanger/artemis/components/KeyChoice.java:146: error: cannot find symbol key_chooser.addItem ( ((Key)keys.get(i)).toString ()); ^ symbol: method get(int) location: variable keys of type KeyVector ./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/plot/UserDataAlgorithm.java:897: error: cannot find symbol private TabixReader reader; ^ symbol: class TabixReader location: class UserDataAlgorithm.TabixIdxGraph ./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/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/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/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/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/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/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/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/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/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/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/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/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/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: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/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: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/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/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/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/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/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/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: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/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: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 ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: 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 feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ 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: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/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 (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/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/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/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ 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: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 52 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/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/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/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/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/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/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: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/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: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/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/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/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/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal ./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); ^ 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/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/FeatureEdit.java:1511: error: cannot find symbol if(possible_keys != null && !possible_keys.contains(key)) ^ symbol: method contains(Key) location: variable possible_keys of type KeyVector ./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/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/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/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/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/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/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/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: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/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 ./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)); ^ 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/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/ReadAndWriteEntry.java:239: error: cannot find symbol qualifierInfo.getValidKeys().add(new_key); ^ symbol: method add(Key) location: class KeyVector ./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/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/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/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/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/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 ./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)); ^ 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/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/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/RunMenu.java:265: error: cannot find symbol public void statusChanged(final ExternalProgramEvent e) ^ symbol: class ExternalProgramEvent ./uk/ac/sanger/artemis/components/RunMenu.java:267: error: cannot find symbol if(e.getType() == ExternalProgramEvent.FINISHED) ^ symbol: variable ExternalProgramEvent ./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/GFFEntryInformation.java:187: error: cannot find symbol valid_keys.add(current_key); ^ symbol: method add(Key) location: variable valid_keys of type KeyVector ./uk/ac/sanger/artemis/io/GFFEntryInformation.java:192: error: cannot find symbol valid_keys.add(current_key); ^ symbol: method add(Key) location: variable valid_keys of type KeyVector ./uk/ac/sanger/artemis/io/GFFEntryInformation.java:193: error: cannot find symbol required_keys.add(current_key); ^ symbol: method add(Key) location: variable required_keys of type KeyVector ./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/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/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/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/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/SelectMenu.java:650: error: cannot find symbol if (!seen_keys.contains (current_feature.getKey ())) { ^ symbol: method contains(Key) location: variable seen_keys of type KeyVector ./uk/ac/sanger/artemis/components/SelectMenu.java:651: error: cannot find symbol seen_keys.add (current_feature.getKey ()); ^ symbol: method add(Key) location: variable seen_keys of type KeyVector ./uk/ac/sanger/artemis/components/SelectMenu.java:657: error: cannot find symbol for (int i = 0 ; i < seen_keys.size () ; ++i) { ^ symbol: method size() location: variable seen_keys of type KeyVector ./uk/ac/sanger/artemis/components/SelectMenu.java:658: error: cannot find symbol selectByKey ((Key)seen_keys.get(i)); ^ symbol: method get(int) location: variable seen_keys of type KeyVector ./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/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/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/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/io/GFFUtils.java:117: error: reference to getSegmentID is ambiguous String segId = gff.getSegmentID(rnew); ^ both method getSegmentID(Range) in GFFStreamFeature and method getSegmentID(RangeVector) in GFFStreamFeature match ./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)); ^ 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/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/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. ./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())); ^ 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/GFFDocumentEntry.java:499: 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)); ^ 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/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/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)); ^ 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/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/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/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: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/RestrictionEnzyme.java:119: 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/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. 3 errors 100 warnings re.add(new Integer(pos.getValue())); ^ ./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/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)) ) ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/Selection.class] Error 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: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: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/AlignmentViewer.java:224: error: cannot find symbol final RangeVector ranges = subject_selection.getSelectionRanges(); ^ symbol: class RangeVector ./uk/ac/sanger/artemis/components/AlignmentViewer.java:240: error: cannot find symbol final RangeVector ranges = query_selection.getSelectionRanges (); ^ symbol: class RangeVector 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. 