X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=3894e210d57d5d66c646773ed9874f22041e9608;hb=66eff479b11806bdcb0852c52344e9a520990921;hp=caef5beb8d941ce188cb6c7314e88007520639d6;hpb=47bbb5bc275d758d86b6c2d2091bf807cb9cd8ec;p=jalview.git

diff --git a/build.xml b/build.xml
index caef5be..3894e21 100755
--- a/build.xml
+++ b/build.xml
@@ -1,21 +1,20 @@
 <?xml version="1.0"?>
 <!--
-   * 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
+   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+   * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
    * 
-   * 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.
+   * 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.
    * 
-   * 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
+   * 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/>.
 -->
 <project name="jalviewX" default="usage" basedir=".">
 	<!-- we use jalopy to format our sources -->
@@ -41,8 +40,8 @@
 		<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"/>
+		<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>
 
 
@@ -73,10 +72,11 @@
 			</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)" -->
+		<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 -->
@@ -85,7 +85,7 @@
 		<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"/>
@@ -99,12 +99,12 @@
 		<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" />
+		<!-- Jalview Applet JMol Jar Dependency -->
+		<property name="jmolJar" value="JmolApplet-12.1.5.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" />
@@ -123,7 +123,7 @@
 				<include name="*.jar"/>
 				<include name="**/*.jar"/>
 			</fileset>
-			
+
 		</path>
 		<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz"/>
 		<!-- The Location of the java 1.1.8 jdk -->
@@ -137,8 +137,8 @@
 			<fileset dir="${java118.home}">
 				<include name="lib/classes.zip"/>
 			</fileset>
-	   	<pathelement location="lib/${jmolJar}"/>
-	  </path>
+			<pathelement location="appletlib/${jmolJar}"/>
+		</path>
 	</target>
 
 
@@ -196,7 +196,7 @@
 
 	<target name="build" depends="prepare">
 		<!-- not efficient yet. -->
-		<javac source="1.4" target="1.4"
+		<javac source="1.5" target="1.5"
         srcdir ="${sourceDir}"
         destdir="${outputDir}"
 				debug="${javac.debug}"
@@ -219,33 +219,25 @@
 
