--- /dev/null
+<?xml version="1.0"?>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+-->
+<project name="jalviewX" default="usage" basedir="."
+ xmlns:if="ant:if"
+ xmlns:unless="ant:unless">
+ <taskdef classpath="${clover.jar}" resource="cloverlib.xml" if:set="clover.jar"/>
+ <clover-env if:set="clover.jar"/>
+
+ <target name="help" depends="usage" />
+ <target name="usage" depends="init">
+ <echo message="~~~Jalview Ant build.xml Usage~~~~" />
+ <echo message="Targets include:" />
+ <echo message="usage - default target, displays this message" />
+ <echo message="buildindices - generates JavaHelpSearch from the help files" />
+ <echo message="build - compiles all necessary files for Application" />
+ <echo message="makedist - compiles and places all necessary jar files into directory dist" />
+ <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
+ <echo message=" this needs a keystore and key."/>
+ <echo message=" Add -Dtimestamp to timestamp signed jars"/>
+ <echo message=" -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
+ <echo message=" See docs/building.html for more information." />
+ <echo message="compileApplet - compiles all necessary files for Applet" />
+ <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
+ <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
+ <echo message=" you can specify particular test groups as a list via -Dtestng-groups=" />
+ <echo message="See docs/building.html and the comments in build file for other targets." />
+ <echo message="note: compile and makeApplet optionally compile/obfuscate applet against a different Java version by specifying -Djava118.home=PathtoJDK/lib which is the lib directory in the JDK install that contains rt.jar " />
+ <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
+ <echo message="Useful -D flags: -Dclover.jar to specify path to openclover for testng coverage report" />
+ </target>
+
+
+ <!-- utils is a class path to additional utilities needed for
+ building docs, jars and webstart stuff -->
+ <!--
+ Userdefined build property defaults
+
+ wsdl.server list (plus namespace mapping info ???) - also want
+ ... to make this a dynamically generatable property
+ WebStart Location
+ Build location - provide a temporary root for speed
+ jarsigner keystore and info
+ Jakarta and axis classpath ?
+ Default argument for starting Jalview (if it exists).
+
+-->
+
+ <target name="init">
+ <path id="axis.classpath">
+ <!-->
+ <fileset dir="/usr/local/axis/lib">
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
+ <include name="**/*.jar"/>
+ <include name="*.jar"/>
+ </fileset> -->
+ </path>
+
+ <!-- Jalview Version String displayed by application on startup and used to check for updates -->
+ <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
+
+ <property name="INSTALLATION" value="Source" />
+
+ <!-- 2.4 (VAMSAS)" -->
+ <!-- Include debugging information in javac true or false -->
+ <property name="javac.debug" value="true" />
+
+ <!-- JarSigner Key Store for Webstart Distribution -->
+ <property name="jalview.keystore" value="./keys/.keystore" />
+ <!-- Keystore Password -->
+ <property name="jalview.keystore.pass" value="alignmentisfun" />
+ <!-- Key Name -->
+ <property name="jalview.key" value="jalview" />
+ <!-- Key Password -->
+ <property name="jalview.key.pass" value="alignmentisfun" />
+ <!-- time stamp server URL -->
+ <property name="jalview.tsaurl" value="" />
+ <!-- locally valid proxy for signing with external time server -->
+ <property name="proxyPort" value="80"/>
+ <property name="proxyHost" value="sqid"/>
+ <!-- key sign/digest algorithms -->
+ <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
+ <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
+
+ <!-- default TestNG groups to run -->
+ <property name="testng-groups" value="Functional" />
+ <!-- Java 9 JVM args -->
+ <condition property="java9">
+ <equals arg1="${ant.java.version}" arg2="9"/>
+ </condition>
+
+ <!-- Don't change anything below here unless you know what you are doing! -->
+ <!-- Url path for WebStart in JNLP file -->
+ <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
+ <!-- Webstart Image - looked for in resources/images -->
+ <property name="WebStartImage" value="JalviewLogo_big.png" />
+ <!-- J2SE version needed for webstart launch -->
+ <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
+ <property name="j2sev" value="1.7+" />
+ <!-- Java Compilation settings - source and target javac version -->
+ <property name="javac.source" value="1.8" />
+ <property name="javac.target" value="1.8" />
+
+ <!-- Permissions for running Java applets and applications. -->
+ <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
+ <property name="application.codebase" value="*.jalview.org" />
+ <!-- and allowing the applet to be deployed from any URL -->
+ <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
+ <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
+ <property name="applet.caller-codebase" value="${applet.codebase}" />
+
+ <!-- build directory configuration -->
+ <property name="libDir" value="lib" />
+ <property name="resourceDir" value="resources" />
+ <property name="helpDir" value="help" />
+ <property name="docDir" value="doc" />
+ <property name="sourceDir" value="src" />
+ <property name="schemaDir" value="schemas" />
+ <property name="outputDir" value="classes" unless:set="clover.jar"/>
+ <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
+ <property name="packageDir" value="dist" />
+ <property name="outputJar" value="jalview.jar" />
+ <!-- Jalview Applet JMol Jar Dependency -->
+ <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
+ <property name="varnaJar" value="VARNAv3-93.jar" />
+ <property name="jsoup" value="jsoup-1.8.1.jar" />
+ <property name="jsonSimple" value="json_simple-1.1.jar" />
+ <property name="javaJson" value="java-json.jar" />
+ <property name="jalviewLiteJar" value="jalviewApplet.jar" />
+ <property name="reportDir" value="test-reports" />
+ <property name="testDir" value="test" />
+ <property name="testOutputDir" value="tests" />
+ <property name="cloverOutputDir" value="clover" if:set="clover.jar" />
+ <!-- switch to indicate if we should obfuscate jalviewLite -->
+ <!-- <property name="donotobfuscate" value="true"/> -->
+ <!-- switch to exclude associations from generated jnlp files -->
+ <!-- <property name="nojnlpfileassocs" value="true"/> -->
+
+ <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
+ <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
+ <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
+ <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
+ <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
+ <property name="WSInterf" value="MsaWS" />
+ <property name="wsdl.Namespace" value="vamsas" />
+ <property name="wsdl.ClientNS" value="ext.vamsas" />
+ <!-- the class path for building the application -->
+ <path id="build.classpath">
+ <fileset dir="utils">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="${libDir}">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar" />
+ </fileset>
+ <fileset dir="appletlib">
+ <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
+ -->
+ <include name="${jmolJar}" />
+ <include name="${varnaJar}" />
+ </fileset>
+ </path>
+ <path id="test.classpath">
+ <pathelement path="${outputDir}" />
+ <path refid="build.classpath" />
+ </path>
+ <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
+ <!-- The Location of the java 1.1.8 jdk -->
+ <property name="java118.home" value="${java.home}" />
+ <!-- jre for 1.4 version -->
+ <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
+
+ <!-- the classpath for building the 1.1 applet -->
+ <path id="jalviewlite.deps">
+ <fileset dir="${java118.home}">
+ <include name="lib/rt.jar" />
+ </fileset>
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar" />
+ </fileset>
+ <pathelement location="appletlib/${jmolJar}" />
+ <pathelement location="lib/${varnaJar}" />
+ <pathelement location="appletlib/${jsoup}" />
+ <pathelement location="appletlib/${jsonSimple}" />
+ <pathelement location="appletlib/${javaJson}" />
+
+ </path>
+ <!-- default location for outputting javadoc -->
+ <property name="javadocDir" value="${packageDir}/javadoc" />
+ </target>
+
+
+ <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
+ <target name="buildPropertiesFile" depends="init">
+ <tstamp prefix="build">
+ <format property="date" pattern="dd MMMM yyyy" />
+ </tstamp>
+ <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
+ <arg value="rev-parse" />
+ <arg value="--short" />
+ <arg value="HEAD" />
+ </exec>
+ <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
+ <arg value="rev-parse" />
+ <arg value="--abbrev-ref" />
