=>> Building biology/artemis build started at Thu Mar 19 08:09:33 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: 13 ---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/13/.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] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is 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] 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] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is 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] 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] bootstrap class path not set in conjunction with -source 8 warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] 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] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] 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] 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] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), 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. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), 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 Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). 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 Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Use -Xlint:-options to suppress this message. unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), 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). Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Use -proc:none to disable annotation processing. path is specified (--processor-path, --processor-module-path), 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. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), 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 CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/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 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 CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/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 4 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/ArtemisUtils.java 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/ChadoCvTermView.java 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/ChadoDAO.java ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal 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 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/ChadoDemo.java warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. Note: ./uk/ac/sanger/artemis/util/FastVector.java uses unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 11 warnings 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 ./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); ^ CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/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 warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings ./uk/ac/sanger/artemis/io/Range.java: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); ^ CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/ChadoTransactionManager.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/CommitFrame.java ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/chado/DbSqlConfig.java ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings ./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 ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 11 warnings 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 CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/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 CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/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 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. ./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/IBatisDAO.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. 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 warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/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 warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), 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. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/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 Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), 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. CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/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 Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), 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 4 warnings Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/DNADraw.java Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. ./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/EmbossCirdnaReader.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/Feature.java warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/GCGraph.java warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings warning: Implicitly compiled files were not subject to annotation processing. Use -proc:none to disable annotation processing or -implicit to specify a policy for implicit compilation. 5 warnings CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/GCSkewGraph.java CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/GeneticMarker.java Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), or annotation processing is enabled explicitly (-proc:only, -proc:full). Use -Xlint:-options to suppress this message. Use -proc:none to disable annotation processing. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is obsolete and will be removed in a future release warning: [options] target value 8 is obsolete and will be removed in a future release warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is 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/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: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), 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/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: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/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/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/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:72: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:146: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal Integer bstart = new Integer((String)stok.nextElement()); ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java:147: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal Integer bend = new Integer((String)stok.nextElement()); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java: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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ uk/ac/sanger/artemis/circular/EmbossCirdnaReader.java: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/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/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ 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/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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/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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ CLASSPATH=lib/commons-lang-2.6.jar:lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/commons-net-3.6.jar:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. javac -source 1.8 -target 1.8 uk/ac/sanger/artemis/circular/Graph.java ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/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:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/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: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: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:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/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: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: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/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/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/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/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: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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/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/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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); ^ ./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); ^ 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: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:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ./uk/ac/sanger/artemis/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/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/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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/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/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/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/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/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/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: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/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/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/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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/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/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/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/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/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/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:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/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/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/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/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: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:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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/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)); ^ warning: [options] bootstrap class path not set in conjunction with -source 8 warning: [options] source value 8 is 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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/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/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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/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/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/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/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/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/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/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:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/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/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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/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:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/Range.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal start_object = new Integer (new_start); ^ ./uk/ac/sanger/artemis/io/Range.java:172: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal end_object = new Integer (new_end); ^ ./uk/ac/sanger/artemis/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: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/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:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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: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/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ^ ./uk/ac/sanger/artemis/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:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/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: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/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: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: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:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: 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))); ^ this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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: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:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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/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:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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: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/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/io/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/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/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/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/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/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))); ^ Note: Annotation processing is enabled because one or more processors were found on the class path. A future release of javac may disable annotation processing unless at least one processor is specified by name (-processor), or a search path is specified (--processor-path, --processor-module-path), 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: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:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/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: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/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/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/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/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/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/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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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: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: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/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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: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: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/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/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: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: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/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/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: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: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:579: 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 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/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); ^ Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./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/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ 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/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/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:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/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 ./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)); ^ cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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/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)); ^ rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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 ./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/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)); ^ featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: 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/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: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: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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ 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/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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/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: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: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: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/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: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/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/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: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: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:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ./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: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/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/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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: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:172: 