X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=caef5beb8d941ce188cb6c7314e88007520639d6;hb=c59e3c344202e84e4547c1e54abc8d50bb680c1f;hp=2082fbdc8ab45c045531119fc9dcfcf7dbb84d5d;hpb=b790acc367d546c31535d7c65799342b5b6e6591;p=jalview.git

diff --git a/build.xml b/build.xml
index 2082fbd..caef5be 100755
--- a/build.xml
+++ b/build.xml
@@ -1,169 +1,550 @@
 <?xml version="1.0"?>
-<project name="jalviewX" default="build" basedir=".">
-  <!-- utils is a class path to additional utilities needed for
-  building docs, jars and webstart stuff -->
-
-
-  
-  <target name="init">
-
-    <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="outputDir" value="classes" />
-    <property name="packageDir" value="dist" />
-    <property name="outputJar" value="jalview.jar" />
-
-    <path id="build.classpath">
-      <fileset dir="utils">
-        <include name="*.jar"/>
-        <include name="**/*.jar"/>
-      </fileset>
-      <fileset dir="${libDir}">
-        <include name="*.jar"/>      
-        <include name="**/*.jar"/>
-      </fileset>
-    </path>
-<!-->    <uptodate property="help.uptodate"
-     targetfile="${helpDir}/helpIndex.xml">
-      <srcfiles
-        dir="${helpDir}"
-        includes="**/*.html" />
-    </uptodate>
-    -->
-  </target>
+<!--
+   * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+   * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+   * 
+   * This program 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 2
+   * of the License, or (at your option) any later version.
+   * 
+   * This program 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 this program; if not, write to the Free Software
+   * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+-->
+<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="clean" depends="init">
-        <!-- not efficient yet. -->
-    <delete dir="${outputDir}"/>
-  </target>
+	<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>
 
-  <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">
+
+	<!-- utils is a class path to additional utilities needed for
+    building docs, jars and webstart stuff -->
+	<!--
+        Userdefined build property defaults
+
+        wsdl.server list (plus namespace mapping info ???)  - also want
+                ... to make this a dynamically generatable property
+        WebStart Location
+        Build location - provide a temporary root for speed
+        jarsigner keystore and info
+        Jakarta and axis classpath ?
+        Default argument for starting Jalview (if it exists).
+
+-->
+
+	<target name="init">
+		<path id="axis.classpath">
+			<!-->
+			<fileset dir="/usr/local/axis/lib">
+				<include name="**/*.jar" />
+			</fileset>
+			<fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
+				<include name="**/*.jar"/>
+				<include name="*.jar"/>
+			</fileset> -->
+      </path>
+		<!-- Jalview Version String displayed by application on startup and used to check for updates -->
+    <property name="JALVIEW_VERSION" value="DEVELOPMENT"/> <!-- 2.4 (VAMSAS)" -->
+		<!-- Include debugging information in javac true or false -->
+		<property name="javac.debug" value="true"/>
+		
+		<!-- JarSigner Key Store for Webstart Distribution -->
+		<property name="jalview.keystore" value="./keys/.keystore"/>
+		<!-- Keystore Password -->
+		<property name="jalview.keystore.pass" value="alignmentisfun"/>
+		<!-- Key Name -->
+		<property name="jalview.key" value="jalview"/>
+		<!-- Key Password -->
+		<property name="jalview.key.pass" value="alignmentisfun"/>
+						
+		<!-- Don't change anything below here unless you know what you are doing! -->
+		<!-- Url path for WebStart in JNLP file -->
+		<property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
+		<!-- build directory configuration -->
+		<property name="libDir" value="lib"/>
+		<property name="resourceDir" value="resources"/>
+		<property name="helpDir" value="help"/>
+		<property name="docDir" value="doc"/>
+		<property name="sourceDir" value="src" />
+		<property name="schemaDir" value="schemas" />
+		<property name="outputDir" value="classes" />
+		<property name="packageDir" value="dist" />
+		<property name="outputJar" value="jalview.jar" />
+	  <!-- Jalview Applet JMol Jar Dependency -->
+    <property name="jmolJar" value="Jmol-11.0.2.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>
+			
+		</path>
+		<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz"/>
+		<!-- The Location of the java 1.1.8 jdk -->
+		<property name="java118.home" value="C:\Sun\jdk1.1.8" />
+		<property name="applet.jre.tools" value="${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>
+	   	<pathelement location="lib/${jmolJar}"/>
+	  </path>
+	</target>
+
+
+	<taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
+	<target name="buildPropertiesFile" depends="init">
+		<tstamp prefix="build">
+			<format property="date" pattern="dd MMMM yyyy"/>
+		</tstamp>
+		<properties file="${outputDir}/.build_properties">