+ <arg value="HEAD" />
+ </exec>
+ <properties file="${outputDir}/.build_properties">
+ <header>
+ ---Jalview Build Details---
+ </header>
+ <property name="VERSION" value="${JALVIEW_VERSION}" />
+ <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
+ <property name="BUILD_DATE" value="${build.date}" />
+ </properties>
+ </target>
+
+
+ <target name="clean" depends="init">
+ <!-- not efficient yet. -->
+ <delete dir="${outputDir}" includes="*,**/*" />
+ </target>
+
+ <target name="distclean" depends="init, clean">
+
+ <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
+ <delete>
+ <fileset dir=".">
+ <include name="${outputJar}" />
+ <include name="#*#" />
+ <include name="#*.*#" />
+ <include name="**/#*#" />
+ <include name="**/#*.*#" />
+ <include name="*~" />
+ <include name="*.*~" />
+ <include name="**/*~" />
+ <include name="**/*.*~" />
+ </fileset>
+ </delete>
+ </target>
+
+ <target name="prepare" depends="init">
+ <mkdir dir="${outputDir}" />
+ <copy todir="${outputDir}">
+ <fileset dir=".">
+ <include name="${docDir}/**/*.*" />
+ <include name="${helpDir}/**/*.*" />
+ <include name="${libDir}/*.jar" />
+ </fileset>
+ <fileset dir="${resourceDir}">
+ <include name="**/*.*" />
+ </fileset>
+ </copy>
+ <mkdir dir="${cloverOutputDir}" if:set="clover.jar"/>
+ </target>
+
+ <target name="build" depends="prepare">
+ <!-- not efficient yet. -->
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
+ <exclude name="jalview/*applet*" />
+ <exclude name="jalview/appletgui/**" />
+ <exclude name="com/stevesoft/**" />
+ </javac>
+ </target>
+
+
+ <target name="testclean" depends="init">
+ <delete dir="${testOutputDir}" includes="*,**/*" />
+ </target>
+
+ <target name="prepareTests" depends="init,testclean">
+ <mkdir dir="${testOutputDir}" />
+ </target>
+
+ <target name="buildTests" depends="build,buildindices,prepareTests">
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
+ </javac>
+ </target>
+
+ <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
+
+ <target name="testng" depends="buildTests">
+ <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
+ verbose="2">
+ <classpath>
+ <pathelement location="${testOutputDir}" />
+ <pathelement location="${clover.jar}" if:set="clover.jar"/>
+ <path refid="test.classpath" />
+ </classpath>
+ <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
+ <jvmarg value="--illegal-access=warn" if:set="java9"/>
+ <classfileset dir="${testOutputDir}" includes="**/*.class" />
+ </testng>
+ </target>
+
+ <target name="buildindices" depends="init, prepare, buildPropertiesFile" unless="help.uptodate">
+ <replace value="${JALVIEW_VERSION}">
+ <replacetoken>
+ <![CDATA[$$Version-Rel$$]]>
+ </replacetoken>
+ <fileset dir="${outputDir}/${helpDir}">
+ <include name="help.jhm" />
+ </fileset>
+ </replace>
+
+ <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
+ <arg line="html" />
+ </java>
+ </target>
+
+ <target name="preparejnlp" depends="makedist">
+ <copy todir="${packageDir}">
+ <fileset dir="${resourceDir}/images">
+ <include name="${WebStartImage}" />
+ </fileset>
+ </copy>
+
+ <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
+
+ <!-- create a dummy jar which will eventually contain the jnlp template -->
+ <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
+ </jar>
+
+ <mkdir dir="${packageDir}/JNLP-INF" />
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
+ <param name="inih" value="*" />
+ <param name="maxh" value="*" />
+ </antcall>
+
+ <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+ <fileset dir="${packageDir}">
+ <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
+ </fileset>
+ </jar>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
+ <param name="inih" value="10M" />
+ <param name="maxh" value="256M" />
+ </antcall>
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
+ <param name="inih" value="800M" />
+ <param name="maxh" value="1024M" />
+ </antcall>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
+ <param name="inih" value="128M" />
+ <param name="maxh" value="512M" />
+ </antcall>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
+ <param name="inih" value="800M" />
+ <param name="maxh" value="1024M" />
+ </antcall>
+
+ <!-- finally, need to postprocess to add in associations at end of 'information' element
+
+ <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
+
+ </xslt>
+
+
+ -->
+ <!--
+ <association mime-type="application-x/ext-file" extensions="fa"/>
+ <association mime-type="application-x/ext-file" extensions="fasta"/>
+ <association mime-type="application-x/ext-file" extensions="mfa"/>
+ <association mime-type="application-x/ext-file" extensions="fastq"/>
+ <association mime-type="application-x/ext-file" extensions="blc"/>
+ <association mime-type="application-x/ext-file" extensions="msf"/>
+ <association mime-type="application-x/ext-file" extensions="pfam"/>
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="stk"/>
+ <association mime-type="application-x/ext-file" extensions="jar"/>-->
+ </target>
+
+ <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
+ tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ </fileset>
+ </signjar>
+ </target>
+ <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ </fileset>
+ </signjar>
+ </target>
+
+ <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
+ <!-- and sign the jars -->
+ <!-- the default keystore details might need to be edited here -->
+ </target>
+
+ <target name="runenv" depends="init">
+ <path id="run.classpath">
+ <pathelement location="${outputDir}" />
+ <fileset dir="${outputDir}">
+ <include name="${libDir}/*.jar" />
+ </fileset>
+ </path>
+ <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
+
+ <echo>java -classpath ${run.classpath} jalview.bin.Jalview
+ </echo>
+ </target>
+
+ <target name="-generatejnlpf">
+ <presetdef name="jnlpf">
+ <jnlp codebase="${WebStartLocation}">
+ <information>
+ <title>Jalview</title>
+ <vendor>The Barton Group</vendor>
+ <homepage href="http://www.jalview.org" />
+ <description>Jalview Multiple Alignment Editor</description>
+ <description kind="short">Jalview</description>
+ <icon href="${WebStartImage}" />
+ <offline_allowed />
+ </information>
+ <resources>
+ <j2se version="1.8+" />
+ <jar main="true" href="jalview.jar"/>
+ <fileset dir="${packageDir}">
+ <exclude name="jalview.jar" />
+ <include name="*.jar" />
+ <include name="*_*.jar" />
+ <exclude name="*quaqua*.jar" />
+ </fileset>
+ <property name="jalview.version" value="${JALVIEW_VERSION}" />
+ </resources>
+ <resources os="Mac OS X">
+ <fileset dir="${packageDir}">
+ <include name="quaqua-filechooser-only-8.0.jar"/>
+ <include name="*quaqua64*.jnilib.jar" />
+ </fileset>
+ </resources>
+
+ <application_desc main_class="jalview.bin.Jalview">
+ </application_desc>
+ <security>
+ <all_permissions />
+ </security>
+ </jnlp>
+ </presetdef>
+
+ <jnlpf toFile="${jnlpFile}" />
+ <!-- add the add-modules j2se attribute for java 9 -->
+ <replace file="${jnlpFile}" value="j2se version="1.8+" initial-heap-size="${inih}" max-heap-size="${maxh}" java-vm-args="--add-modules=java.se.ee --illegal-access=warn"">
+ <replacetoken>j2se version="1.8+"</replacetoken>
+ </replace>
+ </target>
+
+ <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
+ <echo message="Not adding JNLP File Associations" />
+ </target>
+
+ <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
+ <replace file="${jnlpFile}">
+ <replacetoken>
+ <![CDATA[</information>]]></replacetoken>
+ <replacevalue>
+ <![CDATA[
+ <association mime-type="application-x/ext-file" extensions="fa" />
+ <association mime-type="application-x/ext-file" extensions="fasta" />
+ <association mime-type="application-x/ext-file" extensions="mfa" />
+ <association mime-type="application-x/ext-file" extensions="fastq" />
+ <association mime-type="application-x/ext-file" extensions="blc" />
+ <association mime-type="application-x/ext-file" extensions="msf" />
+ <association mime-type="application-x/ext-file" extensions="pfam" />
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="stk"/>
+ <association mime-type="application-x/ext-file" extensions="jvp"/>
+ </information>]]></replacevalue>
+ </replace>
+ <echo message="Added file associations to JNLP file" />
+</target>
+<target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
+</target>
+
+<target name="buildextclients" depends="init">
+ <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
+ <condition property="dontextbuild">
+ <equals arg1="n" arg2="${doextbuild.response}" />
+ </condition>
+ <condition property="dontextbuild">
+ <equals arg1="N" arg2="${doextbuild.response}" />
+ </condition>
+ <fail if="dontextbuild">
+ Build External Client Code process aborted by user. Jalview source is unchanged.
