X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=build.xml;h=8d27614d06f9602b7aca7fcb4b7f23bedc6c157e;hp=19b41e5b413b1ffc0905e5a1e7b8d11b7679c095;hb=refs%2Fheads%2Ffeatures%2FJAL-2388hiddencolumnschanges;hpb=d1d1ca77ce184928fc3b5a1a80e056f867fae73e

diff --git a/build.xml b/build.xml
index 19b41e5..8d27614 100755
--- a/build.xml
+++ b/build.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -19,7 +19,7 @@
 -->
 <project name="jalviewX" default="usage" basedir=".">
   <target name="help" depends="usage" />
-  <target name="usage">
+  <target name="usage" depends="init">
     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
     <echo message="Targets include:" />
     <echo message="usage - default target, displays this message" />
@@ -27,9 +27,14 @@
     <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="              this needs a keystore and key."/>
+    <echo message="              Add -Dtimestamp to timestamp signed jars"/>
+    <echo message="              -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
+    <echo message="              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="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
+    <echo message="      you can specify particular test groups as a list via -Dtestng-groups=" />
     <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" />
@@ -62,8 +67,12 @@
         <include name="*.jar"/>
       </fileset> -->
       </path>
+
     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
+
+    <property name="INSTALLATION" value="Source" />
+
     <!-- 2.4 (VAMSAS)" -->
     <!-- Include debugging information in javac true or false -->
     <property name="javac.debug" value="true" />
@@ -76,15 +85,29 @@
     <property name="jalview.key" value="jalview" />
     <!-- Key Password -->
     <property name="jalview.key.pass" value="alignmentisfun" />
+    <!-- time stamp server URL -->
+    <property name="jalview.tsaurl" value="" />
+    <!-- locally valid proxy for signing with external time server -->
+    <property name="proxyPort" value="80"/>
+    <property name="proxyHost" value="sqid"/>
+    <!-- key sign/digest algorithms -->
+    <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
+    <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
+
+    <!-- default TestNG groups to run -->
+    <property name="testng-groups" value="Functional" />
 
     <!-- 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"/>
+    <property name="WebStartImage" value="JalviewLogo_big.png" />
     <!-- J2SE version needed for webstart launch -->
     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
-    <property name="j2sev" value="1.7+"/>
+    <property name="j2sev" value="1.7+" />
+    <!-- Java Compilation settings - source and target javac version -->
+    <property name="javac.source" value="1.7" />
+    <property name="javac.target" value="1.7" />
 
     <!-- Permissions for running Java applets and applications. -->
     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
@@ -105,9 +128,15 @@
     <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="varnaJar" value="VARNAv3-91.jar" />
+    <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
+    <property name="varnaJar" value="VARNAv3-93.jar" />
+    <property name="jsoup" value="jsoup-1.8.1.jar" />
+    <property name="jsonSimple" value="json_simple-1.1.jar" />
+    <property name="javaJson" value="java-json.jar" />
     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
+    <property name="reportDir" value="test-reports" />
+    <property name="testDir" value="test" />
+    <property name="testOutputDir" value="tests" />
     <!-- switch to indicate if we should obfuscate jalviewLite -->
     <!-- <property name="donotobfuscate" value="true"/> -->
     <!-- switch to exclude associations from generated jnlp files -->
@@ -132,7 +161,7 @@
         <include name="**/*.jar" />
       </fileset>
       <fileset dir="${java.home}/lib">
-        <include name="plugin.jar"/>
+        <include name="plugin.jar" />
       </fileset>
       <fileset dir="appletlib">
         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
@@ -140,7 +169,10 @@
         <include name="${jmolJar}" />
         <include name="${varnaJar}" />
       </fileset>
-
+    </path>
+    <path id="test.classpath">
+      <pathelement path="${outputDir}" />
+      <path refid="build.classpath" />
     </path>
     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
     <!-- The Location of the java 1.1.8 jdk -->
@@ -149,7 +181,7 @@
     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 		-->
     <!-- jre for 1.4 version -->
-    <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
+    <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
 
     <!-- the classpath for building the 1.1 applet -->
     <path id="jalviewlite.deps">
@@ -157,13 +189,17 @@
         <include name="lib/classes.zip" />
       </fileset>
       <fileset dir="${java.home}/lib">
-        <include name="plugin.jar"/>
+        <include name="plugin.jar" />
       </fileset>
       <pathelement location="appletlib/${jmolJar}" />
       <pathelement location="lib/${varnaJar}" />
+      <pathelement location="appletlib/${jsoup}" />
+      <pathelement location="appletlib/${jsonSimple}" />
+      <pathelement location="appletlib/${javaJson}" />
+
     </path>
     <!-- default location for outputting javadoc -->
-    <property name="javadocDir" value="${packageDir}/javadoc"/>
+    <property name="javadocDir" value="${packageDir}/javadoc" />
   </target>
 
