X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;fp=build.xml;h=0000000000000000000000000000000000000000;hb=ca8504cf9d10874dce9f07cf7a9d933853fe0dd0;hp=bed6d684437c5a7c9858d2ca19af96bb388b3b52;hpb=775e7bc104584e88dddcea73fbf02c66f5200c16;p=jalview.git

diff --git a/build.xml b/build.xml
deleted file mode 100755
index bed6d68..0000000
--- a/build.xml
+++ /dev/null
@@ -1,1040 +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" />
-    <!-- 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>
-  </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="${testOutputDir}" includes="**/*.class" />
-    </testng>
-  </target>
-
-  <target name="buildindices" depends="init, prepare" unless="help.uptodate">
-    <replace value="${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="${sourceDir}"/>
-    <arg value="-p"/>
-    <arg value="jalview.xml.binding.uniprot"/>
-  </exec>
-</target>
-
-<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
-  <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
-  <delete>
-    <fileset dir="${sourceDir}/jalview/schemabinding/version2">
-      <include name="*.java" />
-      <include name="descriptors/*.java" />
-    </fileset>
-  </delete>
-  <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-  <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-  <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-  <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-  <!-- 
-		now build the jalview.binding package with the old schema set
-		-->
-  <delete>
-    <fileset dir="${sourceDir}/jalview/binding/">
-      <include name="**" />
-    </fileset>
-  </delete>
-  <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
-  <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
-  <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
-</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="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>
-</project>