+ </fail>
+ <!-- Currently, this doesn't happen automatically.
+ 1. Run WSDL2Java as below, which generates an ext.vamsas +
+ vamsas.<datapackages> fileset.
+ 2. refactor ext.vamsas.SpecificserviceWS* to
+ ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
+ 3. Update the jalview.ws.*WServices classes to reflect the
+ interface type, and all locations of this wsdl type that Jalview
+ might be using.
+
+-->
+ <path id="axisbuild">
+ <path refid="build.classpath" />
+ </path>
+ <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
+ <move todir="./bak">
+ <fileset dir="${sourceDir}" id="client">
+ <include name="${wsdl.ClientNS}/*.*" />
+ </fileset>
+ </move>
+
+ <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
+ <mappingSet>
+ <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
+ <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
+ </mappingSet>
+ </axis-wsdl2java>
+</target>
+
+<target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
+ <fail if="clover.jar">
+ Ignoring request to build jalview distribution with clover-instrumented classes
+ </fail>
+ <!-- make the package jar if not already existing -->
+ <mkdir dir="${packageDir}" />
+ <!-- clean dir if it already existed -->
+ <delete>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ </fileset>
+ </delete>
+ <jar destfile="${packageDir}/${outputJar}" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.Jalview" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Application-Name" value="Jalview Desktop" />
+ <attribute name="Codebase" value="${application.codebase}" />
+ </manifest>
+ <fileset dir="${outputDir}/">
+ <exclude name="cache*/**" />
+ <exclude name="*.jar" />
+ <exclude name="*.jar.*" />
+ <exclude name="**/*.jar" />
+ <exclude name="**/*.jar.*" />
+ </fileset>
+ </jar>
+
+ <copy toDir="${packageDir}" flatten="true">
+ <fileset dir="${outputDir}">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+ </fileset>
+ </copy>
+</target>
+
+
+<!-- jalopy code reformatter -->
+<target name="sourcescrub" depends="init,build">
+ <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
+ <fileset dir="${sourceDir}">
+ <include name="*.java" />
+ <include name="**/*.java" />
+ <include name="**/**/*.java" />
+ </fileset>
+ </jalopy>
+</target>
+
+
+
+<!-- Compile, package and obfuscate Jalview Applet -->
+<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
+
+<target name="compileApplet" depends="init,clean">
+ <mkdir dir="${outputDir}" />
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
+</target>
+
+<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+ <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
+ <copy todir="${outputDir}/lang">
+ <fileset dir="${resourceDir}/lang">
+ <include name="**.*" />
+ </fileset>
+ </copy>
+ <jar destfile="in.jar" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ </manifest>
+ <fileset dir="${outputDir}">
+ <include name="com/**" />
+ <include name="MCview/**" />
+ <include name="jalview/**" />
+ <include name=".build_properties" />
+ <include name="images/link.gif" />
+ <include name="lang/**" />
+ </fileset>
+ </jar>
+</target>
+<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
+</target>
+<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+ <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
+ <delete file="in.jar" />
+</target>
+<target name="-obfuscatereally" unless="donotobfuscate">
+
+ <path id="obfuscateDeps.path">
+ <pathelement location="${applet.jre.tools}" />
+ <pathelement location="appletlib/${jmolJar}" />
+ <pathelement location="lib/${varnaJar}" />
+ <pathelement location="appletlib/${jsoup}" />
+ <pathelement location="appletlib/${jsonSimple}" />
+ <pathelement location="appletlib/${javaJson}" />
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar" />
+ </fileset>
+ </path>
+ <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
+
+ <proguard verbose="true" >
+ <injar file="in.jar" />
+ <outjar file="${jalviewLiteJar}" />
+ <libraryjar refid="obfuscateDeps.path" />
+ <dontwarn />
+ <keep access="public" type="class" name="jalview.bin.JalviewLite">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+ <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+
+ <keep name="jalview.json.binding**">
+ <constructor/>
+ <method name="*"/>
+ </keep>
+
+ <keep access="public" type="class" name="MCview.PDBfile">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+
+ <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+
+ <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+
+
+ <!-- -libraryjars "${obfuscateDeps}"
+ -injars in.jar
+ -outjars jalviewApplet.jar
+ -keep public class jalview.bin.JalviewLite
+ { public * ; } -->
+ </proguard>
+ <delete file="in.jar" />
+</target>
+
+<target name="jaxb-bindings" depends="init" description="Generates JAXB bindings for supported Jalview XML models (needs xjc on the path)">
+ <delete>
+ <fileset dir="${sourceDir}/jalview/xml/binding/jalview">
+ <include name="*.java" />
+ </fileset>
+ </delete>
+ <exec executable="xjc">
+ <arg value="${schemaDir}/jalview.xsd"/>
+ <arg value="-d"/>
+ <arg value="${sourceDir}"/>
+ <arg value="-p"/>
+ <arg value="jalview.xml.binding.jalview"/>
+ </exec>
+ <delete>
+ <fileset dir="${sourceDir}/jalview/xml/binding/embl">
+ <include name="*.java" />
+ </fileset>
+ </delete>
+
+ <exec executable="xjc">
+ <arg value="${schemaDir}/embl.xsd"/>
+ <arg value="-d"/>
+ <arg value="${sourceDir}"/>
+ <arg value="-b"/>
+ <arg value="${schemaDir}/embl_bindings.xml"/>
+ <arg value="-p"/>
+ <arg value="jalview.xml.binding.embl"/>
+ </exec>
+
+ <delete>
+ <fileset dir="${sourceDir}/jalview/xml/binding/uniprot">
+ <include name="*.java" />
+ </fileset>
+ </delete>
+
+ <exec executable="xjc">
+ <arg value="${schemaDir}/uniprot.xsd"/>
+ <arg value="-d"/>
+ <arg value="${sourceDir}"/>
+ <arg value="-p"/>
+ <arg value="jalview.xml.binding.uniprot"/>
+ </exec>
+</target>
+
+<target name="sourcedist" description="create jalview source distribution" depends="init">
+ <delete file="${source.dist.name}" />
+ <!-- temporary copy of source to update timestamps -->
