=>> Building biology/artemis build started at Tue Mar 17 20:48:39 EDT 2026 port directory: /usr/ports/biology/artemis package name: artemis-17.0.1.11_1 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 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: 8c988f802ea2 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: 1500068 Job Id: 09 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 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_15_0_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_15_0_x64-HEAD-ALL/09/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_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=15.0 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 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 libX11-1.8.13,1... [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 libX11-1.8.13,1: .......... 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-1.1.9... [pkg.DaveG.ca] | | `-- Extracting libfontenc-1.1.9: ...... 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 python311-3.11.15: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===== Message from openjdk21-21.0.10+7.1_1: -- This OpenJDK implementation may require procfs(5) mounted on /proc for some applications. If you have not done it yet, please do the following: mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: proc /proc procfs rw 0 0 ===> artemis-17.0.1.11_1 depends on file: /usr/local/openjdk21/bin/java - found ===> Returning to build of artemis-17.0.1.11_1 ===> artemis-17.0.1.11_1 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> artemis-17.0.1.11_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of artemis-17.0.1.11_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for artemis-17.0.1.11_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for artemis-17.0.1.11_1 CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Action.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ActionController.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ActionVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/AlignMatch.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/AlignMatchVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/AlignmentSelectionChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/AlignmentSelectionChangeListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/BlastM8ComparisonData.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ChangeEventVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ChangeListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ClipBoard.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ComparisonData.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ComparisonDataFactory.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ComparisonDataParseException.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Entry.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntryChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntryChangeListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntryGroup.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntryGroupChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntryGroupChangeListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntrySource.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntrySourceVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/EntryVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgram.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramException.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramMonitor.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramThread.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ExternalProgramVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Feature.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureChangeListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureEnumeration.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureFromVectorPredicate.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureKeyPredicate.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureKeyQualifierPredicate.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeaturePatternPredicate.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeaturePredicate.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeaturePredicateConjunction.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeaturePredicateVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureSegment.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureSegmentVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FeatureVector.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/FilteredEntryGroup.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/GotoEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/GotoEventSource.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/GotoListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/LastSegmentException.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Logger.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/MSPcrunchComparisonData.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/MUMmerComparisonData.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/MegaBlastComparisonData.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/OptionChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/OptionChangeListener.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Options.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/ProcessMonitor.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/SSAHAComparisonData.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Selectable.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/Selection.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/SelectionChangeEvent.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/SelectionChangeListener.java 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] 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. 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] 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] 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] 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] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] target value 8 is obsolete and will be removed in a future release 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] 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] 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] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] 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] 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] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] 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] 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] 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] 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] 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. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] 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. 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. 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). 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. 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 Use -Xlint:-options to suppress this message. 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 Use -proc:none to 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] 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 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. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release 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. 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 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 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. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. 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. 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] 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. 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 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 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 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/ChadoCvTermView.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/ChadoDAO.java 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); ^ 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/ChadoDemo.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/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 ./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)); ^ 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java 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/CommitFrame.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/SimpleExternalProgramMonitor.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 5 warnings ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 11 warnings warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 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/DbSqlConfig.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/FeatureForUpdatingResidues.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/FeatureLocLazyQualifierValue.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/GmodDAO.java ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/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 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/JdbcDAO.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. Note: ./uk/ac/sanger/artemis/util/FastVector.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 11 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 ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. Note: ./uk/ac/sanger/artemis/util/FastVector.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 11 warnings 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] 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] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. 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. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] 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. 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. 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. 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: uk/ac/sanger/artemis/SimpleExternalProgramMonitor.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/DNADraw.java 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 6 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/Feature.java ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 6 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/GCGraph.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: 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 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/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. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. 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/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/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/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); ^ Note: uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 14 warnings ./uk/ac/sanger/artemis/io/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/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: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/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/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/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: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)); ^ 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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/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/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/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: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:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/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/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/Bases.java:30: error: cannot access Range import uk.ac.sanger.artemis.io.Range; ^ bad class file: ./uk/ac/sanger/artemis/io/Range.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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/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: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:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/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:172: 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/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/Range.java: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: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: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: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/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/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./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/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/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:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./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: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/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:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/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:172: 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: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/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); ^ 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/circular/Feature.java:23: error: cannot access InvalidRelationException import uk.ac.sanger.artemis.io.InvalidRelationException; ^ bad class file: ./uk/ac/sanger/artemis/io/InvalidRelationException.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: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/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/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/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/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: 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/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: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/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: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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/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 ./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); ^ 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); ^ warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/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/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: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/FeatureChangeEvent.java:42: error: cannot access ChangeEvent public class FeatureChangeEvent extends ChangeEvent ^ bad class file: ./uk/ac/sanger/artemis/ChangeEvent.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/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/FeatureSegment.java:507: error: cannot access LastSegmentException bad class file: ./uk/ac/sanger/artemis/LastSegmentException.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/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: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:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal 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/Entry.java:404: error: cannot access Document public Document getRootDocument() ^ bad class file: ./uk/ac/sanger/artemis/util/Document.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/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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/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: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/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/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: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:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/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/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: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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/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/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/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/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/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/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./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); ^ ./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/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/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/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/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/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: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: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/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: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: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/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/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/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/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/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/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/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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: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:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/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/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/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())); ^ Note: Annotation processing is enabled because one or more processors were found ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ 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/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/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/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java: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: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/components/DisplayAdjustmentEvent.java:37: error: cannot find symbol public class DisplayAdjustmentEvent extends ChangeEvent ^ symbol: class ChangeEvent ./uk/ac/sanger/artemis/components/IndexReferenceEvent.java:5: error: cannot find symbol public class IndexReferenceEvent extends ChangeEvent ^ symbol: class ChangeEvent ./uk/ac/sanger/artemis/components/SegmentBorder.java:114: error: cannot find symbol symbol: class ChangeEvent location: class FeatureDisplay 5 errors 4 warnings ./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: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/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/sequence/Strand.java:123: error: cannot find symbol * for stop codons, otherwise this is used to look for start codons. ^ symbol: class Range location: class MarkerRange ./uk/ac/sanger/artemis/sequence/Strand.java:139: error: cannot find symbol * @param query_codons The codons to search for. Each element of this ^ symbol: class Range location: class MarkerRange ./uk/ac/sanger/artemis/sequence/Strand.java:125: error: cannot find symbol public int [][] getStopOrStartCodons(final Range range, final StringVector query_codons) { ^ symbol: class Range location: class Strand ./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/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:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/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:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/io/KeyVector.java:28: 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/util/StringVector.java:157: error: cannot find symbol tok = argument.substring(idx1,idx2); ^ symbol: class Range location: class Strand ./uk/ac/sanger/artemis/util/StringVector.java:184: error: cannot find symbol * splitting using the given characters. If the argument String is zero ^ symbol: class Range location: class Strand ./uk/ac/sanger/artemis/util/StringVector.java:226: error: cannot find symbol symbol: class Range location: class Strand ./uk/ac/sanger/artemis/sequence/AminoAcidSequence.java:649: error: cannot find symbol return reverseComplementSearchForwardFor(bases_string, start_index); ^ symbol: class Range location: class Strand ./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/sequence/AminoAcidSequence.java:657: error: cannot find symbol * @param bases_string Search this String for the amino acid sequence. ^ symbol: class Range location: class Strand ./uk/ac/sanger/artemis/sequence/AminoAcidSequence.java:662: error: cannot find symbol private int reverseComplementSearchForwardFor(final String bases_string, ^ symbol: class Range location: class Strand ./uk/ac/sanger/artemis/sequence/AminoAcidSequence.java:673: error: cannot find symbol for(int offset = 0; offset < length (); ++offset) ^ symbol: class Range location: class Strand ./uk/ac/sanger/artemis/sequence/Bases.java:216: error: cannot find symbol private Range complementRange (final Range