X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=82cbabb6d6d92e3c763d6fe3cf78ac0b242f9f86;hb=279af6f3b1803de7a1e467b83a7205df18e70d48;hp=990cbe6bbb6f35ca55818216286115e78d916bd4;hpb=23c2823b66abf031af741f12f718e4e72b9bb8f5;p=jalview.git

diff --git a/build.xml b/build.xml
index 990cbe6..82cbabb 100755
--- a/build.xml
+++ b/build.xml
@@ -1,52 +1,53 @@
 <?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 2.8.0b1)
+ * 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~~~~" />
-    <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
+	<!-- 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
     building docs, jars and webstart stuff -->
-  <!--
+	<!--
         Userdefined build property defaults
 
         wsdl.server list (plus namespace mapping info ???)  - also want
@@ -59,41 +60,41 @@
 
 -->
 
-  <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" />
+		<!-- 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+"/>
 
     <!-- Permissions for running Java applets and applications. -->
     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
@@ -102,156 +103,154 @@
     <property name="applet.codebase" value="*" />
     <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="jalviewLiteJar" value="jalviewApplet.jar" />
+		<!-- switch to indicate if we should obfuscate jalviewLite -->
+		<!--<property name="donotobfuscate" value="true"/> -->
+
+		<!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
+		<property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
+		<property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
+		<property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
+		<property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
+		<property name="WSInterf" value="MsaWS" />
+		<property name="wsdl.Namespace" value="vamsas" />
+		<property name="wsdl.ClientNS" value="ext.vamsas" />
+		<!-- the class path for building the application -->
+		<path id="build.classpath">
+			<fileset dir="utils">
+				<include name="*.jar" />
+				<include name="**/*.jar" />
+			</fileset>
+			<fileset dir="${libDir}">
+				<include name="*.jar" />
+				<include name="**/*.jar" />
+			</fileset>
+			<fileset dir="${java.home}/lib">
+				<include name="plugin.jar"/>
+			</fileset>
+			<fileset dir="appletlib">
+				<!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
 				-->
-        <include name="${jmolJar}" />
-      </fileset>
+				<include name="${jmolJar}" />
+			</fileset>
 
-    </path>
-    <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
-    <!-- The Location of the java 1.1.8 jdk -->
-    <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
+		</path>
+		<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
+		<!-- The Location of the java 1.1.8 jdk -->
+		<!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 		-->
-    <property name="java118.home" value="${java.home}" />
-    <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
-		-->
-    <!-- jre for 1.4 version -->
-    <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
-
-    <!-- the classpath for building the 1.1 applet -->
-    <path id="jalviewlite.deps">
-      <fileset dir="${java118.home}">
-        <include name="lib/classes.zip" />
-      </fileset>
-      <fileset dir="${java.home}/lib">
-        <include name="plugin.jar" />
-      </fileset>
-      <pathelement location="appletlib/${jmolJar}" />
-    </path>
+		<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>
     <!-- default location for outputting javadoc -->
-    <property name="javadocDir" value="${packageDir}/javadoc" />
-  </target>
+    <property name="javadocDir" value="${packageDir}/javadoc"/>
+	</target>
 
 
-  <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
-  <target name="buildPropertiesFile" depends="init">
-    <tstamp prefix="build">
-      <format property="date" pattern="dd MMMM yyyy" />
-    </tstamp>
-    <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" />
+			<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" />
 
     <!-- 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"/>
@@ -262,9 +261,9 @@
     </antcall>
           	
   	<jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
-  	      <fileset dir="${packageDir}">
+				<fileset dir="${packageDir}">
   	      	<include name="JNLP-INF"/>
-  	      </fileset>
+				</fileset>
   	</jar>
     
   	<antcall target="writejnlpf">
@@ -285,7 +284,7 @@
   	  <param name="maxh" value="1024M"/>
   	</antcall>
   	
-  	<!-- finally, need to postprocess to add in associations at end of 'information' element 
+			<!-- 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">
 		
@@ -293,9 +292,10 @@
 			
 			
 			-->
-    <!--
+					<!--
 				<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"/>
@@ -312,20 +312,20 @@
           <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 ${run.classpath} jalview.bin.Jalview
       </echo>
-  </target>
+	</target>
   <target name="writejnlpf">
   	<presetdef name="jnlpf">
   	    <jnlp codebase="${WebStartLocation}">
@@ -360,18 +360,18 @@
 
   	    <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="${doextbuild.response}" />
-    </condition>
-    <fail if="dontextbuild">
+	<target name="buildextclients" depends="init">
+		<input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
+		<condition property="dontextbuild">
+			<equals arg1="n" arg2="${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
@@ -381,210 +381,229 @@
      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}/${outputJar}" index="true">
-      <manifest>
-        <attribute name="Main-Class" value="jalview.bin.Jalview" />
+		<path id="axisbuild">
+			<path refid="build.classpath" />
+		</path>
+		<taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
+		<move todir="./bak">
+			<fileset dir="${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}"
+			</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 "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
       -keep public class jalview.bin.JalviewLite
        { public * ; } -->
-    </proguard>
-    <delete file="in.jar" />
-  </target>
-
-  <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
-    <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
-    <delete>
-      <fileset dir="${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=".">
+		<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>
-      <fileset dir="appletlib">
-        <include name="**/*" />
-      </fileset>
-    </copy>
-
+    </signjar>
     <presetdef name="ap_applet.jar">
       <!-- build a signed applet with 'all-permissions' - 
 			  Needs 'param name="permissions' value="all-permissions"' in applet tag
@@ -650,7 +669,7 @@
     </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="${packageDir}/examples/${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}" />
@@ -671,6 +690,7 @@
     <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}" />
@@ -681,6 +701,8 @@
         <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}">
@@ -688,5 +710,4 @@
       </packageset>
     </javadoc>
   </target>
-
 </project>