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: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: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:201: 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:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/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:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/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: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: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: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:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/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/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/chado/ChadoTransactionManager.java:2192: 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/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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: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)); ^ featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/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/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ 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: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())); ^ 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/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal 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/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: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:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/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:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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: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/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: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/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/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: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/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: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: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/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:174: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(0)); ^ ./uk/ac/sanger/artemis/io/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/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./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:175: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(4000)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:177: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(true)); ^ ./uk/ac/sanger/artemis/io/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/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/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/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/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/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/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:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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:339: 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/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/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: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: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/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/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:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/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: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/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); featureLoc.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:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/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))); ^ 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: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/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:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/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/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/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/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/circular/DNADraw.java:174: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./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:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java: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: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: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/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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/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: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/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/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: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: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/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: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/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_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: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/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:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./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:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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: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/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/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:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/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:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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: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: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/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short 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 if(strand.equals( new Short((short)-1)) ) // strand ^ featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./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: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/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/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/circular/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: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:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/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/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: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: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/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: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:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/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:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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)); ^ ./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 ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/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: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: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: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/chado/ChadoTransactionManager.java:2219: 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/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:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ featureloc.setPhase(new Integer(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:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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: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/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:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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: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 ./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:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:724: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:739: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ 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: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: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/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:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/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/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/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/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/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: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/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/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: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: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: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/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/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:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/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: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: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: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:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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: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: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: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:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/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/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/io/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:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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: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/util/DatabaseDocument.java:1940: 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 cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); 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: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()); ^ ./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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ return 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/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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 ./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() ); ^ fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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/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:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/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/circular/DNADraw.java:1079: 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 lineAttr.put("lsize",new Integer(lineSize)); fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ 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/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)); ^ feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:488: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setSignificance(new Double(evalue)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:497: warning: [removal] Double(String) in Double has been deprecated and marked for removal analysisFeature.setRawScore(new Double(score)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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: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"); ^ 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: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:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: 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/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: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/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ 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/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/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/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/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./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/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:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java: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:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !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/circular/DNADraw.java:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/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/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: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:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/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/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:360: warning: [removal] Integer(int) in Integer 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 changes.add(new Integer(ichanged)); progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ uk/ac/sanger/artemis/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/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:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ^ ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal 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/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/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/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:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/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: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/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/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:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/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 ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/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/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/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/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:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/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/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ featureloc.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/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 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/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:861: warning: [removal] Short(short) in Short 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)); ^ 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: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( ^ 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/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:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/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/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: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:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/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/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/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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 ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ 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/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/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:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character 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/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()); ^ Integer feature_id = new Integer(dbxref.getFeature().