X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=ae3dcec6f234886adf94e4beb9334db66452d2f1;hb=9adeaab28df6873e67ebe42e1ccd3a87cf6507af;hp=d28bccadc7c7440562a9203dd78543f21ce6292a;hpb=312d41dad6d0609aee824990e41cab6e5fc4b5f6;p=jalview.git

diff --git a/build.xml b/build.xml
index d28bcca..ae3dcec 100755
--- a/build.xml
+++ b/build.xml
@@ -1,20 +1,53 @@
 <?xml version="1.0"?>
-  <project name="jalviewX" default="build" basedir=".">
-<!-- we use jalopy to format our sources -->
-<taskdef name="jalopy"
+<!--
+   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+   * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+   * 
+   * 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/>.
+-->
+<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>
-
-
-    <!-- utils is a class path to additional utilities needed for
+		<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
@@ -27,183 +60,185 @@
 
 -->
 
-    <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>
-
-      <property name="JALVIEW_VERSION" value="2.03"/>
-      <property name="" value=""/>
-      <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" />
-      <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="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
-        <property name="WSInterf" value="MsaWS" />
-      <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
-      <property name="wsdl.Namespace" value="vamsas" />
-      <property name="wsdl.ClientNS" value="ext.vamsas" />
-
-      <path id="build.classpath">
-        <fileset dir="utils">
-          <include name="*.jar"/>
-          <include name="**/*.jar"/>
-        </fileset>
-        <fileset dir="${libDir}">
-          <include name="*.jar"/>
-          <include name="**/*.jar"/>
-        </fileset>
-<!--        <fileset dir="old_lib_signed">
-<include name="lib_axis.jar"/>
-
-        </fileset>-->
-      </path>
-      <!-->    <uptodate property="help.uptodate"
-      targetfile="${helpDir}/helpIndex.xml">
-      <srcfiles
-                 dir="${helpDir}"
-                 includes="**/*.html" />
-               </uptodate>
-      -->
-    </target>
-
-
-    <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
-    <target name="buildPropertiesFile" depends="init">
-      <tstamp prefix="build">
-        <format property="date" pattern="dd MMMM yyyy hh.mm aa"/>
-      </tstamp>
-      <properties file="${outputDir}/.build_properties">
-        <header>
+		<!-- 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="JmolApplet-12.0.6.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="${java118.home}">
+				<include name="lib/classes.zip"/>
+			</fileset>
+			<pathelement location="appletlib/${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="${resourceDir}">
-          <include name="**/*.*"/>
-        </fileset>
-      </copy>
-    </target>
-
-    <target name="build" depends="prepare">
-      <!-- not efficient yet. -->
-      <javac source="1.4" target="1.4"
+			<property name="VERSION" value="${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="${resourceDir}">
+				<include name="**/*.*"/>
+			</fileset>
+		</copy>
+	</target>
+
+	<target name="build" depends="prepare">
+		<!-- not efficient yet. -->
+		<javac source="1.5" target="1.5"
         srcdir ="${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"
+			<exclude name="jalview/*applet*"/>
+			<exclude name="com/stevesoft/**"/>
+		</javac>
+	</target>
+	<target name="buildindices" depends="init, prepare"
     unless="help.uptodate">
-    <java
+		<java
       classname="com.sun.java.help.search.Indexer"
       classpathref="build.classpath"
       fork="true"
       dir="${outputDir}/${helpDir}"
       >
-      <arg line="html"/>
-    </java>
-    </target>
-
-    <target name="makejars" depends="build, buildPropertiesFile, buildindices">
-      <!-- make the package jar -->
-      <mkdir dir="${packageDir}"/>
-
-      <jar destfile="${packageDir}/${outputJar}">
-        <fileset dir="${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>
-<!-- the default keystore details might need to be edited here -->
-      <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="${WebStartLocation}">
-      <information>
-        <title>Jalview</title>
-        <vendor>The Barton Group</vendor>
-        <homepage href="http://www.jalview.org"/>
-        <description>Jalview Multiple Alignment Editor</description>
-        <description kind="short">Jalview</description>
-        <icon href="logo_big.gif"/>
-        <offline_allowed/>
-	<!--
+			<arg line="html"/>
+		</java>
+	</target>
+
+	<target name="makefulldist" depends="makedist">
+		<!-- the default keystore details might need to be edited here -->
+		<signjar storepass="${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"/>
@@ -212,41 +247,136 @@
         <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"/>
-            <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 ${run.classpath} jalview.bin.Jalview
+			</information>
+			<resources>
+				<j2se version="1.5+" initial_heap_size="10M"/>
+				<fileset dir="${packageDir}">
+					<include name="jalview.jar" />
+				</fileset>
+				<fileset dir="${packageDir}">
+					<include name="*.jar" />
+					<include name="*_*.jar" />
+					<exclude name="jalview.jar" />
+				</fileset>
+				<property name="jalview.version" value="${JALVIEW_VERSION}" />
+			</resources>
+			<application_desc main_class="jalview.bin.Jalview">
+			</application_desc>
+			<security>
+				<all_permissions />
+			</security>
+		</jnlp>
+		<!-- 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 ${run.classpath} jalview.bin.Jalview
       </echo>
-    </target>
-
-    <target name="buildextclients" depends="init">
-<!-- Currently, this doesn't happen automatically.
+			</target>
+
+			<target name="buildextclients" depends="init">
+				<input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
+      validargs="Y,y,n,N" defaultvalue="N"
+      addproperty="doextbuild.response"/>
+				<condition property="dontextbuild">
+					<equals arg1="n" arg2="${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
@@ -256,18 +386,17 @@
      might be using.
 
