de-os-specificised some bits. Commented the file association entries

in jnlp for the moment.

diff --git a/build.xml b/build.xml
index 3c91a2f..dbed685 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -119,8 +119,13 @@
 
     <target name="build" depends="prepare">
       <!-- not efficient yet. -->
-      <javac source="1.4" target="1.4" srcdir="${sourceDir}" destdir="${outputDir}"
-      classpathref="build.classpath" />
+      <javac source="1.4" target="1.4"
+        srcdir ="${sourceDir}"
+        destdir="${outputDir}"
+      classpathref="build.classpath">
+      <exclude name="jalview/*applet*"/>
+       <exclude name="com/stevesoft/**"/>
+      </javac>
     </target>
     <target name="buildindices" depends="init, prepare"
     unless="help.uptodate">
@@ -180,7 +185,8 @@
         <description>Jalview Multiple Alignment Editor</description>
         <description kind="short">Jalview</description>
         <icon href="logo_big.gif"/>
-        <association mime-type="application-x/ext-file" extensions="fa"/>
+       <!--
+       <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"/>
@@ -188,7 +194,8 @@
         <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"/>
-      </information>
+       -->
+       </information>
         <resources>
           <j2se version="1.3+"/>
           <fileset dir="${packageDir}">
@@ -300,7 +307,7 @@
   </target>
 
   <target name="obfuscate" depends="packageApplet">
-    <taskdef resource="proguard/ant/task.properties" classpath="C:/JalviewX/utils/proguard.jar" />
+    <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
     <proguard>
       -libraryjars "${java.home}/lib/rt.jar"
       -injars      in.jar