Merge branch 'JAL-957_jbake' into Release_2_8_Branch

diff --combined build.xml
index ad1b781,990cbe6..2e9fc8d
--- 1/build.xml
--- 2/build.xml
+++ b/build.xml
@@@ -238,13 -238,7 +238,7 @@@
    </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" sigalg="SHA1withRSA">
  
-       <fileset dir="${packageDir}">
-         <include name="*.jar" />
-       </fileset>
-     </signjar>
      <copy todir="${packageDir}">
        <fileset dir="${resourceDir}/images">
          <include name="${WebStartImage}" />
@@@ -253,93 -247,45 +247,45 @@@
  
      <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="${packageDir}/jalview.jnlp" codebase="${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="10M" />
-         <fileset dir="${packageDir}">
-           <include name="jalview.jar" />
-         </fileset>
-         <fileset dir="${packageDir}">
-           <include name="*.jar" />
-           <include name="*_*.jar" />
-           <exclude name="jalview.jar" />
-         </fileset>
-         <property name="jalview.version" value="${JALVIEW_VERSION}" />
-       </resources>
-       <application_desc main_class="jalview.bin.Jalview">
-       </application_desc>
-       <security>
-         <all_permissions />
-       </security>
-     </jnlp>
-     <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
-       <information>
-         <title>Jalview</title>
-         <vendor>The Barton Group</vendor>
-         <homepage href="http://www.jalview.org" />
-         <description>Jalview Multiple Alignment Editor</description>
-         <description kind="short">Jalview</description>
-         <icon href="${WebStartImage}" />
-         <offline_allowed />
-       </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="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
-       <information>
-         <title>Jalview</title>
-         <vendor>The Barton Group</vendor>
-         <homepage href="http://www.jalview.org" />
-         <description>Jalview Multiple Alignment Editor</description>
-         <description kind="short">Jalview</description>
-         <icon href="${WebStartImage}" />
-         <offline_allowed />
-       </information>
-       <resources>
-         <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
-         <fileset dir="${packageDir}">
-           <include name="jalview.jar" />
-         </fileset>
-         <fileset dir="${packageDir}">
-           <include name="*.jar" />
-           <include name="*_*.jar" />
-           <exclude name="jalview.jar" />
-         </fileset>
-         <property name="jalview.version" value="${JALVIEW_VERSION}" />
-       </resources>
-       <application_desc main_class="jalview.bin.Jalview">
-       </application_desc>
-       <security>
-         <all_permissions />
-       </security>
-     </jnlp>
-     <!-- finally, need to postprocess to add in associations at end of 'information' element 
+     <!-- create a dummy jar which will eventually contain the jnlp template -->
+     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+           <fileset dir="${packageDir}">
+             <include name="jalview.jar"/>
+           </fileset>
+     </jar>
+       
+       <mkdir dir="${packageDir}/JNLP-INF"/>
+     <antcall target="writejnlpf">
+        <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+        <param name="inih" value="*" />
+        <param name="maxh" value="*"/>
+     </antcall>
+               
+       <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+             <fileset dir="${packageDir}">
+               <include name="JNLP-INF"/>
+             </fileset>
+       </jar>
+     
+       <antcall target="writejnlpf">
+               <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
+               <param name="inih" value="10M" />
+         <param name="maxh" value="256M"/>
+       </antcall>
+       
+       <antcall target="writejnlpf">
+         <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
+         <param name="inih" value="128M" />
+               <param name="maxh" value="512M"/>
+       </antcall>
+           
+       <antcall target="writejnlpf">
+         <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
+         <param name="inih" value="256M" />
+         <param name="maxh" value="1024M"/>
+       </antcall>
+       
+       <!-- finally, need to postprocess to add in associations at end of 'information' element 
                        
                        <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
                
@@@ -350,7 -296,6 +296,7 @@@
      <!--
                                <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"/>
          <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"/>
@@@ -360,7 -305,13 +306,13 @@@
          <association mime-type="application-x/ext-file" extensions="amsa"/>
          <association mime-type="application-x/ext-file" extensions="stk"/>
          <association mime-type="application-x/ext-file" extensions="jar"/>-->
- 
+     <!-- and sign the jars -->
+     <!-- the default keystore details might need to be edited here -->
+     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
+         <fileset dir="${packageDir}">
+           <include name="*.jar" />
+         </fileset>
+     </signjar>
    </target>
  
    <target name="runenv" depends="init">
@@@ -375,7 -326,40 +327,40 @@@
      <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">