X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=c079df946dde2926f46684f6037106129cc846d1;hb=12e8812e5c9d01ad910e6e1161d7b8886fd94f0e;hp=d11047e98fdb6880791b63bf49cdd575d1e3b57a;hpb=dd1aed40cf00d837d1643918c380546a1dd2d39a;p=jalview.git

diff --git a/build.xml b/build.xml
index d11047e..c079df9 100755
--- a/build.xml
+++ b/build.xml
@@ -1,52 +1,44 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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
+  <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
     building docs, jars and webstart stuff -->
-	<!--
+  <!--
         Userdefined build property defaults
 
         wsdl.server list (plus namespace mapping info ???)  - also want
@@ -59,231 +51,248 @@
 
 -->
 
-	<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" />
-		<!-- Webstart Image - looked for in resources/images -->
-		<property name="WebStartImage" value="JalviewLogo_big.png"/>
-		<!-- J2SE version needed for webstart launch -->
-		<property name="j2sev" value="1.6+"/>
+  	
+    <!-- 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" />
+
+    <!-- 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+"/>
 
     <!-- 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 -->
-    <property name="applet.codebase" value="*" />
+    <!-- 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" />
-		<property name="packageDir" value="dist" />
-		<property name="outputJar" value="jalview.jar" />
-		<!-- Jalview Applet JMol Jar Dependency -->
-		<property name="jmolJar" value="JmolApplet-12.2.4.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 
+    <!-- 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-12.2.4.jar" />
+    <property name="varnaJar" value="VARNAv3-91.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" />
+    <!-- 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="${jmolJar}" />
-			</fileset>
+        <include name="${jmolJar}" />
+        <include name="${varnaJar}" />
+      </fileset>
 
-		</path>
-		<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
-		<!-- The Location of the java 1.1.8 jdk -->
-		<!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
+    </path>
+    <property name="source.dist.name" value="${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" />
 		-->
-		<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>
+    <!-- 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}" />
+      <pathelement location="lib/${varnaJar}" />
+      <pathelement location="lib/${jsoup}" />
+      <pathelement location="lib/${jsonSimple}" />
+      <pathelement location="lib/${javaJson}" />
+      
+    </path>
     <!-- default location for outputting javadoc -->
     <property name="javadocDir" value="${packageDir}/javadoc"/>
-	</target>
+  </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="${outputDir}/.build_properties">
-			<header>
+  <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
+  <target name="buildPropertiesFile" depends="init">
+    <tstamp prefix="build">
+      <format property="date" pattern="dd MMMM yyyy" />
+    </tstamp>
+    <properties file="${outputDir}/.build_properties">
+      <header>
           ---Jalview 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="${outputDir}" includes="*,**/*"/>
-	</target>
-
-	<target name="distclean" depends="init, clean">
-
-		<echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
-		<delete>
-			<fileset dir=".">
-				<include name="${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="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}/${helpDir}">
-			<arg line="html" />
-		</java>
-	</target>
-
-	<target name="makefulldist" depends="makedist">
-		<copy todir="${packageDir}">
-			<fileset dir="${resourceDir}/images">
-				<include name="${WebStartImage}"/>
-			</fileset>
-					</copy>
-		
-		<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
+        </header>    	
+      <property name="VERSION" value="${JALVIEW_VERSION}" />
+      <property name="INSTALLATION" value="${INSTALLATION}" />
+      <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="${resourceDir}">
+        <include name="**/*.*" />
+      </fileset>
+    </copy>
+  </target>
+
+  <target name="build" depends="prepare">
+    <!-- not efficient yet. -->
+    <javac source="1.5" target="1.5" srcdir="${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">
+    <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>
+      <fileset dir="${packageDir}">
+        <include name="jalview.jar" />
+      </fileset>
     </jar>
-  	
-  	<mkdir dir="${packageDir}/JNLP-INF"/>
+
+    <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="*"/>
+      <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="${packageDir}">
-  	      	<include name="JNLP-INF"/>
-				</fileset>
-  	</jar>
-    
-  	<antcall target="writejnlpf">
-  		<param name="jnlpFile" value="${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 
+
+    <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+      <fileset dir="${packageDir}">
+        <include name="JNLP-INF"/>
+      </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">
 		
