From: Ben Soares <bsoares@dundee.ac.uk>
Date: Thu, 10 Oct 2019 14:24:02 +0000 (+0100)
Subject: JAL-3210 Moving j2s components around
X-Git-Tag: Release_2_11_4_0~45^2~18^2~118
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9bd6e3701335e492482b8be2a8028db5b1bc7100;p=jalview.git

JAL-3210 Moving j2s components around
---

diff --git a/.gitignore b/.gitignore
index 46cc0e5..c78ace4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -30,3 +30,6 @@ TESTNG
 *.swp
 /bin
 /doc/building.html
+/.j2s
+/template.html
+
diff --git a/.j2s b/.j2s
deleted file mode 100644
index 93fd157..0000000
--- a/.j2s
+++ /dev/null
@@ -1,20 +0,0 @@
-j2s.compiler.status=enable
-
-#a semicolon-separated list of package-level file paths to be excluded
-j2s.excluded.paths=test;testng;util
-
-#a semicolon-separated list of package (foo.) or class (foo.bar) replacements to be made 
-j2s.class.replacements=org.apache.log4j.->jalview.javascript.log4j.
-
-#output file name for logging methods declared - delete the file to regenerate a listing 
-#j2s.log.methods.declared=swingjs/methodsDeclared.csv
-
-#output file name for logging methods called - delete the file to regenerate a listing
-#j2s.log.methods.called=swingjs/methodsCalled.csv
-
-#if set, every instance of methods called will be logged
-#otherwise, only the first call to a method will be logged 
-#output will be comma-separated: called method,caller class 
-#j2s.log.all.calls=true
-
-
diff --git a/build-libjs.xml b/build-libjs.xml
deleted file mode 100644
index 3fb3cd3..0000000
--- a/build-libjs.xml
+++ /dev/null
@@ -1,67 +0,0 @@
-<?xml version="1.0"?>
-<!--
- * just a crude zip up of non-Jalview classes for development purposes -BH 2018
- *
- * external JAR class treatment for JavaScript: see src2/README_SWINGJS.txt
- * 
- -->
-
-<project name="jalviewX" default="zipall" basedir="."
- xmlns:if="ant:if"
-    xmlns:unless="ant:unless">
-
-  	<!-- inputs directories -->
-    <property name="resource.dir" value="resources" />  	
-    <property name="swingjs.dir" value="swingjs"/>
-	<!-- output directories -->
-  	<property name="site.dir" value="site"/>
-  	<property name="j2s.dir" value="${site.dir}/swingjs/j2s"/>
-  	<property name="libjs.dir" value="libjs"/>
-
-	<target name="zipall" depends="zipvarna,zipmig,zipintervalstore">
-		
-		
-  </target>
-
-  <target name="zipvarna">
-    <!-- VARNA -->
-	    <property name="varna.zip" value="${libjs.dir}/VARNA-site.zip" />	  	  	
-	  	<echo> Zipping up ${varna.zip} </echo>
-	  	<zip destfile="${varna.zip}" basedir="${site.dir}" includes="fr_*.html,swingjs/j2s/fr/**" />
-	</target>
-
-	<target name="zipmig">
-	  <!-- net.miginfo.com MiGLayout -->
-		    <property name="mig.zip" value="${libjs.dir}/MiGLayout-site.zip" />	  	  	
-		  	<echo> Zipping up ${mig.zip} </echo>
-		  	<zip destfile="${mig.zip}" basedir="${site.dir}" includes="swingjs/j2s/net/miginfocom/**" />
-	</target>
-
-	<target name="zipintervalstore">
-	  <!-- intervalstore.impl NCList implementation -->
-		    <property name="intervalstore.zip" value="${libjs.dir}/intervalstore-site.zip" />	  	  	
-		  	<echo> Zipping up ${intervalstore.zip} </echo>
-		  	<zip destfile="${intervalstore.zip}" basedir="${site.dir}" includes="swingjs/j2s/intervalstore/**" />
-	</target>
-
-	<!-- already in SwingJS
-	<target name="zipjson"  already in SwingJS>
-		    <property name="json.zip" value="${libjs.dir}/json-site.zip" />	  	  	
-		  	<echo> Zipping up ${json.zip} </echo>
-		  	<zip destfile="${json.zip}" basedir="${site.dir}" includes="swingjs/j2s/org/json/**" />
-	</target>
-	-->
-
-	<!-- log4j minimal implementation is already in jalview/javascript
-	      and is mapped from org.apache.log4j by the following .j2s line:
-	      
-	      j2s.class.replacements=org.apache.log4j.->jalview.javascript.log4j.
