+ <!-- 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">
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
+ <include name="**/*.jar"/>
+ <include name="*.jar"/>
+ </fileset> -->
+ </path>
+ <!-- Jalview Version String displayed by application on startup and used to check for updates -->
+ <property name="JALVIEW_VERSION" value="DEVELOPMENT"/> <!-- 2.4 (VAMSAS)" -->
+ <!-- Include debugging information in javac true or false -->
+ <property name="javac.debug" value="true"/>
+ <!-- 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"/>
+ <property name="docDir" value="doc"/>
+ <property name="sourceDir" value="src" />
+ <property name="schemaDir" value="schemas" />
+ <property name="outputDir" value="classes" />
+ <property name="packageDir" value="dist" />
+ <property name="outputJar" value="jalview.jar" />
+ <!-- Jalview Applet JMol Jar Dependency -->
+ <property name="jmolJar" value="Jmol-11.0.2.jar" />
+ <property name="jalviewLiteJar" value="jalviewApplet.jar"/>
+ <!-- switch to indicate if we should obfuscate jalviewLite -->
+ <!--<property name="donotobfuscate" value="true"/> -->
+
+ <!-- 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" />
+ <!-- the class path for building the application -->
+ <path id="build.classpath">
+ <fileset dir="utils">
+ <include name="*.jar"/>
+ <include name="**/*.jar"/>
+ </fileset>
+ <fileset dir="${libDir}">
+ <include name="*.jar"/>
+ <include name="**/*.jar"/>
+ </fileset>
+
+ </path>
+ <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz"/>
+ <!-- The Location of the java 1.1.8 jdk -->
+ <property name="java118.home" value="C:\Sun\jdk1.1.8" />
+ <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip"/>
+ <!-- jre for 1.4 version
+ <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
+ -->
+ <!-- the classpath for building the 1.1 applet -->
+ <path id="jalviewlite.deps">
+ <fileset dir="${java118.home}">
+ <include name="lib/classes.zip"/>
+ </fileset>
+ <pathelement location="lib/${jmolJar}"/>
+ </path>
+ </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=".">
+ <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="${outputDir}">
+ <fileset dir=".">
+ <include name="${docDir}/**/*.*"/>
+ <include name="${helpDir}/**/*.*"/>
+ <include name="${libDir}/*.jar"/>
+ </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="${outputDir}"
+ debug="${javac.debug}"
+ classpathref="build.classpath">
+ <exclude name="jalview/*applet*"/>
+ <exclude name="com/stevesoft/**"/>
+ </javac>
+ </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}"
+ >
+ <arg line="html"/>
+ </java>
+ </target>
+
+ <target name="makefulldist" depends="makedist">
+ <!-- the default keystore details might need to be edited here -->
+ <signjar
+ storepass="alignmentisfun"
+ keypass="alignmentisfun"
+ keystore="keys/.keystore"
+ alias="jalview"
+ lazy="false"
+ verbose="false"
+ >
+
+ <fileset dir="${packageDir}">
+ <include name="*.jar"/>
+ </fileset>
+ </signjar>
+ <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
+
+ <!-- codebase="http://www.jalview.org/jalview/webstart" -->
+ <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
+ <jnlp toFile="${packageDir}/jalview.jnlp"
+ codebase="${WebStartLocation}">
+ <information>
+ <title>Jalview</title>
+ <vendor>The Barton Group</vendor>
+ <homepage href="http://www.jalview.org"/>
+ <description>Jalview Multiple Alignment Editor</description>
+ <description kind="short">Jalview</description>
+ <icon href="logo_big.gif"/>
+ <offline_allowed/>
+ <!--
+ <association mime-type="application-x/ext-file" extensions="fa"/>
+ <association mime-type="application-x/ext-file" extensions="fasta"/>
+ <association mime-type="application-x/ext-file" extensions="fastq"/>
+ <association mime-type="application-x/ext-file" extensions="blc"/>
+ <association mime-type="application-x/ext-file" extensions="msf"/>
+ <association mime-type="application-x/ext-file" extensions="pfam"/>
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ -->
+ </information>
+ <resources>
+ <j2se version="1.4+"/>
+ <fileset dir="${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.bin.Jalview">
+ </application_desc>
+ <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"/>
+
+ <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="${doextbuild.response}"/>
+ </condition>
+ <fail if="dontextbuild">
+ Build External Client Code process aborted by user. Jalview source is unchanged.
+ </fail>
+ <!-- Currently, this doesn't happen automatically.
+ 1. Run WSDL2Java as below, which generates an ext.vamsas +
+ vamsas.<datapackages> fileset.
+ 2. refactor ext.vamsas.SpecificserviceWS* to
+ ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
+ 3. Update the jalview.ws.*WServices classes to reflect the
+ interface type, and all locations of this wsdl type that Jalview
+ might be using.
+
+-->
+ <path id="axisbuild">
+ <path refid="build.classpath"/>
+ </path>
+ <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
+ <move todir="./bak">
+ <fileset dir="${sourceDir}" id="client">
+ <include name="${wsdl.ClientNS}/*.*"/>
+ </fileset>
+ </move>
+
+ <axis-wsdl2java
+ output="${sourceDir}"
+ verbose="true"
+ url="${wsdl.MsaWS2}"
+ serverside="false"
+ deployscope="Request"
+ debug="false"
+ helpergen="true"
+ all="true"
+ >
+ <mappingSet>
+ <mapping
+ namespace="${wsdl.Namespace}"
+ package="${wsdl.ClientNS}"
+ />
+ <mapping namespace="http://dataTypes.vamsas"
+ package="${wsdl.ClientNS}"/>
+ </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>
+
+
+
+ <!-- Compile, package and obfuscate Jalview Applet -->
+ <target name="makeApplet" depends="obfuscate"/>
+
+ <target name="compileApplet" depends="init,clean">