X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=dbed685a5ed5018b9bc8db6221028b19996a0936;hb=b2556b24919f5958b771868463fe4bb542f03708;hp=fd4257cd867b77834cb66eacba632e1df9e720f0;hpb=55cbe1bc97dab5eb37c8b6261d966708a142bdce;p=jalview.git

diff --git a/build.xml b/build.xml
index fd4257c..dbed685 100755
--- a/build.xml
+++ b/build.xml
@@ -1,5 +1,16 @@
 <?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 -->
 
@@ -36,11 +47,13 @@
       <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="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.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" />
 
@@ -94,10 +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="**/*.*"/>
@@ -107,8 +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">
@@ -128,6 +145,7 @@
 
       <jar destfile="${packageDir}/${outputJar}">
         <fileset dir="${outputDir}/">
+          <exclude name="cache*/**"/>
           <exclude name="*.jar" />
           <exclude name="*.jar.*" />
           <exclude name="**/*.jar" />
@@ -141,7 +159,7 @@
           <include name="**/*.jar"/>
         </fileset>
       </copy>
-
+<!-- the default keystore details might need to be edited here -->
       <signjar
       storepass="alignmentisfun"
       keypass="alignmentisfun"
@@ -162,12 +180,22 @@
       codebase="${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}">
@@ -179,8 +207,7 @@
           </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>
@@ -200,6 +227,16 @@
     </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"/>
@@ -214,7 +251,7 @@
       <axis-wsdl2java
       output="${sourceDir}"
       verbose="true"
-      url="${wsdl.MsaWS}"
+      url="${wsdl.MsaWS2}"
       serverside="false"
       deployscope="Request"
       debug="false"
@@ -235,4 +272,50 @@
   <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>