jnlp amsa extension and donotobfuscate property conditional for jalviewLite build

diff --git a/build.xml b/build.xml
index c1730a9..ae129ee 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -70,8 +70,12 @@
                <property name="outputDir" value="classes" />
                <property name="packageDir" value="dist" />
                <property name="outputJar" value="jalview.jar" />
-                <!-- Jalview Applet JMol Jar Dependency -->
-                <property name="jmolJar" value="Jmol-11.0.2.jar" />
+         <!-- Jalview Applet JMol Jar Dependency -->
+    <property name="jmolJar" value="Jmol-11.0.2.jar" />
+               <property name="jalviewLiteJar" value="jalviewApplet.jar"/>
+               <!-- switch to indicate if we should obfuscate jalviewLite -->
+               <!--<property name="donotobfuscate" value="true"/> -->
+                               
                <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
                <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
                <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
@@ -222,6 +226,7 @@
         <association mime-type="application-x/ext-file" extensions="pfam"/>
         <association mime-type="application-x/ext-file" extensions="aln"/>
         <association mime-type="application-x/ext-file" extensions="pir"/>
+        <association mime-type="application-x/ext-file" extensions="amsa"/>
        -->
                        </information>
                        <resources>
@@ -381,16 +386,23 @@
         </fileset>
       </jar>
   </target>
-
-  <target name="obfuscate" depends="packageApplet">
-    <path id="obfuscateDeps.path">
+  <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
+  </target>
+       <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">    
+       <copy file="in.jar" tofile="${jalviewLiteJar}" />       
+    <delete file="in.jar"/>
+  </target>
+       <target name="-obfuscatereally" unless="donotobfuscate">
+    
+       <path id="obfuscateDeps.path">
     <pathelement location="${applet.jre.tools}"/>
     <pathelement location="lib/${jmolJar}"/>
     </path>
     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+       
     <proguard>
       <injar file="in.jar"/>
-      <outjar file="jalviewApplet.jar"/>
+      <outjar file="${jalviewLiteJar}"/>
       <libraryjar refid="obfuscateDeps.path"/>
       <keep access="public" type="class"
       name="jalview.bin.JalviewLite">
@@ -402,9 +414,8 @@
       -injars      in.jar
       -outjars     jalviewApplet.jar
       -keep public class jalview.bin.JalviewLite
-       { public * ; }
-       -->
-    </proguard>
+       { public * ; } -->
+      </proguard>
     <delete file="in.jar"/>
   </target>