52 errors 100 warnings ./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)); ^ 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/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")); ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/SimpleEntryGroup.class] Error 1 ./uk/ac/sanger/artemis/components/Navigator.java:758: error: cannot find symbol private boolean overlapsRange(final RangeVector ranges, ^ symbol: class RangeVector location: class Navigator ./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/EditMenu.java:1487: error: cannot find symbol final RangeVector ranges = new RangeVector(); ^ symbol: class RangeVector location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:1487: error: cannot find symbol final RangeVector ranges = new RangeVector(); ^ symbol: class RangeVector location: class EditMenu ./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/EditMenu.java:1930: error: cannot find symbol RangeVector ranges = feature_new.getLocation().getRanges(); ^ symbol: class RangeVector location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:2490: error: cannot find symbol 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 169 total; use -Xmaxerrs if you would like to see more final RangeVector new_ranges = new RangeVector (); ^ symbol: class RangeVector location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:2490: error: cannot find symbol final RangeVector new_ranges = new RangeVector (); ^ symbol: class RangeVector location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:3007: error: cannot find symbol final RangeVector contigRanges = new RangeVector(); ^ symbol: class RangeVector location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:3007: error: cannot find symbol final RangeVector contigRanges = new RangeVector(); ^ symbol: class RangeVector location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:3593: error: cannot find symbol RangeVector ranges = cds_to_fix.getLocation().getRanges(); ^ symbol: class RangeVector location: class EditMenu ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:99: error: cannot find symbol reader = new TabixReader(gffFile.getAbsolutePath()); ^ symbol: class TabixReader location: class IndexedGFFDocumentEntry ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:252: error: package TabixReader does not exist TabixReader.Iterator tabixIterator = 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); ^ 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/FeatureEdit.java:1333: error: cannot find symbol final RangeVector location_ranges = location.getRanges(); ^ symbol: class RangeVector location: class FeatureEdit ./uk/ac/sanger/artemis/components/FeatureEdit.java:1336: error: cannot find symbol final RangeVector new_ranges = new RangeVector(); ^ symbol: class RangeVector location: class FeatureEdit ./uk/ac/sanger/artemis/components/FeatureEdit.java:1336: error: cannot find symbol final RangeVector new_ranges = new RangeVector(); ^ symbol: class RangeVector location: class FeatureEdit gmake: *** [Makefile:47: uk/ac/sanger/artemis/chado/ChadoTransactionManager.class] Error 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/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/GeneViewerPanel.java:750: error: cannot find symbol RangeVector ranges = f.getLocation().getRanges(); ^ symbol: class RangeVector location: class GeneViewerPanel ./uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java:1003: error: cannot find symbol RangeVector ranges = exon.getLocation().getRanges(); ^ symbol: class RangeVector location: class GeneViewerPanel ./uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java:1097: error: cannot find symbol RangeVector ranges = embl_feature.getLocation().getRanges(); ^ symbol: class RangeVector location: class GeneViewerPanel ./uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java:1403: error: cannot find symbol new Location(new RangeVector(range), isComplement), ^ symbol: class RangeVector location: class GeneViewerPanel ./uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java:1525: error: cannot find symbol new Location(new RangeVector(range), ^ symbol: class RangeVector location: class GeneViewerPanel ./uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java:1545: error: cannot find symbol final RangeVector ranges = new RangeVector(); ^ symbol: class RangeVector location: class GeneViewerPanel ./uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java:1545: error: cannot find symbol final RangeVector ranges = new RangeVector(); ^ symbol: class RangeVector location: class GeneViewerPanel ./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/genebuilder/BasicGeneBuilderFrame.java:950: error: cannot find symbol RangeVector ranges = f.getLocation().getRanges(); ^ symbol: class RangeVector location: class BasicGeneBuilderFrame ./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/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/AddMenu.java:774: error: cannot find symbol final RangeVector cds_ranges = cds_location.getRanges (); ^ symbol: class RangeVector location: class AddMenu ./uk/ac/sanger/artemis/components/AddMenu.java:823: error: cannot find symbol final RangeVector intron_ranges = new RangeVector (); ^ symbol: class RangeVector location: class AddMenu ./uk/ac/sanger/artemis/components/AddMenu.java:823: error: cannot find symbol final RangeVector intron_ranges = new RangeVector (); ^ symbol: class RangeVector location: class AddMenu ./uk/ac/sanger/artemis/components/AddMenu.java:1117: error: cannot find symbol final RangeVector cds_ranges = cds_location.getRanges (); ^ symbol: class RangeVector location: class AddMenu ./uk/ac/sanger/artemis/components/AddMenu.java:1124: error: cannot find symbol final RangeVector exon_ranges = new RangeVector (); ^ symbol: class RangeVector location: class AddMenu ./uk/ac/sanger/artemis/components/AddMenu.java:1124: error: cannot find symbol final RangeVector exon_ranges = new RangeVector (); ^ symbol: class RangeVector location: class AddMenu ./uk/ac/sanger/artemis/components/AddMenu.java:1189: error: cannot find symbol final RangeVector ranges = new RangeVector (); ^ symbol: class RangeVector location: class AddMenu ./uk/ac/sanger/artemis/components/AddMenu.java:1189: error: cannot find symbol final RangeVector ranges = new RangeVector (); ^ symbol: class RangeVector location: class AddMenu ./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 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/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/EntryGroupInfoDisplay.java:335: error: cannot find symbol final RangeVector ranges = location.getRanges(); ^ symbol: class RangeVector location: class EntryGroupInfoDisplay 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:961: error: cannot find symbol final RangeVector ranges = location.getRanges(); ^ symbol: class RangeVector 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/genebuilder/ButtonPanel.java:368: error: cannot find symbol final RangeVector location_ranges = location.getRanges(); ^ symbol: class RangeVector location: class ButtonPanel ./uk/ac/sanger/artemis/components/genebuilder/ButtonPanel.java:371: error: cannot find symbol final RangeVector new_ranges = new RangeVector(); ^ symbol: class RangeVector location: class ButtonPanel ./uk/ac/sanger/artemis/components/genebuilder/ButtonPanel.java:371: error: cannot find symbol final RangeVector new_ranges = new RangeVector(); ^ symbol: class RangeVector location: class ButtonPanel 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: 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: 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. 48 errors 100 warnings ./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 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 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 ./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/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 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. ./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); ^ 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/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)); ^ 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. 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 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 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 or override a deprecated API. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 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 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 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 07:04:11 EDT 2026 build time: 00:06:00 !!! build failure encountered !!!