X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=3eae6af3fd4d087af6b75768379f134fa198aaae;hb=e1a4dac21b9e7fb59d123bf3fa4e0f4f594c7f76;hp=38298d2628d0c0bef2191b1907e69d9f137c0e1b;hpb=5fda1eb672af38a5fb8f638f3183dbd0d4a4e4f0;p=jalview.git

diff --git a/build.xml b/build.xml
index 38298d2..3eae6af 100755
--- a/build.xml
+++ b/build.xml
@@ -1,25 +1,24 @@
 <?xml version="1.0"?>
 <!--
-   * 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/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * 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">
+	<taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
 		<classpath>
 			<fileset dir="utils/jalopy/lib">
 				<include name="*.jar" />
@@ -27,21 +26,21 @@
 		</classpath>
 	</taskdef>
 
-	<target name="help" depends="usage"/>
+	<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"/>
+		<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>
 
 
@@ -72,36 +71,40 @@
 			</fileset> -->
       </path>
 		<!-- Jalview Version String displayed by application on startup and used to check for updates -->
-		<property name="JALVIEW_VERSION" value="DEVELOPMENT"/>
+		<property name="JALVIEW_VERSION" value="DEVELOPMENT" />
 		<!-- 2.4 (VAMSAS)" -->
 		<!-- Include debugging information in javac true or false -->
-		<property name="javac.debug" value="true"/>
+		<property name="javac.debug" value="true" />
 
 		<!-- JarSigner Key Store for Webstart Distribution -->
-		<property name="jalview.keystore" value="./keys/.keystore"/>
+		<property name="jalview.keystore" value="./keys/.keystore" />
 		<!-- Keystore Password -->
-		<property name="jalview.keystore.pass" value="alignmentisfun"/>
+		<property name="jalview.keystore.pass" value="alignmentisfun" />
 		<!-- Key Name -->
-		<property name="jalview.key" value="jalview"/>
+		<property name="jalview.key" value="jalview" />
 		<!-- Key Password -->
-		<property name="jalview.key.pass" value="alignmentisfun"/>
+		<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"/>
+		<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+"/>
 		<!-- 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="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"/>
+		<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"/> -->
 
@@ -116,104 +119,110 @@
 		<!-- the class path for building the application -->
 		<path id="build.classpath">
 			<fileset dir="utils">
-				<include name="*.jar"/>
-				<include name="**/*.jar"/>
+				<include name="*.jar" />
+				<include name="**/*.jar" />
 			</fileset>
 			<fileset dir="${libDir}">
-				<include name="*.jar"/>
-				<include name="**/*.jar"/>
+				<include name="*.jar" />
+				<include name="**/*.jar" />
+			</fileset>
+			<fileset dir="${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="${basedir}/jalview-src.tar.gz"/>
+		<property name="source.dist.name" value="${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"/>
+		<!--<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"/>
+				<include name="lib/classes.zip" />
+			</fileset>
+			<fileset dir="${java.home}/lib">
+				<include name="plugin.jar"/>
 			</fileset>
-			<pathelement location="appletlib/${jmolJar}"/>
+			<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"/>
+	<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"/>
+			<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="${build.date}"/>
+			<property name="VERSION" value="${JALVIEW_VERSION}" />
+			<property name="BUILD_DATE" value="${build.date}" />
 		</properties>
 	</target>
 
 
 	<target name="clean" depends="init">
 		<!-- not efficient yet. -->
-		<delete dir="${outputDir}"/>
+		<delete dir="${outputDir}" includes="*,**/*"/>
 	</target>
 
 	<target name="distclean" depends="init, clean">
 
-		<echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
+		<echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 		<delete>
 			<fileset dir=".">
-				<include name="${outputJar}"/>
-				<include name="#*#"/>
-				<include name="#*.*#"/>
-				<include name="**/#*#"/>
-				<include name="**/#*.*#"/>
-				<include name="*~"/>
-				<include name="*.*~"/>
-				<include name="**/*~"/>
-				<include name="**/*.*~"/>
+				<include name="${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="${outputDir}"/>
+		<mkdir dir="${outputDir}" />
 		<copy todir="${outputDir}">
 			<fileset dir=".">
-				<include name="${docDir}/**/*.*"/>
-				<include name="${helpDir}/**/*.*"/>
-				<include name="${libDir}/*.jar"/>
+				<include name="${docDir}/**/*.*" />
+				<include name="${helpDir}/**/*.*" />
+				<include name="${libDir}/*.jar" />
 			</fileset>
 			<fileset dir="${resourceDir}">
-				<include name="**/*.*"/>
+				<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="${javac.debug}"
-      classpathref="build.classpath">
-			<exclude name="jalview/*applet*"/>
-			<exclude name="com/stevesoft/**"/>
+		<javac source="1.5" target="1.5" srcdir="${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"/>
+	<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>
 
