From f298945f07518f90f3400bee0451417872321f54 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 4 Jun 2014 11:25:57 +0100
Subject: [PATCH] JAL-1514 - add jalview.org and dundee to explore if
 liveConnect permissions check is buggy in Java 8

---
 build.xml |  651 +++++++++++++++++++++++++++++++------------------------------
 1 file changed, 327 insertions(+), 324 deletions(-)

diff --git a/build.xml b/build.xml
index 0869a7f..d440331 100755
--- a/build.xml
+++ b/build.xml
@@ -100,7 +100,8 @@
     <!-- 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="*" />
+    <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
+    <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
     <property name="applet.caller-codebase" value="${applet.codebase}" />
 
     <!-- build directory configuration -->
@@ -293,7 +294,7 @@
 			
 			
 			-->
-					<!--
+    <!--
 				<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"/>
@@ -361,8 +362,10 @@
 
     <jnlpf toFile="${jnlpFile}"/>
     <replace file="${jnlpFile}">
-      <replacetoken><![CDATA[</information>]]></replacetoken>
-      <replacevalue><![CDATA[
+      <replacetoken>
+        <![CDATA[</information>]]></replacetoken>
+      <replacevalue>
+        <![CDATA[
         <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" />
@@ -376,20 +379,20 @@
         <association mime-type="application-x/ext-file" extensions="stk"/>
         <association mime-type="application-x/ext-file" extensions="jvp"/>
       </information>]]></replacevalue>
-    </replace>
-  </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">
+  </replace>
+</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
@@ -399,266 +402,266 @@
      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="${wsdl.ClientNS}" />
-      </mappingSet>
-    </axis-wsdl2java>
-  </target>
-
-  <target name="makedist" depends="build, buildPropertiesFile, buildindices">
-    <!-- make the package jar if not already existing -->
-    <mkdir dir="${packageDir}" />
-    <!-- clean dir if it already existed -->
-    <delete>
-      <fileset dir="${packageDir}">
-        <include name="*.jar"/>
-      </fileset>
-    </delete>
-    <jar destfile="${packageDir}/${outputJar}" index="true">
-      <manifest>
-        <attribute name="Main-Class" value="jalview.bin.Jalview" />
-        <attribute name="Permissions" value="all-permissions" />
-        <attribute name="Application-Name" value="Jalview Desktop" />
-        <attribute name="Codebase" value="${application.codebase}" />
-      </manifest>
-      <fileset dir="${outputDir}/">
-        <exclude name="cache*/**" />
-        <exclude name="*.jar" />
-        <exclude name="*.jar.*" />
-        <exclude name="**/*.jar" />
-        <exclude name="**/*.jar.*" />
-      </fileset>
-    </jar>
-
-    <copy toDir="${packageDir}" flatten="true">
-      <fileset dir="${outputDir}">
-        <include name="*.jar" />
-        <include name="**/*.jar" />
-      </fileset>
-    </copy>
-  </target>
-
-
-  <!-- jalopy code reformatter -->
-  <target name="sourcescrub" depends="init,build">
-    <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
-      <fileset dir="${sourceDir}">
-        <include name="*.java" />
-        <include name="**/*.java" />
-        <include name="**/**/*.java" />
-      </fileset>
-    </jalopy>
-  </target>
-
-
-
-  <!-- Compile, package and obfuscate Jalview Applet -->
-  <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
-
-  <target name="compileApplet" depends="init,clean">
-    <mkdir dir="${outputDir}" />
-    <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
+  <path id="axisbuild">
+    <path refid="build.classpath" />
+  </path>
+  <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
+  <move todir="./bak">
+    <fileset dir="${sourceDir}" id="client">
+      <include name="${wsdl.ClientNS}/*.*" />
+    </fileset>
+  </move>
+
+  <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
+    <mappingSet>
+      <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
+      <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
+    </mappingSet>
+  </axis-wsdl2java>
+</target>
+
+<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+  <!-- make the package jar if not already existing -->
+  <mkdir dir="${packageDir}" />
+  <!-- clean dir if it already existed -->
+  <delete>
+    <fileset dir="${packageDir}">
+      <include name="*.jar"/>
+    </fileset>
+  </delete>
+  <jar destfile="${packageDir}/${outputJar}" index="true">
+    <manifest>
+      <attribute name="Main-Class" value="jalview.bin.Jalview" />
+      <attribute name="Permissions" value="all-permissions" />
+      <attribute name="Application-Name" value="Jalview Desktop" />
