X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=build.xml;h=681804dbaf28d07d6ba2c81572745f510e77eff0;hp=f2a9daf1c32e6fc98ad00ad0d386c4165bd5647d;hb=refs%2Fheads%2Fspikes%2Fjims_test;hpb=dfb6a07c452c1c4f2931a1acff753bbe4fc556f0

diff --git a/build.xml b/build.xml
index f2a9daf..681804d 100755
--- a/build.xml
+++ b/build.xml
@@ -1,31 +1,23 @@
 <?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 2.8.2)
+ * Copyright (C) 2014 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~~~~" />
@@ -85,21 +77,21 @@
     <!-- 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" />
+    <property name="WebStartImage" value="JalviewLogo_big.png"/>
     <!-- J2SE version needed for webstart launch -->
-    <property name="j2sev" value="1.6+" />
+    <!-- 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 -->
@@ -114,9 +106,12 @@
     <property name="outputJar" value="jalview.jar" />
     <!-- Jalview Applet JMol Jar Dependency -->
     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
+    <property name="varnaJar" value="VARNAv3-9.jar" />
     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
     <!-- switch to indicate if we should obfuscate jalviewLite -->
-    <!--<property name="donotobfuscate" value="true"/> -->
+    <!-- <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" />
@@ -137,24 +132,24 @@
         <include name="**/*.jar" />
       </fileset>
       <fileset dir="${java.home}/lib">
-        <include name="plugin.jar" />
+        <include name="plugin.jar"/>
       </fileset>
       <fileset dir="appletlib">
         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
 				-->
         <include name="${jmolJar}" />
+        <include name="${varnaJar}" />
       </fileset>
 
     </path>
     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
     <!-- The Location of the java 1.1.8 jdk -->
-    <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
-		-->
+    <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
     <property name="java118.home" value="${java.home}" />
-    <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
+    <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 		-->
     <!-- jre for 1.4 version -->
-    <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
+    <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 
     <!-- the classpath for building the 1.1 applet -->
     <path id="jalviewlite.deps">
@@ -162,12 +157,13 @@
         <include name="lib/classes.zip" />
       </fileset>
       <fileset dir="${java.home}/lib">
-        <include name="plugin.jar" />
+        <include name="plugin.jar"/>
       </fileset>
       <pathelement location="appletlib/${jmolJar}" />
+      <pathelement location="lib/${varnaJar}" />
     </path>
     <!-- default location for outputting javadoc -->
-    <property name="javadocDir" value="${packageDir}/javadoc" />
+    <property name="javadocDir" value="${packageDir}/javadoc"/>
   </target>
 
 
@@ -188,7 +184,7 @@
 
   <target name="clean" depends="init">
     <!-- not efficient yet. -->
-    <delete dir="${outputDir}" includes="*,**/*" />
+    <delete dir="${outputDir}" includes="*,**/*"/>
   </target>
 
   <target name="distclean" depends="init, clean">
@@ -238,107 +234,52 @@
   </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" sigalg="SHA1withRSA">
-
-      <fileset dir="${packageDir}">
-        <include name="*.jar" />
-      </fileset>
-    </signjar>
     <copy todir="${packageDir}">
       <fileset dir="${resourceDir}/images">
-        <include name="${WebStartImage}" />
+        <include name="${WebStartImage}"/>
       </fileset>
     </copy>
 