 	<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"
-      >
+		<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"/>
+				<include name="*.jar" />
 			</fileset>
 		</signjar>
-		<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
+		<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}">
+		<jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 			<information>
 				<title>Jalview</title>
 				<vendor>The Barton Group</vendor>
-				<homepage href="http://www.jalview.org"/>
+				<homepage href="http://www.jalview.org" />
 				<description>Jalview Multiple Alignment Editor</description>
 				<description kind="short">Jalview</description>
-				<icon href="logo_big.gif"/>
-				<offline_allowed/>
+				<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"/>
@@ -259,51 +251,132 @@
 	-->
 			</information>
 			<resources>
-				<j2se version="1.4+"/>
+				<j2se version="1.5+" initial_heap_size="10M"/>
 				<fileset dir="${packageDir}">
-					<include name="jalview.jar"/>
+					<include name="jalview.jar" />
 				</fileset>
 				<fileset dir="${packageDir}">
-					<include name="*.jar"/>
-					<include name="*_*.jar"/>
-					<exclude name="jalview.jar"/>
+					<include name="*.jar" />
+					<include name="*_*.jar" />
+					<exclude name="jalview.jar" />
 				</fileset>
-				<property name="jalview.version" value="${JALVIEW_VERSION}"/>
+				<property name="jalview.version" value="${JALVIEW_VERSION}" />
 			</resources>
 			<application_desc main_class="jalview.bin.Jalview">
 			</application_desc>
 			<security>
-				<all_permissions/>
+				<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 ${run.classpath} jalview.bin.Jalview
+		<!-- the rest of these jnlp tasks are copy and pastes of the above but with different Vm args -->
+					<jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
+				<information>
+					<title>Jalview</title>
+					<vendor>The Barton Group</vendor>
+					<homepage href="http://www.jalview.org" />
+					<description>Jalview Multiple Alignment Editor</description>
+					<description kind="short">Jalview</description>
+					<icon href="logo_big.gif" />
+					<offline_allowed />
+					<!--
+		<association mime-type="application-x/ext-file" extensions="fa"/>
+	        <association mime-type="application-x/ext-file" extensions="fasta"/>
+	        <association mime-type="application-x/ext-file" extensions="fastq"/>
+	        <association mime-type="application-x/ext-file" extensions="blc"/>
+	        <association mime-type="application-x/ext-file" extensions="msf"/>
+	        <association mime-type="application-x/ext-file" extensions="pfam"/>
+	        <association mime-type="application-x/ext-file" extensions="aln"/>
+	        <association mime-type="application-x/ext-file" extensions="pir"/>
+	        <association mime-type="application-x/ext-file" extensions="amsa"/>
+		-->
+				</information>
+				<resources>
+					<j2se version="1.5+" initial_heap_size="64M" max_heap_size="512M"/>
+					<fileset dir="${packageDir}">
+						<include name="jalview.jar" />
+					</fileset>
+					<fileset dir="${packageDir}">
+						<include name="*.jar" />
+						<include name="*_*.jar" />
+						<exclude name="jalview.jar" />
+					</fileset>
+					<property name="jalview.version" value="${JALVIEW_VERSION}" />
+				</resources>
+				<application_desc main_class="jalview.bin.Jalview">
+				</application_desc>
+				<security>
+					<all_permissions />
+				</security>
+			</jnlp>
+			<jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
+					<information>
+						<title>Jalview</title>
+						<vendor>The Barton Group</vendor>
+						<homepage href="http://www.jalview.org" />
+						<description>Jalview Multiple Alignment Editor</description>
+						<description kind="short">Jalview</description>
+						<icon href="logo_big.gif" />
+						<offline_allowed />
+						<!--
+			<association mime-type="application-x/ext-file" extensions="fa"/>
+		        <association mime-type="application-x/ext-file" extensions="fasta"/>
+		        <association mime-type="application-x/ext-file" extensions="fastq"/>
+		        <association mime-type="application-x/ext-file" extensions="blc"/>
+		        <association mime-type="application-x/ext-file" extensions="msf"/>
+		        <association mime-type="application-x/ext-file" extensions="pfam"/>
+		        <association mime-type="application-x/ext-file" extensions="aln"/>
+		        <association mime-type="application-x/ext-file" extensions="pir"/>
+		        <association mime-type="application-x/ext-file" extensions="amsa"/>
+			-->
+					</information>
+					<resources>
+						<j2se version="1.5+" initial_heap_size="256M" max_heap_size="1024M"/>
+						<fileset dir="${packageDir}">
+							<include name="jalview.jar" />
+						</fileset>
+						<fileset dir="${packageDir}">
+							<include name="*.jar" />
+							<include name="*_*.jar" />
+							<exclude name="jalview.jar" />
+						</fileset>
+						<property name="jalview.version" value="${JALVIEW_VERSION}" />
+					</resources>
+					<application_desc main_class="jalview.bin.Jalview">
+					</application_desc>
+					<security>
+						<all_permissions />
+					</security>
+				</jnlp>
+
+			</target>
+
+			<target name="runenv" depends="init">
+				<path id="run.classpath">
+					<pathelement location="${outputDir}"/>
+					<fileset dir="${outputDir}">
+						<include name="${libDir}/*.jar"/>
+					</fileset>
+				</path>
+				<pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
+
+				<echo>java -classpath ${run.classpath} jalview.bin.Jalview
       </echo>
-	</target>
+			</target>
 
-	<target name="buildextclients" depends="init">
-		<input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
+			<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">
+				<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
@@ -313,17 +386,17 @@
      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
+				<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}"
@@ -333,134 +406,142 @@
       helpergen="true"
       all="true"
       >
-			<mappingSet>
-				<mapping
+					<mappingSet>
+						<mapping
         namespace="${wsdl.Namespace}"
         package="${wsdl.ClientNS}"
         />
-				<mapping namespace="http://dataTypes.vamsas"
+						<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="${outputDir}">
-				<include name="*.jar"/>
-				<include name="**/*.jar"/>
-			</fileset>
-		</copy>
-	</target>
-
-
-	<!-- jalopy code reformatter -->
-	<target name="sourcescrub" depends="init,build">
-		<jalopy destdir="jsrc" classpathref="run.classpath"
+					</mappingSet>
+				</axis-wsdl2java>
+			</target>
+
+			<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+				<!-- make the package jar -->
+				<mkdir dir="${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>
+					<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"/>
+			<!-- Compile, package and obfuscate Jalview Applet -->
+			<target name="makeApplet" depends="obfuscate"/>
 
