updated build strategy and checking for portability.

diff --git a/build.xml b/build.xml
index 2082fbd..ff25b09 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -1,168 +1,215 @@
 <?xml version="1.0"?>
-<project name="jalviewX" default="build" basedir=".">
-  <!-- utils is a class path to additional utilities needed for
-  building docs, jars and webstart stuff -->
+  <project name="jalviewX" default="build" basedir=".">
+    <!-- utils is a class path to additional utilities needed for
+    building docs, jars and webstart stuff -->
 
 
-  
-  <target name="init">
 
-    <property name="libDir" value="lib"/>
-    <property name="resourceDir" value="resources"/>
-    <property name="helpDir" value="help"/>
-    <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" />
+    <target name="init">
+      <path id="axis.classpath">
+        <fileset dir="/usr/local/axis/lib">
+          <include name="**/*.jar" />
+        </fileset>
+        <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
+          <include name="**/*.jar"/>
+          <include name="*.jar"/>
+        </fileset>
+      </path>
 
-    <path id="build.classpath">
-      <fileset dir="utils">
-        <include name="*.jar"/>
-        <include name="**/*.jar"/>
-      </fileset>
-      <fileset dir="${libDir}">
-        <include name="*.jar"/>      
-        <include name="**/*.jar"/>
-      </fileset>
-    </path>
-<!-->    <uptodate property="help.uptodate"
-     targetfile="${helpDir}/helpIndex.xml">
+      <property name="libDir" value="lib"/>
+      <property name="resourceDir" value="resources"/>
+      <property name="helpDir" value="help"/>
+      <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" />
+      <property name="wsdl.File" value="http://anaplog.compbio.dundee.ac.uk:8080/axis/services/jpred?wsdl" />
+        <property name="WebStartLocation" value="http://compbio.dundee.ac.uk/~jimp/jalviewtest/"/>
+      <property name="wsdl.Namespace" value="vamsas" />
+      <property name="wsdl.ClientNS" value="ext.vamsas" />  
+
+      <path id="build.classpath">
+        <fileset dir="utils">
+          <include name="*.jar"/>
+          <include name="**/*.jar"/>
+        </fileset>
+        <fileset dir="${libDir}">
+          <include name="*.jar"/>      
+          <include name="**/*.jar"/>
+        </fileset>
+<!--        <fileset dir="old_lib_signed">
+<include name="lib_axis.jar"/> 
+        
+        </fileset>-->
+      </path>
+      <!-->    <uptodate property="help.uptodate"
+      targetfile="${helpDir}/helpIndex.xml">
       <srcfiles
-        dir="${helpDir}"
-        includes="**/*.html" />
-    </uptodate>
-    -->
-  </target>
+                 dir="${helpDir}"
+                 includes="**/*.html" />
+               </uptodate>
+      -->
+    </target>
 
-  <target name="clean" depends="init">
-        <!-- not efficient yet. -->
-    <delete dir="${outputDir}"/>
-  </target>
+    <target name="clean" depends="init">
+      <!-- not efficient yet. -->
+      <delete dir="${outputDir}"/>
+    </target>
 
-  <target name="distclean" depends="init, clean">
+    <target name="distclean" depends="init, clean">
+      
+      <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
+      <delete>
+        <fileset dir=".">
+          <include name="${outputJar}"/>
+          <include name="#*#"/>
+          <include name="#*.*#"/>
+          <include name="**/#*#"/>
+          <include name="**/#*.*#"/>
+          <include name="*~"/>
+          <include name="*.*~"/>
+          <include name="**/*~"/>
+          <include name="**/*.*~"/>
+        </fileset>
+      </delete>
+    </target>
     
-    <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
-    <delete>
-      <fileset dir=".">
-        <include name="${outputJar}"/>
-        <include name="#*#"/>
-        <include name="#*.*#"/>
-        <include name="**/#*#"/>
-        <include name="**/#*.*#"/>
-        <include name="*~"/>
-        <include name="*.*~"/>
-        <include name="**/*~"/>
-        <include name="**/*.*~"/>
-      </fileset>
-    </delete>
-  </target>
-  
-  <target name="prepare" depends="init">
-    <mkdir dir="${outputDir}"/>
-    <copy todir="${outputDir}">
-      <fileset dir=".">
+    <target name="prepare" depends="init">
+      <mkdir dir="${outputDir}"/>
+      <copy todir="${outputDir}">
+        <fileset dir=".">
 
-        <include name="${docDir}/**/*.*"/>
-        <include name="${helpDir}/**/*.*"/>
-        <include name="${libDir}/*.*"/>
-      </fileset>
-      <fileset dir="${resourceDir}">
-        <include name="**/*.*"/>
-      </fileset>
-    </copy>
-  </target>
+          <include name="${docDir}/**/*.*"/>
+          <include name="${helpDir}/**/*.*"/>
+          <include name="${libDir}/*.*"/>
+        </fileset>
+        <fileset dir="${resourceDir}">
+          <include name="**/*.*"/>
+        </fileset>
+      </copy>
+    </target>
 