range) { ^ symbol: class Range location: class Bases ./uk/ac/sanger/artemis/sequence/Bases.java:216: error: cannot find symbol private Range complementRange (final Range range) { ^ symbol: class Range location: class Bases ./uk/ac/sanger/artemis/sequence/Bases.java:270: error: cannot find symbol public AminoAcidSequence getTranslation(final Range range, ^ symbol: class Range location: class Bases ./uk/ac/sanger/artemis/sequence/Bases.java:281: error: cannot find symbol public AminoAcidSequence getSpacedTranslation(final Range range, ^ symbol: class Range location: class Bases ./uk/ac/sanger/artemis/sequence/Bases.java:304: error: cannot find symbol public int [] getMatchingCodons (final Range range, final int direction, ^ symbol: class Range location: class Bases ./uk/ac/sanger/artemis/sequence/Bases.java:508: error: cannot find symbol protected int[] getStopCodons(final Range range, final int direction) ^ symbol: class Range location: class Bases ./uk/ac/sanger/artemis/sequence/Bases.java:664: error: cannot find symbol protected int[][] getStopOrStartCodons(final Range range, ^ symbol: class Range location: class Bases ./uk/ac/sanger/artemis/sequence/Bases.java:884: error: cannot find symbol public String getSubSequence (final Range range, final int direction) { ^ symbol: class Range location: class Bases ./uk/ac/sanger/artemis/sequence/Bases.java:941: error: cannot find symbol public char[] getSubSequenceC(final Range range, final int direction) ^ symbol: class Range location: class Bases ./uk/ac/sanger/artemis/sequence/Bases.java:1005: error: cannot find symbol public Bases truncate (final Range constraint) { ^ symbol: class Range location: class Bases ./uk/ac/sanger/artemis/sequence/Bases.java:1154: error: cannot find symbol public String deleteRange (final Range range) ^ symbol: class Range location: class Bases ./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: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/KeyVector.java:37: error: cannot find symbol public class KeyVector extends FastVector ^ symbol: class FastVector ./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/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/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/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:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/sequence/SequenceChangeEvent.java:57: error: cannot find symbol private Range range; ^ symbol: class Range location: class SequenceChangeEvent ./uk/ac/sanger/artemis/sequence/SequenceChangeEvent.java:94: error: cannot find symbol final Range range) ^ symbol: class Range location: class SequenceChangeEvent ./uk/ac/sanger/artemis/sequence/SequenceChangeEvent.java:104: error: cannot find symbol final Range range, ^ symbol: class Range location: class SequenceChangeEvent ./uk/ac/sanger/artemis/sequence/SequenceChangeEvent.java:166: error: cannot find symbol public Range getRange() ^ symbol: class Range location: class SequenceChangeEvent ./uk/ac/sanger/artemis/sequence/MarkerChangeEvent.java:83: error: cannot find symbol symbol: class Range location: class Feature ./uk/ac/sanger/artemis/sequence/MarkerChangeEvent.java:83: error: cannot find symbol symbol: class Range location: class Feature ./uk/ac/sanger/artemis/FeatureSegment.java:507: error: cannot find symbol symbol: class Range location: class Feature ./uk/ac/sanger/artemis/FeatureSegment.java:507: error: cannot find symbol symbol: class Range location: class Feature ./uk/ac/sanger/artemis/FeatureSegment.java:58: error: cannot find symbol final Range range) ^ symbol: class Range location: class FeatureSegment ./uk/ac/sanger/artemis/FeatureSegment.java:76: error: cannot find symbol public void setRange (final Range range) { ^ symbol: class Range location: class FeatureSegment ./uk/ac/sanger/artemis/FeatureSegment.java:209: error: cannot find symbol public Range getRawRange () { ^ symbol: class Range location: class FeatureSegment ./uk/ac/sanger/artemis/FeatureSegment.java:494: error: cannot find symbol private Range range = null; ^ symbol: class Range location: class FeatureSegment ./uk/ac/sanger/artemis/util/Document.java:210: error: cannot find symbol symbol: class Range location: class Entry ./uk/ac/sanger/artemis/FeatureEnumeration.java:59: error: cannot find symbol symbol: class Range location: class Entry ./uk/ac/sanger/artemis/EntryGroup.java:179: error: cannot find symbol FeatureVector getFeaturesInRange(final Range range) ^ symbol: class Range location: interface EntryGroup ./uk/ac/sanger/artemis/EntryVector.java:132: error: cannot find symbol symbol: class Range location: interface EntryGroup ./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/components/genebuilder/GeneUtils.java:834: error: cannot find symbol final Range range) ^ symbol: class Range location: class GeneUtils ./uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java:1117: error: cannot find symbol protected static Range checkTranscriptBoundary( ^ symbol: class Range location: class GeneUtils ./uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java:1158: error: cannot find symbol protected static Range checkTranscriptBoundary( ^ symbol: class Range location: class GeneUtils ./uk/ac/sanger/artemis/components/genebuilder/GeneUtils.java:1413: error: cannot find symbol private static Range setLocation(final Feature f, ^ symbol: class Range location: class GeneUtils ./uk/ac/sanger/artemis/Selection.java:432: error: cannot find symbol public Range getSelectionRange () { ^ symbol: class Range location: class Selection ./uk/ac/sanger/artemis/chado/ChadoTransaction.java:205: error: cannot find symbol symbol: class Range location: class ChadoTransactionManager ./uk/ac/sanger/artemis/util/DatabaseDocument.java:144: error: cannot find symbol private Range range; ^ symbol: class Range location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:322: error: cannot find symbol final Range range, ^ symbol: class Range location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:955: error: cannot find symbol final Range range, ^ symbol: class Range location: class DatabaseDocument ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/LargeObjectDocument.java:122: error: cannot find symbol symbol: class Range location: class DatabaseDocument ./uk/ac/sanger/artemis/components/variant/CDSFeature.java:16: error: cannot find symbol protected Range lastRange = null; ^ symbol: class Range location: class CDSFeature ./uk/ac/sanger/artemis/components/ZoomScrollBar.java:127: error: cannot find symbol } ^ symbol: class Range location: class FeatureDisplay ./uk/ac/sanger/artemis/components/ZoomScrollBar.java:127: error: cannot find symbol } ^ symbol: class Range location: class FeatureDisplay ./uk/ac/sanger/artemis/components/SegmentBorder.java:114: error: cannot find symbol symbol: class Range location: class FeatureDisplay ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java:1353: error: cannot find symbol final Range range, ^ symbol: class Range location: class GeneViewerPanel ./uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java:1506: error: cannot find symbol final GFFStreamFeature feature, Range range, ^ symbol: class Range location: class GeneViewerPanel ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:328: error: cannot find symbol symbol: class Range location: class DatabaseJPanel ./uk/ac/sanger/artemis/components/database/DatabaseEntrySource.java:128: error: cannot find symbol InputStreamProgressListener progress_listener, Range range) ^ symbol: class Range location: class DatabaseEntrySource ./uk/ac/sanger/artemis/components/database/DatabaseEntrySource.java:238: error: cannot find symbol final Range range) ^ symbol: class Range location: class DatabaseEntrySource ./uk/ac/sanger/artemis/SimpleEntryGroup.java:509: error: cannot find symbol public FeatureVector getFeaturesInRange(Range range) ^ symbol: class Range location: class SimpleEntryGroup ./uk/ac/sanger/artemis/SimpleEntryGroup.java:1013: error: cannot find symbol public EntryGroup truncate(final Range constraint) ^ symbol: class Range location: class SimpleEntryGroup ./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/FilteredEntryGroup.java:338: error: cannot find symbol public FeatureVector getFeaturesInRange(final Range range) ^ symbol: class Range location: class FilteredEntryGroup ./uk/ac/sanger/artemis/FilteredEntryGroup.java:651: error: cannot find symbol public EntryGroup truncate(final Range constraint) ^ symbol: class Range location: class FilteredEntryGroup 61 errors 4 warnings ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/FeatureVector.java:165: error: cannot find symbol private FastVector vector = new FastVector (); ^ symbol: class FastVector location: class FeatureVector ./uk/ac/sanger/artemis/FeatureSegmentVector.java:46: error: cannot find symbol private FastVector vector = new FastVector (); ^ symbol: class FastVector location: class FeatureSegmentVector ./uk/ac/sanger/artemis/io/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)); ^ changes.add(new Integer(ichanged)); ^ ./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/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/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)); ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/chado/ChadoCvTermView.class] Error 1 gmake: *** Waiting for unfinished jobs.... ./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/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/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/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ uk/ac/sanger/artemis/circular/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/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:174: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(0)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:175: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(4000)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:177: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(true)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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/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/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:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./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: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: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: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 Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/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))); ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/SimpleGotoEventSource.class] Error 1 ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/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/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/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./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:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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())); ^ 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/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:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/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/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/circular/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/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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java: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/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:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal majorTicks.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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/ExternalProgram.java:293: warning: [removal] Long(long) in Long 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); 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: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/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./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/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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/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: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/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:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./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/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ^ ./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/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 ./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: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: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: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: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:861: warning: [removal] Short(short) in Short 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/circular/DNADraw.java:724: 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 int index = ticks.indexOf(new Integer(tick)); ^ this.file_length = new Integer(fat.getSize().intValue()); ^ featureloc.setStrand(new Short((short)1)); ^ ./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/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/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/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:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java: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:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Character ('.'); featureIds.add(new Integer(thisFeature.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/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/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/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/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/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/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:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/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: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/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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: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: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/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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: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: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: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/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/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: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: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:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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: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: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:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/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/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/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/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/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/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:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/io/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: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: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: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/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:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ 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/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:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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 ./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/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: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 ./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())); ^ seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/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/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:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ 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/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/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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/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)); ^ ^ featureId = new Integer(featurePub.getFeature().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/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long 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/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/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)); ^ 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/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/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:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/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/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/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:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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/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/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/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:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/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/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: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: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:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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: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 ./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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/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: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/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ 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/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:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/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/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/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/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/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:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/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: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/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/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: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:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/circular/DNADraw.java: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:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: 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())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/chado/ChadoTransactionManager.java:274: 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() ); ^ ./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/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))); ^ chadoFeature.setSeqLen(new Integer( Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./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/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/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/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/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:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:175: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(4000)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java: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/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ uk/ac/sanger/artemis/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:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/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/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: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:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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: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")); ^ fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/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: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:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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/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:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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 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:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: 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/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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())); ^ return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./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/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: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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./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: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/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: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/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/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: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:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/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/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/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: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/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: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: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: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/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/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/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/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/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/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:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ 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: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/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/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/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/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ 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: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: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: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: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: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: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: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: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:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ uk/ac/sanger/artemis/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: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:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/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: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/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:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/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/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: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:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./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: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: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: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: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: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 ./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:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ 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/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/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:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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/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: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/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/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: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/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/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/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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/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:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ^ ./uk/ac/sanger/artemis/io/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: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: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/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/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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: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: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/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/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/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: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: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/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ 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/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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: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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./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/IBatisDAO.java:64: error: cannot access SequenceDaoI public class IBatisDAO extends GmodDAO ^ bad class file: ./org/gmod/schema/dao/SequenceDaoI.class class file truncated at offset 0 Please remove or make sure it appears in the correct subdirectory of the classpath. ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ uk/ac/sanger/artemis/chado/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:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/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/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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/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/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: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:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/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/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/chado/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/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ !seen.contains(new Integer(j))) ^ 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:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/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:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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/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:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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: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: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: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/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/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/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/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:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/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: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); ^ ^ featureId = new Integer(feature_cvterm.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: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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./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:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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/circular/DNADraw.java:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal majorTicks.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/chado/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/circular/DNADraw.java:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/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/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 ^ ./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/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/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: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.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: 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)); ^ 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/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: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:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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: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: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:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/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: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/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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: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/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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 ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/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:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/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: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: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/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: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: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: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: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/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:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/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)); ^ 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 Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/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: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: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: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:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/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/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/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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/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: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/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/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: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: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/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/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 ./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: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: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: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: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/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: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:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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 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)); ^ featureLoc.setFmax(new Integer(max)); ^ rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: 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/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: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/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: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: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: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:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/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/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: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/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:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/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: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)); ^ cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/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/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: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: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/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)); 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/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:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/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/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: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: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/chado/ChadoTransactionManager.java:877: 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.setPhase(new Integer(1)); ^ 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/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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:2209: warning: [removal] Short(short) in Short 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: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: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/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: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())); ^ featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: 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 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:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./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")); ^ 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/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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/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:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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:2217: 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/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: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/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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: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:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ 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: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: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/database/DatabaseJPanel.java:34: error: cannot access Selection import uk.ac.sanger.artemis.Selection; ^ bad class file: ./uk/ac/sanger/artemis/Selection.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/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/database/DatabaseTreeNode.java:37: error: cannot access OrganismProp import org.gmod.schema.organism.OrganismProp; ^ bad class file: ./org/gmod/schema/organism/OrganismProp.class class file truncated at offset 0 Please remove or make sure it appears in the correct subdirectory of the classpath. ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/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/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/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: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/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/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/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ uk/ac/sanger/artemis/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: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:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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: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:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long 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()); ^ 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/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal 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/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/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 featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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( ^ featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./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:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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: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/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 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/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 ./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: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/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: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:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/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/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 fasta_header_positions.set(i, new Integer(new_position[j])); 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: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/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: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:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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/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/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: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: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: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: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: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/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/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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:1478: 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)); ^ ./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: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: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/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/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: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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/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: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: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: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:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ db_id = new Integer(rs.getInt("db_id")); ./uk/ac/sanger/artemis/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/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: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: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: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: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: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: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: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: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: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/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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: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/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: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:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/io/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/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: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/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/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/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: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 ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(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: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: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 ./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/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/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/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:360: 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/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:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/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/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:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/components/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/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/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:172: 