-	       
-	<target name="ziplog4j">
-		  <!- org.apache.log4j ->
-		    <property name="log4j.zip" value="${libjs.dir}/log4j-site.zip" />	  	  	
-		  	<echo> Zipping up ${log4j.zip} </echo>
-		  	<zip destfile="${log4j.zip}" basedir="${site.dir}" includes="swingjs/j2s/org/apache/log4j/**" />
-	</target>
-    -->
-</project>
diff --git a/build-site.xml b/build-site.xml
deleted file mode 100644
index 0cc062d..0000000
--- a/build-site.xml
+++ /dev/null
@@ -1,95 +0,0 @@
-<?xml version="1.0"?>
-<!--
- BH 2018.08.12
-
- - requires tools/ant-contrib.jar
-  
- - creates the site/ directory if it does not exist
- - unzip libjs/*.zip into site/swingjs/j2s
- - unzips swingjs/SwingJS-site.zip into site/
- - copies non-java resources from resources/ into site/swingjs/j2s
- 
--->
-
-<project name="swingjs-project" default="tosite" basedir="."
- xmlns:if="ant:if"
-    xmlns:unless="ant:unless">
-	
-  <target name="tosite">
-  	  	
-  	<!-- input directories -->
-  	
-  	<!-- location of ant-contrib.jar -->
-  	<property name="tools.dir" value = "tools" />
-
- 	<!-- SwingjS_site zip file (could be varied if versioning is needed) -->
-  	<property name="swingjs.zip" value="swingjs/SwingJS-site.zip" />
-
-  	<!-- location of third-party jar contents as precompiled zipped .js files to copy to site/ -->
-  	<property name="libjs.dir" value="libjs" />
- 
-  	<!-- non-Java resources to copy to site/swingjs/j2s -->
-    <property name="resource.dir" value="resources" />  	
-  	
-  	<!-- build_properties datastamp file to copy to site/swingjs/j2s -->
-    <property name="build_properties" value="classes/.build_properties" />  	
- 
-  	<!-- non-Java resources to copy to site/ -->
-    <property name="site-resource.dir" value="site-resources" />  	
-  	
-	<!-- output directories -->
-
-  	<property name="site.dir" value="site" />
-  	<property name="j2s.dir" value="${site.dir}/swingjs/j2s" />
-  	 
-    <!-- <for  ...> construct needs ant-contrib.jar -->
-    <taskdef resource="net/sf/antcontrib/antlib.xml">
-      <classpath>
-        <pathelement location="${tools.dir}/ant-contrib.jar" />
-      </classpath>
-    </taskdef>
-
-	<!-- unzip all libjs zip files into site
-	
-	   all zip files placed in libjs will be processed
-	   
-	 -->
-
-  	<for param="file.zip">
-  	  <path>
-  	    <fileset dir="${libjs.dir}" includes="*.zip"/>
-  	  </path>
-  	  <sequential>
-  	  	 	<unzip src="@{file.zip}" dest="${site.dir}" overwrite="true"/>  	
-  	  </sequential>
-  	</for>
-
-  	<!-- unzip SwingJS-site.zip 
-  	
-  	  we do this separately, as we want it done last 
-  	
-  	-->
-
-  	<unzip src="${swingjs.zip}" dest="${site.dir}/" overwrite="true"/>  	
-
- 	<!-- transfer resources -->
-
-  	<echo> Copying ${resource.dir} files into ${j2s.dir} </echo>
-  	<copy todir="${j2s.dir}">
-      <fileset dir="${resource.dir}">
-      	<include name="**"/>
-  	  </fileset>
-  	  <fileset file="${build_properties}"/>	
-    </copy>
-      		
-  	<echo> Copying ${site-resource.dir} files into ${site.dir} </echo>