@@ -225,6 +234,12 @@
 				<include name="*.jar" />
 			</fileset>
 		</signjar>
+		<copy todir="${packageDir}">
+			<fileset dir="${resourceDir}/images">
+				<include name="${WebStartImage}"/>
+			</fileset>
+					</copy>
+		
 		<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 
 		<!--    codebase="http://www.jalview.org/jalview/webstart" -->
@@ -236,22 +251,39 @@
 				<homepage href="http://www.jalview.org" />
 				<description>Jalview Multiple Alignment Editor</description>
 				<description kind="short">Jalview</description>
-				<icon href="logo_big.gif" />
+				<icon href="${WebStartImage}" />
+				<offline_allowed/>
+			</information>
+			<resources>
+				<j2se version="${j2sev}" 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="${JALVIEW_VERSION}" />
+			</resources>
+			<application_desc main_class="jalview.bin.Jalview">
+			</application_desc>
+			<security>
+				<all_permissions />
+			</security>
+		</jnlp>		
+		<jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
+			<information>
+				<title>Jalview</title>
+				<vendor>The Barton Group</vendor>
+				<homepage href="http://www.jalview.org" />
+				<description>Jalview Multiple Alignment Editor</description>
+				<description kind="short">Jalview</description>
+				<icon href="${WebStartImage}" />
 				<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="10M"/>
+				<j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
 				<fileset dir="${packageDir}">
 					<include name="jalview.jar" />
 				</fileset>
@@ -268,115 +300,82 @@
 				<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="${WebStartLocation}">
-					<information>
-						<title>Jalview</title>
-						<vendor>The Barton Group</vendor>
-						<homepage href="http://www.jalview.org" />
-						<description>Jalview Multiple Alignment Editor</description>
-						<description kind="short">Jalview</description>
-						<icon href="logo_big.gif" />
-						<offline_allowed />
-						<!--
-			<association mime-type="application-x/ext-file" extensions="fa"/>
-		        <association mime-type="application-x/ext-file" extensions="fasta"/>
-		        <association mime-type="application-x/ext-file" extensions="fastq"/>
-		        <association mime-type="application-x/ext-file" extensions="blc"/>
-		        <association mime-type="application-x/ext-file" extensions="msf"/>
-		        <association mime-type="application-x/ext-file" extensions="pfam"/>
-		        <association mime-type="application-x/ext-file" extensions="aln"/>
-		        <association mime-type="application-x/ext-file" extensions="pir"/>
-		        <association mime-type="application-x/ext-file" extensions="amsa"/>
+		<jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
+			<information>
+				<title>Jalview</title>
+				<vendor>The Barton Group</vendor>
+				<homepage href="http://www.jalview.org" />
+				<description>Jalview Multiple Alignment Editor</description>
+				<description kind="short">Jalview</description>
+				<icon href="${WebStartImage}" />
+				<offline_allowed />
+			</information>
+			<resources>
+				<j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
+				<fileset dir="${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>
+			<!-- 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>
+			
+			
 			-->
-					</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 ${run.classpath} jalview.bin.Jalview
+					<!--
+				<association mime-type="application-x/ext-file" extensions="fa"/>
+        <association mime-type="application-x/ext-file" extensions="fasta"/>
+        <association mime-type="application-x/ext-file" extensions="fastq"/>
+        <association mime-type="application-x/ext-file" extensions="blc"/>
+        <association mime-type="application-x/ext-file" extensions="msf"/>
+        <association mime-type="application-x/ext-file" extensions="pfam"/>
+        <association mime-type="application-x/ext-file" extensions="aln"/>
+        <association mime-type="application-x/ext-file" extensions="pir"/>
+        <association mime-type="application-x/ext-file" extensions="amsa"/>
+        <association mime-type="application-x/ext-file" extensions="stk"/>
+        <association mime-type="application-x/ext-file" extensions="jar"/>-->
+	
+	</target>
+
+	<target name="runenv" depends="init">
+		<path id="run.classpath">
+			<pathelement location="${outputDir}" />
+			<fileset dir="${outputDir}">
+				<include name="${libDir}/*.jar" />
+			</fileset>
+		</path>
+		<pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
+
+		<echo>java -classpath ${run.classpath} jalview.bin.Jalview
       </echo>
-			</target>
-
-			<target name="buildextclients" depends="init">
-				<input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
-      validargs="Y,y,n,N" defaultvalue="N"
-      addproperty="doextbuild.response"/>
-				<condition property="dontextbuild">
-					<equals arg1="n" arg2="${doextbuild.response}"/>
-				</condition>
-				<condition property="dontextbuild">
-					<equals arg1="N" arg2="${doextbuild.response}"/>
-				</condition>
-				<fail if="dontextbuild">
+	</target>
+
+	<target name="buildextclients" depends="init">
+		<input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
+		<condition property="dontextbuild">
+			<equals arg1="n" arg2="${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
@@ -386,238 +385,211 @@
      might be using.
 
