updated jalview version of dasobert 1.53e client and added Das Sequence Source discov...

[jalview.git] / build.xml

diff --git a/build.xml b/build.xml
index 9af447e..19ec5f2 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" />
@@ -92,7 +96,7 @@
                        </fileset>
                        
                </path>
-               <property name="source.dist.name" value="jalview-src.tar.gz"/>
+               <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz"/>
                <!-- The Location of the java 1.1.8 jdk -->
                <property name="java118.home" value="C:\Sun\jdk1.1.8" />
                <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip"/>
@@ -202,7 +206,8 @@
                <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
 
                <!--    codebase="http://www.jalview.org/jalview/webstart" -->
-               <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
+               <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
+               <jnlp toFile="${packageDir}/jalview.jnlp" 
       codebase="${WebStartLocation}">
                        <information>
                                <title>Jalview</title>
@@ -221,6 +226,7 @@
         <association mime-type="application-x/ext-file" extensions="pfam"/>
         <association mime-type="application-x/ext-file" extensions="aln"/>
         <association mime-type="application-x/ext-file" extensions="pir"/>
+        <association mime-type="application-x/ext-file" extensions="amsa"/>
        -->
                        </information>
                        <resources>
@@ -357,6 +363,7 @@
     target="1.1"
     srcdir="${sourceDir}" 
     destdir="${outputDir}"
+       debug="${javac.debug}"
     classpath="lib/${jmolJar}"
        includes="jalview/appletgui/**"
        excludes="ext/**,MCview/**,org/**,vamsas/**"
@@ -380,16 +387,23 @@
         </fileset>
       </jar>
   </target>
-
-  <target name="obfuscate" depends="packageApplet">
-    <path id="obfuscateDeps.path">
+  <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
+  </target>
+       <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">    
+       <copy file="in.jar" tofile="${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">
@@ -401,9 +415,8 @@
       -injars      in.jar
       -outjars     jalviewApplet.jar
       -keep public class jalview.bin.JalviewLite
-       { public * ; }
-       -->
-    </proguard>
+       { public * ; } -->
+      </proguard>
     <delete file="in.jar"/>
   </target>
 
@@ -476,11 +489,7 @@
        />
        </target>
        <target name="sourcedist" description="create jalview source distribution" depends="init">
-               <delete>
-                       <fileset dir="${basedir}">
-                               <include name="${source.dist.name}"/>
-                       </fileset>
-               </delete>
+               <delete file="${source.dist.name}"/>
                <tar destfile="${source.dist.name}" compression="gzip">
                        <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
                                <include name="LICENSE"/>