X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=454b9945eb78e08fbb642e6356208ed0e6e60385;hb=3a206ee73908f2339e44fae78d2a7d1f5e384158;hp=5b1066f63b20f1a090c8593eeeacb056c7cd092c;hpb=5aad8085fbd06d2e0f6a97d71e8ed58d0e02e6db;p=jalview.git

diff --git a/build.xml b/build.xml
index 5b1066f..454b994 100755
--- a/build.xml
+++ b/build.xml
@@ -1,52 +1,55 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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=".">
-	<!-- we use jalopy to format our sources -->
-	<taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
-		<classpath>
-			<fileset dir="utils/jalopy/lib">
-				<include name="*.jar" />
-			</fileset>
-		</classpath>
-	</taskdef>
-
-	<target name="help" depends="usage" />
-	<target name="usage">
-		<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. 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="See docs/building.html and the comments in build file for other targets." />
-		<echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
-		<echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
-	</target>
-
-
-	<!-- utils is a class path to additional utilities needed for
+<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
@@ -59,191 +62,329 @@
 
 -->
 
-	<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> -->
+  <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" />
-		<!-- 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" />
-
-		<!-- 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" />
-		<!-- 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" />
-		<property name="packageDir" value="dist" />
-		<property name="outputJar" value="jalview.jar" />
-		<!-- Jalview Applet JMol Jar Dependency -->
-		<property name="jmolJar" value="JmolApplet-12.1.13.jar" />
-		<property name="jalviewLiteJar" value="jalviewApplet.jar" />
-		<!-- switch to indicate if we should obfuscate jalviewLite -->
-		<!--<property name="donotobfuscate" 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}" />
-			</fileset>
 
-		</path>
-		<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
-		<!-- The Location of the java 1.1.8 jdk -->
-		<!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
-		-->
-		<property name="java118.home" value="${java.home}" />
-		    <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
-		--><!-- jre for 1.4 version -->
-		<property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
-		
-		<!-- the classpath for building the 1.1 applet -->
-		<path id="jalviewlite.deps">
-			<fileset dir="${java118.home}">
-				<include name="lib/classes.zip" />
-			</fileset>
-			<fileset dir="${java.home}/lib">
-				<include name="plugin.jar"/>
-			</fileset>
-			<pathelement location="appletlib/${jmolJar}" />
-		</path>
-	</target>
-
-
-	<taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
-	<target name="buildPropertiesFile" depends="init">
-		<tstamp prefix="build">
-			<format property="date" pattern="dd MMMM yyyy" />
-		</tstamp>
-		<properties file="${outputDir}/.build_properties">
-			<header>
+    <!-- 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="BUILD_DATE" value="${build.date}" />
-		</properties>
-	</target>
-
-
-	<target name="clean" depends="init">
-		<!-- not efficient yet. -->
-		<delete dir="${outputDir}" />
-	</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="${resourceDir}">
-				<include name="**/*.*" />
-			</fileset>
-		</copy>
-	</target>
-
-	<target name="build" depends="prepare">
-		<!-- not efficient yet. -->
-		<javac source="1.5" target="1.5" srcdir="${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="buildindices" depends="init, prepare" unless="help.uptodate">
-		<java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
-			<arg line="html" />
-		</java>
-	</target>
-
-	<target name="makefulldist" depends="makedist">
-		<!-- the default keystore details might need to be edited here -->
-		<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
-
-			<fileset dir="${packageDir}">
-				<include name="*.jar" />
-			</fileset>
-		</signjar>
-		<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
-
-		<!--    codebase="http://www.jalview.org/jalview/webstart" -->
-		<!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
-		<jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
-			<information>
-				<title>Jalview</title>
-				<vendor>The Barton Group</vendor>
-				<homepage href="http://www.jalview.org" />
-				<description>Jalview Multiple Alignment Editor</description>
-				<description kind="short">Jalview</description>
-				<icon href="logo_big.gif" />
-				<offline_allowed />
-				<!--
-	<association mime-type="application-x/ext-file" extensions="fa"/>
+      <property name="VERSION" value="${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.jnlp" />
+      <param name="inih" value="10M" />
+      <param name="maxh" value="256M" />