+      <attribute name="Codebase" value="${application.codebase}" />
+    </manifest>
+    <fileset dir="${outputDir}/">
+      <exclude name="cache*/**" />
+      <exclude name="*.jar" />
+      <exclude name="*.jar.*" />
+      <exclude name="**/*.jar" />
+      <exclude name="**/*.jar.*" />
+    </fileset>
+  </jar>
+
+  <copy toDir="${packageDir}" flatten="true">
+    <fileset dir="${outputDir}">
+      <include name="*.jar" />
+      <include name="**/*.jar" />
+    </fileset>
+  </copy>
+</target>
+
+
+<!-- jalopy code reformatter -->
+<target name="sourcescrub" depends="init,build">
+  <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
+    <fileset dir="${sourceDir}">
+      <include name="*.java" />
+      <include name="**/*.java" />
+      <include name="**/**/*.java" />
+    </fileset>
+  </jalopy>
+</target>
+
+
+
+<!-- Compile, package and obfuscate Jalview Applet -->
+<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
+
+<target name="compileApplet" depends="init,clean">
+  <mkdir dir="${outputDir}" />
+  <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
 			classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 			excludes="ext/**,MCview/**,org/**,vamsas/**" />
-  </target>
-
-  <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
-    <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
-    <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
-    <copy todir="${outputDir}/lang">
-      <fileset dir="${resourceDir}/lang">
-        <include name="**.*"/>
-      </fileset>
-    </copy>
-    <jar destfile="in.jar" index="true">
-      <manifest>
-        <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
-        <attribute name="Application-Name" value="JalviewLite" />
-        <attribute name="Codebase" value="${applet.codebase}" />
-      </manifest>
-      <fileset dir="${outputDir}">
-        <include name="com/**" />
-        <include name="MCview/**" />
-        <include name="jalview/**" />
-        <include name=".build_properties" />
-        <include name="images/idwidth.gif" />
-        <include name="images/link.gif" />
-        <include name="lang/**" />
-      </fileset>
-    </jar>
-  </target>
-  <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
-  </target>
-  <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
-    <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
-    <delete file="in.jar" />
-  </target>
-  <target name="-obfuscatereally" unless="donotobfuscate">
-
-    <path id="obfuscateDeps.path">
-      <pathelement location="${applet.jre.tools}" />
-      <pathelement location="appletlib/${jmolJar}" />
-    </path>
-    <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
-
-    <proguard>
-      <injar file="in.jar" />
-      <outjar file="${jalviewLiteJar}" />
-      <libraryjar refid="obfuscateDeps.path" />
-      <dontwarn/>
-      <keep access="public" type="class" name="jalview.bin.JalviewLite">
-        <field access="public" />
-        <method access="public" />
-        <constructor access="public" />
-      </keep>
-      <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
-        <field access="public" />
-        <method access="public" />
-        <constructor access="public" />
-      </keep>
-      <!--      -libraryjars "${obfuscateDeps}"
+</target>
+
+<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+  <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
+  <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
+  <copy todir="${outputDir}/lang">
+    <fileset dir="${resourceDir}/lang">
+      <include name="**.*"/>
+    </fileset>
+  </copy>
+  <jar destfile="in.jar" index="true">
+    <manifest>
+      <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
+      <attribute name="Application-Name" value="JalviewLite" />
+      <attribute name="Codebase" value="${applet.codebase}" />
+    </manifest>
+    <fileset dir="${outputDir}">
+      <include name="com/**" />
+      <include name="MCview/**" />
+      <include name="jalview/**" />
+      <include name=".build_properties" />
+      <include name="images/idwidth.gif" />
+      <include name="images/link.gif" />
+      <include name="lang/**" />
+    </fileset>
+  </jar>
+</target>
+<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
+</target>
+<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+  <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
+  <delete file="in.jar" />
+</target>
+<target name="-obfuscatereally" unless="donotobfuscate">
+
+  <path id="obfuscateDeps.path">
+    <pathelement location="${applet.jre.tools}" />
+    <pathelement location="appletlib/${jmolJar}" />
+  </path>