+ <copy todir="_sourcedist">
+ <fileset dir=".">
+ <exclude name=".*" />
+ <exclude name="**/.*" />
+ <exclude name="*.class" />
+ <exclude name="**/*.class" />
+ <include name="LICENSE" />
+ <include name="README" />
+ <include name="build.xml" />
+ <include name="jalview-jalopy.xml" />
+ <include name="JalviewApplet.jpx" />
+ <include name="JalviewX.jpx" />
+ <include name="nbbuild.xml" />
+ <include name="nbproject/genfiles.properties" />
+ <include name="nbproject/project.properties" />
+ <include name="nbproject/project.xml" />
+ <include name="${sourceDir}/*.java" />
+ <include name="${sourceDir}/**/*.java" />
+ <include name="${sourceDir}/**/*.cdr" />
+ <include name="${libDir}/**/*" />
+ <include name="${resourceDir}/**/*" />
+ <include name="${helpDir}/**/*" />
+ <include name="appletlib/${jmolJar}" />
+ <include name="appletlib/${jsonSimple}" />
+ <include name="appletlib/${javaJson}" />
+ <exclude name="**/*locales" />
+ <exclude name="*locales/**" />
+ <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
+ <exclude name="utils/InstallAnywhere/**Build*/**" />
+ <exclude name="utils/InstallAnywhere/**Build*/**" />
+ <exclude name="utils/InstallAnywhere/.build*.*/**" />
+ <exclude name="utils/InstallAnywhere/**locale*" />
+ <exclude name="utils/InstallAnywhere/**locale*/**" />
+ <exclude name="utils/InstallAnywhere/**locale*/**" />
+ <include name="${schemaDir}/**/*" />
+ <include name="utils/**/*" />
+ <include name="${docDir}/**/*" />
+ <include name="examples/**/*" />
+ </fileset>
+ </copy>
+
+ <tstamp prefix="build">
+ <format property="year" pattern="yyyy" />
+ </tstamp>
+ <!-- each replacetoken CDATA body must be on one line -
+ otherwise the pattern doesn't match -->
+ <replace value="${JALVIEW_VERSION}">
+ <replacetoken>
+ <![CDATA[$$Version-Rel$$]]>
+ </replacetoken>
+ <fileset dir="_sourcedist">
+ <include name="**/*" />
+ </fileset>
+ </replace>
+ <replace dir="_sourcedist" value="${build.year}">
+ <replacetoken>
+ <![CDATA[$$Year-Rel$$]]>
+ </replacetoken>
+ <fileset dir="_sourcedist">
+ <include name="**/*" />
+ </fileset>
+ </replace>
+
+ <tar destfile="${source.dist.name}" compression="gzip">
+ <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
+ </tarfileset>
+ </tar>
+
+ <delete dir="_sourcedist" />
+</target>
+<target name="prepubapplet_1" depends="makeApplet">
+ <copy todir="${packageDir}/examples">
+ <fileset dir="examples">
+ <include name="**/*" />
+ <include name="javascript/*" />
+ <include name="jmol/*" />
+ </fileset>
+ <fileset dir=".">
+ <include name="${jalviewLiteJar}" />
+ </fileset>
+ <fileset dir="appletlib">
+ <include name="**/*" />
+ </fileset>
+ </copy>
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
+ <manifest>
+ <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
+ <!-- <attribute name="Permissions" value="sandbox" /> -->
+ <!--<attribute name="Trusted-Lib" value="true" /> -->
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+ </manifest>
+ </jar>
+
+ <presetdef name="ap_applet.jar">
+ <!-- build a signed applet with 'all-permissions' -
+ Needs 'param name="permissions' value="all-permissions"' in applet tag
+ JalviewLite+JmolApplet linked sequence/structure fails
+ Mixed code warnings are raised
+ -->
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+ <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="applet.jar">
+ <!-- build signed applet with sandbox permissions -
+ Needs 'param name="permissions' value="sandbox"' in applet tag
+ Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
+ -->
+
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="sandbox" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+ <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="tl_applet.jar">
+ <!-- build signed applet with trusted library/trusted permissions -
+ Needs 'param name="permissions' value="all-permissions"' in applet tag
+ j1.7_45:
+ No mixed code warnings raised
+ Jmol/JalviewLite sequence/structure example doesn't link structures
+ Raises dialog asking user to allow page to control applet via LiveConnect javascript
+
+ -->
+
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Trusted-Only" value="true" />
+ <attribute name="Trusted-Library" value="true" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="to_applet.jar">
+ <!-- not fully test variant (yet) -->
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Trusted-Only" value="true" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <!-- create differently privileged artefacts -->
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+ <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
+ <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
+ <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
+ <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
+ <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
+ <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
+ <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
+ <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
+ <!-- finally, create manifest for original jars -->
+ <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+ <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
+ <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
+ <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
+
+ <!-- todo - write examples/downloads for alternate versions of the applet
+ probably don't need to do this now since we don't have alternate versions anymore !-->
+</target>
+<target name="-signapplet" depends="prepubapplet_1">
+ <fileset id="signappletjarset" dir="${packageDir}/examples">
+ <exclude name="u_*.jar" />
+ <include name="${jalviewLiteJar}" />
+ <include name="${jmolJar}" />
+ <include name="${javaJson}" />
+ <include name="${jsonSimple}" />
+ <include name="to_${jalviewLiteJar}" />
+ <include name="to_${jmolJar}" />
+ <include name="to_${javaJson}" />
+ <include name="to_${jsonSimple}" />
+ <include name="tl_${jalviewLiteJar}" />
+ <include name="tl_${jmolJar}" />
+ <include name="tl_${javaJson}" />
+ <include name="tl_${jsonSimple}" />
+ <include name="ap_${jalviewLiteJar}" />