+    </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="256M" />
+      <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"/>
@@ -251,133 +392,130 @@
         <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"/>
-	-->
-			</information>
-			<resources>
-				<j2se version="1.5+" initial_heap_size="10M" />
-				<fileset dir="${packageDir}">
-					<include name="jalview.jar" />
-				</fileset>
-				<fileset dir="${packageDir}">
-					<include name="*.jar" />
-					<include name="*_*.jar" />
-					<exclude name="jalview.jar" />
-				</fileset>
-				<property name="jalview.version" value="${JALVIEW_VERSION}" />
-			</resources>
-			<application_desc main_class="jalview.bin.Jalview">
-			</application_desc>
-			<security>
-				<all_permissions />
-			</security>
-		</jnlp>
-		<!-- the rest of these jnlp tasks are copy and pastes of the above but with different Vm args -->
-		<jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
-			<information>
-				<title>Jalview</title>
-				<vendor>The Barton Group</vendor>
-				<homepage href="http://www.jalview.org" />
-				<description>Jalview Multiple Alignment Editor</description>
-				<description kind="short">Jalview</description>
-				<icon href="logo_big.gif" />
-				<offline_allowed />
-				<!--
-		<association mime-type="application-x/ext-file" extensions="fa"/>
-	        <association mime-type="application-x/ext-file" extensions="fasta"/>
-	        <association mime-type="application-x/ext-file" extensions="fastq"/>
-	        <association mime-type="application-x/ext-file" extensions="blc"/>
-	        <association mime-type="application-x/ext-file" extensions="msf"/>
-	        <association mime-type="application-x/ext-file" extensions="pfam"/>
-	        <association mime-type="application-x/ext-file" extensions="aln"/>
-	        <association mime-type="application-x/ext-file" extensions="pir"/>
-	        <association mime-type="application-x/ext-file" extensions="amsa"/>
-		-->
-			</information>
-			<resources>
-				<j2se version="1.5+" initial_heap_size="64M" max_heap_size="512M" />
-				<fileset dir="${packageDir}">
-					<include name="jalview.jar" />
-				</fileset>
-				<fileset dir="${packageDir}">
-					<include name="*.jar" />
-					<include name="*_*.jar" />
-					<exclude name="jalview.jar" />
-				</fileset>
-				<property name="jalview.version" value="${JALVIEW_VERSION}" />
-			</resources>
-			<application_desc main_class="jalview.bin.Jalview">
-			</application_desc>
-			<security>
-				<all_permissions />
-			</security>
-		</jnlp>
-		<jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${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="logo_big.gif" />
-				<offline_allowed />
-				<!--
-			<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="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"/>
-			-->
-			</information>
-			<resources>
-				<j2se version="1.5+" initial_heap_size="256M" max_heap_size="1024M" />
-				<fileset dir="${packageDir}">
-					<include name="jalview.jar" />
-				</fileset>
-				<fileset dir="${packageDir}">
-					<include name="*.jar" />
-					<include name="*_*.jar" />
-					<exclude name="jalview.jar" />
-				</fileset>
-				<property name="jalview.version" value="${JALVIEW_VERSION}" />
-			</resources>
-			<application_desc main_class="jalview.bin.Jalview">
-			</application_desc>
-			<security>
-				<all_permissions />
-			</security>
-		</jnlp>
-
-	</target>
-
-	<target name="runenv" depends="init">
-		<path id="run.classpath">
-			<pathelement location="${outputDir}" />
-			<fileset dir="${outputDir}">
-				<include name="${libDir}/*.jar" />
-			</fileset>
-		</path>
-		<pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
-
-		<echo>java -classpath ${run.classpath} jalview.bin.Jalview
+        <association mime-type="application-x/ext-file" extensions="stk"/>
+        <association mime-type="application-x/ext-file" extensions="jar"/>-->
+  </target>
+
+  <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
+    <signjar storepass="${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="${packageDir}">
+        <include name="*.jar" />
+      </fileset>
+    </signjar>
+  </target>
+  <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
+    <signjar storepass="${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 ${run.classpath} jalview.bin.Jalview
       </echo>
-	</target>
-
-	<target name="buildextclients" depends="init">
-		<input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
-		<condition property="dontextbuild">
-			<equals arg1="n" arg2="${doextbuild.response}" />
-		</condition>
-		<condition property="dontextbuild">
-			<equals arg1="N" arg2="${doextbuild.response}" />
-		</condition>
-		<fail if="dontextbuild">
+  </target>
+
+  <target name="-generatejnlpf">
+    <presetdef name="jnlpf">
+      <jnlp codebase="${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.
