X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=dbed685a5ed5018b9bc8db6221028b19996a0936;hb=9961c690ef2e43c0bbd12ff37d691c413c2968d0;hp=ef22f31e1fea4ead652ac97d472f6fe6dc92c1b7;hpb=b99914def4f8ca33b194b943298c82bc2698a1a6;p=jalview.git

diff --git a/build.xml b/build.xml
index ef22f31..dbed685 100755
--- a/build.xml
+++ b/build.xml
@@ -1,9 +1,31 @@
 <?xml version="1.0"?>
   <project name="jalviewX" default="build" basedir=".">
+<!-- we use jalopy to format our sources -->
+<taskdef name="jalopy"
+         classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
+  <classpath>
+    <fileset dir="utils/jalopy/lib">
+      <include name="*.jar" />
+    </fileset>
+  </classpath>
+</taskdef>
+
+
     <!-- 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 +38,7 @@
         </fileset> -->
       </path>
 
+      <property name="" value=""/>
       <property name="libDir" value="lib"/>
       <property name="resourceDir" value="resources"/>
       <property name="helpDir" value="help"/>
@@ -24,10 +47,15 @@
       <property name="outputDir" value="classes" />
       <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="WebStartLocation" value="http://www.compbio.dundee.ac.uk/~jimp/jalviewtest"/>
+      <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" />
+      <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
+      <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
+      <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
+        <property name="WSInterf" value="MsaWS" />
+      <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
       <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 +63,12 @@
           <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 +86,7 @@
     </target>
 
     <target name="distclean" depends="init, clean">
-      
+
       <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
       <delete>
         <fileset dir=".">
@@ -74,15 +102,14 @@
         </fileset>
       </delete>
     </target>
-    
+
     <target name="prepare" depends="init">
       <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="**/*.*"/>
@@ -92,10 +119,15 @@
 
     <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" 
+    <target name="buildindices" depends="init, prepare"
     unless="help.uptodate">
     <java
       classname="com.sun.java.help.search.Indexer"
@@ -106,14 +138,18 @@
       <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="cache*/**"/>
           <exclude name="*.jar" />
+          <exclude name="*.jar.*" />
+          <exclude name="**/*.jar" />
+          <exclude name="**/*.jar.*" />
         </fileset>
       </jar>
 
@@ -123,8 +159,8 @@
           <include name="**/*.jar"/>
         </fileset>
       </copy>
-
-      <signjar 
+<!-- the default keystore details might need to be edited here -->
+      <signjar
       storepass="alignmentisfun"
       keypass="alignmentisfun"
       keystore="keys/.keystore"
@@ -138,18 +174,28 @@
       </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>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}">
@@ -161,12 +207,11 @@
           </fileset>
         </resources>
         <application_desc main_class="jalview.bin.Jalview">
-          <argument>http://www.compbio.dundee.ac.uk/~andrew/jalview/glut.msf</argument>
-        </application_desc>
+          </application_desc>
         <security>
           <all_permissions/>
-        </security>  
-      </jnlp>        
+        </security>
+      </jnlp>
     </target>
     <target name="runenv" depends="init">
       <path id="run.classpath">
@@ -176,15 +221,25 @@
         </fileset>
       </path>
       <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
-      
+
       <echo>java -classpath ${run.classpath} jalview.bin.Jalview
       </echo>
     </target>
-    
+
     <target name="buildextclients" depends="init">
+<!-- Currently, this doesn't happen automatically.
+     1. Run WSDL2Java as below, which generates an ext.vamsas +
+     vamsas.<datapackages> fileset.
+     2. refactor ext.vamsas.SpecificserviceWS* to
+     ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
+     3. Update the jalview.ws.*WServices classes to reflect the
+     interface type, and all locations of this wsdl type that Jalview
+     might be using.
+
+-->
       <path id="axisbuild">
         <!--        <path refid="axis.classpath"/> -->
-        <path refid="build.classpath"/>        
+        <path refid="build.classpath"/>
       </path>
       <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
       <move todir="./bak">
@@ -192,27 +247,75 @@
           <include name="${wsdl.ClientNS}/*.*"/>
         </fileset>
       </move>
-      
+
       <axis-wsdl2java
       output="${sourceDir}"
       verbose="true"
-      url="${wsdl.File}" 
+      url="${wsdl.MsaWS2}"
       serverside="false"
       deployscope="Request"
       debug="false"
+      helpergen="true"
+      all="true"
       >
       <mappingSet>
-        <mapping 
+        <mapping
         namespace="${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>
+  <!-- jalopy code reformatter -->
+  <target name="sourcescrub" depends="init,build">
+    <jalopy destdir="jsrc" classpathref="run.classpath"
+      convention="jalview-jalopy.xml">
+      <fileset dir="${sourceDir}">
+        <include name="*.java"/>
+        <include name="**/*.java"/>
+        <include name="**/**/*.java"/>
+      </fileset>
+      </jalopy>
   </target>
+
+
+
+  <!-- Compile, package and obfuscate Jalview Applet -->
+  <target name="makeApplet" depends="obfuscate"/>
+
+  <target name="compileApplet" depends="init,clean">
+    <mkdir dir="${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>