loads of changes. Jalopy source formatting, better WS client build (but still not...

diff --git a/build.xml b/build.xml
index 303437d..4ab3257 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -1,5 +1,14 @@
 <?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 -->
 
@@ -36,13 +45,13 @@
       <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="wsdl.MsaWS2" value="http://anaplog.compbio.dundee.ac.uk:8080/axis/services/ClustalWS?wsdl" />
-      <property name="wsdl.MsaWS2" value="http://anaplog.compbio.dundee.ac.uk:8080/axis/services/ClustalWS?wsdl" />
+      <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.compbio.dundee.ac.uk/~jimp/jalviewtest"/>
+      <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
       <property name="wsdl.Namespace" value="vamsas" />
       <property name="wsdl.ClientNS" value="ext.vamsas" />
 
@@ -143,7 +152,7 @@
           <include name="**/*.jar"/>
         </fileset>
       </copy>
-
+<!-- the default keystore details might need to be edited here -->
       <signjar
       storepass="alignmentisfun"
       keypass="alignmentisfun"
@@ -181,8 +190,7 @@
           </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>
@@ -202,7 +210,7 @@
     </target>
 
     <target name="buildextclients" depends="init">
-<!-- Currently, we do not do this automatically.
+<!-- 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
@@ -210,7 +218,7 @@
      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"/> -->
@@ -247,4 +255,16 @@
   <target name="package" depends="init, build">
 
   </target>
+  <!-- jalopy code reformatter -->
+  <target name="sourcescrub" depends="init,build">
+    <jalopy destdir="jsrc" classpathref="run.classpath"
+      convention="jalviewCodeConvention.xml">
+      <fileset dir="${sourceDir}">
+        <include name="*.java"/>
+        <include name="**/*.java"/>
+        <include name="**/**/*.java"/>
+      </fileset>
+      </jalopy>
+  </target>
+
 </project>