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)); ^ return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: 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/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ featureLoc.setFmin(new Integer(min)); ^ ./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: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: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: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: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/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/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: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:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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: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: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/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java: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/io/GFFDocumentEntry.java:43: error: cannot access CvTerm import org.gmod.schema.cv.CvTerm; ^ bad class file: ./org/gmod/schema/cv/CvTerm.class class file truncated at offset 0 Please remove or make sure it appears in the correct subdirectory of the classpath. ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:495: error: cannot find symbol private CvTerm getCvTermFromCache(final Hashtable cvTermCache, ^ symbol: class CvTerm location: class GFFDocumentEntry ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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: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/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/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/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/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: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: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/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/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/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:807: 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/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java:40: error: cannot access CvTerm import java.util.Enumeration; ^ bad class file: ./org/gmod/schema/cv/CvTerm.class ./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: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: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/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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ 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/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/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/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ class file truncated at offset 0 Please remove or make sure it appears in the correct subdirectory of the classpath. ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) 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: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: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:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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: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)); ^ ./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: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: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 return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/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/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: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/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/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: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: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:103: error: cannot find symbol private static Hashtable cvterms; ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1816: error: cannot find symbol private static CvTerm getCvTerm(final int id, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1833: error: cannot find symbol public static CvTerm getCvTermByCvTermName(final String cvterm_name) ./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: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); ^ ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1851: error: cannot find symbol public static CvTerm getCvTermByCvTermId(final int cvTermId, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1889: error: cannot find symbol public static CvTerm getCvTermByCvAndCvTerm(final String cvterm_name, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1911: error: cannot find symbol public static CvTerm getCvTermByCvPartAndCvTerm(final String cvterm_name, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1929: error: cannot find symbol private static Hashtable getCvterms(final GmodDAO dao) ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2006: error: cannot find symbol public static Vector getCvterms(final String search_str, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2035: error: cannot find symbol public static CvTerm getCvtermFromGoId(final String goId) ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/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: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/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:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/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/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java: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: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: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: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:2135: error: cannot find symbol public void insertCvTerm(CvTerm cvTerm) ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: 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/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/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:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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 ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ hideVcfList.remove(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:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/io/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: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/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: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: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/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/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal ./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: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: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: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/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 ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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"))); ^ else if(strand.equals( new Short((short)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/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: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:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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: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 ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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)); ^ featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: 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)); ^ featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./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: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:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ 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/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/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/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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/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: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())); ^ (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/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: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: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: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/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/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/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/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java: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/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/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/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: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/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( ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal 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/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/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:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/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/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: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:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ^ ./uk/ac/sanger/artemis/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:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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 ./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: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 ^ featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/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: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/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/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/ChadoTransactionManager.java:947: 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/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)); ^ return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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: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:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/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: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/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:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/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/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:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/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:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); 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:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ^ ./uk/ac/sanger/artemis/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:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/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/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/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java: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: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/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:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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: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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ 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()); ^ parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal 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: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:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ uk/ac/sanger/artemis/chado/JdbcDAO.java: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: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)); ^ Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/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/ChadoTransaction.java:205: error: cannot find symbol symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransaction.java:205: error: cannot find symbol deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/chado/ChadoTransaction.java:205: error: cannot find symbol symbol: class CvTerm location: class ChadoTransactionManager ./uk/ac/sanger/artemis/util/DatabaseDocument.java:103: error: cannot find symbol private static Hashtable cvterms; ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1816: error: cannot find symbol private static CvTerm getCvTerm(final int id, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1833: error: cannot find symbol public static CvTerm getCvTermByCvTermName(final String cvterm_name) ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1851: error: cannot find symbol public static CvTerm getCvTermByCvTermId(final int cvTermId, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1889: error: cannot find symbol public static CvTerm getCvTermByCvAndCvTerm(final String cvterm_name, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1911: error: cannot find symbol public static CvTerm getCvTermByCvPartAndCvTerm(final String cvterm_name, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1929: error: cannot find symbol private static Hashtable getCvterms(final GmodDAO dao) ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2006: error: cannot find symbol public static Vector getCvterms(final String search_str, ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2035: error: cannot find symbol public static CvTerm getCvtermFromGoId(final String goId) ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2135: error: cannot find symbol public void insertCvTerm(CvTerm cvTerm) ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/chado/IBatisDAO.java:372: error: cannot find symbol CvTerm cvTerm, boolean not) ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/IBatisDAO.java:400: error: cannot find symbol String name, CvTerm type) ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/IBatisDAO.java:674: error: cannot find symbol public CvTerm getCvTermByNameAndCvName(String cvTermName, String name) ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/IBatisDAO.java:686: error: cannot find symbol public CvTerm getCvTermById(final int cvTermId) ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1162: error: cannot find symbol private void insertCvTerm(final CvTerm cvTerm) ^ symbol: class CvTerm location: class IBatisDAO ./uk/ac/sanger/artemis/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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/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/chado/JdbcDAO.java:345: error: cannot find symbol CvTerm cvTerm, boolean not) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:493: error: cannot find symbol String name, CvTerm cvTerm) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:903: error: cannot find symbol final CvTerm cvTerm) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:1223: error: cannot find symbol public CvTerm getCvTermByNameAndCvName(String cvTermName, String name) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/JdbcDAO.java:1228: error: cannot find symbol public CvTerm getCvTermById(final int cvTermId) ^ symbol: class CvTerm location: class JdbcDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:218: error: cannot find symbol public List getPossibleMatches(String arg0, CvTerm arg1, int arg2) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:307: error: cannot find symbol public CvTerm getCvTermByDbXRef(DbXRef arg0) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:351: error: cannot find symbol public CvTerm getGoCvTermByAcc(String value) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:363: error: cannot find symbol public CvTerm getGoCvTermByAccViaDb(final String id) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:369: error: cannot find symbol public List getFeatureCvTermsByFeatureAndCvTermAndNot(Feature arg0, CvTerm arg1, boolean arg2) ^ symbol: class CvTerm location: class GmodDAO ./uk/ac/sanger/artemis/chado/GmodDAO.java:414: error: cannot find symbol public List getPubPropByPubAndCvTerm(Pub arg0, CvTerm arg1) ^ symbol: class CvTerm location: class GmodDAO ./org/gmod/schema/dao/SequenceDaoI.java:113: error: cannot find symbol CvTerm cvTerm, boolean not); ^ symbol: class CvTerm location: interface SequenceDaoI ./org/gmod/schema/dao/SequenceDaoI.java:146: error: cannot find symbol public Synonym getSynonymByNameAndCvTerm(String name, CvTerm type); ^ symbol: class CvTerm location: interface SequenceDaoI ./org/gmod/schema/dao/SequenceDaoI.java:230: error: cannot find symbol public List getPossibleMatches(String name,CvTerm cvTerm, int limit); ^ symbol: class CvTerm location: interface SequenceDaoI ./org/gmod/schema/dao/CvDaoI.java:55: error: cannot find symbol public abstract CvTerm getCvTermById(int id); ^ symbol: class CvTerm location: interface CvDaoI ./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)); ^ ./org/gmod/schema/dao/CvDaoI.java:66: error: cannot find symbol public abstract List getCvTermByNameInCv(String cvTermName, Cv cv); ^ symbol: class CvTerm location: interface CvDaoI ./org/gmod/schema/dao/CvDaoI.java:75: error: cannot find symbol public abstract CvTerm getGoCvTermByAcc(String value); ^ symbol: class CvTerm location: interface CvDaoI ./org/gmod/schema/dao/CvDaoI.java:84: error: cannot find symbol public abstract CvTerm getGoCvTermByAccViaDb(final String id); ^ symbol: class CvTerm location: interface CvDaoI ./org/gmod/schema/dao/CvDaoI.java:91: error: cannot find symbol public abstract List getCvTerms(); ^ symbol: class CvTerm location: interface CvDaoI ./uk/ac/sanger/artemis/circular/DNADraw.java:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./org/gmod/schema/dao/CvDaoI.java:100: error: cannot find symbol public abstract CvTerm getCvTermByNameAndCvName(String cvTermName, String name); ^ symbol: class CvTerm location: interface CvDaoI ./org/gmod/schema/dao/CvDaoI.java:108: error: cannot find symbol public abstract CvTerm getCvTermByDbXRef(DbXRef dbXRef); ^ symbol: class CvTerm location: interface CvDaoI ./org/gmod/schema/dao/PubDaoI.java:64: error: cannot find symbol public abstract List getPubPropByPubAndCvTerm(Pub pub,CvTerm cvTerm); ^ symbol: class CvTerm location: interface PubDaoI ./uk/ac/sanger/artemis/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:495: error: cannot find symbol private CvTerm getCvTermFromCache(final Hashtable cvTermCache, ^ symbol: class CvTerm location: class GFFDocumentEntry ./uk/ac/sanger/artemis/components/genebuilder/cv/AbstractCvBox.java:177: error: cannot find symbol } ^ symbol: class CvTerm location: class CVPanel ./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: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:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java: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/cv/GoBox.java:241: error: cannot find symbol public static CvTerm getGOCvTerm(String term) ^ symbol: class CvTerm location: class GoBox ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:311: error: cannot find symbol protected static Vector getCvTerms() ^ symbol: class CvTerm location: class HistoryBox ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:328: error: cannot find symbol public static CvTerm getDefaultTerm() ^ symbol: class CvTerm location: class HistoryBox ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:703: error: cannot find symbol private static CvTerm getCvTerm(String cvTermName) ^ symbol: class CvTerm location: class ArtemisUtils ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermsComparator.java:31: error: cannot find symbol public class CvTermsComparator implements Comparator ^ symbol: class CvTerm ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermsComparator.java:33: error: cannot find symbol public int compare(CvTerm cvTerm1, CvTerm cvTerm2) ^ symbol: class CvTerm location: class CvTermsComparator ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermsComparator.java:33: error: cannot find symbol public int compare(CvTerm cvTerm1, CvTerm cvTerm2) ^ symbol: class CvTerm location: class CvTermsComparator 50 errors 4 warnings ./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/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: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: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:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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: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/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: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: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/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/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: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:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./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: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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = 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: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/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: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/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/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/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ^ ./uk/ac/sanger/artemis/io/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: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:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/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/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:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:724: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:739: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/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/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:181: 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: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/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:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ 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/circular/DNADraw.java:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal majorTicks.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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: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/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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); ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/circular/DNADraw.class] Error 1 gmake: *** Waiting for unfinished jobs.... ./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/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./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/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/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/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/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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/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/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:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/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/circular/DNADraw.java:724: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:739: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int index = ticks.indexOf(new Integer(tick)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java: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/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: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/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/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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: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: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: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/genebuilder/cv/CVPanel.java:624: error: cannot find symbol private void addCvTermQualifier(CvTerm cvterm, ^ symbol: class CvTerm location: class CVPanel ./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/circular/DNADraw.java:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/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/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/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/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: 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/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/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:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/components/alignment/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/LocationLexer.java:181: 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/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ./uk/ac/sanger/artemis/io/LocationLexer.java: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 ('.'); ^ this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/chado/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:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/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:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/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/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: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: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/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:241: error: cannot find symbol public static CvTerm getGOCvTerm(String term) ^ symbol: class CvTerm location: class GoBox ./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:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java: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/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/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/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/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/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()); ^ return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/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/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/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/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/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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/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:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/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/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/components/alignment/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: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/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/LocationLexer.java:181: 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: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: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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/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:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/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/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/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/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/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:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/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: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/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: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 ./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()); ^ 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/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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/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: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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ return (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/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/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:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean 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/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: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:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java: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:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java: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/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/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:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/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/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/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/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 featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/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: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/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:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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: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/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/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/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/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/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/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()); ^ featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal 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/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/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/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/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/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal 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/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:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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/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/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()); ^ featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/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/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/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java: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: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: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:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/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/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/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/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/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/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/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:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/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: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:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/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/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/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: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/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/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./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:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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: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:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/io/LocationLexer.java: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/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: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/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/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/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/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/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ return new Character (current_char); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./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: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: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:201: 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: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:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/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/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: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/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/components/alignment/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: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:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/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/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/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/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 featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer 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/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/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 return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./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:326: warning: [removal] Long(long) in Long 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)); ^ 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:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./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); ^ 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: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/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal 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/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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: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/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/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: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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/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/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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal ./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)); ^ 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)) ) ^ fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/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/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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/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:689: 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/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()); ^ progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./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/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/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/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/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/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/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: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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short 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/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:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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: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)); ^ featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/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/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:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/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:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long 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)); ^ return new Integer (24); ^ ./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)); ^ file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/chado/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/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:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/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:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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/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/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()); ^ featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java: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/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()); ^ this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/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: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/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/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)); ^ lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./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:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1642: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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/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/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 ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/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 ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ 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/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/Options.java: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/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"))); ^ featureloc.setFmax(new Integer(range_new.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/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/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/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:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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: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: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/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:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/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: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/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal read_succeeded = new Boolean(true); 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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: 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/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/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); ^ db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/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/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:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/chado/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:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/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/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:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/components/filetree/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/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/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/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/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/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: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/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java: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/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ file_number_hash.put(base_directory, new Long(old_file_number + 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/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/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/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java: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:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/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/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: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/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/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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/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/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/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/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/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: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/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/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/components/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/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: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/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/io/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/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/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/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:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/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())); ^ progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/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/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:164: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character (current_char); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:181: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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/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: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/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/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/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/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:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/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)); ^ 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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/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: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/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/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/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/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/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/chado/ChadoTransactionManager.java:583: 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/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:450: warning: [removal] Boolean(boolean) in Boolean 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()); ^ 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/ActionController.java:57: error: cannot access Action private Action current_action = null; ^ bad class file: ./uk/ac/sanger/artemis/Action.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/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()); ^ deleted.add(new Integer(ideleted)); ^ ./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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./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 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:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/io/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:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java: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:946: 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 fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./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/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java: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/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 ./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:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/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)); ^ return new Character ('<'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/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: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: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:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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: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/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/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/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/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/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/components/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:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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/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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/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/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/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/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()); ^ return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/io/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: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/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/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/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/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/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:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java: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 ./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 featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/components/filetree/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:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: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); ^ 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/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/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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: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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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/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: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: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: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/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:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/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/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:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java: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/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:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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/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/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/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:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java:341: 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/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()); ^ final Vector v = (Vector)hash.get(new Integer(clusterFeature.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/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: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/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/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: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/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/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/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ lineAttr.put("lsize", new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java: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/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java: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/circular/DNADraw.java:175: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(4000)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:176: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(5)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:177: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(true)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/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: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/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:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./uk/ac/sanger/artemis/io/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: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: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: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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/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/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/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/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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: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/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: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/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/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/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/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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean 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/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ read_succeeded = new Boolean(true); ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal ^ return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:428: error: cannot find symbol final CvTerm cvTerm = getCvTermFromCache(cvTermCache, matchFeature, f); ^ symbol: class CvTerm location: class GFFDocumentEntry ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/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())); ^ getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./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: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 ./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() ); ^ 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/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/io/GFFDocumentEntry.java:500: error: cannot find symbol final CvTerm cvTerm; ^ symbol: class CvTerm location: class GFFDocumentEntry ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:503: error: cannot find symbol cvTerm = (CvTerm) cvTermCache.get(cvTermId); ^ symbol: class CvTerm location: class GFFDocumentEntry ./uk/ac/sanger/artemis/circular/DNADraw.java:804: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal majorTicks.