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/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:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./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/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ changes.add(new Integer(ichanged)); ^ featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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/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: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 ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/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 ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/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/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: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: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/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/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: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: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/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: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/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: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/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: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: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:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_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: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: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: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: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: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: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: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()); ^ ./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:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/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/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/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: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: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/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/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/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: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: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/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/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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: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/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: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 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: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: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: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/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:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: 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)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ return 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 ./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)); ^ 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: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:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/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: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:933: 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 featureCvTermId = new Integer( ^ 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: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: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: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: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:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./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: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: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: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 ./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: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 featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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())); ^ featureloc.setStrand(new Short((short)1)); ^ uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/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:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ return dao.getSimilarityMatches(new Integer(srcFeatureId)); ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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.setPhase(new Integer(1)); ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/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/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:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ^ ./uk/ac/sanger/artemis/chado/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: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:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/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/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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/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:1078: 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( 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/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:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/io/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: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/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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.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:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./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 ./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: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/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:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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())); ^ 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)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/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:1249: 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() ); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/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:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java: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/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: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/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/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: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: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:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/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: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:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/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: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:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/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/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ 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)); ^ return_object = new Integer(start_value); ./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/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/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/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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: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: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/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)); ^ hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/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: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/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/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/EntryEdit.java:129: error: cannot find symbol private Selection selection = null; ^ symbol: class Selection location: class EntryEdit uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/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/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/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/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 ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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/io/KeyVector.java:51: error: cannot find symbol add (new_key); ^ symbol: method add(Key) location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:59: error: cannot find symbol final KeyVector new_key_vector = (KeyVector)clone(); ^ symbol: method clone() location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:72: error: cannot find symbol for (int i = 0; i < size (); ++i) ^ symbol: method size() location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:76: error: cannot find symbol for(int j = i + 1 ; j < size () ; ++j) ^ symbol: method size() location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:78: error: cannot find symbol if(((Key)get(j)).compareTo( (Key)get(smallest)) < 0) ^ symbol: method get(int) location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:78: error: cannot find symbol ./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())); ^ if(((Key)get(j)).compareTo( (Key)get(smallest)) < 0) ^ symbol: method get(int) location: class KeyVector ./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/KeyVector.java:84: error: cannot find symbol final Key tmp = (Key)get(i); ^ symbol: method get(int) location: class KeyVector ./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 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: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/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/KeyVector.java:85: error: cannot find symbol setElementAt (get(smallest), i); ^ symbol: method get(int) location: class KeyVector ./uk/ac/sanger/artemis/io/KeyVector.java:86: error: cannot find symbol setElementAt (tmp, smallest); ^ symbol: method setElementAt(Key,int) location: class KeyVector ./uk/ac/sanger/artemis/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/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: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: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()); ^ ./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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/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/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: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/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:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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/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: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:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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: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/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: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/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:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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: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/GFFDocumentEntry.java:437: 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)); ^ (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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/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/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/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/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: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/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 ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ 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/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/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:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ^ ./uk/ac/sanger/artemis/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/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/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:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./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/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/EntryEdit.java:740: error: cannot find symbol public Selection getSelection() ^ symbol: class Selection location: class EntryEdit ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/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")); ^ 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/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/components/EntryEdit.java:2077: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EntryEdit ./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/EntryEdit.java:2114: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EntryEdit ./uk/ac/sanger/artemis/components/EntryEdit.java:2137: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EntryEdit ./uk/ac/sanger/artemis/components/EntryEdit.java:2196: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EntryEdit ./uk/ac/sanger/artemis/components/SelectionInfoDisplay.java:60: error: cannot find symbol final Selection selection) ^ symbol: class Selection location: class SelectionInfoDisplay ./uk/ac/sanger/artemis/components/SelectionInfoDisplay.java:313: error: cannot find symbol static String markerRangeText(final Selection current_selection, ^ symbol: class Selection location: class SelectionInfoDisplay ./uk/ac/sanger/artemis/components/SelectionInfoDisplay.java:462: error: cannot find symbol private Selection getSelection () ^ symbol: class Selection location: class SelectionInfoDisplay ./uk/ac/sanger/artemis/components/SelectionInfoDisplay.java:485: error: cannot find symbol private final Selection selection; ^ symbol: class Selection location: class SelectionInfoDisplay ./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/components/alignment/BamView.java:200: error: cannot find symbol private Selection selection; ^ symbol: class Selection location: class BamView ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:3732: error: cannot find symbol protected Selection getSelection() ^ symbol: class Selection location: class BamView ./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/components/FeatureList.java:122: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class FeatureList ./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/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/BasePlotGroup.java:78: error: cannot find symbol private Selection selection; ^ symbol: class Selection location: class BasePlotGroup ./uk/ac/sanger/artemis/components/BasePlotGroup.java:95: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class BasePlotGroup ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/components/BasePlotGroup.java:403: error: cannot find symbol private Selection getSelection() ^ symbol: class Selection location: class BasePlotGroup ./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/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/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/BasePlot.java:108: error: cannot find symbol private Selection selection; ^ symbol: class Selection location: class BasePlot ./uk/ac/sanger/artemis/components/BasePlot.java:173: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class BasePlot ./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:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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/BasePlot.java:968: error: cannot find symbol ./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)); ^ private Selection getSelection() ^ symbol: class Selection location: class BasePlot ./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/FeatureDisplay.java:324: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class FeatureDisplay ./uk/ac/sanger/artemis/components/FeatureDisplay.java:345: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class FeatureDisplay ./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/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/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/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/components/EntryGroupPanel.java:64: error: cannot find symbol private Selection selection; ^ symbol: class Selection location: class EntryGroupPanel ./uk/ac/sanger/artemis/components/EntryGroupPanel.java:86: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EntryGroupPanel ./uk/ac/sanger/artemis/components/EntryGroupPanel.java:138: error: cannot find symbol public Selection getSelection() ^ symbol: class Selection location: class EntryGroupPanel ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:151: error: cannot find symbol public static boolean setOrganismProps(Set op, final boolean isMitochondrial) ^ symbol: class OrganismProp location: class DatabaseTreeNode ./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/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/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/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: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( ^ Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/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: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: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/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/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/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/components/genebuilder/GeneUtils.java:49: error: cannot access FeaturePub import org.gmod.schema.sequence.FeaturePub; ^ bad class file: ./org/gmod/schema/sequence/FeaturePub.class class file truncated at offset 0 Please remove or make sure it appears in the correct subdirectory of the classpath. ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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: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:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/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:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java: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/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: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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/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/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: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: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:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java: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: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/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: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:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/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:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/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: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/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:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/components/genebuilder/ProteinMapPanel.java:95: error: cannot find symbol final Selection selection) ^ symbol: class Selection location: class ProteinMapPanel ./uk/ac/sanger/artemis/components/genebuilder/MapPanel.java:45: error: cannot find symbol protected Selection selection; ^ symbol: class Selection location: class MapPanel ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/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: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/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: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/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/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:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/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:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ./uk/ac/sanger/artemis/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:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/components/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: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:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/DocumentEntry.java:58: error: cannot find symbol void save (final Document document) ^ symbol: class Document location: interface DocumentEntry ./uk/ac/sanger/artemis/io/DocumentEntry.java:85: error: cannot find symbol Document getDocument (); ^ symbol: class Document location: interface DocumentEntry ./uk/ac/sanger/artemis/io/DatabaseDocumentEntry.java:44: error: cannot find symbol public DatabaseDocumentEntry(final Document doc, ^ symbol: class Document location: class DatabaseDocumentEntry ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:69: error: cannot find symbol GFFDocumentEntry(final Document document, final ReadListener listener) ^ symbol: class Document location: class GFFDocumentEntry ./uk/ac/sanger/artemis/io/SimpleDocumentEntry.java:68: error: cannot find symbol private Document document = null; ^ symbol: class Document location: class SimpleDocumentEntry ./uk/ac/sanger/artemis/io/SimpleDocumentEntry.java:109: error: cannot find symbol final Document document, ^ symbol: class Document location: class SimpleDocumentEntry ./uk/ac/sanger/artemis/io/SimpleDocumentEntry.java:1082: error: cannot find symbol public Document getDocument() ^ symbol: class Document location: class SimpleDocumentEntry ./uk/ac/sanger/artemis/io/SimpleDocumentEntry.java:1091: error: cannot find symbol public void setDocument(final Document document) ^ symbol: class Document location: class SimpleDocumentEntry ./uk/ac/sanger/artemis/io/SimpleDocumentEntry.java:1117: error: cannot find symbol public void save(final Document document) ^ symbol: class Document location: class SimpleDocumentEntry ./uk/ac/sanger/artemis/io/EmblDocumentEntry.java:55: error: cannot find symbol final Document document, ^ symbol: class Document location: class EmblDocumentEntry ./uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java:84: error: cannot find symbol ./uk/ac/sanger/artemis/io/ValidateFeature.java:125: error: cannot find symbol final Selection sel, ^ symbol: class Selection location: class ValidateFeature ./uk/ac/sanger/artemis/io/ValidateFeature.java:149: error: cannot find symbol final Selection sel, ^ symbol: class Selection location: class ValidateFeature ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ final Document document, final ReadListener listener) ^ symbol: class Document location: class PublicDBDocumentEntry ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:67: error: cannot find symbol private Document document; ^ symbol: class Document location: class IndexedGFFDocumentEntry ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:89: error: cannot find symbol public IndexedGFFDocumentEntry(final Document document) ^ symbol: class Document location: class IndexedGFFDocumentEntry ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:1100: error: cannot find symbol public void save(Document document) throws IOException ^ symbol: class Document location: class IndexedGFFDocumentEntry ./uk/ac/sanger/artemis/io/IndexedGFFDocumentEntry.java:1127: error: cannot find symbol public Document getDocument() ^ symbol: class Document location: class IndexedGFFDocumentEntry ./uk/ac/sanger/artemis/io/DocumentEntryFactory.java:76: error: cannot find symbol final Document document, ^ symbol: class Document location: class DocumentEntryFactory ./uk/ac/sanger/artemis/components/UserDefinedQualifiers.java:480: error: cannot find symbol private QualifierVector loadQualifiers(final Document doc) throws IOException ^ symbol: class Document location: class UserDefinedQualifiers ^ ./uk/ac/sanger/artemis/components/UserDefinedQualifiers.java:494: error: cannot find symbol private QualifierVector loadObo(final Document doc) throws IOException 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/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/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: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: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); ^ ^ symbol: class Document location: class UserDefinedQualifiers ./uk/ac/sanger/artemis/components/UserDefinedQualifiers.java:660: error: cannot find symbol private void createObo(Document doc) ^ symbol: class Document location: class UserDefinedQualifiers ./uk/ac/sanger/artemis/components/UserDefinedQualifiers.java:845: error: cannot find symbol Document doc; ^ symbol: class Document location: class UserDefinedQualifiers.QualifierList ./uk/ac/sanger/artemis/plot/CodonUsageWeight.java:157: error: cannot find symbol private void readDataFromStream (final Document document) ^ symbol: class Document location: class CodonUsageWeight ./uk/ac/sanger/artemis/editor/FastaTextPane.java:57: error: cannot find symbol private Document document; ^ symbol: class Document location: class FastaTextPane ./uk/ac/sanger/artemis/editor/FastaTextPane.java:79: error: cannot find symbol public FastaTextPane(Document document) ^ symbol: class Document location: class FastaTextPane ./uk/ac/sanger/artemis/components/EntryFileDialog.java:228: error: cannot find symbol final Document file_document, ^ symbol: class Document location: class EntryFileDialog ./uk/ac/sanger/artemis/components/EntryFileDialog.java:275: error: cannot find symbol final Document entry_document, ^ symbol: class Document location: class EntryFileDialog ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/ViewMenu.java:1643: error: cannot find symbol public static Document getSearchDocument(Feature this_feature, String program, String fileName) ^ symbol: class Document location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1705: error: cannot find symbol private static String getDocumentContents(Document document) throws IOException ^ symbol: class Document location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1871: error: cannot find symbol private static Document checkRemoteNode(final Feature this_feature, ^ symbol: class Document location: class ViewMenu ./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: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:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/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/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal 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: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: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: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: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: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: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: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/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/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/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 ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/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/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/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)); ^ 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:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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)); ^ hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/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/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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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/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: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/FeatureListFrame.java:57: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class FeatureListFrame ./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/ViewMenu.java:75: error: cannot find symbol private Selection selection = null; ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:98: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:613: error: cannot find symbol final Selection selection, ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:755: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:818: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:882: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:944: error: cannot find symbol protected static void showIntrons(final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:973: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1019: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1063: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1119: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1190: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1266: error: cannot find symbol final Selection selection, final EntryGroup entry_group, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1308: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1356: error: cannot find symbol final Key key, final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1389: error: cannot find symbol final Selection selection, final EntryGroup entry_group, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1442: error: cannot find symbol final Selection selection, final EntryGroup entry_group, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1477: error: cannot find symbol final Selection selection) ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1502: error: cannot find symbol final Selection selection) ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1531: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class ViewMenu ./uk/ac/sanger/artemis/components/SelectionMenu.java:53: error: cannot find symbol private Selection selection; ^ symbol: class Selection location: class SelectionMenu ./uk/ac/sanger/artemis/components/SelectionMenu.java:67: error: cannot find symbol final Selection selection) ^ symbol: class Selection location: class SelectionMenu ./uk/ac/sanger/artemis/components/SelectionMenu.java:100: error: cannot find symbol final Selection selection) ^ symbol: class Selection location: class SelectionMenu ./uk/ac/sanger/artemis/components/SelectionMenu.java:141: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class SelectionMenu ./uk/ac/sanger/artemis/components/SelectionMenu.java:179: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class SelectionMenu ./uk/ac/sanger/artemis/components/SelectionMenu.java:270: error: cannot find symbol final Selection selection) ^ symbol: class Selection location: class SelectionMenu ./uk/ac/sanger/artemis/components/SelectionMenu.java:286: error: cannot find symbol protected Selection getSelection() ^ symbol: class Selection location: class SelectionMenu featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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 ./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:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ return new Character ('.'); ^ ./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:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java: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/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/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( 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/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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: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/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/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/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:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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)); ^ hideVcfList.add(new Integer(thisBamIndex)); ^ 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/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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/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: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)); ^ ./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/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/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/circular/DNADraw.java:174: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java: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: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/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/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/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:193: 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/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: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/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/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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/FeatureSegmentVector.java:46: error: cannot find symbol ./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/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: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:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:739: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ private FastVector vector = new FastVector (); ^ symbol: class FastVector location: class FeatureSegmentVector ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java: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/FeatureSegmentVector.java:155: error: cannot find symbol return_vector.vector = (FastVector) vector.clone (); ^ symbol: class FastVector location: class FeatureSegmentVector ./uk/ac/sanger/artemis/FeatureVector.java:145: error: cannot find symbol return_vector.vector = (FastVector) vector.clone (); ^ symbol: class FastVector location: class FeatureVector ./uk/ac/sanger/artemis/FeatureVector.java:165: error: cannot find symbol private FastVector vector = new FastVector (); ^ symbol: class FastVector location: class FeatureVector ./uk/ac/sanger/artemis/chado/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/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) 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); ^ ./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:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ 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/Options.java:1433: error: cannot find symbol valid_keys.add(current_key); ^ symbol: method add(Key) location: variable valid_keys of type KeyVector ./uk/ac/sanger/artemis/Options.java:1438: error: cannot find symbol valid_keys.add(current_key); ^ symbol: method add(Key) location: variable valid_keys of type KeyVector ./uk/ac/sanger/artemis/Options.java:1439: error: cannot find symbol required_keys.add(current_key); ^ symbol: method add(Key) location: variable required_keys of type KeyVector ./uk/ac/sanger/artemis/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/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/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/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/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/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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: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/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/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/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:739: 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/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:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ int index = ticks.indexOf(new Integer(tick)); ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/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: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/circular/DNADraw.java:1537: 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 ^ lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./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: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: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/chado/IBatisDAO.java:1383: 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/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/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); ^ Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./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/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/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/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/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/ExternalProgram.java:293: warning: [removal] Long(long) in Long 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( ^ 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: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/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/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/components/genebuilder/GeneUtils.java:438: error: cannot find symbol for(int i=0; i'); ^ ./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:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ return new Integer (120); ^ ./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:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./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: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/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:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/components/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()); ^ 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: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:1353: warning: [removal] Short(short) in Short 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 ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ 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()); ^ else if(strand.equals( 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/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/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)); ^ 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/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/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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/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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal ./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/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/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/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/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()); ^ 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:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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: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/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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/components/alignment/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/ChadoTransaction.java:205: error: cannot find symbol symbol: class FeaturePub location: class ChadoTransactionManager ./uk/ac/sanger/artemis/util/DatabaseDocument.java:827: error: cannot find symbol final List list) ^ symbol: class FeaturePub location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:826: error: cannot find symbol private Hashtable> getFeaturePubs(final GmodDAO dao, ^ symbol: class FeaturePub location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1233: error: cannot find symbol final Hashtable> featurePubs, ^ symbol: class FeaturePub location: class DatabaseDocument ./uk/ac/sanger/artemis/chado/IBatisDAO.java:990: error: cannot find symbol private void insertFeaturePub(final FeaturePub featurePub) ^ symbol: class FeaturePub location: class IBatisDAO 6 errors 4 warnings ./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:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./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: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/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/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: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/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/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/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/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java: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/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/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/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:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ uk/ac/sanger/artemis/circular/DNADraw.java: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/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)); ^ changes.add(new Integer(ichanged)); ./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/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/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: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/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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: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: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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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))); ^ 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/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/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/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: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/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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())); ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/circular/Feature.class] Error 1 uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/circular/Feature.java:106: error: cannot find symbol catch(InvalidRelationException e) ^ symbol: class InvalidRelationException