-  <target name="build" depends="prepare">
-            <!-- not efficient yet. -->
-     <javac source="1.4" target="1.4" srcdir="${sourceDir}" destdir="${outputDir}"
-        classpathref="build.classpath" />
-  </target>
-  <target name="buildindices" depends="init, prepare" 
-   unless="help.uptodate">
+    <target name="build" depends="prepare">
+      <!-- not efficient yet. -->
+      <javac source="1.4" target="1.4" 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}"
-     >
+      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}"/>
+    </target>
     
-    <jar destfile="${packageDir}/${outputJar}">
-      <fileset dir="${outputDir}">
-        <exclude name="*.jar" />
-      </fileset>
-    </jar>
+    <target name="makejars" depends="build, buildindices">
+      <!-- make the package jar -->
+      <mkdir dir="${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>
+      <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"
-    >
+      <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="${packageDir}">
         <include name="*.jar"/>
       </fileset>
-    </resources>
-    <application_desc main_class="jalview.gui.AlignFrame">
-      <argument>http://www.compbio.dundee.ac.uk/~andrew/jalview/glut.msf</argument>
-      <argument>URL</argument>
-      <argument>MSF</argument>
+      </signjar>
+      <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
+      
+      <!--    codebase="http://www.jalview.org/jalview/webstart" -->
+      <jnlp toFile="${packageDir}/Jalview.jnlp" href="Jalview.jnlp"
+      codebase="${WebStartLocation}">
+      <information>
+        <title>Jalview</title>
+        <vendor>M Clamp</vendor>
+        <homepage href="www.jalview.org"/>
+        <description>Jalview Multiple Alignment Editor</description>
+        <description kind="short">Jalview</description>
+        <icon href="BartonGroupBanner.gif"/>
+      </information>
+        <resources>
+          <j2se version="1.3+"/>
+          <fileset dir="${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">
+        <security>
+          <all_permissions/>
+        </security>  
+      </jnlp>        
+    </target>
+    <target name="runenv" depends="init">
       <path id="run.classpath">
         <pathelement location="${outputDir}"/>
         <fileset dir="${outputDir}">
-        <include name="${libDir}/*.jar"/>
-      </fileset>
-    </path>
-    <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
+          <include name="${libDir}/*.jar"/>
+        </fileset>
+      </path>
+      <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
+      
+      <echo>java -classpath ${run.classpath} jalview.bin.Jalview
+      </echo>
+    </target>
     
-    <echo>java -classpath ${run.classpath} jalview.bin.Jalview
-    </echo>
-</target>
-  
+    <target name="buildextclients" depends="init">
+      <path id="axisbuild">
+        <!--        <path refid="axis.classpath"/> -->
+        <path refid="build.classpath"/>        
+      </path>
+      <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
+      <move todir="./bak">
+        <fileset dir="${sourceDir}" id="client">
+          <include name="${wsdl.ClientNS}/*.*"/>
+        </fileset>
+      </move>
+      
+      <axis-wsdl2java
+      output="${sourceDir}"
+      verbose="true"
+      url="${wsdl.File}" 
+      serverside="false"
+      deployscope="Request"
+      debug="false"
+      >
+      <mappingSet>
+        <mapping 
+        namespace="${wsdl.Namespace}"
+        package="${wsdl.ClientNS}"
+        />
+        <mapping namespace="http://dataTypes.vamsas"
+        package="${wsdl.ClientNS}"/>
+        </mappingSet>      
+    </axis-wsdl2java>
 
+  </target>
   <target name="package" depends="init, build">
     
   </target>

diff --git a/lib/axis.jar b/lib/axis.jar
index 4f62367..90bb798 100755 (executable)
Binary files a/lib/axis.jar and b/lib/axis.jar differ

diff --git a/utils/axis-ant.jar b/utils/axis-ant.jar
index 9cb30a9..be9d3fe 100755 (executable)
Binary files a/utils/axis-ant.jar and b/utils/axis-ant.jar differ

diff --git a/utils/jarunsigner.pl b/utils/jarunsigner.pl
index f18f94c..283aed2 100755 (executable)
--- a/utils/jarunsigner.pl
+++ b/utils/jarunsigner.pl
@@ -24,8 +24,8 @@ while (scalar @jarfiles) {
     system("rm -Rf *");
     system("jar xf $jarfile");
     system("mv $jarfile $jarfile.bak");
-    system("rm META-INF/*.SF");
-    system("rm META-INF/*.RSA");
+    system("find META-INF \\( -name \"*.SF\" \\) -exec rm \\{\\} \\;");
+    system("find META-INF \\( -name \"*.RSA\" \\) -exec rm \\{\\} \\;");
     system("jar cf $jarfile *");
 }