X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=4985f91f2fd3e29cf6a513771a85f4bece4bff84;hb=b31d6ded1992d8d8ea16f4321672b432b425693c;hp=ff25b0964fac315560dad6f04ce8de16024aae76;hpb=1156f593e261b3c082e56d783c756aefb08d4d0b;p=jalview.git

diff --git a/build.xml b/build.xml
index ff25b09..4985f91 100755
--- a/build.xml
+++ b/build.xml
@@ -1,21 +1,63 @@
 <?xml version="1.0"?>
-  <project name="jalviewX" default="build" basedir=".">
+  <project name="jalviewX" default="usage" 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>
+
+   <target name="help" depends="usage"/>
+   <target name="usage">
+     <echo message="~~~Jalview Ant build.xml Usage~~~~"/>
+     <echo message="Targets include:"/>
+     <echo message="usage - default target, displays this message"/>
+     <echo message="buildindices - generates JavaHelpSearch from the help files"/>
+     <echo message="build - compiles all necessary files for Application"/>
+     <echo message="makedist - compiles and places all necessary jar files into directory dist"/>
+     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution"/>
+     <echo message="              this needs a keystore and key. See docs/building.html for more information."/>
+     <echo message="compileApplet - compiles all necessary files for Applet"/>
+     <echo message="makeApplet - compiles, then packages and obfuscates the Applet"/>
+     <echo message="See docs/building.html and the comments in build file for other targets."/>
+   </target>
+
+
     <!-- 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">
-        <fileset dir="/usr/local/axis/lib">
+<!-->        <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>
+        </fileset> -->
       </path>
-
+      <!-- Jalview Version String displayed by application on startup and used to check for updates -->
+      <property name="JALVIEW_VERSION" value="ANNOTATION_TEST"/>
+      <!-- Don't change anything below here unless you know what you are doing! -->
+      <!-- Url path for WebStart in JNLP file -->
+      <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
+      <!-- build directory configuration -->
       <property name="libDir" value="lib"/>
       <property name="resourceDir" value="resources"/>
       <property name="helpDir" value="help"/>
@@ -24,41 +66,50 @@
       <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/"/>
+      <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
+      <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="WSInterf" value="MsaWS" />
       <property name="wsdl.Namespace" value="vamsas" />
-      <property name="wsdl.ClientNS" value="ext.vamsas" />  
-
+      <property name="wsdl.ClientNS" value="ext.vamsas" />
+      <!-- the class path for building the application -->
       <path id="build.classpath">
         <fileset dir="utils">
           <include name="*.jar"/>
           <include name="**/*.jar"/>
         </fileset>
         <fileset dir="${libDir}">
-          <include name="*.jar"/>      
+          <include name="*.jar"/>
           <include name="**/*.jar"/>
         </fileset>
-<!--        <fileset dir="old_lib_signed">
-<include name="lib_axis.jar"/> 
-        
-        </fileset>-->
       </path>
-      <!-->    <uptodate property="help.uptodate"
-      targetfile="${helpDir}/helpIndex.xml">
-      <srcfiles
-                 dir="${helpDir}"
-                 includes="**/*.html" />
-               </uptodate>
-      -->
     </target>
 
+
+    <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
+    <target name="buildPropertiesFile" depends="init">
+      <tstamp prefix="build">
+        <format property="date" pattern="dd MMMM yyyy"/>
+      </tstamp>
+      <properties file="${outputDir}/.build_properties">
+        <header>
+          ---Jalview Build Details---
+        </header>
+        <property name="VERSION" value="${JALVIEW_VERSION}"/>
+        <property name="BUILD_DATE" value="${build.date}"/>
+      </properties>
+    </target>
+
+
     <target name="clean" depends="init">
       <!-- not efficient yet. -->
       <delete dir="${outputDir}"/>
     </target>
 
     <target name="distclean" depends="init, clean">
-      
+
       <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
       <delete>
         <fileset dir=".">
@@ -74,15 +125,14 @@
         </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 +142,15 @@
 
     <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"
@@ -106,25 +161,10 @@
       <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}">
-          <exclude name="*.jar" />
-        </fileset>
-      </jar>
 