 
@@ -172,11 +208,22 @@
     <tstamp prefix="build">
       <format property="date" pattern="dd MMMM yyyy" />
     </tstamp>
+    <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
+      <arg value="rev-parse" />
+      <arg value="--short" />
+      <arg value="HEAD" />
+    </exec>
+    <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
+      <arg value="rev-parse" />
+      <arg value="--abbrev-ref" />
+      <arg value="HEAD" />
+    </exec>
     <properties file="${outputDir}/.build_properties">
       <header>
           ---Jalview Build Details---
         </header>
       <property name="VERSION" value="${JALVIEW_VERSION}" />
+      <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
       <property name="BUILD_DATE" value="${build.date}" />
     </properties>
   </target>
@@ -184,7 +231,7 @@
 
   <target name="clean" depends="init">
     <!-- not efficient yet. -->
-    <delete dir="${outputDir}" includes="*,**/*"/>
+    <delete dir="${outputDir}" includes="*,**/*" />
   </target>
 
   <target name="distclean" depends="init, clean">
@@ -221,22 +268,50 @@
 
   <target name="build" depends="prepare">
     <!-- not efficient yet. -->
-    <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
+    <javac source="${javac.source}" target="${javac.target}" srcdir="${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="testclean" depends="init">
+    <delete dir="${testOutputDir}" includes="*,**/*" />
+  </target>
+
+  <target name="prepareTests" depends="init,testclean">
+    <mkdir dir="${testOutputDir}" />
+  </target>
+
+  <target name="buildTests" depends="build,buildindices,prepareTests">
+    <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
+    </javac>
+  </target>
+
+  <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
+
+  <target name="testng" depends="buildTests">
+    <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
+      verbose="2">
+      <classpath>
+        <pathelement location="${testOutputDir}" />
+        <path refid="test.classpath" />
+      </classpath>
+      <classfileset dir="${testOutputDir}" includes="**/*.class" />
+    </testng>
+  </target>
+
   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
       <arg line="html" />
     </java>
   </target>
 
-  <target name="makefulldist" depends="makedist">
+  <target name="preparejnlp" depends="makedist">
     <copy todir="${packageDir}">
       <fileset dir="${resourceDir}/images">
-        <include name="${WebStartImage}"/>
+        <include name="${WebStartImage}" />
       </fileset>
     </copy>
 
@@ -249,35 +324,35 @@
       </fileset>
     </jar>
 
-    <mkdir dir="${packageDir}/JNLP-INF"/>
+    <mkdir dir="${packageDir}/JNLP-INF" />
     <antcall target="writejnlpf">
-      <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+      <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
       <param name="inih" value="*" />
-      <param name="maxh" value="*"/>
+      <param name="maxh" value="*" />
     </antcall>
 
     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
       <fileset dir="${packageDir}">
-        <include name="JNLP-INF"/>
+        <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
       </fileset>
     </jar>
 
     <antcall target="writejnlpf">
-      <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
+      <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
       <param name="inih" value="10M" />
-      <param name="maxh" value="256M"/>
+      <param name="maxh" value="256M" />
     </antcall>
 
     <antcall target="writejnlpf">
-      <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
+      <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
       <param name="inih" value="128M" />
-      <param name="maxh" value="512M"/>
+      <param name="maxh" value="512M" />
     </antcall>
 
     <antcall target="writejnlpf">
-      <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
+      <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
       <param name="inih" value="256M" />
-      <param name="maxh" value="1024M"/>
+      <param name="maxh" value="1024M" />
     </antcall>
 
     <!-- finally, need to postprocess to add in associations at end of 'information' element 
@@ -301,14 +376,28 @@
         <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">
+  </target>
+
+  <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
+    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
+      tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
       <fileset dir="${packageDir}">
         <include name="*.jar" />
       </fileset>
     </signjar>
   </target>
+  <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
+    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
+      <fileset dir="${packageDir}">
+        <include name="*.jar" />
+      </fileset>
+    </signjar>
+  </target>
+
+  <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
+    <!-- and sign the jars -->
+    <!-- the default keystore details might need to be edited here -->
+  </target>
 
