<?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 -->
-
-
-
- <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" />
-
- <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">
- <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="${resourceDir}">
- <include name="**/*.*"/>
- </fileset>
- </copy>
- </target>
-
- <target name="build" depends="prepare">
- <!-- not efficient yet. -->
- <javac srcdir="${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="${packageDir}/Jalview.jnlp" href="Jalview.jnlp"
- codebase="file://">
- <information>
- <title>Jalview</title>
- <vendor>M Clamp</vendor>
- <homepage href="www.jalview.org"/>
- <description>Jalview Multiple Alignment Editor</description>
- <description kind="short">Jalview</description>
- <icon href="BartonGroupBanner.gif"/>
- </information>
- <resources>
- <j2se version="1.3+"/>
- <fileset dir="${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>
- </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="package" depends="init, build">
-
- </target>
-</project>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<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."/>
+ <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk."/>
+ <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation"/>
+ </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">
+ <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"/>
+
+ <!-- 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"/>
+ <!-- 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-12.1.11_dev.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="appletlib/${jmolJar}"/>
+ </path>
+ </target>
+
+
+ <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
+ <target name="buildPropertiesFile" depends="init">
+ <tstamp prefix="build">
+ <format property="date" pattern="dd MMMM yyyy"/>
+ </tstamp>
+ <properties file="${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="1.5" target="1.5"
+ 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}/${helpDir}"
+ >
+ <arg line="html"/>
+ </java>
+ </target>
+
+ <target name="makefulldist" depends="makedist">
+ <!-- the default keystore details might need to be edited here -->
+ <signjar storepass="${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>
+ <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="1.5+" 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="${JALVIEW_VERSION}" />
+ </resources>
+ <application_desc main_class="jalview.bin.Jalview">
+ </application_desc>
+ <security>
+ <all_permissions />
+ </security>
+ </jnlp>
+ <!-- the rest of these jnlp tasks are copy and pastes of the above but with different Vm args -->
+ <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
+ <information>
+ <title>Jalview</title>
+ <vendor>The Barton Group</vendor>
+ <homepage href="http://www.jalview.org" />
+ <description>Jalview Multiple Alignment Editor</description>
+ <description kind="short">Jalview</description>
+ <icon href="logo_big.gif" />
+ <offline_allowed />
+ <!--
+ <association mime-type="application-x/ext-file" extensions="fa"/>
+ <association mime-type="application-x/ext-file" extensions="fasta"/>
+ <association mime-type="application-x/ext-file" extensions="fastq"/>
+ <association mime-type="application-x/ext-file" extensions="blc"/>
+ <association mime-type="application-x/ext-file" extensions="msf"/>
+ <association mime-type="application-x/ext-file" extensions="pfam"/>
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ -->
+ </information>
+ <resources>
+ <j2se version="1.5+" initial_heap_size="64M" max_heap_size="512M"/>
+ <fileset dir="${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="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="1.5+" 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="${JALVIEW_VERSION}" />
+ </resources>
+ <application_desc main_class="jalview.bin.Jalview">
+ </application_desc>
+ <security>
+ <all_permissions />
+ </security>
+ </jnlp>
+
+ </target>
+
+ <target name="runenv" depends="init">
+ <path id="run.classpath">
+ <pathelement location="${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="${sourceDir}">
+ <include name="*.java"/>
+ <include name="**/*.java"/>
+ <include name="**/**/*.java"/>
+ </fileset>
+ </jalopy>
+ </target>
+
+
+
+ <!-- Compile, package and obfuscate Jalview Applet -->
+ <target name="makeApplet" depends="obfuscate"/>
+
+ <target name="compileApplet" depends="init,clean">
+ <mkdir dir="${outputDir}"/>
+ <javac source="1.5"