+  <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+
+  <proguard>
+    <injar file="in.jar" />
+    <outjar file="${jalviewLiteJar}" />
+    <libraryjar refid="obfuscateDeps.path" />
+    <dontwarn/>
+    <keep access="public" type="class" name="jalview.bin.JalviewLite">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+    <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+    <!--      -libraryjars "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
       -keep public class jalview.bin.JalviewLite
        { public * ; } -->
-    </proguard>
-    <delete file="in.jar" />
-  </target>
-
-  <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
-    <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
-    <delete>
-      <fileset dir="${sourceDir}/jalview/schemabinding/version2">
-        <include name="*.java" />
-        <include name="descriptors/*.java" />
-      </fileset>
-    </delete>
-    <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-    <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-    <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-    <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-    <!-- 
+  </proguard>
+  <delete file="in.jar" />
+</target>
+
+<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
+  <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
+  <delete>
+    <fileset dir="${sourceDir}/jalview/schemabinding/version2">
+      <include name="*.java" />
+      <include name="descriptors/*.java" />
+    </fileset>
+  </delete>
+  <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+  <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+  <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+  <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
+  <!-- 
 		now build the jalview.binding package with the old schema set
 		-->
-    <delete>
-      <fileset dir="${sourceDir}/jalview/binding/">
-        <include name="**" />
-      </fileset>
-    </delete>
-    <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
-    <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
-    <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
-  </target>
-  <target name="sourcedist" description="create jalview source distribution" depends="init">
-    <delete file="${source.dist.name}" />
-    <tar destfile="${source.dist.name}" compression="gzip">
-      <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
-        <include name="LICENSE" />
-        <include name="README" />
-        <include name="build.xml" />
-        <include name="jalview-jalopy.xml" />
-        <include name="JalviewApplet.jpx" />
-        <include name="JalviewX.jpx" />
-        <include name="nbbuild.xml"/>
-        <include name="nbproject/genfiles.properties"/>
-        <include name="nbproject/project.properties"/>
-        <include name="nbproject/project.xml"/>
-        <include name="${sourceDir}/*.java" />
-        <include name="${sourceDir}/**/*.java" />
-        <include name="${sourceDir}/**/*.cdr" />
-        <include name="${libDir}/**/*" />
-        <include name="${resourceDir}/**/*" />
-        <include name="${helpDir}/**/*" />
-        <include name="appletlib/${jmolJar}" />
-        <exclude name="**/*locales" />
-        <exclude name="*locales/**" />
-        <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
-        <exclude name="utils/InstallAnywhere/**Build*/**" />
-        <exclude name="utils/InstallAnywhere/**Build*/**" />
-        <exclude name="utils/InstallAnywhere/**locale*" />
-        <exclude name="utils/InstallAnywhere/**locale*/**" />
-        <include name="${schemaDir}/**/*" />
-        <include name="utils/**/*" />
-        <include name="${docDir}/**/*" />
-        <include name="examples/**/*" />
-      </tarfileset>
-    </tar>
-  </target>
-  <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
-    <copy todir="${packageDir}/examples">
-      <fileset dir="examples">
-        <include name="**/*"/>
-        <include name="javascript/*"/>
-        <include name="jmol/*"/>
-      </fileset>
-      <fileset dir=".">
-        <include name="${jalviewLiteJar}" />
-      </fileset>
-      <fileset dir="appletlib">
-        <include name="**/*"/>
-      </fileset>
-    </copy>
-    <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
-    <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
-      <manifest>
-        <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
-        <!--          <attribute name="Permissions" value="sandbox" /> -->
-        <!--<attribute name="Trusted-Lib" value="true" /> -->
-        <attribute name="Codebase" value="${applet.codebase}"/>
-        <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
-      </manifest>
