X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=ba538c206da91312ac17d748d21793fadcf28b72;hb=d5538cea7610ca0658449f0bcdb8a7063c3c90fe;hp=0226383a27c2bf0072938238e2faac5a10e1c022;hpb=56d4c1b68866f75613556f7f93da4eb8ce463f42;p=jalview.git

diff --git a/build.xml b/build.xml
index 0226383..ba538c2 100755
--- a/build.xml
+++ b/build.xml
@@ -1,35 +1,53 @@
 <?xml version="1.0"?>
-  <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."/>
-   </target>
-
-
-    <!-- utils is a class path to additional utilities needed for
-    building docs, jars and webstart stuff -->
-
 <!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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
+    building docs, jars and webstart stuff -->
+	<!--
         Userdefined build property defaults
 
         wsdl.server list (plus namespace mapping info ???)  - also want
@@ -42,210 +60,318 @@
 
 -->
 
-    <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="2.2"/>
-      <!-- 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="outputDir" value="classes" />
-      <property name="packageDir" value="dist" />
-      <property name="outputJar" value="jalview.jar" />
-      <!-- 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="${libDir}">
-          <include name="*.jar"/>
-          <include name="**/*.jar"/>
-        </fileset>
+	<target name="init">
+		<path id="axis.classpath">
+			<!-->
+			<fileset dir="/usr/local/axis/lib">
+				<include name="**/*.jar" />
+			</fileset>
+			<fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
+				<include name="**/*.jar"/>
+				<include name="*.jar"/>
+			</fileset> -->
       </path>
-    </target>
-
-
-    <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
-    <target name="buildPropertiesFile" depends="init">
-      <tstamp prefix="build">
-        <format property="date" pattern="dd MMMM yyyy"/>
-      </tstamp>
-      <properties file="${outputDir}/.build_properties">
-        <header>
+		<!-- Jalview 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 -->
+    <property name="application.codebase" value="*.jalview.org" />
+    <!-- and allowing the applet to be deployed from any URL -->
+    <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="${java.home}/lib">
+				<include name="plugin.jar"/>
+			</fileset>
+			<fileset dir="appletlib">
+				<!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
+				-->
+				<include name="${jmolJar}" />
+			</fileset>
+
+		</path>
+		<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
+		<!-- The Location of the java 1.1.8 jdk -->
+		<!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
+		-->
+		<property name="java118.home" value="${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>
+
+
+	<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="${outputDir}"
-      classpathref="build.classpath">
-      <exclude name="jalview/*applet*"/>
-       <exclude name="com/stevesoft/**"/>
-      </javac>
-    </target>
-    <target name="buildindices" depends="init, prepare"
-    unless="help.uptodate">
-    <java
-      classname="com.sun.java.help.search.Indexer"
-      classpathref="build.classpath"
-      fork="true"
-      dir="${outputDir}/${helpDir}"
-      >
-      <arg line="html"/>
-    </java>
-    </target>
-
-    <target name="makefulldist" depends="makedist">
- <!-- the default keystore details might need to be edited here -->
-      <signjar
-      storepass="alignmentisfun"
-      keypass="alignmentisfun"
-      keystore="keys/.keystore"
-      alias="jalview"
-      lazy="false"
-      verbose="false"
-      >
-
-      <fileset dir="${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/>
-	<!--
-	<association mime-type="application-x/ext-file" extensions="fa"/>
+			<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>
+    </jar>
+  	
+  	<mkdir dir="${packageDir}/JNLP-INF"/>
+    <antcall target="writejnlpf">
+       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+       <param name="inih" value="*" />
+       <param name="maxh" value="*"/>
+    </antcall>
+          	
+  	<jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+				<fileset dir="${packageDir}">
+  	      	<include name="JNLP-INF"/>
+				</fileset>
+  	</jar>
+    
+  	<antcall target="writejnlpf">
+  		<param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
+  		<param name="inih" value="10M" />
+  	  <param name="maxh" value="256M"/>
+  	</antcall>
+  	
+  	<antcall target="writejnlpf">
+  	  <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
+  	  <param name="inih" value="128M" />
+  		<param name="maxh" value="512M"/>
+  	</antcall>
+  	    
+  	<antcall target="writejnlpf">
+  	  <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
+  	  <param name="inih" value="256M" />
+  	  <param name="maxh" value="1024M"/>
+  	</antcall>
+  	
+			<!-- finally, need to postprocess to add in associations at end of 'information' element 
+			
+			<xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
+		
+		</xslt>
+			
+			
+			-->
+					<!--
+				<association mime-type="application-x/ext-file" extensions="fa"/>
         <association mime-type="application-x/ext-file" extensions="fasta"/>
+        <association mime-type="application-x/ext-file" extensions="mfa"/>
         <association mime-type="application-x/ext-file" extensions="fastq"/>
         <association mime-type="application-x/ext-file" extensions="blc"/>
         <association mime-type="application-x/ext-file" extensions="msf"/>
         <association mime-type="application-x/ext-file" extensions="pfam"/>
         <association mime-type="application-x/ext-file" extensions="aln"/>
         <association mime-type="application-x/ext-file" extensions="pir"/>
-	-->
-       </information>
-        <resources>
-          <j2se version="1.4+"/>