+ <include name="ap_${jmolJar}" />
+ <include name="ap_${javaJson}" />
+ <include name="ap_${jsonSimple}" />
+ </fileset>
+</target>
+<target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+ <fileset refid="signappletjarset" />
+ </signjar>
+</target>
+
+<target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
+ <fileset refid="signappletjarset" />
+ </signjar>
+</target>
+
+<target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
+<target name="pubapplet" description="Dummy target to keep legacy Jalview build system happy. We don't actually publish the applet anymore."/>
+
+<target name="_pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
+
+ <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+ <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+ <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
+ <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
+ <!-- finally, replace any launchApp servlet tags with a version specification -->
+ <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
+ <replacetoken>
+ <![CDATA[http://www.jalview.org/services/launchApp"]]>
+ </replacetoken>
+ <fileset dir="${packageDir}/examples">
+ <include name="**/*.html" />
+ </fileset>
+ </replace>
+ <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
+ <replacetoken>
+ <![CDATA[http://www.jalview.org/services/launchApp']]>
+ </replacetoken>
+ <fileset dir="${packageDir}/examples">
+ <include name="**/*.html" />
+ </fileset>
+ </replace>
+
+</target>
+<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+ <javadoc destdir="${javadocDir}">
+ <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+ </packageset>
+ </javadoc>
+</target>
+<target name="linkcheck" depends="init,prepare">
+ <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
+ <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
+ <arg file="${helpDir}"/>
+ <arg value="-nointernet" />
+ </java>
+</target>
+
+<target name="eclipse-install" depends="init,prepare">
+
+ <property name="eclipseTempFile" value="eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
+ <property name="eclipseInstallURL" value="http://mirror.csclub.uwaterloo.ca/eclipse/technology/epp/downloads/release/oxygen/R/eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
+ <property name="java2scriptURL" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.core/dist/dropins/net.sf.j2s.core.jar?raw=true"/>
+
+ <get url="${eclipseInstallURL}" dest="${eclipseTempFile}"/>
+ <untar compression="gzip" src="${eclipseTempFile}" dest="${eclipse-inst}"/>
+
+ <!-- not needed since we ship transpiler with source
+ <get url="${java2scriptURL}" dest="eclipse-inst/dropins/net.sf.j2s.core.jar" /> -->
+
+</target>
+
+<target name="build-site" depends="init,prepare,compile-site,unzip-to-site,make-j2s-cores">
+ <!-- tarball -->
+ <tar compression="gzip" destfile="site.tar.gz">
+ <tarfileset dir="site" />
+ </tar>
+</target>
+<target name="prepare-site" depends="init,prepare,buildPropertiesFile">
+ <property name="swingjsdir" value="swingjs"/>
+ <property name="eclipse-inst" value="/home/bamboo/buildtools/eclipse/eclipse-js"/>
+ <property name="eclipse-exec" value="${eclipse-inst}/eclipse"/>
+ <property name="site" value="site"/>
+ <!-- where the eclipse js workspace has been initialised -->
+ <property name="eclipse-work" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace"/>
+ <!-- git repository linked to project in workspace -->
+ <property name="eclipse-workrepo" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace/jalview-js"/>
+</target>
+ <target name="clean-site" depends="prepare-site">
+ <delete dir="${eclipse-workrepo}/${site}"/>
+ <mkdir dir="${eclipse-workrepo}/${site}"/>
+ </target>
+<target name="compile-site" depends="prepare-site,clean-site">
+ <!-- update transpiler -->
+ <copy file="${swingjsdir}/net.sf.j2s.core.jar" todir="${eclipse-inst}/dropins" overwrite="true" failonerror="true"/>
+ <!-- update the git repo linked to the eclipse workspace -->
+ <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="true">
+ <arg value="rev-parse" />
+ <arg value="--short" />
+ <arg value="HEAD" />
+ </exec>
+ <!-- update and checkout the same commit in the workspace project -->
+ <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
+ <arg value="reset" />
+ <arg value="--hard" />
+ </exec>
+ <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
+ <arg value="pull" />
+ </exec>
+ <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
+ <arg value="checkout" />
+ <arg value="${git.commit}" />
+ </exec>
+ <!-- custom classpath for .js builds -->
+ <copy file=".classpath.js" tofile="${eclipse-workrepo}/.classpath" overwrite="true"/>
+ <!-- clean eclipse log -->
+ <delete file="${eclipse-work}/.metadata/.log"/>
+
+ <!-- execute the eclipse build - the build may fail but valid javascript may still be produced, so we ignore return codes -->
+ <exec executable="${eclipse-exec}" failonerror="no">
+ <arg value="-nosplash"/>
+ <arg value="--launcher.suppressErrors"/>
+ <arg value="-application"/>
+ <arg value="org.eclipse.jdt.apt.core.aptBuild"/>
+ <arg value="-data"/>
+ <arg value="${eclipse-work}"/>
+ </exec>
+ <!-- report log -->
+ <exec executable="/bin/cat">
+ <arg value="${eclipse-work}/.metadata/.log"/>
+ </exec>
+ <!-- TODO: run jslint and something else here to check we have a complete set of .js files for java -->
+ <!-- possibly compare timestamps between .js files and their mate in source - any newer or not present triggers a new build -->
+ <!-- <mkdir dir="${packageDir}/${site}" /> -->
+ <!-- <property name="swingjs.zipurl" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.java.core/dist/SwingJS-site.zip?raw=true" /> -->
+
+ <!-- and reset the .classpath -->
+ <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
+ <arg value="checkout" />
+ <arg value="${git.commit}"/>
+ <arg value="--"/>
+ <arg value=".classpath" />
+ </exec>
+
+ <!-- finally copy artefacts from eclipse project checkout to the build site -->
+ <copy todir="${site}">
+ <fileset dir="${eclipse-workrepo}/site"/>
+ </copy>
+</target>