-  	<copy todir="${site.dir}">
-      <fileset dir="${site-resource.dir}">
-      	<include name="**"/>
-  	</fileset>
-    </copy>
-      		
-</target>
-	
-
-</project>
diff --git a/build.xml b/build.xml
deleted file mode 100755
index 327cc33..0000000
--- a/build.xml
+++ /dev/null
@@ -1,1124 +0,0 @@
-<?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=&quot;1.8+&quot; initial-heap-size=&quot;${inih}&quot; max-heap-size=&quot;${maxh}&quot; java-vm-args=&quot;--add-modules=java.se.ee --illegal-access=warn&quot;">
-      <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=${JALVIEW_VERSION}&quot;">
-    <replacetoken>
-      <![CDATA[http://www.jalview.org/services/launchApp"]]>
-    </replacetoken>
-    <fileset dir="${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="${eclipse-workrepo}/site"/>
-  </copy>  
-</target>
-<target name="unzip-to-site" depends="prepare-site">
-  <ant antfile="build-site.xml"/>
-</target>
-
-  <target name="make-j2s-cores" depends="">
-    <ant antfile="buildcore.xml" target="build-all-cores"/>
-  </target>
-</project>
diff --git a/buildcore.xml b/buildcore.xml
deleted file mode 100644
index 3c21f43..0000000
--- a/buildcore.xml
+++ /dev/null
@@ -1,92 +0,0 @@
-<project name="JSmol" default="toJs" basedir=".">
-
-  <taskdef resource="net/sf/antcontrib/antcontrib.properties">
-    <classpath>
-      <pathelement location="./utils/ant-contrib-1.0b3.jar" />
-    </classpath>
-  </taskdef>
-
-  <target name="build-all-cores" id="build-all-cores" depends="toJs">
-    <foreach target="CallToJs" param="classlist">
-      <path>
-        <fileset dir="./classlists/" includes="*.txt" />
-      </path>
-    </foreach>
-  </target>
-
-  <target name="CallToJs" id="CallToJs" description="Don't call this directly - used by build-all-cores to configure the toJs task for each set of classes in classlist">
-    <basename property="core.name.txt" file="${classlist}"/>
-    <propertyregex property="core.name" input="${core.name.txt}" replace="" regexp="\.txt"/>
-    <antcall target="toJs"/>
-  </target>
-
-  <target name="toJs" id="toJs">
-    <!-- sensible defaults for default target -->
-    <property name="site" value="site"/>
-    <property name="site.path" value="${site}/swingjs" />
-    <property name="core.name" value="_jalview" />
-    <property name="classlist"  
-      description="Class list .txt generated by java2script classloader to be bundled into corefile - default is _j2sclasslist.txt" 
-      value="_j2sclasslist.txt" />
-    <!-- create a NON svn local directory only containing JS files
-  	
-  	<echo>Deleting the site directory.</echo>
-   	 	<delete quiet="true" dir="site" />
-    -->
-
-    <!-- make core files -->
-
-    <echo>Building core file '${core.name}' - warnings are OK; "does not exist" is trouble</echo>
-    <echo>Reading core class list from file ${classlist}</echo>
-    <loadresource property="coreclasses">
-      <file file="${classlist}"/>
-    </loadresource>
-
-    <antcall target="call-core">
