stopped duplicate jars appearing in jalview.jar

beginning of 'automatic ws client' generation.

diff --git a/build.xml b/build.xml
index ef22f31..fd4257c 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -3,7 +3,18 @@
     <!-- utils is a class path to additional utilities needed for
     building docs, jars and webstart stuff -->
 
+<!--
+        Userdefined build property defaults
 
+        wsdl.server list (plus namespace mapping info ???)  - also want
+                ... to make this a dynamically generatable property
+        WebStart Location
+        Build location - provide a temporary root for speed
+        jarsigner keystore and info
+        Jakarta and axis classpath ?
+        Default argument for starting Jalview (if it exists).
+
+-->
 
     <target name="init">
       <path id="axis.classpath">
@@ -16,6 +27,7 @@
         </fileset> -->
       </path>
 
+      <property name="" value=""/>
       <property name="libDir" value="lib"/>
       <property name="resourceDir" value="resources"/>
       <property name="helpDir" value="help"/>
@@ -25,9 +37,12 @@
       <property name="packageDir" value="dist" />
       <property name="outputJar" value="jalview.jar" />
       <property name="wsdl.File" value="http://anaplog.compbio.dundee.ac.uk:8080/axis/services/jpred?wsdl" />
+      <property name="wsdl.Files" value="http://anaplog.compbio.dundee.ac.uk:8080/axis/services/vamsas?wsdlFiles" />
+      <property name="wsdl.MsaWS" value="http://anaplog.compbio.dundee.ac.uk:8080/axis/services/MuscleWS?wsdl" />
+
       <property name="WebStartLocation" value="http://www.compbio.dundee.ac.uk/~jimp/jalviewtest"/>
       <property name="wsdl.Namespace" value="vamsas" />
-      <property name="wsdl.ClientNS" value="ext.vamsas" />  
+      <property name="wsdl.ClientNS" value="ext.vamsas" />
 
       <path id="build.classpath">
         <fileset dir="utils">
@@ -35,12 +50,12 @@
           <include name="**/*.jar"/>
         </fileset>
         <fileset dir="${libDir}">
-          <include name="*.jar"/>      
+          <include name="*.jar"/>
           <include name="**/*.jar"/>
         </fileset>
 <!--        <fileset dir="old_lib_signed">
-<include name="lib_axis.jar"/> 
-        
+<include name="lib_axis.jar"/>
+
         </fileset>-->
       </path>
       <!-->    <uptodate property="help.uptodate"
@@ -58,7 +73,7 @@
     </target>
 
     <target name="distclean" depends="init, clean">
-      
+
       <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
       <delete>
         <fileset dir=".">
@@ -74,7 +89,7 @@
         </fileset>
       </delete>
     </target>
-    
+
     <target name="prepare" depends="init">
       <mkdir dir="${outputDir}"/>
       <copy todir="${outputDir}">
@@ -95,7 +110,7 @@
       <javac source="1.4" target="1.4" srcdir="${sourceDir}" destdir="${outputDir}"
       classpathref="build.classpath" />
     </target>
-    <target name="buildindices" depends="init, prepare" 
+    <target name="buildindices" depends="init, prepare"
     unless="help.uptodate">
     <java
       classname="com.sun.java.help.search.Indexer"
@@ -106,14 +121,17 @@
       <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}">
+        <fileset dir="${outputDir}/">
           <exclude name="*.jar" />
+          <exclude name="*.jar.*" />
+          <exclude name="**/*.jar" />
+          <exclude name="**/*.jar.*" />
         </fileset>
       </jar>
 
@@ -124,7 +142,7 @@
         </fileset>
       </copy>
 
-      <signjar 
+      <signjar
       storepass="alignmentisfun"
       keypass="alignmentisfun"
       keystore="keys/.keystore"
@@ -138,13 +156,13 @@
       </fileset>
       </signjar>
       <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
-      
+
       <!--    codebase="http://www.jalview.org/jalview/webstart" -->
       <jnlp toFile="${packageDir}/Jalview.jnlp" href="Jalview.jnlp"
       codebase="${WebStartLocation}">
       <information>
         <title>Jalview</title>
-        <vendor>M Clamp</vendor>
+        <vendor>Barton Group</vendor>
         <homepage href="www.jalview.org"/>
         <description>Jalview Multiple Alignment Editor</description>
         <description kind="short">Jalview</description>
@@ -165,8 +183,8 @@
         </application_desc>
         <security>
           <all_permissions/>
-        </security>  
-      </jnlp>        
+        </security>
+      </jnlp>
     </target>
     <target name="runenv" depends="init">
       <path id="run.classpath">
@@ -176,15 +194,15 @@
         </fileset>
       </path>
       <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
-      
+
       <echo>java -classpath ${run.classpath} jalview.bin.Jalview
       </echo>
     </target>
-    
+
     <target name="buildextclients" depends="init">
       <path id="axisbuild">
         <!--        <path refid="axis.classpath"/> -->
-        <path refid="build.classpath"/>        
+        <path refid="build.classpath"/>
       </path>
       <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
       <move todir="./bak">
@@ -192,27 +210,29 @@
           <include name="${wsdl.ClientNS}/*.*"/>
         </fileset>
       </move>
-      
+
       <axis-wsdl2java
       output="${sourceDir}"
       verbose="true"
-      url="${wsdl.File}" 
+      url="${wsdl.MsaWS}"
       serverside="false"
       deployscope="Request"
       debug="false"
+      helpergen="true"
+      all="true"
       >
       <mappingSet>
-        <mapping 
+        <mapping
         namespace="${wsdl.Namespace}"
         package="${wsdl.ClientNS}"
         />
         <mapping namespace="http://dataTypes.vamsas"
         package="${wsdl.ClientNS}"/>
-        </mappingSet>      
+        </mappingSet>
     </axis-wsdl2java>
 
   </target>
   <target name="package" depends="init, build">
-    
+
   </target>
 </project>