+<target name="unzip-to-site" depends="prepare-site">
+ <ant antfile="build-site.xml"/>
+</target>
+
+ <target name="make-j2s-cores" depends="">
+ <ant antfile="buildcore.xml" target="build-all-cores"/>
+ </target>
+</project>
--- /dev/null
+java/applet/Applet.js
+java/applet/AppletContext.js
+java/applet/AppletStub.js
+java/applet/JSApplet.js
+java/awt/ActiveEvent.js
+java/awt/Adjustable.js
+java/awt/AWTEvent.js
+java/awt/AWTEventMulticaster.js
+java/awt/AWTKeyStroke.js
+java/awt/BasicStroke.js
+java/awt/BorderLayout.js
+java/awt/Button.js
+java/awt/Color.js
+java/awt/color/ColorSpace.js
+java/awt/Component.js
+java/awt/ComponentOrientation.js
+java/awt/Container.js
+java/awt/ContainerOrderFocusTraversalPolicy.js
+java/awt/Cursor.js
+java/awt/DefaultFocusTraversalPolicy.js
+java/awt/DefaultKeyboardFocusManager.js
+java/awt/Dialog.js
+java/awt/Dimension.js
+java/awt/dnd/peer/DropTargetPeer.js
+java/awt/event/ActionListener.js
+java/awt/event/AdjustmentEvent.js
+java/awt/event/AdjustmentListener.js
+java/awt/event/AWTEventListener.js
+java/awt/event/ComponentAdapter.js
+java/awt/event/ComponentEvent.js
+java/awt/event/ComponentListener.js
+java/awt/event/ContainerListener.js
+java/awt/event/FocusEvent.js
+java/awt/event/FocusListener.js
+java/awt/event/HierarchyBoundsListener.js
+java/awt/event/HierarchyListener.js
+java/awt/event/InputEvent.js
+java/awt/event/InputMethodListener.js
+java/awt/event/InvocationEvent.js
+java/awt/event/ItemEvent.js
+java/awt/event/ItemListener.js
+java/awt/event/KeyListener.js
+java/awt/event/MouseEvent.js
+java/awt/event/MouseListener.js
+java/awt/event/MouseMotionListener.js
+java/awt/event/MouseWheelListener.js
+java/awt/event/TextListener.js
+java/awt/event/WindowAdapter.js
+java/awt/event/WindowEvent.js
+java/awt/event/WindowFocusListener.js
+java/awt/event/WindowListener.js
+java/awt/event/WindowStateListener.js
+java/awt/EventDispatchThread.js
+java/awt/EventFilter.js
+java/awt/EventQueue.js
+java/awt/EventQueueItem.js
+java/awt/FlowLayout.js
+java/awt/FocusTraversalPolicy.js
+java/awt/Font.js
+java/awt/font/FontRenderContext.js
+java/awt/FontMetrics.js
+java/awt/Frame.js
+java/awt/geom/AffineTransform.js
+java/awt/geom/Dimension2D.js
+java/awt/geom/Path2D.js
+java/awt/geom/PathIterator.js
+java/awt/geom/Point2D.js
+java/awt/geom/Rectangle2D.js
+java/awt/geom/RectangularShape.js
+java/awt/geom/RectIterator.js
+java/awt/GraphicsCallback.js
+java/awt/GraphicsConfiguration.js
+java/awt/GraphicsDevice.js
+java/awt/GraphicsEnvironment.js
+java/awt/image/ImageObserver.js
+java/awt/Insets.js
+java/awt/ItemSelectable.js
+java/awt/JSComponent.js
+java/awt/JSDialog.js
+java/awt/JSFrame.js
+java/awt/JSPanel.js
+java/awt/KeyboardFocusManager.js
+java/awt/KeyEventDispatcher.js
+java/awt/KeyEventPostProcessor.js
+java/awt/Label.js
+java/awt/LayoutManager.js
+java/awt/LayoutManager2.js
+java/awt/LightweightDispatcher.js
+java/awt/Paint.js
+java/awt/Panel.js
+java/awt/peer/ComponentPeer.js
+java/awt/peer/ContainerPeer.js
+java/awt/peer/FramePeer.js
+java/awt/peer/KeyboardFocusManagerPeer.js
+java/awt/peer/LightweightPeer.js
+java/awt/peer/WindowPeer.js
+java/awt/Point.js
+java/awt/Queue.js
+java/awt/Rectangle.js
+java/awt/RenderingHints.js
+java/awt/Scrollbar.js
+java/awt/ScrollPane.js
+java/awt/Shape.js
+java/awt/Stroke.js
+java/awt/TextArea.js
+java/awt/TextComponent.js
+java/awt/TextField.js
+java/awt/Toolkit.js
+java/awt/Transparency.js
+java/awt/Window.js
+java/beans/ChangeListenerMap.js
+java/beans/PropertyChangeEvent.js
+java/beans/PropertyChangeListener.js
+java/beans/PropertyChangeSupport.js
+java/lang/AbstractStringBuilder.js
+java/lang/Class.js
+java/lang/Enum.js
+java/lang/Iterable.js
+java/lang/reflect/Constructor.js
+java/lang/reflect/Method.js
+java/lang/StringBuffer.js
+java/lang/StringBuilder.js
+java/lang/Thread.js
+java/lang/ThreadGroup.js
+java/math/RoundingMode.js
+java/net/URL.js
+java/net/URLStreamHandlerFactory.js
+java/text/CharacterIterator.js
+java/text/DecimalFormat.js
+java/text/DecimalFormatSymbols.js
+java/text/DigitList.js
+java/text/FieldPosition.js
+java/text/Format.js
+java/text/NumberFormat.js
+java/util/AbstractCollection.js
+java/util/AbstractList.js
+java/util/AbstractMap.js
+java/util/AbstractSequentialList.js
+java/util/AbstractSet.js
+java/util/ArrayList.js
+java/util/Arrays.js
+java/util/Collection.js
+java/util/Collections.js
+java/util/Deque.js
+java/util/Dictionary.js
+java/util/Enumeration.js
+java/util/EventListener.js
+java/util/EventObject.js
+java/util/HashMap.js
+java/util/HashSet.js
+java/util/Hashtable.js
+java/util/IdentityHashMap.js
+java/util/Iterator.js
+java/util/LinkedHashMap.js
+java/util/LinkedList.js
+java/util/List.js
+java/util/ListResourceBundle.js
+java/util/Locale.js
+java/util/Map.js
+java/util/Objects.js
+java/util/Queue.js
+java/util/Random.js
+java/util/RandomAccess.js
+java/util/ResourceBundle.js
+java/util/Set.js
+java/util/Vector.js
+javajs/api/JSFunction.js
+javajs/util/AjaxURLConnection.js
+javajs/util/AjaxURLStreamHandlerFactory.js
+javajs/util/AU.js
+javajs/util/JSThread.js
+javajs/util/Lst.js
+javajs/util/PT.js
+javajs/util/SB.js
+javax/swing/AbstractAction.js
+javax/swing/AbstractButton.js
+javax/swing/AbstractListModel.js
+javax/swing/Action.js
+javax/swing/ActionMap.js
+javax/swing/AncestorNotifier.js
+javax/swing/ArrayTable.js
+javax/swing/border/AbstractBorder.js
+javax/swing/border/BevelBorder.js
+javax/swing/border/Border.js
+javax/swing/border/CompoundBorder.js
+javax/swing/border/EmptyBorder.js
+javax/swing/border/EtchedBorder.js
+javax/swing/border/LineBorder.js
+javax/swing/BorderFactory.js
+javax/swing/BoundedRangeModel.js
+javax/swing/BoxLayout.js
+javax/swing/ButtonGroup.js
+javax/swing/ButtonModel.js
+javax/swing/ClientPropertyKey.js
+javax/swing/ComboBoxModel.js
+javax/swing/DefaultBoundedRangeModel.js
+javax/swing/DefaultButtonModel.js
+javax/swing/DefaultComboBoxModel.js
+javax/swing/DefaultSingleSelectionModel.js
+javax/swing/DropMode.js
+javax/swing/event/AncestorEvent.js
+javax/swing/event/AncestorListener.js
+javax/swing/event/CaretEvent.js
+javax/swing/event/CaretListener.js
