- <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://www.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="${helpDir}"
- includes="**/*.html" />
- </uptodate>
- -->
- </target>
-
- <target name="clean" depends="init">
- <!-- not efficient yet. -->
- <delete dir="${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}/*.*"/>
- </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="${outputDir}"
- classpathref="build.classpath" />
- </target>
- <target name="buildindices" depends="init, prepare"
- unless="help.uptodate">
- <java
- classname="com.sun.java.help.search.Indexer"
- classpathref="build.classpath"
- fork="true"
- dir="${outputDir}/${helpDir}"
- >
- <arg line="html"/>
- </java>
- </target>
-
- <target name="makejars" depends="build, buildindices">
- <!-- make the package jar -->
- <mkdir dir="${packageDir}"/>
-
- <jar destfile="${packageDir}/${outputJar}">
- <fileset dir="${outputDir}">
- <exclude name="*.jar" />
- </fileset>
- </jar>
-
- <copy toDir="${packageDir}" flatten="true">
- <fileset dir="${outputDir}">
- <include name="*.jar"/>
- <include name="**/*.jar"/>
- </fileset>
- </copy>
-
- <signjar
- storepass="alignmentisfun"
- keypass="alignmentisfun"
- keystore="keys/.keystore"
- alias="jalview"
- lazy="false"
- verbose="false"
- >
-
- <fileset dir="${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="${packageDir}/Jalview.jnlp" href="Jalview.jnlp"
- codebase="${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="${packageDir}">
- <include name="jalview.jar"/>
- </fileset>
- <fileset dir="${packageDir}">
- <include name="*.jar"/>
- <exclude name="jalview.jar"/>
- </fileset>
- </resources>
- <application_desc main_class="jalview.bin.Jalview">
- <argument>http://www.compbio.dundee.ac.uk/~andrew/jalview/glut.msf</argument>
- </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
+ <!-- JarSigner Key Store for Webstart Distribution -->
+ <property name="jalview.keystore" value="./keys/.keystore" />
+ <!-- Keystore Password -->
+ <property name="jalview.keystore.pass" value="alignmentisfun" />
+ <!-- Key Name -->
+ <property name="jalview.key" value="jalview" />
+ <!-- Key Password -->
+ <property name="jalview.key.pass" value="alignmentisfun" />
+
+ <!-- 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" />
+ <!-- Webstart Image - looked for in resources/images -->
+ <property name="WebStartImage" value="JalviewLogo_big.png"/>
+ <!-- J2SE version needed for webstart launch -->
+ <property name="j2sev" value="1.6+"/>
+ <!-- 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="JmolApplet-12.2.4.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>
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar"/>
+ </fileset>
+ <fileset dir="appletlib">
+ <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
+ -->
+ <include name="${jmolJar}" />
+ </fileset>
+
+ </path>
+ <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
+ <!-- The Location of the java 1.1.8 jdk -->
+ <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
+ -->
+ <property name="java118.home" value="${java.home}" />
+ <!--<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="${java118.home}">
+ <include name="lib/classes.zip" />
+ </fileset>
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar"/>
+ </fileset>
+ <pathelement location="appletlib/${jmolJar}" />
+ </path>
+ <!-- default location for outputting javadoc -->
+ <property name="javadocDir" value="${packageDir}/javadoc"/>
+ </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}" includes="*,**/*"/>
+ </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="${resourceDir}">
+ <include name="**/*.*" />
+ </fileset>
+ </copy>
+ </target>
+
+ <target name="build" depends="prepare">
+ <!-- not efficient yet. -->
+ <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
+ <exclude name="jalview/*applet*" />
+ <exclude name="jalview/appletgui/**" />
+ <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="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ </fileset>
+ </signjar>
+ <copy todir="${packageDir}">
+ <fileset dir="${resourceDir}/images">
+ <include name="${WebStartImage}"/>
+ </fileset>
+ </copy>
+
+ <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="${WebStartImage}" />
+ <offline_allowed/>
+ </information>
+ <resources>
+ <j2se version="${j2sev}" initial_heap_size="10M" />
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ <include name="*_*.jar" />
+ <exclude name="jalview.jar" />
+ </fileset>
+ <property name="jalview.version" value="${JALVIEW_VERSION}" />
+ </resources>
+ <application_desc main_class="jalview.bin.Jalview">
+ </application_desc>
+ <security>
+ <all_permissions />
+ </security>
+ </jnlp>
+ <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
+ <information>
+ <title>Jalview</title>
+ <vendor>The Barton Group</vendor>
+ <homepage href="http://www.jalview.org" />
+ <description>Jalview Multiple Alignment Editor</description>
+ <description kind="short">Jalview</description>
+ <icon href="${WebStartImage}" />
+ <offline_allowed />
+ </information>
+ <resources>
+ <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ <include name="*_*.jar" />
+ <exclude name="jalview.jar" />
+ </fileset>
+ <property name="jalview.version" value="${JALVIEW_VERSION}" />
+ </resources>
+ <application_desc main_class="jalview.bin.Jalview">
+ </application_desc>
+ <security>
+ <all_permissions />
+ </security>
+ </jnlp>
+ <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${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="${WebStartImage}" />
+ <offline_allowed />
+ </information>
+ <resources>
+ <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ <include name="*_*.jar" />
+ <exclude name="jalview.jar" />
+ </fileset>
+ <property name="jalview.version" value="${JALVIEW_VERSION}" />
+ </resources>
+ <application_desc main_class="jalview.bin.Jalview">
+ </application_desc>
+ <security>
+ <all_permissions />
+ </security>
+ </jnlp>
+ <!-- finally, need to postprocess to add in associations at end of 'information' element
+
+ <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
+
+ </xslt>
+
+
+ -->
+ <!--
+ <association mime-type="application-x/ext-file" extensions="fa"/>
+ <association mime-type="application-x/ext-file" extensions="fasta"/>
+ <association mime-type="application-x/ext-file" extensions="fastq"/>
+ <association mime-type="application-x/ext-file" extensions="blc"/>
+ <association mime-type="application-x/ext-file" extensions="msf"/>
+ <association mime-type="application-x/ext-file" extensions="pfam"/>
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="stk"/>
+ <association mime-type="application-x/ext-file" extensions="jar"/>-->
+
+ </target>
+
+ <target name="runenv" depends="init">
+ <path id="run.classpath">
+ <pathelement location="${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