   <target name="runenv" depends="init">
     <path id="run.classpath">
@@ -337,16 +426,21 @@
         </information>
         <resources>
           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+          <jar main="true" href="jalview.jar"/>
           <fileset dir="${packageDir}">
-            <include name="jalview.jar" />
-          </fileset>
-          <fileset dir="${packageDir}">
+            <exclude name="jalview.jar" />
             <include name="*.jar" />
             <include name="*_*.jar" />
-            <exclude name="jalview.jar" />
+            <exclude name="*jnilib.jar" />
           </fileset>
           <property name="jalview.version" value="${JALVIEW_VERSION}" />
         </resources>
+        <resources os="Mac OS X">
+          <fileset dir="${packageDir}">
+            <include name="*quaqua*.jnilib.jar" />
+          </fileset>
+        </resources>
+
         <application_desc main_class="jalview.bin.Jalview">
         </application_desc>
         <security>
@@ -355,12 +449,12 @@
       </jnlp>
     </presetdef>
 
-    <jnlpf toFile="${jnlpFile}"/>
+    <jnlpf toFile="${jnlpFile}" />
 
   </target>
 
   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
-    <echo message="Not adding JNLP File Associations"/>
+    <echo message="Not adding JNLP File Associations" />
   </target>
 
   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
@@ -383,7 +477,7 @@
         <association mime-type="application-x/ext-file" extensions="jvp"/>
       </information>]]></replacevalue>
   </replace>
-  <echo message="Added file associations to JNLP file"/>
+  <echo message="Added file associations to JNLP file" />
 </target>
 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 </target>
@@ -427,13 +521,13 @@
   </axis-wsdl2java>
 </target>
 
-<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+<target name="makedist" depends="build, buildPropertiesFile, linkcheck, 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"/>
+      <include name="*.jar" />
     </fileset>
   </delete>
   <jar destfile="${packageDir}/${outputJar}" index="true">
@@ -475,13 +569,11 @@
 
 
 <!-- Compile, package and obfuscate Jalview Applet -->
-<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
+<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/**,jalview/ext/paradise/**" />
+  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 </target>
 