-  <target name="compileApplet" depends="init,clean">
-    <mkdir dir="${outputDir}"/>
-    <javac source="1.2"
-    target="1.1"
+			<target name="compileApplet" depends="init,clean">
+				<mkdir dir="${outputDir}"/>
+				<javac source="1.5"
+    target="1.5"
     srcdir="${sourceDir}" 
     destdir="${outputDir}"
    	debug="${javac.debug}"
-    classpath="lib/${jmolJar}"
+    classpath="appletlib/${jmolJar}"
        includes="jalview/appletgui/**"
        excludes="ext/**,MCview/**,org/**,vamsas/**"
        />
-  </target>
-
-  <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
-  <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
-  <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
-       <jar destfile="in.jar">
-        <manifest>
-            <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
-        </manifest>
-        <fileset dir="${outputDir}">
-          <include name="com/**"/>
-          <include name="MCview/**"/>
-          <include name="jalview/**"/>
-          <include name=".build_properties"/>
-          <include name="images/idwidth.gif"/>
-          <include name="images/link.gif"/>
-        </fileset>
-      </jar>
-  </target>
-  <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
-  </target>
-	<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">    
-  	<copy file="in.jar" tofile="${jalviewLiteJar}" />    	
-    <delete file="in.jar"/>
-  </target>
-	<target name="-obfuscatereally" unless="donotobfuscate">
-    
-  	<path id="obfuscateDeps.path">
-    <pathelement location="${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"
+			</target>
+
+			<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+				<copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
+				<copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
+				<jar destfile="in.jar">
+					<manifest>
+						<attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
+					</manifest>
+					<fileset dir="${outputDir}">
+						<include name="com/**"/>
+						<include name="MCview/**"/>
+						<include name="jalview/**"/>
+						<include name=".build_properties"/>
+						<include name="images/idwidth.gif"/>
+						<include name="images/link.gif"/>
+					</fileset>
+				</jar>
+			</target>
+			<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
+			</target>
+			<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+				<copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true"/>
+				<delete file="in.jar"/>
+			</target>
+			<target name="-obfuscatereally" unless="donotobfuscate">
+
+				<path id="obfuscateDeps.path">
+					<pathelement location="${applet.jre.tools}"/>
+					<pathelement location="appletlib/${jmolJar}"/>
+				</path>
+				<taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+
+				<proguard>
+					<injar file="in.jar"/>
+					<outjar file="${jalviewLiteJar}"/>
+					<libraryjar refid="obfuscateDeps.path"/>
+					<keep access="public" type="class"
       name="jalview.bin.JalviewLite">
-        <field access="public"/>
-        <method access="public"/>
-        <constructor access="public"/>
-      </keep>
-<!--      -libraryjars "${obfuscateDeps}"
+						<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>
+				</proguard>
+				<delete file="in.jar"/>
+			</target>
 
-	<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
-		<taskdef name="castor-srcgen"
+			<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"
+				<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" 
@@ -468,7 +549,7 @@
 						verbose="true"
 						properties="${schemaDir}/jalview.properties"
 		/>
-		<castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
+				<castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd"
 			      todir="${sourceDir}"
 			      package="jalview.schemabinding.version2"
 			      warnings="false" 
@@ -476,7 +557,7 @@
 						verbose="true"
 						properties="${schemaDir}/jalview.properties"
 		/>
-		<castor-srcgen file="${schemaDir}/jalview.xsd"
+				<castor-srcgen file="${schemaDir}/jalview.xsd"
 			      todir="${sourceDir}"
 			      package="jalview.schemabinding.version2"
 			      warnings="false" 
@@ -485,23 +566,23 @@
 						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"
+				<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="${schemaDir}/JalviewUserColours.xsd"
+		/>
+				<castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
 			      todir="${sourceDir}"
 			      package="jalview.binding"
 			      warnings="false" 
@@ -509,7 +590,7 @@
 						verbose="true"
 						properties="${schemaDir}/jalview.nodesc.properties"
 		/>
-		<castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
+				<castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
 			      todir="${sourceDir}"
 			      package="jalview.binding"
 			      warnings="false" 
@@ -517,34 +598,35 @@
 						verbose="true"
 						properties="${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>
+			</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}/**/*"/>
+						<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}/**/*"/>
+					</tarfileset>
+				</tar>
+			</target>
+		</project>