 -->
-				<path id="axisbuild">
-					<path refid="build.classpath"/>
-				</path>
-				<taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
-				<move todir="./bak">
-					<fileset dir="${sourceDir}" id="client">
-						<include name="${wsdl.ClientNS}/*.*"/>
-					</fileset>
-				</move>
-
-				<axis-wsdl2java
-      output="${sourceDir}"
-      verbose="true"
-      url="${wsdl.MsaWS2}"
-      serverside="false"
-      deployscope="Request"
-      debug="false"
-      helpergen="true"
-      all="true"
-      >
-					<mappingSet>
-						<mapping
-        namespace="${wsdl.Namespace}"
-        package="${wsdl.ClientNS}"
-        />
-						<mapping namespace="http://dataTypes.vamsas"
-        package="${wsdl.ClientNS}"/>
-					</mappingSet>
-				</axis-wsdl2java>
-			</target>
-
-			<target name="makedist" depends="build, buildPropertiesFile, buildindices">
-				<!-- make the package jar -->
-				<mkdir dir="${packageDir}"/>
-
-				<jar destfile="${packageDir}/${outputJar}">
-					<manifest>
-						<attribute name="Main-Class" value="jalview.bin.Jalview"/>
-					</manifest>
-					<fileset dir="${outputDir}/">
-						<exclude name="cache*/**"/>
-						<exclude name="*.jar" />
-						<exclude name="*.jar.*" />
-						<exclude name="**/*.jar" />
-						<exclude name="**/*.jar.*" />
-					</fileset>
-				</jar>
-
-				<copy toDir="${packageDir}" flatten="true">
-					<fileset dir="${outputDir}">
-						<include name="*.jar"/>
-						<include name="**/*.jar"/>
-					</fileset>
-				</copy>
-			</target>
-
-
-			<!-- jalopy code reformatter -->
-			<target name="sourcescrub" depends="init,build">
-				<jalopy destdir="jsrc" classpathref="run.classpath"
-      convention="jalview-jalopy.xml">
-					<fileset dir="${sourceDir}">
-						<include name="*.java"/>
-						<include name="**/*.java"/>
-						<include name="**/**/*.java"/>
-					</fileset>
-				</jalopy>
-			</target>
-
-
-
-			<!-- Compile, package and obfuscate Jalview Applet -->
-			<target name="makeApplet" depends="obfuscate"/>
-
-			<target name="compileApplet" depends="init,clean">
-				<mkdir dir="${outputDir}"/>
-				<javac source="1.2"
-    target="1.1"
-    srcdir="${sourceDir}" 
-    destdir="${outputDir}"
-   	debug="${javac.debug}"
-    classpath="lib/${jmolJar}"
-       includes="jalview/appletgui/**"
-       excludes="ext/**,MCview/**,org/**,vamsas/**"
-       />
-			</target>
-
-			<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
-				<copy file="${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"
-      name="jalview.bin.JalviewLite">
-						<field access="public"/>
-						<method access="public"/>
-						<constructor access="public"/>
-					</keep>
-					<!--      -libraryjars "${obfuscateDeps}"
+		<path id="axisbuild">
+			<path refid="build.classpath" />
+		</path>
+		<taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
+		<move todir="./bak">
+			<fileset dir="${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}">
+			<manifest>
+				<attribute name="Main-Class" value="jalview.bin.Jalview" />
+        <attribute name="Permissions" value="all-permissions" />
+        <!--<attribute name="Trusted-Lib" value="true" /> -->
+        <attribute name="Application-Name" value="Jalview Desktop"/>
+        <attribute name="Codebase" value="*"/>
+			</manifest>
+			<fileset dir="${outputDir}/">
+				<exclude name="cache*/**" />
+				<exclude name="*.jar" />
+				<exclude name="*.jar.*" />
+				<exclude name="**/*.jar" />
+				<exclude name="**/*.jar.*" />
+			</fileset>
+		</jar>
+
+		<copy toDir="${packageDir}" flatten="true">
+			<fileset dir="${outputDir}">
+				<include name="*.jar" />
+				<include name="**/*.jar" />
+			</fileset>
+		</copy>
+	</target>
+
+
+	<!-- jalopy code reformatter -->
+	<target name="sourcescrub" depends="init,build">