 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
@@ -489,7 +581,7 @@
   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
   <copy todir="${outputDir}/lang">
     <fileset dir="${resourceDir}/lang">
-      <include name="**.*"/>
+      <include name="**.*" />
     </fileset>
   </copy>
   <jar destfile="in.jar" index="true">
@@ -520,14 +612,21 @@
   <path id="obfuscateDeps.path">
     <pathelement location="${applet.jre.tools}" />
     <pathelement location="appletlib/${jmolJar}" />
+    <pathelement location="lib/${varnaJar}" />
+    <pathelement location="appletlib/${jsoup}" />
+    <pathelement location="appletlib/${jsonSimple}" />
+    <pathelement location="appletlib/${javaJson}" />
+    <fileset dir="${java.home}/lib">
+      <include name="plugin.jar" />
+    </fileset>
   </path>
   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 
-  <proguard>
+  <proguard verbose="true" >
     <injar file="in.jar" />
     <outjar file="${jalviewLiteJar}" />
     <libraryjar refid="obfuscateDeps.path" />
-    <dontwarn/>
+    <dontwarn />
     <keep access="public" type="class" name="jalview.bin.JalviewLite">
       <field access="public" />
       <method access="public" />
@@ -538,6 +637,31 @@
       <method access="public" />
       <constructor access="public" />
     </keep>
+
+    <keep name="jalview.json.binding**">
+      <constructor/>
+      <method name="*"/>
+    </keep>
+
+    <keep access="public" type="class" name="MCview.PDBfile">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+
+    <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+
+    <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+
+
     <!--      -libraryjars "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
@@ -573,18 +697,23 @@
 </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">
+  <!-- temporary copy of source to update timestamps -->
+  <copy todir="_sourcedist">
+    <fileset dir=".">
+      <exclude name=".*" />
+      <exclude name="**/.*" />
+      <exclude name="*.class" />
+      <exclude name="**/*.class" />
       <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="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="${sourceDir}/**/*.cdr" />
@@ -592,49 +721,76 @@
       <include name="${resourceDir}/**/*" />
       <include name="${helpDir}/**/*" />
       <include name="appletlib/${jmolJar}" />
+      <include name="appletlib/${jsonSimple}" />
+      <include name="appletlib/${javaJson}" />
       <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/.build*.*/**" />
       <exclude name="utils/InstallAnywhere/**locale*" />
       <exclude name="utils/InstallAnywhere/**locale*/**" />
+      <exclude name="utils/InstallAnywhere/**locale*/**" />
       <include name="${schemaDir}/**/*" />
       <include name="utils/**/*" />
       <include name="${docDir}/**/*" />
       <include name="examples/**/*" />
+    </fileset>
+  </copy>
+
+  <tstamp prefix="build">
+    <format property="year" pattern="yyyy" />
+  </tstamp>
+  <!-- each replacetoken CDATA body must be on one line - 
+       otherwise the pattern doesn't match -->
+  <replace value="${JALVIEW_VERSION}">
+    <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
+    <fileset dir="_sourcedist">
+      <include name="**/*" />
+    </fileset>
+  </replace>
+  <replace dir="_sourcedist" value="${build.year}">
+    <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
+    <fileset dir="_sourcedist">
+      <include name="**/*" />
+    </fileset>
+  </replace>
+
+  <tar destfile="${source.dist.name}" compression="gzip">
+    <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
     </tarfileset>
   </tar>
+
+  <delete dir="_sourcedist" />
 </target>
-<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
+<target name="prepubapplet_1" depends="makeApplet">
   <copy todir="${packageDir}/examples">
     <fileset dir="examples">
-      <include name="**/*"/>
-      <include name="javascript/*"/>
-      <include name="jmol/*"/>
+      <include name="**/*" />
+      <include name="javascript/*" />
+      <include name="jmol/*" />
     </fileset>
     <fileset dir=".">
       <include name="${jalviewLiteJar}" />
     </fileset>
     <fileset dir="appletlib">
-      <include name="**/*"/>
+      <include name="**/*" />
     </fileset>
   </copy>
-  <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
     <manifest>
-      <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
+      <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
       <!--          <attribute name="Permissions" value="sandbox" /> -->
       <!--<attribute name="Trusted-Lib" value="true" /> -->
-      <attribute name="Codebase" value="${applet.codebase}"/>
-      <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+      <attribute name="Codebase" value="${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
@@ -700,40 +856,101 @@
   </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="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
-  <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
+  <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
+  <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
+  <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
+  <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
+  <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
+  <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
+  <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
   <!-- finally, create manifest for original jars -->
   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
+  <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
+  <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 
-  <!-- todo - write examples/downloads for alternate versions of the applet -->
+  <!-- todo - write examples/downloads for alternate versions of the applet 
+    probably don't need to do this now since we don't have alternate versions anymore !-->
+</target>
+<target name="-signapplet" depends="prepubapplet_1">
+  <fileset id="signappletjarset" dir="${packageDir}/examples">
+    <exclude name="u_*.jar" />
+    <include name="${jalviewLiteJar}" />
+    <include name="${jmolJar}" />
+    <include name="${javaJson}" />
+    <include name="${jsonSimple}" />
+    <include name="to_${jalviewLiteJar}" />
+    <include name="to_${jmolJar}" />
+    <include name="to_${javaJson}" />
+    <include name="to_${jsonSimple}" />
+    <include name="tl_${jalviewLiteJar}" />
+    <include name="tl_${jmolJar}" />
+    <include name="tl_${javaJson}" />
+    <include name="tl_${jsonSimple}" />
+    <include name="ap_${jalviewLiteJar}" />
+    <include name="ap_${jmolJar}" />
+    <include name="ap_${javaJson}" />
+    <include name="ap_${jsonSimple}" />
+  </fileset>
+</target>
+<target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+    <fileset refid="signappletjarset" />
+  </signjar>
+</target>
 
-    <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_${jmolJar}" />
-    </fileset>
+<target name="-signapplettsa" if="timestamp" depends="-signapplet">
+  <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
+    <fileset refid="signappletjarset" />
   </signjar>
+</target>
+
+<target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
+
+<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
+
   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+  <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
+  <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
+  <!-- finally, replace any launchApp servlet tags with a version specification -->
+  <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
+    <replacetoken>
+      <![CDATA[http://www.jalview.org/services/launchApp"]]>
+    </replacetoken>
+    <fileset dir="${packageDir}/examples">
+      <include name="**/*.html" />
+    </fileset>
+  </replace>
+  <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
+    <replacetoken>
+      <![CDATA[http://www.jalview.org/services/launchApp']]>
+    </replacetoken>
+    <fileset dir="${packageDir}/examples">
+      <include name="**/*.html" />
+    </fileset>
+  </replace>
+
 </target>
 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
   <javadoc destdir="${javadocDir}">
@@ -741,4 +958,11 @@
     </packageset>
   </javadoc>
 </target>
+<target name="linkcheck" depends="init,prepare">
+  <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
+  <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
+    <arg file="${helpDir}"/>
+    <arg value="-nointernet"/>
+  </java>
+</target>
 </project>