+javax/swing/event/ChangeEvent.js
+javax/swing/event/ChangeListener.js
+javax/swing/event/DocumentEvent.js
+javax/swing/event/DocumentListener.js
+javax/swing/event/EventListenerList.js
+javax/swing/event/ListDataEvent.js
+javax/swing/event/ListDataListener.js
+javax/swing/event/UndoableEditEvent.js
+javax/swing/event/UndoableEditListener.js
+javax/swing/InputMap.js
+javax/swing/JApplet.js
+javax/swing/JButton.js
+javax/swing/JCheckBox.js
+javax/swing/JCheckBoxMenuItem.js
+javax/swing/JComboBox.js
+javax/swing/JComponent.js
+javax/swing/JFrame.js
+javax/swing/JLabel.js
+javax/swing/JLayeredPane.js
+javax/swing/JMenu.js
+javax/swing/JMenuBar.js
+javax/swing/JMenuItem.js
+javax/swing/JPanel.js
+javax/swing/JPopupMenu.js
+javax/swing/JRadioButtonMenuItem.js
+javax/swing/JRootPane.js
+javax/swing/JScrollBar.js
+javax/swing/JScrollPane.js
+javax/swing/JSeparator.js
+javax/swing/JTextArea.js
+javax/swing/JTextField.js
+javax/swing/JToggleButton.js
+javax/swing/JViewport.js
+javax/swing/KeyboardManager.js
+javax/swing/KeyStroke.js
+javax/swing/ListModel.js
+javax/swing/LookAndFeel.js
+javax/swing/MenuElement.js
+javax/swing/MutableComboBoxModel.js
+javax/swing/plaf/ActionMapUIResource.js
+javax/swing/plaf/basic/BasicBorders.js
+javax/swing/plaf/BorderUIResource.js
+javax/swing/plaf/ColorUIResource.js
+javax/swing/plaf/ComponentUI.js
+javax/swing/plaf/DimensionUIResource.js
+javax/swing/plaf/FontUIResource.js
+javax/swing/plaf/InputMapUIResource.js
+javax/swing/plaf/InsetsUIResource.js
+javax/swing/plaf/UIResource.js
+javax/swing/RepaintManager.js
+javax/swing/RootPaneContainer.js
+javax/swing/Scrollable.js
+javax/swing/ScrollPaneConstants.js
+javax/swing/ScrollPaneLayout.js
+javax/swing/SingleSelectionModel.js
+javax/swing/SizeRequirements.js
+javax/swing/SwingConstants.js
+javax/swing/SwingPaintEventDispatcher.js
+javax/swing/SwingUtilities.js
+javax/swing/text/AbstractDocument.js
+javax/swing/text/AttributeSet.js
+javax/swing/text/Caret.js
+javax/swing/text/DefaultCaret.js
+javax/swing/text/DefaultEditorKit.js
+javax/swing/text/Document.js
+javax/swing/text/EditorKit.js
+javax/swing/text/Element.js
+javax/swing/text/GapContent.js
+javax/swing/text/GapVector.js
+javax/swing/text/JTextComponent.js
+javax/swing/text/MutableAttributeSet.js
+javax/swing/text/PlainDocument.js
+javax/swing/text/PlainView.js
+javax/swing/text/Position.js
+javax/swing/text/Segment.js
+javax/swing/text/SegmentCache.js
+javax/swing/text/SimpleAttributeSet.js
+javax/swing/text/Style.js
+javax/swing/text/StyleConstants.js
+javax/swing/text/StyleContext.js
+javax/swing/text/TabExpander.js
+javax/swing/text/TextAction.js
+javax/swing/text/Utilities.js
+javax/swing/text/View.js
+javax/swing/tree/TreeNode.js
+javax/swing/UIDefaults.js
+javax/swing/UIManager.js
+javax/swing/undo/AbstractUndoableEdit.js
+javax/swing/undo/CompoundEdit.js
+javax/swing/undo/UndoableEdit.js
+javax/swing/ViewportLayout.js
+javax/swing/WindowConstants.js
+sun/awt/AppContext.js
+sun/awt/AWTAccessor.js
+sun/awt/AWTAutoShutdown.js
+sun/awt/CausedFocusEvent.js
+sun/awt/ComponentFactory.js
+sun/awt/KeyboardFocusManagerPeerProvider.js
+sun/awt/MostRecentKeyValue.js
+sun/awt/MostRecentThreadAppContext.js
+sun/awt/PaintEventDispatcher.js
+sun/awt/PostEventQueue.js
+sun/awt/RequestFocusController.js
+sun/awt/SunToolkit.js
+sun/awt/WindowClosingListener.js
+sun/awt/WindowClosingSupport.js
+sun/font/FontDesignMetrics.js
+sun/swing/DefaultLookup.js
+sun/swing/SwingLazyValue.js
+sun/text/resources/FormatData.js
+sun/text/resources/FormatData_en.js
+sun/util/resources/LocaleData.js
+swingjs/a2s/A2SContainer.js
+swingjs/a2s/A2SEvent.js
+swingjs/a2s/A2SListener.js
+swingjs/a2s/Applet.js
+swingjs/a2s/Button.js
+swingjs/a2s/Label.js
+swingjs/a2s/Panel.js
+swingjs/a2s/Scrollbar.js
+swingjs/a2s/ScrollPane.js
+swingjs/a2s/TextArea.js
+swingjs/a2s/TextField.js
+swingjs/api/Interface.js
+swingjs/api/js/DOMNode.js
+swingjs/api/js/HTML5CanvasContext2D.js
+swingjs/api/js/JSInterface.js
+swingjs/api/JSMinimalAbstractDocument.js
+swingjs/jquery/JQueryUI.js
+swingjs/JSAbstractDocument.js
+swingjs/JSApp.js
+swingjs/JSApplet.js
+swingjs/JSAppletThread.js
+swingjs/JSAppletViewer.js
+swingjs/JSDocumentEvent.js
+swingjs/JSFocusPeer.js
+swingjs/JSFontMetrics.js
+swingjs/JSFrameViewer.js
+swingjs/JSGraphics2D.js
+swingjs/JSGraphicsConfiguration.js
+swingjs/JSGraphicsEnvironment.js
+swingjs/JSMouse.js
+swingjs/JSNullComponentPeer.js
+swingjs/JSPlainDocument.js
+swingjs/JSScreenDevice.js
+swingjs/JSThreadGroup.js
+swingjs/JSToolkit.js
+swingjs/JSUtil.js
+swingjs/plaf/ButtonListener.js
+swingjs/plaf/DefaultMenuLayout.js
+swingjs/plaf/HTML5LookAndFeel.js
+swingjs/plaf/JSAppletUI.js
+swingjs/plaf/JSButtonUI.js
+swingjs/plaf/JSCheckBoxMenuItemUI.js
+swingjs/plaf/JSCheckBoxUI.js
+swingjs/plaf/JSComboBoxUI.js
+swingjs/plaf/JSComponentUI.js
+swingjs/plaf/JSEventHandler.js
+swingjs/plaf/JSFrameUI.js
+swingjs/plaf/JSGraphicsUtils.js
+swingjs/plaf/JSLabelUI.js
+swingjs/plaf/JSLayeredPaneUI.js
+swingjs/plaf/JSLightweightUI.js
+swingjs/plaf/JSMenuBarUI.js
+swingjs/plaf/JSMenuItemUI.js
+swingjs/plaf/JSMenuUI.js
+swingjs/plaf/JSPanelUI.js
+swingjs/plaf/JSPopupMenuSeparatorUI.js
+swingjs/plaf/JSPopupMenuUI.js
+swingjs/plaf/JSRadioButtonMenuItemUI.js
+swingjs/plaf/JSRadioButtonUI.js
+swingjs/plaf/JSRootPaneUI.js
+swingjs/plaf/JSScrollBarUI.js
+swingjs/plaf/JSScrollPaneUI.js
+swingjs/plaf/JSSeparatorUI.js
+swingjs/plaf/JSSliderUI.js
+swingjs/plaf/JSTextAreaUI.js
+swingjs/plaf/JSTextFieldUI.js
+swingjs/plaf/JSTextUI.js
+swingjs/plaf/JSTextViewUI.js
+swingjs/plaf/JSViewportUI.js
+swingjs/plaf/JSWindowUI.js
+swingjs/plaf/LazyActionMap.js
+swingjs/plaf/Resizer.js
+swingjs/plaf/TextListener.js
--- /dev/null
+java/applet/Applet.js
+java/applet/AppletContext.js
+java/applet/AppletStub.js
+java/applet/JSApplet.js
+java/awt/ActiveEvent.js
+java/awt/Adjustable.js
+java/awt/AWTEvent.js
+java/awt/AWTEventMulticaster.js
+java/awt/AWTKeyStroke.js
+java/awt/BasicStroke.js
+java/awt/BorderLayout.js
+java/awt/Button.js
+java/awt/Color.js
+java/awt/color/ColorSpace.js
+java/awt/Component.js