@@ -291,9 +300,10 @@
 			
 			
 			-->
-					<!--
+    <!--
 				<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"/>
@@ -306,70 +316,109 @@
     <!-- and sign the jars -->
     <!-- 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" sigalg="SHA1withRSA">
-        <fileset dir="${packageDir}">
-          <include name="*.jar" />
-        </fileset>
+      <fileset dir="${packageDir}">
+        <include name="*.jar" />
+      </fileset>
     </signjar>
-	</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 ${run.classpath} jalview.bin.Jalview
+  </target>
+
+  <target name="runenv" depends="init">
+    <path id="run.classpath">
+      <pathelement location="${outputDir}" />
+      <fileset dir="${outputDir}">
+        <include name="${libDir}/*.jar" />
+      </fileset>
+    </path>
+    <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
+
+    <echo>java -classpath ${run.classpath} jalview.bin.Jalview
       </echo>
-	</target>
-  <target name="writejnlpf">
-  	<presetdef name="jnlpf">
-  	    <jnlp codebase="${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="${WebStartImage}" />
-  	        <offline_allowed />
-  	      </information>
-  	      <resources>
-  	        <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
-  	        <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="${JALVIEW_VERSION}" />
-  	      </resources>
-  	      <application_desc main_class="jalview.bin.Jalview">
-  	      </application_desc>
-  	      <security>
-  	        <all_permissions />
-  	      </security>
-  	    </jnlp>
-  	    </presetdef>
-
-  	    <jnlpf toFile="${jnlpFile}"/>
   </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 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="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+          <fileset dir="${packageDir}">
+            <include name="jalview.jar" />
+          </fileset>
+          <fileset dir="${packageDir}">
+            <include name="*.jar" />
+            <include name="*_*.jar" />
+            <exclude name="jalview.jar" />
+          	<exclude name="*jnilib.jar"/>
+          </fileset>
+      	</resources>
+        <resources os="Mac OS X">
+          <property name="jalview.version" value="${JALVIEW_VERSION}" />
+        	<fileset dir="${packageDir}">
+        		<include name="*quaqua*.jnilib.jar"/>
+        	</fileset>
+        </resources>
+      	
+        <application_desc main_class="jalview.bin.Jalview">
+        </application_desc>
+        <security>
+          <all_permissions />
+        </security>
+      </jnlp>
+    </presetdef>
+
+    <jnlpf toFile="${jnlpFile}"/>
+
+  </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
@@ -379,263 +428,270 @@
      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}/${outputJar}" index="true">
-			<manifest>
-				<attribute name="Main-Class" value="jalview.bin.Jalview" />
-        <attribute name="Permissions" value="all-permissions" />
-        <attribute name="Application-Name" value="Jalview Desktop" />
-        <attribute name="Codebase" value="${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="${outputDir}" />
-		<javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
+  <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}/${outputJar}" index="true">
+    <manifest>
+      <attribute name="Main-Class" value="jalview.bin.Jalview" />
+      <attribute name="Permissions" value="all-permissions" />
+      <attribute name="Application-Name" value="Jalview Desktop" />
+      <attribute name="Codebase" value="${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="${outputDir}" />
+  <javac source="1.5" target="1.5" srcdir="${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" />
-		<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/idwidth.gif" />
-				<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/${jmolJar}" />
-		</path>
-		<taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
-
-		<proguard>
-			<injar file="in.jar" />
-			<outjar file="${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>
-			<!--      -libraryjars "${obfuscateDeps}"
+			excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
+</target>
+
+<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+  <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
+  <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
+  <copy todir="${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="${outputDir}">
+      <include name="com/**" />
+      <include name="MCview/**" />
+      <include name="jalview/**" />
+      <include name=".build_properties" />
+      <include name="images/idwidth.gif" />
+      <include name="images/link.gif" />
+      <include name="lang/**" />
+    </fileset>
+  </jar>
+</target>
+<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
+</target>
+<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+  <copy file="in.jar" tofile="${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="appletlib/${jsonSimple}" />
+    <pathelement location="appletlib/${javaJson}" />
+  </path>
+  <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+
+  <proguard>
+    <injar file="in.jar" />
+    <outjar file="${jalviewLiteJar}" />
+    <libraryjar refid="obfuscateDeps.path" />
+    <dontwarn/>
+    <keep access="public" type="class" name="jalview.bin.JalviewLite">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+    <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+    <!--      -libraryjars "${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="**/*"/>
-	  	<include name="javascript/*"/>
+  <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="**/*"/>
+      <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/${jmolJar}">
-	    	<manifest>
-	        <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
-	        <!--          <attribute name="Permissions" value="sandbox" /> -->
-	        <!--<attribute name="Trusted-Lib" value="true" /> -->
-	        <attribute name="Codebase" value="${applet.codebase}"/>
-	        <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
-	    	  </manifest>
-	    	</jar>
-    <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
-      <fileset dir="${packageDir}/examples">
-        <include name="*.jar" />
-      </fileset>
-    </signjar>
-    <presetdef name="ap_applet.jar">
-      <!-- build a signed applet with 'all-permissions' - 
+    </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="${applet.caller-codebase}"/>
+    </manifest>
+  </jar>
+  <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+    <fileset dir="${packageDir}/examples">
+      <include name="*.jar" />
+    </fileset>
+  </signjar>
+  <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="${applet.codebase}" />
-        </manifest>
-      </jar>
-    </presetdef>
-    <presetdef name="applet.jar">
-      <!-- build signed applet with sandbox permissions -
+    <jar update="true" index="true">
+      <manifest>
+        <attribute name="Application-Name" value="JalviewLite" />
+        <attribute name="Permissions" value="all-permissions" />
+        <attribute name="Codebase" value="${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="${applet.codebase}" />
-        </manifest>
-      </jar>
-    </presetdef>
-    <presetdef name="tl_applet.jar">
-      <!-- build signed applet with trusted library/trusted permissions -
+    <jar update="true" index="true">
+      <manifest>
+        <attribute name="Application-Name" value="JalviewLite" />
+        <attribute name="Permissions" value="sandbox" />
+        <attribute name="Codebase" value="${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 
@@ -644,66 +700,106 @@
 			       