+			<header>
+          ---Jalview Build Details---
+        </header>
+			<property name="VERSION" value="${JALVIEW_VERSION}"/>
+			<property name="BUILD_DATE" value="${build.date}"/>
+		</properties>
+	</target>
+
+
+	<target name="clean" depends="init">
+		<!-- not efficient yet. -->
+		<delete dir="${outputDir}"/>
+	</target>
+
+	<target name="distclean" depends="init, clean">
+
+		<echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
+		<delete>
+			<fileset dir=".">
+				<include name="${outputJar}"/>
+				<include name="#*#"/>
+				<include name="#*.*#"/>
+				<include name="**/#*#"/>
+				<include name="**/#*.*#"/>
+				<include name="*~"/>
+				<include name="*.*~"/>
+				<include name="**/*~"/>
+				<include name="**/*.*~"/>
+			</fileset>
+		</delete>
+	</target>
+
+	<target name="prepare" depends="init">
+		<mkdir dir="${outputDir}"/>
+		<copy todir="${outputDir}">
+			<fileset dir=".">
+				<include name="${docDir}/**/*.*"/>
+				<include name="${helpDir}/**/*.*"/>
+				<include name="${libDir}/*.jar"/>
+			</fileset>
+			<fileset dir="${resourceDir}">
+				<include name="**/*.*"/>
+			</fileset>
+		</copy>
+	</target>
+
+	<target name="build" depends="prepare">
+		<!-- not efficient yet. -->
+		<javac source="1.4" target="1.4"
+        srcdir ="${sourceDir}"
+        destdir="${outputDir}"
+				debug="${javac.debug}"
+      classpathref="build.classpath">
+			<exclude name="jalview/*applet*"/>
+			<exclude name="com/stevesoft/**"/>
+		</javac>
+	</target>
+	<target name="buildindices" depends="init, prepare"
+    unless="help.uptodate">
+		<java
+      classname="com.sun.java.help.search.Indexer"
+      classpathref="build.classpath"
+      fork="true"
+      dir="${outputDir}/${helpDir}"
+      >
+			<arg line="html"/>
+		</java>
+	</target>
+
+	<target name="makefulldist" depends="makedist">
+		<!-- the default keystore details might need to be edited here -->
+		<signjar
+      storepass="${jalview.keystore.pass}"
+      keypass="${jalview.key.pass}"
+      keystore="${jalview.keystore}"
+      alias="${jalview.key}"
+      lazy="false"
+      verbose="false"
+      >
+
+			<fileset dir="${packageDir}">
+				<include name="*.jar"/>
+			</fileset>
+		</signjar>
+		<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
+
+		<!--    codebase="http://www.jalview.org/jalview/webstart" -->
+		<!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
+		<jnlp toFile="${packageDir}/jalview.jnlp" 
+      codebase="${WebStartLocation}">
+			<information>
+				<title>Jalview</title>
+				<vendor>The Barton Group</vendor>
+				<homepage href="http://www.jalview.org"/>
+				<description>Jalview Multiple Alignment Editor</description>
+				<description kind="short">Jalview</description>
+				<icon href="logo_big.gif"/>
+				<offline_allowed/>
+				<!--
+	<association mime-type="application-x/ext-file" extensions="fa"/>
+        <association mime-type="application-x/ext-file" extensions="fasta"/>
+        <association mime-type="application-x/ext-file" extensions="fastq"/>
+        <association mime-type="application-x/ext-file" extensions="blc"/>
+        <association mime-type="application-x/ext-file" extensions="msf"/>
+        <association mime-type="application-x/ext-file" extensions="pfam"/>
+        <association mime-type="application-x/ext-file" extensions="aln"/>
+        <association mime-type="application-x/ext-file" extensions="pir"/>
+        <association mime-type="application-x/ext-file" extensions="amsa"/>
+	-->
+			</information>
+			<resources>
+				<j2se version="1.4+"/>
+				<fileset dir="${packageDir}">
+					<include name="jalview.jar"/>
+				</fileset>
+				<fileset dir="${packageDir}">
+					<include name="*.jar"/>
+					<include name="*_*.jar"/>
+					<exclude name="jalview.jar"/>
+				</fileset>
+				<property name="jalview.version" value="${JALVIEW_VERSION}"/>
+			</resources>
+			<application_desc main_class="jalview.bin.Jalview">
+			</application_desc>
+			<security>
+				<all_permissions/>
+			</security>
+		</jnlp>
+	</target>
+	<target name="runenv" depends="init">
+		<path id="run.classpath">
+			<pathelement location="${outputDir}"/>
+			<fileset dir="${outputDir}">
+				<include name="${libDir}/*.jar"/>
+			</fileset>
+		</path>
+		<pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
+
+		<echo>java -classpath ${run.classpath} jalview.bin.Jalview
+      </echo>
+	</target>
+
+	<target name="buildextclients" depends="init">
+		<input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
+      validargs="Y,y,n,N" defaultvalue="N"
+      addproperty="doextbuild.response"/>
+		<condition property="dontextbuild">
+			<equals arg1="n" arg2="${doextbuild.response}"/>
+		</condition>
+		<condition property="dontextbuild">
+			<equals arg1="N" arg2="${doextbuild.response}"/>
+		</condition>
+		<fail if="dontextbuild">
+        Build External Client Code process aborted by user. Jalview source is unchanged.
