<?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">
</fileset> -->
</path>
+ <property name="JALVIEW_VERSION" value="2.07"/>
+ <property name="" value=""/>
<property name="libDir" value="lib"/>
<property name="resourceDir" value="resources"/>
<property name="helpDir" value="help"/>
<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">
<include name="**/*.jar"/>
</fileset>
<fileset dir="${libDir}">
- <include name="*.jar"/>
+ <include name="*.jar"/>
<include name="**/*.jar"/>
</fileset>
+ <fileset dir="../VamsasClient/packages">
+ <include name="*.jar"/>
+ <include name="**/*.jar"/>
+ </fileset>
<!-- <fileset dir="old_lib_signed">
-<include name="lib_axis.jar"/>
-
+<include name="lib_axis.jar"/>
+
</fileset>-->
</path>
<!--> <uptodate property="help.uptodate"
-->
</target>
+
+ <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
+ <target name="buildPropertiesFile" depends="init">
+ <tstamp prefix="build">
+ <format property="date" pattern="dd MMMM yyyy"/>
+ </tstamp>
+ <properties file="${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="${outputDir}"/>
</target>
<target name="distclean" depends="init, clean">
-
+
<echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
<delete>
<fileset dir=".">
</fileset>
</delete>
</target>
-
+
<target name="prepare" depends="init">
<mkdir dir="${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="**/*.*"/>
</fileset>
+ <fileset dir="../VamsasClient/packages/">
+ <include name="**/*.jar"/>
+ </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" />
+ <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"
<arg line="html"/>
</java>
</target>
-
- <target name="makejars" depends="build, buildindices">
+
+ <target name="makejars" depends="build, buildPropertiesFile, buildindices">
<!-- make the package jar -->
<mkdir dir="${packageDir}"/>
-
+
<jar destfile="${packageDir}/${outputJar}">
- <fileset dir="${outputDir}">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.Jalview"/>
+ </manifest>
+ <fileset dir="${outputDir}/">
+ <exclude name="cache*/**"/>
<exclude name="*.jar" />
+ <exclude name="*.jar.*" />
+ <exclude name="**/*.jar" />
+ <exclude name="**/*.jar.*" />
</fileset>
</jar>
<include name="**/*.jar"/>
</fileset>
</copy>
-
- <signjar
+<!-- the default keystore details might need to be edited here -->
+ <signjar
storepass="alignmentisfun"
keypass="alignmentisfun"
keystore="keys/.keystore"
</fileset>
</signjar>
<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
-
+
<!-- codebase="http://www.jalview.org/jalview/webstart" -->
- <jnlp toFile="${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="${packageDir}">
<include name="jalview.jar"/>
</fileset>
<include name="*.jar"/>
<exclude name="jalview.jar"/>
</fileset>
+ <property name="jalview.version" value="${JALVIEW_VERSION}"/>
</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">
</fileset>
</path>
<pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
-
+
<echo>java -classpath ${run.classpath} jalview.bin.Jalview
</echo>
</target>
-
+
<target name="buildextclients" depends="init">
+<!-- Currently, this doesn't happen automatically.
+ 1. Run WSDL2Java as below, which generates an ext.vamsas +
+ vamsas.<datapackages> fileset.
+ 2. refactor ext.vamsas.SpecificserviceWS* to
+ ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
+ 3. Update the jalview.ws.*WServices classes to reflect the
+ interface type, and all locations of this wsdl type that Jalview
+ might be using.
+
+-->
<path id="axisbuild">
<!-- <path refid="axis.classpath"/> -->
- <path refid="build.classpath"/>
+ <path refid="build.classpath"/>
</path>
<taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
<move todir="./bak">
<include name="${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, 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>
git://source.jalview.org / jalview.git / blobdiff