-    </jar>
-    <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
-      <fileset dir="${packageDir}/examples">
-        <include name="*.jar" />
-      </fileset>
-    </signjar>
-    <presetdef name="ap_applet.jar">
-      <!-- build a signed applet with 'all-permissions' - 
+  <delete>
+    <fileset dir="${sourceDir}/jalview/binding/">
+      <include name="**" />
+    </fileset>
+  </delete>
+  <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+  <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+  <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+</target>
+<target name="sourcedist" description="create jalview source distribution" depends="init">
+  <delete file="${source.dist.name}" />
+  <tar destfile="${source.dist.name}" compression="gzip">
+    <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+      <include name="LICENSE" />
+      <include name="README" />
+      <include name="build.xml" />
+      <include name="jalview-jalopy.xml" />
+      <include name="JalviewApplet.jpx" />
+      <include name="JalviewX.jpx" />
+      <include name="nbbuild.xml"/>
+      <include name="nbproject/genfiles.properties"/>
+      <include name="nbproject/project.properties"/>
+      <include name="nbproject/project.xml"/>
+      <include name="${sourceDir}/*.java" />
+      <include name="${sourceDir}/**/*.java" />
+      <include name="${sourceDir}/**/*.cdr" />
+      <include name="${libDir}/**/*" />
+      <include name="${resourceDir}/**/*" />
+      <include name="${helpDir}/**/*" />
+      <include name="appletlib/${jmolJar}" />
+      <exclude name="**/*locales" />
+      <exclude name="*locales/**" />
+      <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
+      <exclude name="utils/InstallAnywhere/**Build*/**" />
+      <exclude name="utils/InstallAnywhere/**Build*/**" />
+      <exclude name="utils/InstallAnywhere/**locale*" />
+      <exclude name="utils/InstallAnywhere/**locale*/**" />
+      <include name="${schemaDir}/**/*" />
+      <include name="utils/**/*" />
+      <include name="${docDir}/**/*" />
+      <include name="examples/**/*" />
+    </tarfileset>
+  </tar>
+</target>
+<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
+  <copy todir="${packageDir}/examples">
+    <fileset dir="examples">
+      <include name="**/*"/>
+      <include name="javascript/*"/>
+      <include name="jmol/*"/>
+    </fileset>
+    <fileset dir=".">
+      <include name="${jalviewLiteJar}" />
+    </fileset>
+    <fileset dir="appletlib">
+      <include name="**/*"/>
+    </fileset>
+  </copy>
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
+    <manifest>
+      <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
+      <!--          <attribute name="Permissions" value="sandbox" /> -->
+      <!--<attribute name="Trusted-Lib" value="true" /> -->
+      <attribute name="Codebase" value="${applet.codebase}"/>
+      <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+    </manifest>
+  </jar>
+  <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+    <fileset dir="${packageDir}/examples">
+      <include name="*.jar" />
+    </fileset>
+  </signjar>
+  <presetdef name="ap_applet.jar">
+    <!-- build a signed applet with 'all-permissions' - 
 			  Needs 'param name="permissions' value="all-permissions"' in applet tag
 			  JalviewLite+JmolApplet linked sequence/structure fails
 			  Mixed code warnings are raised
 			  -->
-      <jar update="true" index="true">
-        <manifest>
-          <attribute name="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="${applet.codebase}" />
-        </manifest>
-      </jar>
-    </presetdef>
-    <presetdef name="applet.jar">
-      <!-- build signed applet with sandbox permissions -
+    <jar update="true" index="true">
+      <manifest>
+        <attribute name="Application-Name" value="JalviewLite" />
+        <attribute name="Permissions" value="all-permissions" />
+        <attribute name="Codebase" value="${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="${applet.codebase}" />
-        </manifest>
-      </jar>
-    </presetdef>
-    <presetdef name="tl_applet.jar">
-      <!-- build signed applet with trusted library/trusted permissions -
+    <jar update="true" index="true">
+      <manifest>
+        <attribute name="Application-Name" value="JalviewLite" />
+        <attribute name="Permissions" value="sandbox" />
+        <attribute name="Codebase" value="${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 
@@ -667,68 +670,68 @@
 			       
 			      -->
 
-      <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>
+    <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>
-- 
1.7.10.2