-          <fileset dir="${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="${libDir}/*.jar"/>
+        <association mime-type="application-x/ext-file" extensions="amsa"/>
+        <association mime-type="application-x/ext-file" extensions="stk"/>
+        <association mime-type="application-x/ext-file" extensions="jar"/>-->
+    <!-- and sign the jars -->
+    <!-- the default keystore details might need to be edited here -->
+    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
+        <fileset dir="${packageDir}">
+          <include name="*.jar" />
         </fileset>
-      </path>
-      <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
-
-      <echo>java -classpath ${run.classpath} jalview.bin.Jalview
+    </signjar>
+	</target>
+
+	<target name="runenv" depends="init">
+		<path id="run.classpath">
+			<pathelement location="${outputDir}" />
+			<fileset dir="${outputDir}">
+				<include name="${libDir}/*.jar" />
+			</fileset>
+		</path>
+		<pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
+
+		<echo>java -classpath ${run.classpath} jalview.bin.Jalview
       </echo>
-    </target>
-
-    <target name="buildextclients" depends="init">
-      <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
-      validargs="Y,y,n,N" defaultvalue="N"
-      addproperty="doextbuild.response"/>
-      <condition property="dontextbuild">
-        <equals arg1="n" arg2="${doextbuild.response}"/>
-      </condition>
-      <condition property="dontextbuild">
-        <equals arg1="N" arg2="${doextbuild.response}"/>
-      </condition>
-      <fail if="dontextbuild">
+	</target>
+  <target name="writejnlpf">
+  	<presetdef name="jnlpf">
+  	    <jnlp codebase="${WebStartLocation}">
+  	      <information>
+  	        <title>Jalview</title>
+  	        <vendor>The Barton Group</vendor>
+  	        <homepage href="http://www.jalview.org" />
+  	        <description>Jalview Multiple Alignment Editor</description>
+  	        <description kind="short">Jalview</description>
+  	        <icon href="${WebStartImage}" />
+  	        <offline_allowed />
+  	      </information>
+  	      <resources>
+  	        <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+  	        <fileset dir="${packageDir}">
+  	          <include name="jalview.jar" />
+  	        </fileset>
+  	        <fileset dir="${packageDir}">
+  	          <include name="*.jar" />
+  	          <include name="*_*.jar" />
+  	          <exclude name="jalview.jar" />
+  	        </fileset>
+  	        <property name="jalview.version" value="${JALVIEW_VERSION}" />
+  	      </resources>
+  	      <application_desc main_class="jalview.bin.Jalview">
+  	      </application_desc>
+  	      <security>
+  	        <all_permissions />
+  	      </security>
+  	    </jnlp>
+  	    </presetdef>
+
+  	    <jnlpf toFile="${jnlpFile}"/>
+  </target>
+	<target name="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
@@ -255,116 +381,333 @@
      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}">
+		<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" />
+		<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" />
+		<!-- 
+		now build the jalview.binding package with the old schema set
+		-->
+		<delete>
+			<fileset dir="${sourceDir}/jalview/binding/">
+				<include name="**" />
+			</fileset>
+		</delete>
+		<castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+		<castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+		<castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+	</target>
+	<target name="sourcedist" description="create jalview source distribution" depends="init">
+		<delete file="${source.dist.name}" />
+		<tar destfile="${source.dist.name}" compression="gzip">
+			<tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+				<include name="LICENSE" />
+				<include name="README" />
+				<include name="build.xml" />
+				<include name="jalview-jalopy.xml" />
+				<include name="JalviewApplet.jpx" />
+				<include name="JalviewX.jpx" />
+				<include name="nbbuild.xml"/>
+				<include name="nbproject/genfiles.properties"/>
+        <include name="nbproject/project.properties"/>
+        <include name="nbproject/project.xml"/>
+				<include name="${sourceDir}/*.java" />
+				<include name="${sourceDir}/**/*.java" />
+				<include name="${sourceDir}/**/*.cdr" />
+				<include name="${libDir}/**/*" />
+				<include name="${resourceDir}/**/*" />
+				<include name="${helpDir}/**/*" />
+				<include name="appletlib/${jmolJar}" />
+				<exclude name="**/*locales" />
+				<exclude name="*locales/**" />
+				<exclude name="utils/InstallAnywhere/**Build.iap_xml" />
+				<exclude name="utils/InstallAnywhere/**Build*/**" />
+				<exclude name="utils/InstallAnywhere/**Build*/**" />
+				<exclude name="utils/InstallAnywhere/**locale*" />
+				<exclude name="utils/InstallAnywhere/**locale*/**" />
+				<include name="${schemaDir}/**/*" />
+				<include name="utils/**/*" />
+				<include name="${docDir}/**/*" />
+				<include name="examples/**/*" />
+			</tarfileset>
+		</tar>
+	</target>
+	<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
+	  <copy todir="${packageDir}/examples">
+	  <fileset dir="examples">
+	  	<include name="**/*"/>
+	  	<include name="javascript/*"/>
+      <include name="jmol/*"/>
+	  </fileset>
+	  	<fileset dir=".">
+        <include name="${jalviewLiteJar}" />
+	  		</fileset>
+	  	<fileset dir="appletlib">
+	  	      <include name="**/*"/>
+	  	        </fileset>
+	  </copy>
+	    <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+	    <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
+	    	<manifest>
+	        <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
+	        <!--          <attribute name="Permissions" value="sandbox" /> -->
+	        <!--<attribute name="Trusted-Lib" value="true" /> -->
+	        <attribute name="Codebase" value="${applet.codebase}"/>