+		<jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
+			<fileset dir="${sourceDir}">
+				<include name="*.java" />
+				<include name="**/*.java" />
+				<include name="**/**/*.java" />
+			</fileset>
+		</jalopy>
+	</target>
+
+
+
+	<!-- Compile, package and obfuscate Jalview Applet -->
+	<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
+
+	<target name="compileApplet" depends="init,clean">
+		<mkdir dir="${outputDir}" />
+		<javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
+			classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
+			excludes="ext/**,MCview/**,org/**,vamsas/**" />
+	</target>
+
+	<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+		<copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
+		<copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
+		<jar destfile="in.jar">
+			<manifest>
+				<attribute name="Main-Class" value="jalview.bin.JalviewLite" />
+			</manifest>
+			<fileset dir="${outputDir}">
+				<include name="com/**" />
+				<include name="MCview/**" />
+				<include name="jalview/**" />
+				<include name=".build_properties" />
+				<include name="images/idwidth.gif" />
+				<include name="images/link.gif" />
+			</fileset>
+		</jar>
+	</target>
+	<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
+	</target>
+	<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+		<copy file="in.jar" tofile="${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}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
       -keep public class jalview.bin.JalviewLite
        { public * ; } -->
-				</proguard>
-				<delete file="in.jar"/>
-			</target>
-
-			<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
-				<taskdef name="castor-srcgen"
-			  classname="org.castor.anttask.CastorCodeGenTask"
-		      classpathref="build.classpath" />
-				<delete>
-					<fileset dir="${sourceDir}/jalview/schemabinding/version2">
-						<include name="*.java"/>
-						<include name="descriptors/*.java"/>
-					</fileset>
-				</delete>
-				<castor-srcgen file="${schemaDir}/vamsas.xsd"
-			      todir="${sourceDir}"
-			      package="jalview.schemabinding.version2"
-			      warnings="false" 
-				  	nodesc="false"
-						verbose="true"
-						properties="${schemaDir}/jalview.properties"
-		/>
-				<castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
-			      todir="${sourceDir}"
-			      package="jalview.schemabinding.version2"
-			      warnings="false" 
-				  	nodesc="false"
-						verbose="true"
-						properties="${schemaDir}/jalview.properties"
-		/>
-				<castor-srcgen file="${schemaDir}/jalview.xsd"
-			      todir="${sourceDir}"
-			      package="jalview.schemabinding.version2"
-			      warnings="false" 
-					  nodesc="false"
-						verbose="true"
-						properties="${schemaDir}/jalview.properties"
-			
-		/>
-				<!-- 
+		</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="${source.dist.name}" compression="gzip">
-					<tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
-						<include name="LICENSE"/>
-						<include name="README"/>
-						<include name="build.xml"/>
-						<include name="jalview-jalopy.xml"/>
-						<include name="JalviewApplet.jpx"/>
-						<include name="JalviewX.jpx"/>
-						<include name="${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="${docDir}/**/*"/>
-					</tarfileset>
-				</tar>
-			</target>
-		</project>
+		<delete>
+			<fileset dir="${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="jalviewApplet.jar"/>
+	  		</fileset>
+	  	<fileset dir="appletlib">
+	  	      <include name="**/*"/>
+	  	        </fileset>
+	  </copy>
+	  		
+	</target>
+	<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+	 <javadoc destdir="${javadocDir}">
+	 	<packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+	 	</packageset>
+	 	</javadoc>
+	</target>
+	
+</project>