location: class Feature ./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/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: 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/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/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:201: warning: [removal] Character(char) in Character 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 return new Character ('.'); ^ ./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: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/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/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: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/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./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/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/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/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: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:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/chado/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: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/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/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/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/io/FuzzyRange.java:297: 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/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/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/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/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); ^ 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: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/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/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/components/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:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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/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 ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/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/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: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/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:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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/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/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: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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal ./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/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ 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/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/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/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/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/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:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ uk/ac/sanger/artemis/circular/DNADraw.java: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: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/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./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()); ^ ./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:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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: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/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/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/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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean 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/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/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/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/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); ^ read_succeeded = new Boolean(true); ^ ./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:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ./uk/ac/sanger/artemis/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: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: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:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/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/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: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: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: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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/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:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/alignment/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/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: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/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: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/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/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/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/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java: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: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: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: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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal 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/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/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/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/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/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/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/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/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double 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 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/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/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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: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/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/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/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/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/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./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/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ 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/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/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/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()); ^ fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./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: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: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: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: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/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/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/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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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: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:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./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/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/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/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()); ^ 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/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/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/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/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:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/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/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal 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: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:947: 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/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:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/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/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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: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/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/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ 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/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: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: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/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/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/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/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/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new 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/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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/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/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/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java: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 ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/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:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/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/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); 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(); ^ return new Integer (window_size / 8); ^ ./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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/io/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/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/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: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/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/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/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./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: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/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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/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: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/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/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/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/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/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/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/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/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/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/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/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/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/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/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/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/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/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: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/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:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/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/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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/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/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ 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/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: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/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/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: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/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); ^ 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/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: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: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/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:946: 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()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/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/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/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:2559: warning: [removal] Short(short) in Short 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()); ^ 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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ 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/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/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/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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 (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/circular/Wizard.java:708: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize", new Integer(1)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:709: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular", new Boolean(true)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:710: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start", new Integer(0)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:711: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end", new Integer(entry.getBases().getLength())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java: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/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( ^ 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); ^ 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: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: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: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/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:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/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: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/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/components/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:199: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(null); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ^ ./uk/ac/sanger/artemis/io/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/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/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/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/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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/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/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ featureloc.setFmax(new Integer(range_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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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)); ^ getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ 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/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/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/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:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java: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 ./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)); ^ return new Float (0); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./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/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/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/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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/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/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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/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/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: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/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/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/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/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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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:538: error: cannot find symbol srcFeature = dao.getFeatureById(srcfeatureid); ^ symbol: method getFeatureById(int) location: variable dao of type GmodDAO ./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:544: error: cannot find symbol srcFeature = dao.getFeatureById(Integer.parseInt(srcFeatureId)); ^ symbol: method getFeatureById(int) location: variable dao of type GmodDAO ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java: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/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java: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/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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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/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: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: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: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/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/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal ./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)); ^ 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/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/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/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: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:689: error: cannot find symbol ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final List featList = dao.getFeaturesByLocatedOnFeature(child); 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:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ symbol: method getFeaturesByLocatedOnFeature(Feature) location: variable dao of type GmodDAO ./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: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:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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: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/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: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/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/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/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:961: error: cannot find symbol List featuresInRange = dao.getFeaturesByRange(range.getStart()-1, ^ symbol: method getFeaturesByRange(int,int,int,Feature,) location: variable dao of type GmodDAO ./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/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/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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:1060: error: cannot find symbol List features = dao.getFeaturesByUniqueName(search_gene); ^ symbol: method getFeaturesByUniqueName(String) location: variable dao of type GmodDAO 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/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: 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)); ^ 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: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/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: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/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/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:1167: error: cannot find symbol chadoFeature = (Feature)dao.getFeatureById(featureId); ^ symbol: method getFeatureById(int) location: variable dao of type GmodDAO ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1181: error: cannot find symbol dao.getFeatureDbXRefsByFeatureUniquename(chadoFeature.getUniqueName())); ^ symbol: method getFeatureDbXRefsByFeatureUniquename(String) location: variable dao of type GmodDAO ./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:1184: error: cannot find symbol dao.getFeatureSynonymsByFeatureUniquename(chadoFeature.getUniqueName())); ^ symbol: method getFeatureSynonymsByFeatureUniquename(String) location: variable dao of type GmodDAO ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1187: error: cannot find symbol dao.getFeatureCvTermsByFeature(chadoFeature)); ^ symbol: method getFeatureCvTermsByFeature(Feature) location: variable dao of type GmodDAO ./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:1190: error: cannot find symbol dao.getFeatureCvTermDbXRefByFeature(chadoFeature)); ^ symbol: method getFeatureCvTermDbXRefByFeature(Feature) location: variable dao of type GmodDAO ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1197: error: cannot find symbol dao.getFeatureCvTermPubByFeature(chadoFeature)); ^ symbol: method getFeatureCvTermPubByFeature(Feature) location: variable dao of type GmodDAO ./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: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/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/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/ArtemisUtils.java:661: 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/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/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/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/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: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/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ 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/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: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/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/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/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: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: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: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/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: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/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: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 ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Float (0); featureId = new Integer(alias.