fixed some of the jar/wsdl deployment problems.

diff --git a/build.xml b/build.xml
index be92845..76e2d1d 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -3,6 +3,8 @@
   <!-- utils is a class path to additional utilities needed for
   building docs, jars and webstart stuff -->
 
+
+  
   <target name="init">
 
     <property name="libDir" value="lib"/>
@@ -11,6 +13,7 @@
     <property name="docDir" value="doc"/>
     <property name="sourceDir" value="src" />
     <property name="outputDir" value="classes" />
+    <property name="packageDir" value="dist" />
     <property name="outputJar" value="jalview.jar" />
 
     <path id="build.classpath">
@@ -23,7 +26,13 @@
         <include name="**/*.jar"/>
       </fileset>
     </path>
-
+<!-->    <uptodate property="help.uptodate"
+     targetfile="${helpDir}/helpIndex.xml">
+      <srcfiles
+        dir="${helpDir}"
+        includes="**/*.html" />
+    </uptodate>
+    -->
   </target>
 
   <target name="clean" depends="init">
@@ -69,6 +78,77 @@
      <javac srcdir="${sourceDir}" destdir="${outputDir}"
         classpathref="build.classpath" />
   </target>
+  <target name="buildindices" depends="init, prepare" 
+   unless="help.uptodate">
+    <java
+     classname="com.sun.java.help.search.Indexer"
+     classpathref="build.classpath"
+     fork="true"
+     dir="${outputDir}/${helpDir}"
+     >
+      <arg line="html"/>
+    </java>
+  </target>
+  
+  <target name="makejars" depends="build, buildindices">
+    <!-- make the package jar -->
+    <mkdir dir="${packageDir}"/>
+    
+    <jar destfile="${packageDir}/${outputJar}">
+      <fileset dir="${outputDir}">
+        <exclude name="*.jar" />
+      </fileset>
+    </jar>
+
+    <copy toDir="${packageDir}" flatten="true">
+      <fileset dir="${outputDir}">
+        <include name="*.jar"/>
+        <include name="**/*.jar"/>
+      </fileset>
+    </copy>
+
+    <signjar 
+    storepass="alignmentisfun"
+    keypass="alignmentisfun"
+    keystore="keys/.keystore"
+    alias="jalview"
+    lazy="false"
+    verbose="false"
+    >
+
+    <fileset dir="${packageDir}">
+      <include name="*.jar"/>
+    </fileset>
+    </signjar>
+    <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
+    
+    <!--    codebase="http://www.jalview.org/jalview/webstart" -->
+    <jnlp toFile="${packageDir}/Jalview.jnlp" href="Jalview.jnlp"
+    codebase="file://">
+    <information>
+      <title>Jalview</title>
+      <vendor>M Clamp</vendor>
+      <homepage href="www.jalview.org"/>
+      <description>Jalview Multiple Alignment Editor</description>
+      <description kind="short">Jalview</description>
+      <icon href="BartonGroupBanner.gif"/>
+    </information>
+    <resources>
+      <j2se version="1.3+"/>
+      <fileset dir="${packageDir}">
+        <include name="*.jar"/>
+      </fileset>
+    </resources>
+    <application_desc main_class="jalview.gui.AlignFrame">
+      <argument>http://www.compbio.dundee.ac.uk/~andrew/jalview/glut.msf</argument>
+      <argument>URL</argument>
+      <argument>MSF</argument>
+        </application_desc>
+    <security>
+      <all_permissions/>
+    </security>  
+    </jnlp>        
+  </target>
   <target name="runenv" depends="init">
       <path id="run.classpath">
         <pathelement location="${outputDir}"/>