-      <copy toDir="${packageDir}" flatten="true">
-        <fileset dir="${outputDir}">
-          <include name="*.jar"/>
-          <include name="**/*.jar"/>
-        </fileset>
-      </copy>
-
-      <signjar 
+    <target name="makefulldist" depends="makedist">
+ <!-- the default keystore details might need to be edited here -->
+      <signjar
       storepass="alignmentisfun"
       keypass="alignmentisfun"
       keystore="keys/.keystore"
@@ -138,33 +178,46 @@
       </fileset>
       </signjar>
       <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
-      
+
       <!--    codebase="http://www.jalview.org/jalview/webstart" -->
-      <jnlp toFile="${packageDir}/Jalview.jnlp" href="Jalview.jnlp"
+      <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
       codebase="${WebStartLocation}">
       <information>
         <title>Jalview</title>
-        <vendor>M Clamp</vendor>
-        <homepage href="www.jalview.org"/>
+        <vendor>The Barton Group</vendor>
+        <homepage href="http://www.jalview.org"/>
         <description>Jalview Multiple Alignment Editor</description>
         <description kind="short">Jalview</description>
-        <icon href="BartonGroupBanner.gif"/>
-      </information>
+        <icon href="logo_big.gif"/>
+        <offline_allowed/>
+	<!--
+	<association mime-type="application-x/ext-file" extensions="fa"/>
+        <association mime-type="application-x/ext-file" extensions="fasta"/>
+        <association mime-type="application-x/ext-file" extensions="fastq"/>
+        <association mime-type="application-x/ext-file" extensions="blc"/>
+        <association mime-type="application-x/ext-file" extensions="msf"/>
+        <association mime-type="application-x/ext-file" extensions="pfam"/>
+        <association mime-type="application-x/ext-file" extensions="aln"/>
+        <association mime-type="application-x/ext-file" extensions="pir"/>
+	-->
+       </information>
         <resources>
-          <j2se version="1.3+"/>
+          <j2se version="1.4+"/>
+          <fileset dir="${packageDir}">
+            <include name="jalview.jar"/>
+          </fileset>
           <fileset dir="${packageDir}">
             <include name="*.jar"/>
+            <exclude name="jalview.jar"/>
           </fileset>
+          <property name="jalview.version" value="${JALVIEW_VERSION}"/>
         </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>
+        <application_desc main_class="jalview.bin.Jalview">
+          </application_desc>
         <security>
           <all_permissions/>
-        </security>  
-      </jnlp>        
+        </security>
+      </jnlp>
     </target>
     <target name="runenv" depends="init">
       <path id="run.classpath">
@@ -174,15 +227,36 @@
         </fileset>
       </path>
       <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
-      
+
       <echo>java -classpath ${run.classpath} jalview.bin.Jalview
       </echo>
     </target>
-    
+
     <target name="buildextclients" depends="init">
+      <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
+      validargs="Y,y,n,N" defaultvalue="N"
+      addproperty="doextbuild.response"/>
+      <condition property="dontextbuild">
+        <equals arg1="n" arg2="${doextbuild.response}"/>
+      </condition>
+      <condition property="dontextbuild">
+        <equals arg1="N" arg2="${doextbuild.response}"/>
+      </condition>
+      <fail if="dontextbuild">
+        Build External Client Code process aborted by user. Jalview source is unchanged.
+      </fail>
+<!-- Currently, this doesn't happen automatically.
+     1. Run WSDL2Java as below, which generates an ext.vamsas +
+     vamsas.<datapackages> fileset.
+     2. refactor ext.vamsas.SpecificserviceWS* to
+     ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
+     3. Update the jalview.ws.*WServices classes to reflect the
+     interface type, and all locations of this wsdl type that Jalview
+     might be using.
+
+-->
       <path id="axisbuild">
-        <!--        <path refid="axis.classpath"/> -->
-        <path refid="build.classpath"/>        
+        <path refid="build.classpath"/>
       </path>
       <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
       <move todir="./bak">
@@ -190,27 +264,105 @@
           <include name="${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="makedist" depends="build, buildPropertiesFile, buildindices">
+      <!-- make the package jar -->
+      <mkdir dir="${packageDir}"/>
+
+      <jar destfile="${packageDir}/${outputJar}">
+        <manifest>
+             <attribute name="Main-Class" value="jalview.bin.Jalview"/>
+        </manifest>
+        <fileset dir="${outputDir}/">
+          <exclude name="cache*/**"/>
+          <exclude name="*.jar" />
+          <exclude name="*.jar.*" />
+          <exclude name="**/*.jar" />
+          <exclude name="**/*.jar.*" />
+        </fileset>
+      </jar>
+
+      <copy toDir="${packageDir}" flatten="true">
+        <fileset dir="${outputDir}">
+          <include name="*.jar"/>
+          <include name="**/*.jar"/>
+        </fileset>
+      </copy>
+  </target>
+
 
+  <!-- jalopy code reformatter -->
+  <target name="sourcescrub" depends="init,build">
+    <jalopy destdir="jsrc" classpathref="run.classpath"
+      convention="jalview-jalopy.xml">
+      <fileset dir="${sourceDir}">
+        <include name="*.java"/>
+        <include name="**/*.java"/>
+        <include name="**/**/*.java"/>
+      </fileset>
+      </jalopy>
   </target>
-  <target name="package" depends="init, build">
-    
+
+
+
+  <!-- Compile, package and obfuscate Jalview Applet -->
+  <target name="makeApplet" depends="obfuscate"/>
+
+  <target name="compileApplet" depends="init,clean">
+    <mkdir dir="${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, buildPropertiesFile">
+  <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
+       <jar destfile="in.jar">
+        <manifest>
+            <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
+        </manifest>
+        <fileset dir="${outputDir}">
+          <include name="com/**"/>
+          <include name="MCview/**"/>
+          <include name="jalview/**"/>
+          <include name=".build_properties"/>
+          <include name="images/idwidth.gif"/>
+        </fileset>
+      </jar>
+  </target>
+
+  <target name="obfuscate" depends="packageApplet">
+    <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+    <proguard>
+      -libraryjars "${java.home}/lib/rt.jar"
+      -injars      in.jar
+      -outjars     jalviewApplet.jar
+      -keep public class jalview.bin.JalviewLite
+       { public * ; }
+    </proguard>
+    <delete file="in.jar"/>
+  </target>
+
+
 </project>