+java/awt/ComponentOrientation.js
+java/awt/Container.js
+java/awt/ContainerOrderFocusTraversalPolicy.js
+java/awt/Cursor.js
+java/awt/DefaultFocusTraversalPolicy.js
+java/awt/DefaultKeyboardFocusManager.js
+java/awt/Dialog.js
+java/awt/Dimension.js
+java/awt/dnd/peer/DropTargetPeer.js
+java/awt/event/ActionListener.js
+java/awt/event/AdjustmentEvent.js
+java/awt/event/AdjustmentListener.js
+java/awt/event/AWTEventListener.js
+java/awt/event/ComponentAdapter.js
+java/awt/event/ComponentEvent.js
+java/awt/event/ComponentListener.js
+java/awt/event/ContainerListener.js
+java/awt/event/FocusEvent.js
+java/awt/event/FocusListener.js
+java/awt/event/HierarchyBoundsListener.js
+java/awt/event/HierarchyListener.js
+java/awt/event/InputEvent.js
+java/awt/event/InputMethodListener.js
+java/awt/event/InvocationEvent.js
+java/awt/event/ItemEvent.js
+java/awt/event/ItemListener.js
+java/awt/event/KeyListener.js
+java/awt/event/MouseEvent.js
+java/awt/event/MouseListener.js
+java/awt/event/MouseMotionListener.js
+java/awt/event/MouseWheelListener.js
+java/awt/event/TextListener.js
+java/awt/event/WindowAdapter.js
+java/awt/event/WindowEvent.js
+java/awt/event/WindowFocusListener.js
+java/awt/event/WindowListener.js
+java/awt/event/WindowStateListener.js
+java/awt/EventDispatchThread.js
+java/awt/EventFilter.js
+java/awt/EventQueue.js
+java/awt/EventQueueItem.js
+java/awt/FlowLayout.js
+java/awt/FocusTraversalPolicy.js
+java/awt/Font.js
+java/awt/font/FontRenderContext.js
+java/awt/FontMetrics.js
+java/awt/Frame.js
+java/awt/geom/AffineTransform.js
+java/awt/geom/Dimension2D.js
+java/awt/geom/Path2D.js
+java/awt/geom/PathIterator.js
+java/awt/geom/Point2D.js
+java/awt/geom/Rectangle2D.js
+java/awt/geom/RectangularShape.js
+java/awt/geom/RectIterator.js
+java/awt/GraphicsCallback.js
+java/awt/GraphicsConfiguration.js
+java/awt/GraphicsDevice.js
+java/awt/GraphicsEnvironment.js
+java/awt/image/ImageObserver.js
+java/awt/Insets.js
+java/awt/ItemSelectable.js
+java/awt/JSComponent.js
+java/awt/JSDialog.js
+java/awt/JSFrame.js
+java/awt/JSPanel.js
+java/awt/KeyboardFocusManager.js
+java/awt/KeyEventDispatcher.js
+java/awt/KeyEventPostProcessor.js
+java/awt/Label.js
+java/awt/LayoutManager.js
+java/awt/LayoutManager2.js
+java/awt/LightweightDispatcher.js
+java/awt/Paint.js
+java/awt/Panel.js
+java/awt/peer/ComponentPeer.js
+java/awt/peer/ContainerPeer.js
+java/awt/peer/FramePeer.js
+java/awt/peer/KeyboardFocusManagerPeer.js
+java/awt/peer/LightweightPeer.js
+java/awt/peer/WindowPeer.js
+java/awt/Point.js
+java/awt/Queue.js
+java/awt/Rectangle.js
+java/awt/RenderingHints.js
+java/awt/Scrollbar.js
+java/awt/ScrollPane.js
+java/awt/Shape.js
+java/awt/Stroke.js
+java/awt/TextArea.js
+java/awt/TextComponent.js
+java/awt/TextField.js
+java/awt/Toolkit.js
+java/awt/Transparency.js
+java/awt/Window.js
+java/beans/ChangeListenerMap.js
+java/beans/PropertyChangeEvent.js
+java/beans/PropertyChangeListener.js
+java/beans/PropertyChangeSupport.js
+java/lang/AbstractStringBuilder.js
+java/lang/Class.js
+java/lang/Enum.js
+java/lang/Iterable.js
+java/lang/reflect/Constructor.js
+java/lang/reflect/Method.js
+java/lang/StringBuffer.js
+java/lang/StringBuilder.js
+java/lang/Thread.js
+java/lang/ThreadGroup.js
+java/math/RoundingMode.js
+java/net/URL.js
+java/net/URLStreamHandlerFactory.js
+java/text/CharacterIterator.js
+java/text/DecimalFormat.js
+java/text/DecimalFormatSymbols.js
+java/text/DigitList.js
+java/text/FieldPosition.js
+java/text/Format.js
+java/text/NumberFormat.js
+java/util/AbstractCollection.js
+java/util/AbstractList.js
+java/util/AbstractMap.js
+java/util/AbstractSequentialList.js
+java/util/AbstractSet.js
+java/util/ArrayList.js
+java/util/Arrays.js
+java/util/Collection.js
+java/util/Collections.js
+java/util/Deque.js
+java/util/Dictionary.js
+java/util/Enumeration.js
+java/util/EventListener.js
+java/util/EventObject.js
+java/util/HashMap.js
+java/util/HashSet.js
+java/util/Hashtable.js
+java/util/IdentityHashMap.js
+java/util/Iterator.js
+java/util/LinkedHashMap.js
+java/util/LinkedList.js
+java/util/List.js
+java/util/ListResourceBundle.js
+java/util/Locale.js
+java/util/Map.js
+java/util/Objects.js
+java/util/Queue.js
+java/util/Random.js
+java/util/RandomAccess.js
+java/util/ResourceBundle.js
+java/util/Set.js
+java/util/Vector.js
+javajs/api/JSFunction.js
+javajs/util/AjaxURLConnection.js
+javajs/util/AjaxURLStreamHandlerFactory.js
+javajs/util/AU.js
+javajs/util/JSThread.js
+javajs/util/Lst.js
+javajs/util/PT.js
+javajs/util/SB.js
+javax/swing/AbstractAction.js
+javax/swing/AbstractButton.js
+javax/swing/AbstractListModel.js
+javax/swing/Action.js
+javax/swing/ActionMap.js
+javax/swing/AncestorNotifier.js
+javax/swing/ArrayTable.js
+javax/swing/border/AbstractBorder.js
+javax/swing/border/BevelBorder.js
+javax/swing/border/Border.js
+javax/swing/border/CompoundBorder.js
+javax/swing/border/EmptyBorder.js
+javax/swing/border/EtchedBorder.js
+javax/swing/border/LineBorder.js
+javax/swing/BorderFactory.js
+javax/swing/BoundedRangeModel.js
+javax/swing/BoxLayout.js
+javax/swing/ButtonGroup.js
+javax/swing/ButtonModel.js
+javax/swing/ClientPropertyKey.js
+javax/swing/ComboBoxModel.js
+javax/swing/DefaultBoundedRangeModel.js
+javax/swing/DefaultButtonModel.js
+javax/swing/DefaultComboBoxModel.js
+javax/swing/DefaultSingleSelectionModel.js
+javax/swing/DropMode.js
+javax/swing/event/AncestorEvent.js
+javax/swing/event/AncestorListener.js
+javax/swing/event/CaretEvent.js
+javax/swing/event/CaretListener.js
+javax/swing/event/ChangeEvent.js
+javax/swing/event/ChangeListener.js
+javax/swing/event/DocumentEvent.js
+javax/swing/event/DocumentListener.js
+javax/swing/event/EventListenerList.js
+javax/swing/event/ListDataEvent.js
+javax/swing/event/ListDataListener.js
+javax/swing/event/UndoableEditEvent.js
+javax/swing/event/UndoableEditListener.js
+javax/swing/InputMap.js
+javax/swing/JApplet.js
+javax/swing/JButton.js
+javax/swing/JCheckBox.js
+javax/swing/JCheckBoxMenuItem.js
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git://source.jalview.org / jalview.git / commitdiff