+      </fail>
+		<!-- Currently, this doesn't happen automatically.
+     1. Run WSDL2Java as below, which generates an ext.vamsas +
+     vamsas.<datapackages> fileset.
+     2. refactor ext.vamsas.SpecificserviceWS* to
+     ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
+     3. Update the jalview.ws.*WServices classes to reflect the
+     interface type, and all locations of this wsdl type that Jalview
+     might be using.
+
+-->
+		<path id="axisbuild">
+			<path refid="build.classpath"/>
+		</path>
+		<taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
+		<move todir="./bak">
+			<fileset dir="${sourceDir}" id="client">
+				<include name="${wsdl.ClientNS}/*.*"/>
+			</fileset>
+		</move>
+
+		<axis-wsdl2java
+      output="${sourceDir}"
+      verbose="true"
+      url="${wsdl.MsaWS2}"
+      serverside="false"
+      deployscope="Request"
+      debug="false"
+      helpergen="true"
+      all="true"
+      >
+			<mappingSet>
+				<mapping
+        namespace="${wsdl.Namespace}"
+        package="${wsdl.ClientNS}"
+        />
+				<mapping namespace="http://dataTypes.vamsas"
+        package="${wsdl.ClientNS}"/>
+			</mappingSet>
+		</axis-wsdl2java>
+	</target>
+
+	<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+		<!-- make the package jar -->
+		<mkdir dir="${packageDir}"/>
+
+		<jar destfile="${packageDir}/${outputJar}">
+			<manifest>
+				<attribute name="Main-Class" value="jalview.bin.Jalview"/>
+			</manifest>
+			<fileset dir="${outputDir}/">
+				<exclude name="cache*/**"/>
+				<exclude name="*.jar" />
+				<exclude name="*.jar.*" />
+				<exclude name="**/*.jar" />
+				<exclude name="**/*.jar.*" />
+			</fileset>
+		</jar>
+
+		<copy toDir="${packageDir}" flatten="true">
+			<fileset dir="${outputDir}">
+				<include name="*.jar"/>
+				<include name="**/*.jar"/>
+			</fileset>
+		</copy>
+	</target>
+
+
+	<!-- jalopy code reformatter -->
+	<target name="sourcescrub" depends="init,build">
+		<jalopy destdir="jsrc" classpathref="run.classpath"
+      convention="jalview-jalopy.xml">
+			<fileset dir="${sourceDir}">
+				<include name="*.java"/>
+				<include name="**/*.java"/>
+				<include name="**/**/*.java"/>
+			</fileset>
+		</jalopy>
+	</target>
+
+
+
+  <!-- Compile, package and obfuscate Jalview Applet -->
+  <target name="makeApplet" depends="obfuscate"/>
+
+  <target name="compileApplet" depends="init,clean">
     <mkdir dir="${outputDir}"/>
-    <copy todir="${outputDir}">
-      <fileset dir=".">
-
-        <include name="${docDir}/**/*.*"/>
-        <include name="${helpDir}/**/*.*"/>
-        <include name="${libDir}/*.*"/>
-      </fileset>
-      <fileset dir="${resourceDir}">
-        <include name="**/*.*"/>
-      </fileset>
-    </copy>
+    <javac source="1.2"
+    target="1.1"
+    srcdir="${sourceDir}" 
+    destdir="${outputDir}"
+   	debug="${javac.debug}"
+    classpath="lib/${jmolJar}"
+       includes="jalview/appletgui/**"
+       excludes="ext/**,MCview/**,org/**,vamsas/**"
+       />
   </target>
 
-  <target name="build" depends="prepare">
-            <!-- not efficient yet. -->
-     <javac source="1.4" target="1.4" srcdir="${sourceDir}" destdir="${outputDir}"
-        classpathref="build.classpath" />
+  <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+  <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
+  <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
+       <jar destfile="in.jar">
+        <manifest>
+            <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
+        </manifest>
+        <fileset dir="${outputDir}">
+          <include name="com/**"/>
+          <include name="MCview/**"/>
+          <include name="jalview/**"/>
+          <include name=".build_properties"/>