-      <param name="call-core.name" value="${core.name}" />
-      <param name="call-core.list" value="
-			core/coreswingjs.js
-         	${coreclasses}
-        	" />
-    </antcall>
-    <antcall target="publish-core-template"/>
-  </target>
-
-  <target name="publish-core-template" id="publish-core-template" description="Creates a new file ${template.name}_${core.name} from ${template.html} in ${site} which include core file ${core.name} in the Info block">
-    <!-- TODO: extend to process all html templates -->
-    <property name="template.html" value="jalview_bin_Jalview.html"/>
-    <property name="template.name" value="JalviewJS"/>
-
-    <echo>......Now copying ${site}/${template.html} as ${$template.name}_${core.name}.html with core:"${core.name}", added to the Info block.</echo>
-    <copy file="${site}/${template.html}" tofile="${site}/${template.name}_${core.name}.html"/>
-    <replace token="NONE" value="${core.name}" file="${site}/${template.name}_${core.name}.html"/>
-
-  </target>
-
-
-  <target name="call-core" id="call-core">
-    <echo>......Creating core${call-core.name}.js</echo>
-    <concat destfile="${site.path}/js/core/tmp.js">
-      <filelist dir="${site.path}/j2s" files="${call-core.list}" />
-    </concat>
-
-    <replace dir="${site.path}/js/core" includes="tmp.js" token="Clazz." value="Clazz_"/>
-    <replace dir="${site.path}/js/core" includes="tmp.js" token="Clazz__" value="Clazz._"/>
-    <echo>......Generating ${site.path}/j2s/core/core${call-core.name}.js</echo>
-    <concat destfile="${site.path}/j2s/core/core${call-core.name}.js">
-      <filelist dir="${site.path}/js" files="
-	   		core/coretop2.js
-	   		core/tmp.js
-	   		core/corebottom2.js
-	   		" />
-    </concat>
-    <echo>......Generating ${site.path}/j2s/core/core${call-core.name}.z.js</echo>
-    <java jar="tools/closure_compiler.jar" fork="true" dir="${site.path}/j2s/core" failonerror="false">
-      <arg line="--js core${call-core.name}.js --js_output_file core${call-core.name}.z.js" />
-    </java>
-    <delete quiet="true" file="${site.path}/js/core/tmp.js" />
-  </target>
-
-
-
-</project>
diff --git a/swingjs/DEV_NOTES.txt b/swingjs/DEV_NOTES.txt
deleted file mode 100644
index 751d81c..0000000
--- a/swingjs/DEV_NOTES.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-This is sources/net.sf.j2s.java.core/dist/DEV_NOTES.txt
-
-_j2sclasslist.txt 
-
-the list of .js files concatenated into coreswingjs.js and minified to coreswingjs.z.js
-
-
-SwingJS-site.zip
-
-the full site directory for SwingJS including all files not in the test/ directory.
diff --git a/swingjs/README.txt b/swingjs/README.txt
deleted file mode 100644
index f45850b..0000000
--- a/swingjs/README.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-The swingjs directory contains the current transpiler (net.sf.j2s.core.jar) 
-and the run-time core site files (SwingJS-site.zip)
-
-In addition are version directories -- for example, ver/3.1.1 and ver/3.2.1
-
-The second of these, ver/3.2.1, adds Java 8 functionality.