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/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/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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/ExternalProgram.java:326: warning: [removal] Long(long) in Long 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/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/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/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ 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:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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/util/DatabaseDocument.java:2152: error: cannot find symbol Feature feature = dao.getFeatureById(Integer.parseInt(srcFeatureId)); ^ symbol: method getFeatureById(int) location: variable dao of type GmodDAO ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal 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:2165: error: cannot find symbol (Feature)(getDAOOnly().getFeaturesByAnyCurrentName(id).get(0)); ^ symbol: method getFeaturesByAnyCurrentName(String) location: class GmodDAO ./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: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 rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2299: error: cannot find symbol return (Feature) dao.getFeatureByUniqueName(uniqueName, null); ^ symbol: method getFeatureByUniqueName(String,) location: variable dao of type GmodDAO ./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/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/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/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/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/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/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/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 ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2865: error: cannot find symbol feature = dao.getFeatureByUniqueName(uniquename, ^ symbol: method getFeatureByUniqueName(String,String) location: variable dao of type GmodDAO ./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/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/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:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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:3010: error: cannot find symbol = dao.getFeatureByUniqueName(uniquename, tsn.getFeatureKey()); ^ symbol: method getFeatureByUniqueName(String,String) location: variable dao of type GmodDAO ./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/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/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/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:3098: error: cannot find symbol final Feature feature = dao.getFeatureByUniqueName(uniquename, keyName); ^ symbol: method getFeatureByUniqueName(String,String) location: variable dao of type GmodDAO ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: 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); ^ 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:3267: error: cannot find symbol featureList.add(dao.getFeatureByUniqueName(args[0], "polypeptide")); ^ symbol: method getFeatureByUniqueName(String,String) location: variable dao of type GmodDAO ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/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:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./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/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:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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/plot/CodonUsageAlgorithm.java:183: 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 final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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/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 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: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:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/io/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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java: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/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:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/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/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/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 ./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()); ^ 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/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/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:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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/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/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/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: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/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/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: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: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: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/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal ./uk/ac/sanger/artemis/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/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: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:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/circular/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/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 ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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: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/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ final Vector v = (Vector)hash.get(new Integer(clusterFeature.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/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ 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/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/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/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/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/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/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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/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/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:708: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize", new Integer(1)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:709: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular", new Boolean(true)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:710: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start", new Integer(0)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:711: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end", new Integer(entry.getBases().getLength())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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: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/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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = 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/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: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/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/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/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/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./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:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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 final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/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/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./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: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/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/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/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:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang 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/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)); ^ SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:199: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(null); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/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/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/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/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./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/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java: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/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 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/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/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/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/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/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/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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) { ^ 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/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/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 ./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)); ^ if (getUserKeys () != null && getUserKeys ().contains (key)) { ^ symbol: method contains(Key) location: class KeyVector ./uk/ac/sanger/artemis/util/DatabaseDocument.java:325: error: cannot find symbol this((String)originalDocument.getLocation(), ^ symbol: method getLocation() location: variable originalDocument of type DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:348: error: cannot find symbol this((String)originalDocument.getLocation(), ^ symbol: method getLocation() location: variable originalDocument of type DatabaseDocument ./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/util/DatabaseDocument.java:392: error: cannot find symbol setLocation(location.substring(0,index+1) + schema); ^ symbol: method setLocation(String) location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:407: error: cannot find symbol System.setProperty("chado", (String)getLocation()); ^ symbol: method getLocation() location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:408: error: cannot find symbol logger4j.debug((String)getLocation()); ^ symbol: method getLocation() location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:439: error: cannot find symbol return new DatabaseDocument( ((String)getLocation()) + name, pfield); ^ symbol: method getLocation() location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:450: error: cannot find symbol int ind = ((String) getLocation()).indexOf("?"); ^ symbol: method getLocation() location: class DatabaseDocument ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:451: error: cannot find symbol String name = ((String) getLocation()).substring(0, ind); ^ symbol: method getLocation() location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:470: error: cannot find symbol return new DatabaseDocument( (String)getLocation(), pfield, ^ symbol: method getLocation() location: class DatabaseDocument ./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:566: error: cannot find symbol logger4j.debug("RETRIEVE SOURCE FEATURE FROM: "+getLocation()); ^ symbol: method getLocation() location: class DatabaseDocument ./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/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:1057: error: cannot find symbol reset((String)getLocation(), schema_search.get(0)); ^ symbol: method getLocation() location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/components/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: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/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/components/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/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/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:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:708: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize", new Integer(1)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:709: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular", new Boolean(true)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:710: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start", new Integer(0)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:711: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end", new Integer(entry.getBases().getLength())); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2495: error: cannot find symbol getLocation()+"\n"+ ^ symbol: method getLocation() location: class DatabaseDocument ./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:2516: error: cannot find symbol getLocation()+"\n"+ ^ symbol: method getLocation() location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2641: error: cannot find symbol jdbcDAO = new JdbcDAO((String)getLocation(), pfield); ^ symbol: method getLocation() location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2648: error: cannot find symbol System.setProperty("chado", (String)getLocation()); ^ symbol: method getLocation() location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2663: error: cannot find symbol String url = (String)getLocation(); ^ symbol: method getLocation() location: class DatabaseDocument ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/database/DatabaseJPanel.java:772: error: cannot find symbol Selection selection = ee.getSelection(); ^ symbol: class Selection location: class DatabaseJPanel ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:155: error: cannot find symbol final Iterator it = op.iterator(); ^ symbol: class OrganismProp location: class DatabaseTreeNode ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:158: error: cannot find symbol OrganismProp organismProp = it.next(); ^ symbol: class OrganismProp location: class DatabaseTreeNode ./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/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/EntryEdit.java:167: error: cannot find symbol selection = new Selection(null); ^ symbol: class Selection location: class EntryEdit ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:199: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(null); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./uk/ac/sanger/artemis/components/SelectMenu.java:120: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class SelectMenu ./uk/ac/sanger/artemis/components/SelectMenu.java:144: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class SelectMenu ./uk/ac/sanger/artemis/components/SelectMenu.java:411: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class SelectMenu ./uk/ac/sanger/artemis/components/GotoMenu.java:112: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class GotoMenu ./uk/ac/sanger/artemis/components/GotoMenu.java:223: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class GotoMenu ./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/EditMenu.java:118: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:150: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:888: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:904: error: cannot find symbol private static void redo(final JFrame frame, final Selection selection, ^ symbol: class Selection location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:932: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:994: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:1123: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:1378: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:1645: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:1829: error: cannot find symbol final Selection selection, ^ symbol: class Selection location: class EditMenu ./uk/ac/sanger/artemis/components/EditMenu.java:1954: error: cannot find symbol private void addQualifiers (final JFrame frame, final Selection selection) { ^ symbol: class Selection location: class EditMenu ./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/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/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/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/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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/GenbankDocumentEntry.java:54: error: cannot find symbol final Document document, ^ symbol: class Document location: class GenbankDocumentEntry ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/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/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/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/io/BlastDocumentEntry.java:52: error: cannot find symbol public BlastDocumentEntry (final Document document, ^ symbol: class Document location: class BlastDocumentEntry ./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/Options.java:304: error: cannot find symbol final Document options_document = ^ symbol: class Document location: class Options ./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/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/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 ./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 (24); ^ ./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: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: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/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/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/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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/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:236: error: cannot find symbol final Document document = ((DocumentEntry)feature.getEntry()).getDocument(); ^ symbol: class Document location: class ClusterLazyQualifierValue ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java: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/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java: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/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/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/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: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: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: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/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/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/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/plot/UserDataAlgorithm.java:116: error: cannot find symbol public UserDataAlgorithm (final Strand strand, final Document doc, ^ symbol: class Document location: class UserDataAlgorithm ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:206: error: cannot find symbol private static boolean isIndexed(Document doc) ^ symbol: class