+          <include name="images/idwidth.gif"/>
+          <include name="images/link.gif"/>
+        </fileset>
+      </jar>
   </target>
-  <target name="buildindices" depends="init, prepare" 
-   unless="help.uptodate">
-    <java
-     classname="com.sun.java.help.search.Indexer"
-     classpathref="build.classpath"
-     fork="true"
-     dir="${outputDir}/${helpDir}"
-     >
-      <arg line="html"/>
-    </java>
+  <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
   </target>
-  
-  <target name="makejars" depends="build, buildindices">
-    <!-- make the package jar -->
-    <mkdir dir="${packageDir}"/>
-    
-    <jar destfile="${packageDir}/${outputJar}">
-      <fileset dir="${outputDir}">
-        <exclude name="*.jar" />
-      </fileset>
-    </jar>
-
-    <copy toDir="${packageDir}" flatten="true">
-      <fileset dir="${outputDir}">
-        <include name="*.jar"/>
-        <include name="**/*.jar"/>
-      </fileset>
-    </copy>
-
-    <signjar 
-    storepass="alignmentisfun"
-    keypass="alignmentisfun"
-    keystore="keys/.keystore"
-    alias="jalview"
-    lazy="false"
-    verbose="false"
-    >
-
-    <fileset dir="${packageDir}">
-      <include name="*.jar"/>
-    </fileset>
-    </signjar>
-    <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
-    
-    <!--    codebase="http://www.jalview.org/jalview/webstart" -->
-    <jnlp toFile="${packageDir}/Jalview.jnlp" href="Jalview.jnlp"
-    codebase="file://">
-    <information>
-      <title>Jalview</title>
-      <vendor>M Clamp</vendor>
-      <homepage href="www.jalview.org"/>
-      <description>Jalview Multiple Alignment Editor</description>
-      <description kind="short">Jalview</description>
-      <icon href="BartonGroupBanner.gif"/>
-    </information>
-    <resources>
-      <j2se version="1.3+"/>
-      <fileset dir="${packageDir}">
-        <include name="*.jar"/>
-      </fileset>
-    </resources>
-    <application_desc main_class="jalview.gui.AlignFrame">
-      <argument>http://www.compbio.dundee.ac.uk/~andrew/jalview/glut.msf</argument>
-      <argument>URL</argument>
-      <argument>MSF</argument>
-        </application_desc>
-    <security>
-      <all_permissions/>
-    </security>  
-    </jnlp>        
+	<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">    
+  	<copy file="in.jar" tofile="${jalviewLiteJar}" />    	
+    <delete file="in.jar"/>
   </target>
-  <target name="runenv" depends="init">
-      <path id="run.classpath">
-        <pathelement location="${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="package" depends="init, build">
+	<target name="-obfuscatereally" unless="donotobfuscate">
     
+  	<path id="obfuscateDeps.path">
+    <pathelement location="${applet.jre.tools}"/>
+    <pathelement location="lib/${jmolJar}"/>
+    </path>
+    <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+  	
+    <proguard>
+      <injar file="in.jar"/>
+      <outjar file="${jalviewLiteJar}"/>
+      <libraryjar refid="obfuscateDeps.path"/>
+      <keep access="public" type="class"
+      name="jalview.bin.JalviewLite">
+        <field access="public"/>
+        <method access="public"/>
+        <constructor access="public"/>
+      </keep>
+<!--      -libraryjars "${obfuscateDeps}"
+      -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}/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="${sourceDir}/*.java"/>
+				<include name="${sourceDir}/**/*.java"/>
+				<include name="${sourceDir}/**/*.cdr"/>
+				<include name="${libDir}/**/*"/>						
+				<include name="${resourceDir}/**/*"/>						
+				<include name="${helpDir}/**/*"/>						
+				<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}/**/*"/>						
+			</tarfileset>
+		</tar>
+	</target>
 </project>