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:811: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer tk = new Integer(i); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/chado/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 ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); 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/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java:1079: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./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/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/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: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/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long 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); feature_count_hash.put(base_directory, new Long(new_number)); ^ ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/circular/Wizard.java: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/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/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/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/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/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:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:675: error: cannot find symbol CvTerm cvTerm; ^ symbol: class CvTerm location: class DatabaseDocument ./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: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:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/components/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/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/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: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/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: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/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:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/circular/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/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/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/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/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/circular/DNADraw.java:1537: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(asCircular.isSelected())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java: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/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/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/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/circular/Wizard.java: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/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:1635: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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/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/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/chado/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/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:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/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:1512: error: cannot find symbol CvTerm cvterm = getCvTerm( feature_cvterm.getCvTerm().getCvTermId(), dao, gene_builder); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/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: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/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1835: error: cannot find symbol Enumeration enum_cvterm = cvterms.elements(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1838: error: cannot find symbol CvTerm cvterm = enum_cvterm.nextElement(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1872: error: cannot find symbol Enumeration enum_cvterm = cvterms.elements(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1875: error: cannot find symbol CvTerm cvterm = enum_cvterm.nextElement(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1892: error: cannot find symbol final Enumeration enum_cvterm = cvterms.elements(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1895: error: cannot find symbol final CvTerm cvterm = enum_cvterm.nextElement(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/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:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1914: error: cannot find symbol Enumeration enum_cvterm = cvterms.elements(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1917: error: cannot find symbol CvTerm cvterm = enum_cvterm.nextElement(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1933: error: cannot find symbol final List cvterm_list = dao.getCvTerms(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1934: error: cannot find symbol final Iterator it = cvterm_list.iterator(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1935: error: cannot find symbol cvterms = new Hashtable(cvterm_list.size()); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1939: error: cannot find symbol final CvTerm cvterm = it.next(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2010: error: cannot find symbol final Vector cvterm_match = new Vector(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/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/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2010: error: cannot find symbol 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(); ^ final Vector cvterm_match = new Vector(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2015: error: cannot find symbol CvTerm cvterm = cvterms.get(key); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2041: error: cannot find symbol CvTerm cvTerm = cvterms.get(key); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2083: error: cannot find symbol final Enumeration enum_cvterm = cvterms.elements(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2086: error: cannot find symbol final CvTerm cvTerm = enum_cvterm.nextElement(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2111: error: cannot find symbol List synonymCvTerms = doc.getDAO().getCvTermByNameInCv(null, cv); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2123: error: cannot find symbol Enumeration cvterm_enum = cvterms.elements(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2126: error: cannot find symbol CvTerm cvterm = cvterm_enum.nextElement(); ^ symbol: class CvTerm location: class DatabaseDocument ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] SecurityManager in java.lang has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:198: warning: [removal] getSecurityManager() in System has been deprecated and marked for removal SecurityManager sm = System.getSecurityManager(); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:199: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(null); ^ ./uk/ac/sanger/artemis/components/EntryFileDialog.java:203: warning: [removal] setSecurityManager(SecurityManager) in System has been deprecated and marked for removal System.setSecurityManager(sm); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/components/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/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 read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/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/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/sequence/Marker.java:193: warning: [removal] finalize() in Object has been deprecated and marked for removal public void finalize () { ^ ./uk/ac/sanger/artemis/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/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:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/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: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:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/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/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 ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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: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/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)); ^ 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: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/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/chado/ArtemisUtils.java:518: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("-1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:520: warning: [removal] Short(String) in Short has been deprecated and marked for removal strand = new Short("1"); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:661: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(fmin)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:663: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(fmax)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:668: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(-1)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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/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:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/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/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:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/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: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:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/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: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/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/alignment/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/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2219: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2221: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/chado/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/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/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/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/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/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/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./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/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java: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/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:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2192: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(range_new.getEnd())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2217: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/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/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: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: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/io/LocationLexer.java:172: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('>'); ^ ./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/LocationLexer.java:181: 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/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/LocationLexer.java:193: warning: [removal] Character(char) in Character has been deprecated and marked for removal ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Character ('.'); return new Float (2); ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:201: warning: [removal] Character(char) in Character has been deprecated and marked for removal return new Character ('.'); ^ ^ ./uk/ac/sanger/artemis/io/LocationLexer.java:253: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return new Integer (integer_string); ^ ./uk/ac/sanger/artemis/util/DatabaseLocationParser.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal int db_port = new Integer(port); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/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: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/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:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./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()); ^ Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/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/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:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/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/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:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ^ ./uk/ac/sanger/artemis/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: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/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/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1825: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return cvterms.get(new Integer(id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./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/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/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/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/io/Location.java:850: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return_object = new Integer(start_value); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/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/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/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/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(thisMatch.getFeatureId()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/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/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: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: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: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: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:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java: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: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/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java: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:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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: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 read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ./uk/ac/sanger/artemis/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:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/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:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java: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: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: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/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 ./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())); ^ hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/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/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: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/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/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./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/ArtemisUtils.java:446: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal subjectFeature.setSeqLen(new Integer(length)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2140: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvTerm.getCvTermId()), cvTerm); ^ ./uk/ac/sanger/artemis/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/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:1940: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal cvterms.put(new Integer(cvterm.getCvTermId()), cvterm); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:2424: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return dao.getSimilarityMatches(new Integer(srcFeatureId)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/UI.java:74: warning: [removal] stop() in Thread has been deprecated and marked for removal mask.stop(); ^ ./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/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/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/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/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: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/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/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: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/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/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: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/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ^ ./uk/ac/sanger/artemis/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/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/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/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/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/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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/components/filetree/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:583: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal deleted.add(new Integer(ideleted)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/MatchPanel.java:622: error: cannot find symbol CvTerm cvTerm = featureCvTerm.getCvTerm(); ^ symbol: class CvTerm location: class MatchPanel ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ ./uk/ac/sanger/artemis/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/RawStreamSequence.java:308: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal !seen.contains(new Integer(j))) ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:310: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(new_position[j])); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/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/database/DatabaseTreeNode.java:203: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal List sequenceList = dbDoc.getResidueFeatures(new Integer(getOrganism().getOrganismId())); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java: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: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/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: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: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/io/UI.java:74: warning: [removal] stop() in Thread has been deprecated and marked for removal mask.stop(); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:289: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new Integer (start); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:297: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new Integer (end); ^ ./uk/ac/sanger/artemis/io/FuzzyRange.java:299: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_end_object = new UpperInteger (new Integer (end)); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/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/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2074: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal db_id = new Integer(rs.getInt("db_id")); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:2095: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal dbxref_id = new Integer(rs.getInt("dbxref_id")); ^ ./uk/ac/sanger/artemis/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/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/chado/ChadoTransactionManager.java:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/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/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/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/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: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:2193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(range_new.getStart()-1)); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2207: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) -1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:2209: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short) 1)); ^ ./uk/ac/sanger/artemis/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:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1478: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureCvTermId = new Integer( feature_cvterm.getFeatureCvTermId() ); ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:807: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(alias.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:837: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(featurePub.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureId = new Integer(feature_cvterm.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:901: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermDbXRefId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:933: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureCvTermId = new Integer( ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:968: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureIds.add(new Integer(thisFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:972: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(range.getStart())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:973: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(range.getEnd())); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1078: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal parent = dao.getLazyFeatureNoResiduesById(new Integer(src_id)); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1103: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer idInt = new Integer(id); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1249: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureId = new Integer(feat.getFeatureId()); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1280: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer featureRelationShipId = new Integer( fr.getFeatureRelationshipId() ); ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1351: warning: [removal] Short(short) in Short has been deprecated and marked for removal if(strand.equals( new Short((short)-1)) ) // strand ^ ./uk/ac/sanger/artemis/util/DatabaseDocument.java:1353: warning: [removal] Short(short) in Short has been deprecated and marked for removal else if(strand.equals( new Short((short)1)) ) ^ ./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 ./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/genebuilder/cv/CvTermSelector.java:49: error: cannot find symbol private CvTerm cvTerm; ^ symbol: class CvTerm location: class CvTermSelector ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermSelector.java:50: error: cannot find symbol private Vector terms; ^ symbol: class CvTerm location: class CvTermSelector ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermSelector.java:310: error: cannot find symbol private Vector getTermsForGoId() ^ symbol: class CvTerm location: class CvTermSelector ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermSelector.java:407: error: cannot find symbol private CvTerm getCvTermFromSelectedItem() ^ symbol: class CvTerm location: class CvTermSelector ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermSelector.java:429: error: cannot find symbol private CvTerm addCvTermToDb(final DatabaseDocument doc) ^ symbol: class CvTerm location: class CvTermSelector ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermSelector.java:458: error: cannot find symbol protected CvTerm getCvTerm() ^ symbol: class CvTerm location: class CvTermSelector 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: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/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/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:311: error: cannot find symbol protected static Vector getCvTerms() ^ symbol: class CvTerm location: class HistoryBox ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:328: error: cannot find symbol public static CvTerm getDefaultTerm() ^ symbol: class CvTerm location: class HistoryBox ./uk/ac/sanger/artemis/util/DatabaseDocument.java: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/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/editor/HitInfo.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(startQuery)); ^ ./uk/ac/sanger/artemis/editor/HitInfo.java:275: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal queryPosition.add(new Integer(endQuery)); ^ ./uk/ac/sanger/artemis/io/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/genebuilder/AutoCompleteComboDocument.java:222: error: cannot find symbol itemStr = ((CvTerm)item).getName(); ^ symbol: class CvTerm location: class AutoCompleteComboDocument ./uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java:803: error: cannot find symbol if(list.getSelectedItem() instanceof CvTerm) ^ symbol: class CvTerm location: class PropertiesPanel ./uk/ac/sanger/artemis/components/genebuilder/gff/PropertiesPanel.java:804: error: cannot find symbol synonymName = ((CvTerm)list.getSelectedItem()).getName(); ^ symbol: class CvTerm location: class PropertiesPanel ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:211: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:274: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal chadoFeature.setSeqLen(new Integer( ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:360: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal changes.add(new Integer(ichanged)); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java: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/JdbcDAO.java:952: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(rs.getInt("fmin"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:953: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(rs.getInt("fmax"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:954: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short(rs.getShort("strand"))); ^ ./uk/ac/sanger/artemis/chado/JdbcDAO.java:960: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(phase)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/components/alignment/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:689: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal feature_relationship_rank_store.put(seq_id, new Integer(rank)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:861: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:863: warning: [removal] Short(short) in Short has been deprecated and marked for removal featureloc.setStrand(new Short((short)-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:875: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(0)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:877: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:879: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setPhase(new Integer(2)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:946: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmin(new Integer(segment.getRawRange().getStart()-1)); ^ ./uk/ac/sanger/artemis/chado/ChadoTransactionManager.java:947: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureloc.setFmax(new Integer(segment.getRawRange().getEnd())); ^ ./uk/ac/sanger/artemis/chado/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/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/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:291: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal new_start_object = new LowerInteger (new Integer (start)); ./uk/ac/sanger/artemis/components/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: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/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/IBatisDAO.java:339: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(min)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmax(new Integer(max)); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:688: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return (CvTerm)sqlMap.queryForObject("getCvtermByCvTermId", new Integer(cvTermId)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/chado/IBatisDAO.java:1383: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer feature_id = new Integer(dbxref.getFeature().getFeatureId()); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/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/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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/chado/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/chado/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/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/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:141: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/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: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/components/filetree/RemoteFileNode.java:91: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal this.file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:309: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java:321: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal file_length = new Integer(fat.getSize().intValue()); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:169: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.remove(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.addElement(new Integer(nbase)); ^ ./uk/ac/sanger/artemis/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/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:314: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal seen.add(new Integer(j)); ^ ./uk/ac/sanger/artemis/io/RawStreamSequence.java:340: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal fasta_header_positions.set(i, new Integer(length-range.getEnd())); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:49: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setValue((new Long(bytesSoFar)).intValue()); ^ ./uk/ac/sanger/artemis/j2ssh/FTProgress.java:58: warning: [removal] Long(long) in Long has been deprecated and marked for removal progress.setMaximum((new Long(bytesTotal)).intValue()); ^ ./uk/ac/sanger/artemis/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/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/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/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/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/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)); ^ 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/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/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/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/FileSystemModel.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return file.isFile() ? new Integer((int)file.length()) : null; ^ ./uk/ac/sanger/artemis/io/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. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/circular/SequenceData.java:61: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_default = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:62: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_remote = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:63: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_listFile = new Boolean(false); ^ ./uk/ac/sanger/artemis/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/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/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/LineAttribute.java:83: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal lineAttr.put("circular",new Boolean(draw.isCircular())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:98: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(s)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:125: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(e)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:151: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lsize)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:168: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(size)); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:184: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(size)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:226: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start.getValue())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:227: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end.getValue())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:228: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize.getValue())); ^ ./uk/ac/sanger/artemis/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/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/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/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ ./uk/ac/sanger/artemis/chado/ArtemisUtils.java:667: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal featureLoc.setFmin(new Integer(-1)); ^ ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:142: error: cannot find symbol CvTerm cvTerm = getGOCvTerm(term); ^ symbol: class CvTerm location: class GoBox ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:243: error: cannot find symbol CvTerm cvTerm = DatabaseDocument.getCvTermByCvTermName(term); ^ symbol: class CvTerm location: class GoBox ./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)); ^ 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:249: error: cannot find symbol CvTerm thisCvTerm = DatabaseDocument.getCvTermByCvAndCvTerm(term, ^ symbol: class CvTerm location: class GoBox ./uk/ac/sanger/artemis/components/genebuilder/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:867: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.remove(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/variant/VCFview.java:869: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal hideVcfList.add(new Integer(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ 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())); ^ ./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/RestrictionEnzyme.java:119: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal re.add(new Integer(pos.getValue())); ^ ./uk/ac/sanger/artemis/chado/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/SequenceData.java:61: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_default = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:62: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_remote = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:63: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_listFile = new Boolean(false); ^ ./uk/ac/sanger/artemis/chado/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/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/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/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: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/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/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 ./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); ^ lineAttr.put("lsize",new Integer(lsize)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:168: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(size)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:184: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(size)); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:226: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("start",new Integer(start.getValue())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:227: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("end",new Integer(end.getValue())); ^ ./uk/ac/sanger/artemis/circular/LineAttribute.java:228: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal lineAttr.put("lsize",new Integer(lineSize.getValue())); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:293: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(new_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:296: warning: [removal] Long(long) in Long has been deprecated and marked for removal feature_count_hash.put(base_directory, new Long(1)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:326: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(directory, new Long(old_file_number)); ^ ./uk/ac/sanger/artemis/ExternalProgram.java:364: warning: [removal] Long(long) in Long has been deprecated and marked for removal file_number_hash.put(base_directory, new Long(old_file_number + 1)); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java: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/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/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/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/circular/DNADraw.java: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/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/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; ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. ./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 ()); ^ Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java: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); ^ ./uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java:267: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/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/plot/AGWindowAlgorithm.java:106: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:121: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:136: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:144: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (100); ^ ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:152: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:162: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 10); ^ ./uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java:174: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (getStrand ().getBases ().getAverageAGPercent ()); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:177: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(120); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:194: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(500); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:211: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(24); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:222: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(window_size / 8); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:233: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float(100); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float(0); ^ ./uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java:252: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float(getStrand().getBases().getAverageGCPercent()); ^ ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:224: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(240); ^ ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:241: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(600); ^ ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:258: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(48); ^ ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:269: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer(window_size / 8); ^ ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:280: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float(100); ^ ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:289: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float(0); ^ ./uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java:299: warning: [removal] Float(double) in Float has been deprecated and marked for removal return new Float(52.7); ^ ./uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.java:115: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (30); ^ ./uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.java:130: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (5000); ^ ./uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.java:145: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (10); ^ ./uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.java:155: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 10); ^ ./uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.java:166: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (1); ^ ./uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.java:174: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (-1); ^ ./uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.java:190: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (g_minus_c/g_plus_c); ^ ./uk/ac/sanger/artemis/plot/GCDeviationAlgorithm.java:192: warning: [removal] Float(double) in Float has been deprecated and marked for removal return new Float (0.0); ^ ./uk/ac/sanger/artemis/plot/ATDeviationAlgorithm.java:118: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (30); ^ ./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/plot/ATDeviationAlgorithm.java:133: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (5000); ^ ./uk/ac/sanger/artemis/plot/ATDeviationAlgorithm.java:148: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (10); ^ ./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); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more 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/plot/CodonUsageAlgorithm.java:183: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (120); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:198: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (500); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:213: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (24); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:223: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal return new Integer (window_size / 8); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:234: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (2); ^ ./uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java:242: warning: [removal] Float(float) in Float has been deprecated and marked for removal return new Float (0); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/alignment/BamView.java:2557: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.remove(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/components/alignment/BamView.java:2559: warning: [removal] Short(short) in Short has been deprecated and marked for removal hideBamList.add(new Short(thisBamIndex)); ^ ./uk/ac/sanger/artemis/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)); ^ 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/ClusterLazyQualifierValue.java:191: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Vector v = (Vector)hash.get(new Integer(clusterFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:97: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer srcFeatureId = new Integer(featureLoc.getSrcFeatureId()); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:108: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal matchFeatures.put(new Integer(thisMatchFeature.getFeatureId()), thisMatchFeature); ^ ./uk/ac/sanger/artemis/chado/FeatureLocLazyQualifierValue.java:120: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer srcFeatureId = new Integer(srcFeature.getFeatureId()); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ ./uk/ac/sanger/artemis/components/genebuilder/ortholog/OrthoParalogTable.java:1079: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal return (new Integer(rank1)).compareTo(new Integer(rank2)); ^ 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/io/GFFDocumentEntry.java:437: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal (List) hashFeatureLocs.get(new Integer(matchFeature.getFeatureId())); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:499: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal final Integer cvTermId = new Integer(matchFeature.getCvTerm().getCvTermId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:579: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal Integer featureId = new Integer(featureLoc.getFeatureByFeatureId().getFeatureId()); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:664: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal rank = new Integer(0); ^ ./uk/ac/sanger/artemis/io/GFFDocumentEntry.java:667: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal rank = new Integer((String) (rankQualifier.getValues().get(0))); ^ ./uk/ac/sanger/artemis/components/alignment/PopupMessageFrame.java:46: warning: [removal] Float(float) in Float has been deprecated and marked for removal getRootPane().putClientProperty("Window.alpha", new Float(0.8f)); ^ 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/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/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: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/UI.java:74: warning: [removal] stop() in Thread has been deprecated and marked for removal mask.stop(); ^ 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/CvTermSelector.java:298: error: cannot find symbol if(((CvTerm)termList.getSelectedItem()).getName().equals("") && ^ symbol: class CvTerm location: class CvTermSelector ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermSelector.java:312: error: cannot find symbol CvTerm cvTerm = ^ symbol: class CvTerm location: class CvTermSelector ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermSelector.java:315: error: cannot find symbol terms = new Vector(); ^ symbol: class CvTerm location: class CvTermSelector ./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)); ^ 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/CvTermSelector.java:414: error: cannot find symbol CvTerm thisCvTerm = (CvTerm) terms.get(i); ^ symbol: class CvTerm location: class CvTermSelector ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermSelector.java:414: error: cannot find symbol CvTerm thisCvTerm = (CvTerm) terms.get(i); ^ symbol: class CvTerm location: class CvTermSelector ./uk/ac/sanger/artemis/components/genebuilder/cv/CvTermSelector.java:420: error: cannot find symbol return (CvTerm) termList.getSelectedItem(); ^ symbol: class CvTerm location: class CvTermSelector ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:318: error: cannot find symbol Vector cvTerms = getCvTerms(); ^ symbol: class CvTerm location: class HistoryBox ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:322: error: cannot find symbol CvTerm cvTerm = cvTerms.get(i); ^ symbol: class CvTerm location: class HistoryBox ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:330: error: cannot find symbol CvTerm cvterm = ^ symbol: class CvTerm location: class HistoryBox ./uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java:331: error: cannot find symbol (CvTerm) DatabaseDocument.getCvterms("", ChadoTransactionManager.HISTORY_CV, false).get(0); ^ symbol: class CvTerm location: class HistoryBox ./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/ControlledCurationBox.java:75: error: cannot find symbol CvTerm cvTerm = DatabaseDocument.getCvTermByCvPartAndCvTerm(term,cvName); ^ symbol: class CvTerm location: class ControlledCurationBox 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/Options.java:450: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(true); ^ ./uk/ac/sanger/artemis/Options.java:454: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal read_succeeded = new Boolean(false); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 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/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/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())); ^ 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. 66 errors 100 warnings ./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/cv/GoBox.java:393: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal values_index.add(new Integer(i)); ^ gmake: *** [Makefile:47: uk/ac/sanger/artemis/circular/GCSkewGraph.class] Error 1 Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/circular/RestrictionEnzyme.java:119: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal re.add(new Integer(pos.getValue())); ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more ./uk/ac/sanger/artemis/circular/SequenceData.java:61: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_default = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:62: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_remote = new Boolean(false); ^ ./uk/ac/sanger/artemis/circular/SequenceData.java:63: warning: [removal] Boolean(boolean) in Boolean has been deprecated and marked for removal s_listFile = new Boolean(false); ^ 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: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())); ^ 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/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())); ^ 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. 1 error 100 warnings Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more gmake: *** [Makefile:47: uk/ac/sanger/artemis/circular/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 Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files additionally use or override a deprecated API that is marked for removal. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 100 warnings only showing the first 100 warnings, of 101 total; use -Xmaxwarns if you would like to see more 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 Thu Mar 19 08:11:46 EDT 2026 build time: 00:02:14 !!! build failure encountered !!!