     <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="${WebStartImage}" />
-        <offline_allowed />
-      </information>
-      <resources>
-        <j2se version="${j2sev}" 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="${JALVIEW_VERSION}" />
-      </resources>
-      <application_desc main_class="jalview.bin.Jalview">
-      </application_desc>
-      <security>
-        <all_permissions />
-      </security>
-    </jnlp>
-    <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
-      <information>
-        <title>Jalview</title>
-        <vendor>The Barton Group</vendor>
-        <homepage href="http://www.jalview.org" />
-        <description>Jalview Multiple Alignment Editor</description>
-        <description kind="short">Jalview</description>
-        <icon href="${WebStartImage}" />
-        <offline_allowed />
-      </information>
-      <resources>
-        <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
-        <fileset dir="${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="${WebStartImage}" />
-        <offline_allowed />
-      </information>
-      <resources>
-        <j2se version="${j2sev}" 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="${JALVIEW_VERSION}" />
-      </resources>
-      <application_desc main_class="jalview.bin.Jalview">
-      </application_desc>
-      <security>
-        <all_permissions />
-      </security>
-    </jnlp>
+    <!-- create a dummy jar which will eventually contain the jnlp template -->
+    <jar destfile="${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="${packageDir}">
+        <include name="JNLP-INF"/>
+      </fileset>
+    </jar>
+
+    <antcall target="writejnlpf">
+      <param name="jnlpFile" value="${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">
@@ -350,6 +291,7 @@
     <!--
 				<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"/>
@@ -359,7 +301,13 @@
         <association mime-type="application-x/ext-file" extensions="amsa"/>
         <association mime-type="application-x/ext-file" extensions="stk"/>
         <association mime-type="application-x/ext-file" extensions="jar"/>-->
-
+    <!-- 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>
+    </signjar>
   </target>
 
   <target name="runenv" depends="init">
@@ -375,18 +323,83 @@
       </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 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="${packageDir}">
+            <include name="*.jar" />
+            <include name="*_*.jar" />
+            <exclude name="jalview.jar" />
+          </fileset>
+          <property name="jalview.version" value="${JALVIEW_VERSION}" />
+        </resources>
+        <application_desc main_class="jalview.bin.Jalview">
+        </application_desc>
+        <security>
+          <all_permissions />
+        </security>
+      </jnlp>
+    </presetdef>
+
+    <jnlpf toFile="${jnlpFile}"/>
+
+  </target>
+
+  <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
+    <echo message="Not adding JNLP File Associations"/>
+  </target>
+
+  <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
+    <replace file="${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
@@ -396,244 +409,266 @@
      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}" 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" 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" />
-      </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 "${obfuscateDeps}"
+  <path id="axisbuild">
+    <path refid="build.classpath" />
+  </path>
+  <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
+  <move todir="./bak">
+    <fileset dir="${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="${javac.debug}" 
+			classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
+			excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
+</target>
+
+<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+  <copy file="${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}" />
+  </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/*" />
-        <include name="jmol/*" />
-      </fileset>
-      <fileset dir=".">
-        <include name="${jalviewLiteJar}" />
-      </fileset>
-      <fileset dir="appletlib">
-        <include name="**/*" />
-      </fileset>
-    </copy>
-
-    <presetdef name="ap_applet.jar">
-      <!-- build a signed applet with 'all-permissions' - 
+  <delete>
+    <fileset dir="${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' - 
 			  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" jarfile="@{jarfile}">
-        <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 
@@ -642,57 +677,68 @@
 			       
 			      -->
 
-      <jar update="true" index="true" jarfile="@{jarfile}">
-        <manifest>
-          <attribute name="Application-Name" value="JalviewLite" />
-          <attribute name="Permissions" value="all-permissions" />
-          <attribute name="Codebase" value="${applet.codebase}" />
-          <attribute name="Trusted-Only" value="true" />
-          <attribute name="Trusted-Library" value="true" />
-        </manifest>
-      </jar>
-    </presetdef>
-    <presetdef name="to_applet.jar">
-      <!-- not fully test variant (yet) -->
-      <jar update="true" index="true" jarfile="@{jarfile}">
-        <manifest>
-          <attribute name="Application-Name" value="JalviewLite" />
-          <attribute name="Permissions" value="all-permissions" />
-          <attribute name="Codebase" value="${applet.codebase}" />
-          <attribute name="Trusted-Only" value="true" />
-        </manifest>
-      </jar>
-    </presetdef>
-    <!-- create differently privileged artefacts -->
-    <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${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="${packageDir}/examples">
-        <include name="*.jar" />
-      </fileset>
-    </signjar>
-  </target>
-  <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
-    <javadoc destdir="${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/${jalviewLiteJar}" tofile="${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">
+      <exclude name="u_*.jar"/>
+      <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>
+  <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+  <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+</target>
+<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+  <javadoc destdir="${javadocDir}">
+    <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+    </packageset>
+  </javadoc>
+</target>
 </project>