Put all libraries in Project space

[jalview.git] / build.xml

diff --git a/build.xml b/build.xml
index 4ab3257..dbed685 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -9,6 +9,8 @@
     </fileset>
   </classpath>
 </taskdef>
+
+
     <!-- utils is a class path to additional utilities needed for
     building docs, jars and webstart stuff -->
 
@@ -105,10 +107,9 @@
       <mkdir dir="${outputDir}"/>
       <copy todir="${outputDir}">
         <fileset dir=".">
-
           <include name="${docDir}/**/*.*"/>
           <include name="${helpDir}/**/*.*"/>
-          <include name="${libDir}/*.*"/>
+          <include name="${libDir}/*.jar"/>
         </fileset>
         <fileset dir="${resourceDir}">
           <include name="**/*.*"/>
@@ -118,8 +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">
@@ -139,6 +145,7 @@
 
       <jar destfile="${packageDir}/${outputJar}">
         <fileset dir="${outputDir}/">
+          <exclude name="cache*/**"/>
           <exclude name="*.jar" />
           <exclude name="*.jar.*" />
           <exclude name="**/*.jar" />
@@ -173,12 +180,22 @@
       codebase="${WebStartLocation}">
       <information>
         <title>Jalview</title>
-        <vendor>Barton Group</vendor>
+        <vendor>The Barton Group</vendor>
         <homepage href="www.jalview.org"/>
         <description>Jalview Multiple Alignment Editor</description>
         <description kind="short">Jalview</description>
-        <icon href="BartonGroupBanner.gif"/>
-      </information>
+        <icon href="logo_big.gif"/>
+       <!--
+       <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"/>
+        <association mime-type="application-x/ext-file" extensions="msf"/>
+        <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>
         <resources>
           <j2se version="1.3+"/>
           <fileset dir="${packageDir}">
@@ -258,7 +275,7 @@
   <!-- jalopy code reformatter -->
   <target name="sourcescrub" depends="init,build">
     <jalopy destdir="jsrc" classpathref="run.classpath"
-      convention="jalviewCodeConvention.xml">
+      convention="jalview-jalopy.xml">
       <fileset dir="${sourceDir}">
         <include name="*.java"/>
         <include name="**/*.java"/>
@@ -267,4 +284,38 @@
       </jalopy>
   </target>
 
+
+
+  <!-- Compile, package and obfuscate Jalview Applet -->
+  <target name="makeApplet" depends="obfuscate"/>
+
+  <target name="compileApplet" depends="init,clean">
+    <mkdir dir="${outputDir}"/>
+    <javac source="1.2" target="1.1" srcdir="${sourceDir}" destdir="${outputDir}"
+       includes="jalview/analysis/**,jalview/appletgui/**,jalview/datamodel/**jalview/jbappletgui/**,jalview/math/**,jalview/schemes/**"
+       excludes="ext/**,MCview/**,org/**,vamsas/**"/>
+  </target>
+
+  <target name="packageApplet" depends="compileApplet">
+       <jar destfile="in.jar">
+        <fileset dir="${outputDir}">
+          <include name="com/**"/>
+          <include name="jalview/**"/>
+          <include name="${resourceDir}/images/idwidth.gif"/>
+        </fileset>
+      </jar>
+  </target>
+
+  <target name="obfuscate" depends="packageApplet">
+    <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+    <proguard>
+      -libraryjars "${java.home}/lib/rt.jar"
+      -injars      in.jar
+      -outjars     jalviewApplet.jar
+      -keep public class jalview.bin.JalviewLite
+    </proguard>
+    <delete file="in.jar"/>
+  </target>
+
+
 </project>