 			      -->
 
-      <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}"/>
-    <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
-    <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
-    <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
-    <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
-    <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
-    <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
-    <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
-    <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
-    <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
-    <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
-    <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
-    <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
-    <!-- finally, create manifest for original jars -->
-    <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
-    <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
-
-    <!-- todo - write examples/downloads for alternate versions of the applet -->
-    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
-
-      <fileset dir="${packageDir}/examples">
-        <include name="${jalviewLiteJar}" />
-        <include name="${jmolJar}" />
-        <include name="to_${jalviewLiteJar}" />
-        <include name="to_${jmolJar}" />
-        <include name="tl_${jalviewLiteJar}" />
-        <include name="tl_${jmolJar}" />
-        <include name="ap_${jalviewLiteJar}" />
-        <include name="ap_${jmolJar}" />
-      </fileset>
-    </signjar>
-	</target>
-	<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
-	 <javadoc destdir="${javadocDir}">
-	 	<packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
-	 	</packageset>
-	 	</javadoc>
-	</target>
-	
+    <jar update="true" index="true">
+      <manifest>
+        <attribute name="Application-Name" value="JalviewLite" />
+        <attribute name="Permissions" value="all-permissions" />
+        <attribute name="Codebase" value="${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/${jsonSimple}" />
+
+  <!-- todo - write examples/downloads for alternate versions of the applet -->
+  <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+
+    <fileset dir="${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>
+  </signjar>
+  <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+  <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+	<!-- finally, replace any launchApp servlet tags with a version specification -->
+	<replace value="http://www.jalview.org/services/launchApp?version=${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>
 </project>