-
-
diff --git a/swingjs/_j2sclasslist.txt b/swingjs/_j2sclasslist.txt
deleted file mode 100644
index fb9da31..0000000
--- a/swingjs/_j2sclasslist.txt
+++ /dev/null
@@ -1,389 +0,0 @@
-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
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-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
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-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
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-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
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-javax/swing/RepaintManager.js
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-javax/swing/Scrollable.js
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-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
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-javax/swing/text/DefaultEditorKit.js
-javax/swing/text/Document.js
-javax/swing/text/EditorKit.js
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-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
diff --git a/swingjs/ver/3.2.4/net.sf.j2s.core.jar b/swingjs/ver/3.2.4/net.sf.j2s.core.jar
deleted file mode 100644
index ec67d8c..0000000
Binary files a/swingjs/ver/3.2.4/net.sf.j2s.core.jar and /dev/null differ
diff --git a/swingjs/ver/3.2.4/timestamp b/swingjs/ver/3.2.4/timestamp
deleted file mode 100644
index 0bfc11c..0000000
--- a/swingjs/ver/3.2.4/timestamp
+++ /dev/null
@@ -1 +0,0 @@
-20190422120213 
diff --git a/template.html b/template.html
deleted file mode 100644
index e959685..0000000
--- a/template.html
+++ /dev/null
@@ -1,33 +0,0 @@
-<!DOCTYPE html>
-<html>
-<head>
-<title>SwingJS test _NAME_</title>
-<meta charset="utf-8" />
-<script src="swingjs/swingjs2.js"></script>
-<script>
-if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs folder in the same directory as ' + document.location.href)
-Info = {
-  code: _CODE_,
-  main: _MAIN_,
-  core: "NONE",
-	width: 850,
-	height: 550,
-  readyFunction: null,
-	serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php',
-	j2sPath: 'swingjs/j2s',
-	console:'sysoutdiv',
-	allowjavascript: true
-}
-</script>
-</head>
-<body>
-<script>
-SwingJS.getApplet('testApplet', Info)
-getClassList = function(){J2S._saveFile('_j2sclasslist.txt', Clazz.ClassFilesLoaded.sort().join('\n'))}
-</script>
-<div style="position:absolute;left:900px;top:30px;width:600px;height:300px;">
-<div id="sysoutdiv" style="border:1px solid green;width:100%;height:95%;overflow:auto"></div>
-This is System.out. <a href="javascript:testApplet._clearConsole()">clear it</a> <br>Add ?j2snocore to URL to see full class list; ?j2sdebug to use uncompressed j2s/core files <br><a href="javascript:getClassList()">get _j2sClassList.txt</a>
-</div>
-</body>
-</html>
diff --git a/swingjs/SwingJS-site.zip b/utils/jalviewjs/SwingJS-site.zip
similarity index 100%
rename from swingjs/SwingJS-site.zip
rename to utils/jalviewjs/SwingJS-site.zip
diff --git a/utils/jalviewjs/eclipse/dropins/com.seeq.eclipse.importprojects-1.4.0.jar b/utils/jalviewjs/eclipse/dropins/com.seeq.eclipse.importprojects-1.4.0.jar
new file mode 100644
index 0000000..69d7603
Binary files /dev/null and b/utils/jalviewjs/eclipse/dropins/com.seeq.eclipse.importprojects-1.4.0.jar differ
diff --git a/swingjs/net.sf.j2s.core.jar b/utils/jalviewjs/eclipse/dropins/net.sf.j2s.core-3.2.4.jar
similarity index 100%
rename from swingjs/net.sf.j2s.core.jar
rename to utils/jalviewjs/eclipse/dropins/net.sf.j2s.core-3.2.4.jar
diff --git a/libjs/MiGLayout-site.zip b/utils/jalviewjs/libjs/MiGLayout-site.zip
similarity index 100%
rename from libjs/MiGLayout-site.zip
rename to utils/jalviewjs/libjs/MiGLayout-site.zip
diff --git a/libjs/VARNA-site.zip b/utils/jalviewjs/libjs/VARNA-site.zip