+  <!-- 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
@@ -387,198 +525,467 @@
      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="${wsdl.ClientNS}" />
-			</mappingSet>
-		</axis-wsdl2java>
-	</target>
-
-	<target name="makedist" depends="build, buildPropertiesFile, buildindices">
-		<!-- make the package jar if not already existing -->
-		<mkdir dir="${packageDir}" />
-		<!-- clean dir if it already existed -->
-		<delete>
-			<fileset dir="${packageDir}">
-				<include name="*.jar"/>
-			</fileset>
-		</delete>
-		<jar destfile="${packageDir}/${outputJar}">
-			<manifest>
-				<attribute name="Main-Class" value="jalview.bin.Jalview" />
-			</manifest>
-			<fileset dir="${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="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
-			classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
-			excludes="ext/**,MCview/**,org/**,vamsas/**" />
-	</target>
-
-	<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
-		<copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
-		<copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
-		<jar destfile="in.jar">
-			<manifest>
-				<attribute name="Main-Class" value="jalview.bin.JalviewLite" />
-			</manifest>
-			<fileset dir="${outputDir}">
-				<include name="com/**" />
-				<include name="MCview/**" />
-				<include name="jalview/**" />
-				<include name=".build_properties" />
-				<include name="images/idwidth.gif" />
-				<include name="images/link.gif" />
-			</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/${jmolJar}" />
-		</path>
-		<taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
-
-		<proguard>
-			<injar file="in.jar" />
-			<outjar file="${jalviewLiteJar}" />
-			<libraryjar refid="obfuscateDeps.path" />
-			<keep access="public" type="class" name="jalview.bin.JalviewLite">
-				<field access="public" />
-				<method access="public" />
-				<constructor access="public" />
-			</keep>
-			<!--      -libraryjars "${obfuscateDeps}"
+  <path id="axisbuild">
+    <path refid="build.classpath" />
+  </path>
+  <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
+  <move todir="./bak">
+    <fileset dir="${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 "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
       -keep public class jalview.bin.JalviewLite
        { public * ; } -->
-		</proguard>
-		<delete file="in.jar" />
-	</target>
-
-	<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
-		<taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
-		<delete>
-			<fileset dir="${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" />
-		<!-- 
+  </proguard>
+  <delete file="in.jar" />
+</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}" />
-		<tar destfile="${source.dist.name}" compression="gzip">
-			<tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
-				<include name="LICENSE" />
-				<include name="README" />
-				<include name="build.xml" />
-				<include name="jalview-jalopy.xml" />
-				<include name="JalviewApplet.jpx" />
-				<include name="JalviewX.jpx" />
-				<include name="nbbuild.xml"/>
-				<include name="nbproject/genfiles.properties"/>
-        <include name="nbproject/project.properties"/>
-        <include name="nbproject/project.xml"/>
-				<include name="${sourceDir}/*.java" />
-				<include name="${sourceDir}/**/*.java" />
-				<include name="${sourceDir}/**/*.cdr" />
-				<include name="${libDir}/**/*" />
-				<include name="${resourceDir}/**/*" />
-				<include name="${helpDir}/**/*" />
-				<include name="appletlib/${jmolJar}" />
-				<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/**locale*" />
-				<exclude name="utils/InstallAnywhere/**locale*/**" />
-				<include name="${schemaDir}/**/*" />
-				<include name="utils/**/*" />
-				<include name="${docDir}/**/*" />
-				<include name="examples/**/*" />
-			</tarfileset>
-		</tar>
-	</target>
-	<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
-	  <copy todir="${packageDir}/examples">
-	  <fileset dir="examples">
-	  	<include name="**/*"/>
-	  </fileset>
-	  	<fileset dir=".">
-	  	<include name="jalviewApplet.jar"/>
-	  		</fileset>
-	  	<fileset dir="appletlib">
-	  	      <include name="**/*"/>
-	  	        </fileset>
-	  </copy>
-	  		
-	</target>
+  <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" unless="timestamp" depends="-signapplet">
+  <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">
+  <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>