Document location: class UserDataAlgorithm ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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/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/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)) ) ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/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/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/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/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/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/chado/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/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/UserDefinedQualifiers.java:456: error: cannot find symbol Document doc = new URLDocument( ^ symbol: class Document location: class UserDefinedQualifiers ./uk/ac/sanger/artemis/components/UserDefinedQualifiers.java:469: error: cannot find symbol Document doc = new FileDocument(new File(fileName)); ^ symbol: class Document location: class UserDefinedQualifiers ./uk/ac/sanger/artemis/components/UserDefinedQualifiers.java:546: error: cannot find symbol if(!doc.getLocation().equals(urlDoc.getLocation())) ^ symbol: method getLocation() location: variable urlDoc of type URLDocument ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:211: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/alignment/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/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/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/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/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/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/components/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: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/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: 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())); ^ List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/io/ReadAndWriteEntry.java:239: error: cannot find symbol qualifierInfo.getValidKeys().add(new_key); ^ symbol: method add(Key) location: class 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/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/CodonUsageWeight.java:239: error: cannot find symbol final Document current_dir_document = new FileDocument (usage_file); ^ symbol: class Document location: class CodonUsageWeight ./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/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/io/UI.java:74: warning: [removal] stop() in Thread has been deprecated and marked for removal mask.stop(); ^ ./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/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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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: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/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/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/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/database/DatabaseJPanel.java:682: error: cannot find symbol ((String)doc.getLocation()).replaceAll("[/:=\\?]", "_")); ^ symbol: method getLocation() location: variable doc of type DatabaseDocument ./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/components/database/DatabaseTreeNode.java:245: error: cannot find symbol ((String)dbDoc.getLocation()).replaceAll("[/:=\\?]", "_")); ^ symbol: method getLocation() location: variable dbDoc of type DatabaseDocument 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 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/EntryEdit.java:2148: error: cannot find symbol final Document dbDoc = ^ symbol: class Document location: class EntryEdit ./uk/ac/sanger/artemis/editor/HitInfo.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(startQuery)); ^ ./uk/ac/sanger/artemis/editor/HitInfo.java:275: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(endQuery)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/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/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/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/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/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/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/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/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/alignment/BamView.java:3543: error: cannot find symbol final Document entry_document = DocumentFactory.makeDocument(entryFileName); ^ symbol: class Document location: class BamView ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/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. 52 errors 100 warnings ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./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); ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/chado/ArtemisUtils.class] Error 1 ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/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())); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/io/UI.java:74: warning: [removal] stop() in Thread 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)); ^ mask.stop(); ^ ./uk/ac/sanger/artemis/util/FileDocument.java:107: error: cannot find symbol final File read_file = (File) getLocation (); ^ symbol: method getLocation() location: class FileDocument ./uk/ac/sanger/artemis/util/FileDocument.java:111: error: cannot find symbol getProgressListeners ()); ^ symbol: method getProgressListeners() location: class FileDocument ./uk/ac/sanger/artemis/util/FileDocument.java:128: error: cannot find symbol getProgressListeners ())); ^ symbol: method getProgressListeners() location: class FileDocument ./uk/ac/sanger/artemis/util/FileDocument.java:140: error: cannot find symbol final File write_file = (File) getLocation (); ^ symbol: method getLocation() location: class FileDocument ./uk/ac/sanger/artemis/util/FileDocument.java:157: error: cannot find symbol return (File) getLocation (); ^ symbol: method getLocation() location: class FileDocument ./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/UI.java:74: warning: [removal] stop() in Thread has been deprecated and marked for removal mask.stop(); ^ ./uk/ac/sanger/artemis/io/ValidateFeature.java:1086: error: cannot find symbol final Document doc = DocumentFactory.makeDocument(seq); ^ symbol: class Document location: class ValidateFeature ./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/editor/DataViewInternalFrame.java:93: error: cannot find symbol Document document = null; ^ symbol: class Document location: class DataViewInternalFrame ./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())); ^ 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/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/util/URLDocument.java:111: error: cannot find symbol final URL url = (URL) getLocation (); ^ symbol: method getLocation() location: class URLDocument ./uk/ac/sanger/artemis/util/URLDocument.java:118: error: cannot find symbol getProgressListeners ()); ^ symbol: method getProgressListeners() location: class URLDocument ./uk/ac/sanger/artemis/util/URLDocument.java:142: error: cannot find symbol return (URL) getLocation (); ^ symbol: method getLocation() location: class URLDocument ./uk/ac/sanger/artemis/components/ArtemisMain.java:212: error: cannot find symbol entry_document.addInputStreamProgressListener(progress_listener); ^ symbol: method addInputStreamProgressListener(InputStreamProgressListener) location: variable entry_document of type TextDocument ./uk/ac/sanger/artemis/components/ArtemisMain.java:330: error: cannot find symbol final Document entry_document; ^ symbol: class Document location: class ArtemisMain ./uk/ac/sanger/artemis/components/ArtemisMain.java:408: error: cannot find symbol final Document entry_document = ^ symbol: class Document location: class ArtemisMain ./uk/ac/sanger/artemis/components/ArtemisMain.java:511: error: cannot find symbol final Document location_document = ^ symbol: class Document location: class ArtemisMain ./uk/ac/sanger/artemis/io/BioJavaEntry.java:30: error: cannot find symbol public BioJavaEntry(final Document document, ^ symbol: class Document location: class BioJavaEntry ./uk/ac/sanger/artemis/io/BioJavaEntry.java:38: error: cannot find symbol final Document document, ^ symbol: class Document location: class BioJavaEntry ./uk/ac/sanger/artemis/io/BioJavaEntry.java:121: error: cannot find symbol public Document getDocument () { ^ symbol: class Document location: class BioJavaEntry ./uk/ac/sanger/artemis/io/BioJavaEntry.java:128: error: cannot find symbol public void setDocument (final Document document) { ^ symbol: class Document location: class BioJavaEntry ./uk/ac/sanger/artemis/io/BioJavaEntry.java:136: error: cannot find symbol public void save (Document document) throws IOException { ^ symbol: class Document location: class BioJavaEntry Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/io/BioJavaEntry.java:429: error: cannot find symbol private Document document = null; ^ symbol: class Document location: class BioJavaEntry ./uk/ac/sanger/artemis/components/ArtemisMain.java:603: error: cannot find symbol final Document entry_document = ^ symbol: class Document location: class ArtemisMain ./uk/ac/sanger/artemis/components/ArtemisMain.java:664: error: cannot find symbol final Document feature_document = ^ symbol: class Document location: class ArtemisMain ./uk/ac/sanger/artemis/util/RemoteFileDocument.java:120: error: cannot find symbol getProgressListeners()); ^ symbol: method getProgressListeners() location: class RemoteFileDocument ./uk/ac/sanger/artemis/util/RemoteFileDocument.java:191: error: cannot find symbol return (RemoteFileNode)getLocation(); ^ symbol: method getLocation() location: class RemoteFileDocument ./uk/ac/sanger/artemis/io/GenbankTblOutputStream.java:75: error: cannot find symbol final Writer writer = fileDocument.getWriter(); ^ symbol: method getWriter() location: variable fileDocument of type FileDocument 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/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/components/ViewMenu.java:1593: error: cannot find symbol Document document = getSearchDocument(this_feature, program_name, file_name); ^ symbol: class Document location: class ViewMenu ./uk/ac/sanger/artemis/components/SearchResultViewer.java:61: error: cannot find symbol final Document document) ^ symbol: class Document location: class SearchResultViewer ./uk/ac/sanger/artemis/components/ViewMenu.java:1647: error: cannot find symbol Document root_document = entry.getRootDocument(); ^ symbol: class Document location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1651: error: cannot find symbol Document document = null; ^ symbol: class Document location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1660: error: cannot find symbol final Document[] possible_documents = new Document[] { ^ symbol: class Document location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1660: error: cannot find symbol final Document[] possible_documents = new Document[] { ^ symbol: class Document location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1675: error: cannot find symbol final Document this_document = possible_documents[k]; ^ symbol: class Document location: class ViewMenu ./uk/ac/sanger/artemis/components/ViewMenu.java:1684: error: cannot find symbol final Document gzip_document = new FileDocument(gzip_file); ^ symbol: class Document location: class ViewMenu ./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/ViewMenu.java:1880: error: cannot find symbol Document document = null; ^ symbol: class Document location: class ViewMenu ./uk/ac/sanger/artemis/util/TextDocument.java:140: error: cannot find symbol getProgressListeners()); ^ symbol: method getProgressListeners() location: class TextDocument Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/circular/Wizard.java:512: error: cannot find symbol final Document entry_document = DocumentFactory.makeDocument(entryFileName); ^ symbol: class Document location: class Wizard ./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/DocumentEntryAutosaveThread.java:97: error: cannot find symbol final Document save_document = new FileDocument (save_file); ^ symbol: class Document location: class DocumentEntryAutosaveThread ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./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()); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/filetree/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/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/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)); ^ 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/editor/HitInfo.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(startQuery)); ^ ./uk/ac/sanger/artemis/editor/HitInfo.java:275: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(endQuery)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more 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/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more 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/ProjectProperty.java:163: error: cannot find symbol final Document doc = ^ symbol: class Document location: class ProjectProperty ./uk/ac/sanger/artemis/circular/GeneticMarker.java:510: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal arow.add(new Integer(b.getBstart())); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:511: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal arow.add(new Integer(b.getBend())); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:513: warning: [removal] Float(float) in Float has been deprecated and marked for removal arow.add(new Float(b.getStrokeSize())); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:514: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal arow.add(new Boolean(b.isArrowHead())); ^ ./uk/ac/sanger/artemis/circular/GeneticMarker.java:515: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal arow.add(new Boolean(b.isArrowTail())); ^ ./uk/ac/sanger/artemis/circular/RestrictionEnzyme.java:119: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal re.add(new Integer(pos.getValue())); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:61: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_default = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:62: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_remote = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:63: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_listFile = new Boolean(false); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/GraphMenu.java:262: error: reference to addUserPlot is ambiguous addUserPlot (plots[i], false); ^ both method addUserPlot(String,boolean) in GraphMenu and method addUserPlot(Document,boolean) in GraphMenu match ./uk/ac/sanger/artemis/components/GraphMenu.java:265: error: reference to addUserPlot is ambiguous addUserPlot (logplots[i], true); ^ both method addUserPlot(String,boolean) in GraphMenu and method addUserPlot(Document,boolean) in GraphMenu match 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 220 total; use -Xmaxerrs if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more 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 gmake: *** [Makefile:47: uk/ac/sanger/artemis/circular/GeneticMarker.class] Error 1 Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:462: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setIdentity(new Double(id)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/circular/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())); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/circular/RestrictionEnzyme.java:119: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal re.add(new Integer(pos.getValue())); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:61: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_default = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:62: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_remote = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:63: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_listFile = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:64: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(jcirc.isSelected())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:75: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(jcirc.isSelected())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:83: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(draw.isCircular())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:98: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(s)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:125: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(e)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:151: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lsize)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/circular/LineAttribute.java:168: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(size)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:184: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(size)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:226: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start.getValue())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:227: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end.getValue())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:228: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize.getValue())); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 errors 100 warnings only showing the first 100 errors, of 105 total; use -Xmaxerrs 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)); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1868: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal removals.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1897: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal removals.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1982: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[0] = new Integer(start); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:1983: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[1] = new Integer(this_start-1); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:2026: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[0] = new Integer(start+1); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:2027: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[1] = new Integer(next_start-1); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:2036: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[0] = new Integer(start+1); ^ ./uk/ac/sanger/artemis/components/AlignmentViewer.java:2037: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[1] = new Integer(length); ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/circular/GCGraph.class] Error 1 Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/AddMenu.java:417: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[0] = new Integer(istart); ^ ./uk/ac/sanger/artemis/components/AddMenu.java:418: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal coords[1] = new Integer(jend); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:795: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (default_window_size); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (100); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:821: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (1); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:834: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 10); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:844: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (data_max); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:852: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (data_min); ^ ./uk/ac/sanger/artemis/plot/UserDataAlgorithm.java:860: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (average_value); ^ 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/plot/GCWindowAlgorithm.java:106: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:121: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:136: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:146: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 10); ^ ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:157: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (100); ^ ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:165: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java:174: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (getStrand ().getBases ().getAverageGCPercent ()); ^ ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (1000); ^ ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:218: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (5000); ^ ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:233: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (100); ^ ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:242: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (1); ^ ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:251: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (getStrand ().getBases ().getAverageGCPercent ()); ^ ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:259: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (100); ^ 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 Tue Mar 17 20:51:05 EDT 2026 build time: 00:02:29 !!! build failure encountered !!!