similarity index 100%
rename from libjs/VARNA-site.zip
rename to utils/jalviewjs/libjs/VARNA-site.zip
diff --git a/libjs/intervalstore-site.zip b/utils/jalviewjs/libjs/intervalstore-site.zip
similarity index 100%
rename from libjs/intervalstore-site.zip
rename to utils/jalviewjs/libjs/intervalstore-site.zip
diff --git a/libjs/jmol-app.zip b/utils/jalviewjs/libjs/jmol-app.zip
similarity index 100%
rename from libjs/jmol-app.zip
rename to utils/jalviewjs/libjs/jmol-app.zip
diff --git a/site-resources/examples/PF00111_seed.stk b/utils/jalviewjs/site-resources/examples/PF00111_seed.stk
similarity index 100%
rename from site-resources/examples/PF00111_seed.stk
rename to utils/jalviewjs/site-resources/examples/PF00111_seed.stk
diff --git a/site-resources/examples/RF00031_folded.stk b/utils/jalviewjs/site-resources/examples/RF00031_folded.stk
similarity index 100%
rename from site-resources/examples/RF00031_folded.stk
rename to utils/jalviewjs/site-resources/examples/RF00031_folded.stk
diff --git a/site-resources/examples/exampleFeatures.txt b/utils/jalviewjs/site-resources/examples/exampleFeatures.txt
similarity index 100%
rename from site-resources/examples/exampleFeatures.txt
rename to utils/jalviewjs/site-resources/examples/exampleFeatures.txt
diff --git a/site-resources/examples/jaxbtest.jvx b/utils/jalviewjs/site-resources/examples/jaxbtest.jvx
similarity index 100%
rename from site-resources/examples/jaxbtest.jvx
rename to utils/jalviewjs/site-resources/examples/jaxbtest.jvx
diff --git a/site-resources/examples/rna_ss_test.stk b/utils/jalviewjs/site-resources/examples/rna_ss_test.stk
similarity index 100%
rename from site-resources/examples/rna_ss_test.stk
rename to utils/jalviewjs/site-resources/examples/rna_ss_test.stk
diff --git a/site-resources/examples/uniref50.fa b/utils/jalviewjs/site-resources/examples/uniref50.fa
similarity index 100%
rename from site-resources/examples/uniref50.fa
rename to utils/jalviewjs/site-resources/examples/uniref50.fa
diff --git a/site-resources/jalview_bin_JalviewJS2.html b/utils/jalviewjs/site-resources/jalview_bin_JalviewJS2.html
similarity index 100%
rename from site-resources/jalview_bin_JalviewJS2.html
rename to utils/jalviewjs/site-resources/jalview_bin_JalviewJS2.html
diff --git a/site-resources/jalview_bin_JalviewJS_core.html b/utils/jalviewjs/site-resources/jalview_bin_JalviewJS_core.html
similarity index 100%
rename from site-resources/jalview_bin_JalviewJS_core.html
rename to utils/jalviewjs/site-resources/jalview_bin_JalviewJS_core.html
diff --git a/site-resources/jalview_bin_JalviewJS_embedded.html b/utils/jalviewjs/site-resources/jalview_bin_JalviewJS_embedded.html
similarity index 100%
rename from site-resources/jalview_bin_JalviewJS_embedded.html
rename to utils/jalviewjs/site-resources/jalview_bin_JalviewJS_embedded.html
diff --git a/site-resources/jalview_bin_JalviewJS_embedded_core.html b/utils/jalviewjs/site-resources/jalview_bin_JalviewJS_embedded_core.html
similarity index 100%
rename from site-resources/jalview_bin_JalviewJS_embedded_core.html
rename to utils/jalviewjs/site-resources/jalview_bin_JalviewJS_embedded_core.html
diff --git a/utils/jalviewjs/urls.txt b/utils/jalviewjs/urls.txt
new file mode 100644
index 0000000..7a8cf0a
--- /dev/null
+++ b/utils/jalviewjs/urls.txt
@@ -0,0 +1,11 @@
+# see https://github.com/seeq12/eclipse-import-projects-plugin
+# see https://github.com/java2script/java2script
+
+for x in \
+https://github.com/seeq12/eclipse-import-projects-plugin/raw/master/jar/com.seeq.eclipse.importprojects_1.4.0.jar \
+https://github.com/BobHanson/java2script/raw/master/sources/net.sf.j2s.core/dist/swingjs/SwingJS-site.zip \
+https://github.com/BobHanson/java2script/raw/master/sources/net.sf.j2s.core/dist/swingjs/net.sf.j2s.core.jar
+do
+  wget "$x"
+done
+