X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=31419c8ad24a78cb7661b9923f8c4c523f6bf2c9;hb=8b985fad9a206fb678e8f84f65a1659c00e49d93;hp=6cfaf4e5de36fde1f3de79de25b578fd5f467cac;hpb=205a4ac63d5d8ffcf5cf8d3556b5aca94f6cce06;p=jalview.git

diff --git a/build.xml b/build.xml
index 6cfaf4e..31419c8 100755
--- a/build.xml
+++ b/build.xml
@@ -1,20 +1,21 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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 -->
@@ -85,11 +86,24 @@
 		<!-- 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+"/>
+<!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
+		<property name="j2sev" value="1.7+"/>
+
+    <!-- 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="${applet.codebase}" />
+
 		<!-- build directory configuration -->
 		<property name="libDir" value="lib" />
 		<property name="resourceDir" value="resources" />
@@ -101,7 +115,8 @@
 		<property name="packageDir" value="dist" />
 		<property name="outputJar" value="jalview.jar" />
 		<!-- Jalview Applet JMol Jar Dependency -->
-		<property name="jmolJar" value="JmolApplet-12.1.13.jar" />
+		<property name="jmolJar" value="JmolApplet-12.2.4.jar" />
+		<property name="varnaJar" value="VARNAv3-9.jar" />
 		<property name="jalviewLiteJar" value="jalviewApplet.jar" />
 		<!-- switch to indicate if we should obfuscate jalviewLite -->
 		<!--<property name="donotobfuscate" value="true"/> -->
@@ -131,6 +146,7 @@
 				<!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
 				-->
 				<include name="${jmolJar}" />
+				<include name="${varnaJar}" />
 			</fileset>
 
 		</path>
@@ -152,6 +168,8 @@
 				<include name="plugin.jar"/>
 			</fileset>
 			<pathelement location="appletlib/${jmolJar}" />
+      <pathelement location="lib/${varnaJar}" />
+
 		</path>
     <!-- default location for outputting javadoc -->
     <property name="javadocDir" value="${packageDir}/javadoc"/>
@@ -225,223 +243,64 @@
 	</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="${packageDir}">
-				<include name="*.jar" />
+		<copy todir="${packageDir}">
+			<fileset dir="${resourceDir}/images">
+				<include name="${WebStartImage}"/>
 			</fileset>
-		</signjar>
+					</copy>
+		
 		<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="${packageDir}/jalview_noa.jnlp" codebase="${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"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>-->
-			</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="${packageDir}/jalview.jnlp" codebase="${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"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
-			</information>
-			<resources>
-				<j2se version="${j2sev}" initial_heap_size="10M"/>
+    <!-- create a dummy jar which will eventually contain the jnlp template -->
+    <jar destfile="${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="${packageDir}">
-					<include name="*.jar" />
-					<include name="*_*.jar" />
-					<exclude name="jalview.jar" />
+  	      	<include name="JNLP-INF"/>
 				</fileset>
-				<property name="jalview.version" value="${JALVIEW_VERSION}" />
-			</resources>
-			<application_desc main_class="jalview.bin.Jalview">
-			</application_desc>
-			<security>
-				<all_permissions />
-			</security>
-		</jnlp>
+  	</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">
 		
-		<jnlp toFile="${packageDir}/jalview_noa_1G.jnlp" codebase="${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"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>-->
-			</information>
-			<resources>
-				<j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
-				<fileset dir="${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="${packageDir}/jalview_1G.jnlp" codebase="${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"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
-			</information>
-			<resources>
-				<j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
-				<fileset dir="${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="${packageDir}/jalview_noac_2G.jnlp" codebase="${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"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
+		</xslt>
+			
+			
 			-->
-			</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>
-		<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="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"/>
@@ -450,26 +309,14 @@
         <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"/>
-			</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>
-
+        <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>
+    </signjar>
 	</target>
 
 	<target name="runenv" depends="init">
@@ -484,7 +331,40 @@
 		<echo>java -classpath ${run.classpath} jalview.bin.Jalview
       </echo>
 	</target>
-
+  <target name="writejnlpf">
+  	<presetdef name="jnlpf">
+  	    <jnlp codebase="${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">
@@ -533,9 +413,12 @@
 				<include name="*.jar"/>
 			</fileset>
 		</delete>
-		<jar destfile="${packageDir}/${outputJar}">
+		<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*/**" />
@@ -575,15 +458,19 @@
 		<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/**" />
+			excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 	</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">
+		<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/**" />
@@ -592,6 +479,7 @@
 				<include name=".build_properties" />
 				<include name="images/idwidth.gif" />
 				<include name="images/link.gif" />
+				<include name="lang/**" />
 			</fileset>
 		</jar>
 	</target>
@@ -613,11 +501,17 @@
 			<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
@@ -694,19 +588,131 @@
       <include name="jmol/*"/>
 	  </fileset>
 	  	<fileset dir=".">
-	  	<include name="jalviewApplet.jar"/>
+        <include name="${jalviewLiteJar}" />
 	  		</fileset>
 	  	<fileset dir="appletlib">
 	  	      <include name="**/*"/>
 	  	        </fileset>
 	  </copy>
-	  		
-	</target>
-	<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
-	 <javadoc destdir="${javadocDir}">
-	 	<packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
-	 	</packageset>
-	 	</javadoc>
-	</target>
-	
+	    <jar update="true" index="true" jarfile="${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="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="${applet.codebase}" />
+        </manifest>
+      </jar>
+    </presetdef>
+    <presetdef name="applet.jar">
+      <!-- build signed applet with sandbox permissions -
+			  Needs 'param name="permissions' value="sandbox"' in applet tag
+			 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag 
+			-->
+
+      <jar update="true" index="true">
+        <manifest>
+          <attribute name="Application-Name" value="JalviewLite" />
+          <attribute name="Permissions" value="sandbox" />
+          <attribute name="Codebase" value="${applet.codebase}" />
+          <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+          <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
+        </manifest>
+      </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="sourcedoc" description="Create jalview source documentation pages" depends="init">
+    <javadoc destdir="${javadocDir}">
+      <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+      </packageset>
+    </javadoc>
+  </target>
 </project>