+	        <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+	    	  </manifest>
+	    	</jar>
+    <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+      <fileset dir="${packageDir}/examples">
+        <include name="*.jar" />
+      </fileset>
+    </signjar>
+    <presetdef name="ap_applet.jar">
+      <!-- build a signed applet with 'all-permissions' - 
+			  Needs 'param name="permissions' value="all-permissions"' in applet tag
+			  JalviewLite+JmolApplet linked sequence/structure fails
+			  Mixed code warnings are raised
+			  -->
+      <jar update="true" index="true">
         <manifest>
-             <attribute name="Main-Class" value="jalview.bin.Jalview"/>
+          <attribute name="Application-Name" value="JalviewLite" />
+          <attribute name="Permissions" value="all-permissions" />
+          <attribute name="Codebase" value="${applet.codebase}" />
+          <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+          <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
         </manifest>
-        <fileset dir="${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"/>
-  <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
-       <jar destfile="in.jar">
+    </presetdef>
+    <presetdef name="applet.jar">
+      <!-- build signed applet with sandbox permissions -
+			  Needs 'param name="permissions' value="sandbox"' in applet tag
+			 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag 
+			-->
+
+      <jar update="true" index="true">
         <manifest>
-            <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
+          <attribute name="Application-Name" value="JalviewLite" />
+          <attribute name="Permissions" value="sandbox" />
+          <attribute name="Codebase" value="${applet.codebase}" />
+          <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+          <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
         </manifest>
-        <fileset dir="${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>
+    </presetdef>
+    <presetdef name="tl_applet.jar">
+      <!-- build signed applet with trusted library/trusted permissions -
+			        Needs 'param name="permissions' value="all-permissions"' in applet tag
+			       j1.7_45:
+			       No mixed code warnings raised 
+			       Jmol/JalviewLite sequence/structure example doesn't link structures
+			       Raises dialog asking user to allow page to control applet via LiveConnect javascript
+			       
+			      -->
+
+      <jar update="true" index="true">
+        <manifest>
+          <attribute name="Application-Name" value="JalviewLite" />
+          <attribute name="Permissions" value="all-permissions" />
+          <attribute name="Codebase" value="${applet.codebase}" />
+          <attribute name="Trusted-Only" value="true" />
+          <attribute name="Trusted-Library" value="true" />
+        </manifest>
+      </jar>
+    </presetdef>
+    <presetdef name="to_applet.jar">
+      <!-- not fully test variant (yet) -->
+      <jar update="true" index="true">
+        <manifest>
+          <attribute name="Application-Name" value="JalviewLite" />
+          <attribute name="Permissions" value="all-permissions" />
+          <attribute name="Codebase" value="${applet.codebase}" />
+          <attribute name="Trusted-Only" value="true" />
+        </manifest>
+      </jar>
+    </presetdef>
+    <!-- create differently privileged artefacts -->
+    <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
+    <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
+    <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+    <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
+    <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+    <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
+    <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+    <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
+    <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+    <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
+    <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
+    <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
+    <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
+    <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
+    <!-- finally, create manifest for original jars -->
+    <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+    <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
+
+    <!-- todo - write examples/downloads for alternate versions of the applet -->
+    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+
+      <fileset dir="${packageDir}/examples">
+        <exclude name="u_*.jar"/>
+        <include name="${jalviewLiteJar}" />
+        <include name="${jmolJar}" />
+        <include name="to_${jalviewLiteJar}" />
+        <include name="to_${jmolJar}" />
+        <include name="tl_${jalviewLiteJar}" />
+        <include name="tl_${jmolJar}" />
+        <include name="ap_${jalviewLiteJar}" />
+        <include name="ap_${jmolJar}" />
+      </fileset>
+    </signjar>
+    <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+    <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
   </target>
-
-  <target name="obfuscate" depends="packageApplet">
-    <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
-    <proguard>
-      -libraryjars "${java.home}/lib/rt.jar"
-      -injars      in.jar
-      -outjars     jalviewApplet.jar
-      -keep public class jalview.bin.JalviewLite
-       { public * ; }
-    </proguard>
-    <delete file="in.jar"/>
+  <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+    <javadoc destdir="${javadocDir}">
+      <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+      </packageset>
+    </javadoc>
   </target>
-
-
 </project>