 -->
-      <path id="axisbuild">
-        <!--        <path refid="axis.classpath"/> -->
-        <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}"
@@ -277,66 +406,219 @@
       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="${wsdl.ClientNS}"/>
-        </mappingSet>
-    </axis-wsdl2java>
-
-  </target>
-  <target name="package" depends="init, build">
-
-  </target>
-  <!-- jalopy code reformatter -->
-  <target name="sourcescrub" depends="init,build">
-    <jalopy destdir="jsrc" classpathref="run.classpath"
+					</mappingSet>
+				</axis-wsdl2java>
+			</target>
+
+			<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+				<!-- make the package jar -->
+				<mkdir dir="${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>
-
-
-
-  <!-- Compile, package and obfuscate Jalview Applet -->
-  <target name="makeApplet" depends="obfuscate"/>
-
-  <target name="compileApplet" depends="init,clean">
-    <mkdir dir="${outputDir}"/>
-    <javac source="1.2" target="1.1" srcdir="${sourceDir}" destdir="${outputDir}"
-       includes="jalview/analysis/**,jalview/appletgui/**,jalview/datamodel/**jalview/jbappletgui/**,jalview/math/**,jalview/schemes/**"
-       excludes="ext/**,MCview/**,org/**,vamsas/**"/>
-  </target>
-
-  <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
-  <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
-       <jar destfile="in.jar">
-        <fileset dir="${outputDir}">
-          <include name="com/**"/>
-          <include name="jalview/**"/>
-          <include name=".build_properties"/>
-          <include name="images/idwidth.gif"/>
-        </fileset>
-      </jar>
-  </target>
-
-  <target name="obfuscate" depends="packageApplet">
-    <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
-    <proguard>
-      -libraryjars "${java.home}/lib/rt.jar"
+					<fileset dir="${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="${outputDir}"/>
+				<javac source="1.2"
+    target="1.1"
+    srcdir="${sourceDir}" 
+    destdir="${outputDir}"
+   	debug="${javac.debug}"
+    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="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 "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
       -keep public class jalview.bin.JalviewLite
-    </proguard>
-    <delete file="in.jar"/>
-  </target>
-
-
-</project>
+       { public * ; } -->
+				</proguard>
+				<delete file="in.jar"/>
+			</target>
+
+			<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
+				<taskdef name="castor-srcgen"
+			  classname="org.castor.anttask.CastorCodeGenTask"
+		      classpathref="build.classpath" />
+				<delete>
+					<fileset dir="${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="${helpDir}/**/*"/>
+						<include name="appletlib/${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>