+ target="1.5"
+ srcdir="${sourceDir}"
+ destdir="${outputDir}"
+ debug="${javac.debug}"
+ classpath="appletlib/${jmolJar}"
+ includes="jalview/appletgui/**"
+ excludes="ext/**,MCview/**,org/**,vamsas/**"
+ />
+ </target>
+
+ <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+ <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
+ <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
+ <jar destfile="in.jar">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
+ </manifest>
+ <fileset dir="${outputDir}">
+ <include name="com/**"/>
+ <include name="MCview/**"/>
+ <include name="jalview/**"/>
+ <include name=".build_properties"/>
+ <include name="images/idwidth.gif"/>
+ <include name="images/link.gif"/>
+ </fileset>
+ </jar>
+ </target>
+ <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
+ </target>
+ <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+ <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true"/>
+ <delete file="in.jar"/>
+ </target>
+ <target name="-obfuscatereally" unless="donotobfuscate">
+
+ <path id="obfuscateDeps.path">
+ <pathelement location="${applet.jre.tools}"/>
+ <pathelement location="appletlib/${jmolJar}"/>
+ </path>
+ <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+
+ <proguard>
+ <injar file="in.jar"/>
+ <outjar file="${jalviewLiteJar}"/>
+ <libraryjar refid="obfuscateDeps.path"/>
+ <keep access="public" type="class"
+ name="jalview.bin.JalviewLite">
+ <field access="public"/>
+ <method access="public"/>
+ <constructor access="public"/>
+ </keep>
+ <!-- -libraryjars "${obfuscateDeps}"
+ -injars in.jar
+ -outjars jalviewApplet.jar
+ -keep public class jalview.bin.JalviewLite
+ { public * ; } -->
+ </proguard>
+ <delete file="in.jar"/>
+ </target>
+
+ <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
+ <taskdef name="castor-srcgen"
+ classname="org.castor.anttask.CastorCodeGenTask"
+ classpathref="build.classpath" />
+ <delete>
+ <fileset dir="${sourceDir}/jalview/schemabinding/version2">
+ <include name="*.java"/>
+ <include name="descriptors/*.java"/>
+ </fileset>
+ </delete>
+ <castor-srcgen file="${schemaDir}/vamsas.xsd"
+ todir="${sourceDir}"
+ package="jalview.schemabinding.version2"
+ warnings="false"
+ nodesc="false"
+ verbose="true"
+ properties="${schemaDir}/jalview.properties"
+ />
+ <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
+ todir="${sourceDir}"
+ package="jalview.schemabinding.version2"
+ warnings="false"
+ nodesc="false"
+ verbose="true"
+ properties="${schemaDir}/jalview.properties"
+ />
+ <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd"
+ todir="${sourceDir}"
+ package="jalview.schemabinding.version2"
+ warnings="false"
+ nodesc="false"
+ verbose="true"
+ properties="${schemaDir}/jalview.properties"
+ />
+ <castor-srcgen file="${schemaDir}/jalview.xsd"
+ todir="${sourceDir}"
+ package="jalview.schemabinding.version2"
+ warnings="false"
+ nodesc="false"
+ verbose="true"
+ properties="${schemaDir}/jalview.properties"
+
+ />
+ <!--
+ now build the jalview.binding package with the old schema set
+ -->
+ <delete>
+ <fileset dir="${sourceDir}/jalview/binding/">
+ <include name="**"/>
+ </fileset>
+ </delete>
+ <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd"
+ todir="${sourceDir}"
+ package="jalview.binding"
+ warnings="false"
+ nodesc="true"
+ verbose="true"
+ properties="${schemaDir}/jalview.nodesc.properties"
+ />
+ <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
+ todir="${sourceDir}"
+ package="jalview.binding"
+ warnings="false"
+ nodesc="true"
+ verbose="true"
+ properties="${schemaDir}/jalview.nodesc.properties"
+ />
+ <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
+ todir="${sourceDir}"
+ package="jalview.binding"
+ warnings="false"
+ nodesc="true"
+ verbose="true"
+ properties="${schemaDir}/jalview.nodesc.properties"
+ />
+ </target>
+ <target name="sourcedist" description="create jalview source distribution" depends="init">
+ <delete file="${source.dist.name}"/>
+ <tar destfile="${source.dist.name}" compression="gzip">
+ <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+ <include name="LICENSE"/>
+ <include name="README"/>
+ <include name="build.xml"/>
+ <include name="jalview-jalopy.xml"/>
+ <include name="JalviewApplet.jpx"/>
+ <include name="JalviewX.jpx"/>
+ <include name="${sourceDir}/*.java"/>
+ <include name="${sourceDir}/**/*.java"/>
+ <include name="${sourceDir}/**/*.cdr"/>
+ <include name="${libDir}/**/*"/>
+ <include name="${resourceDir}/**/*"/>
+ <include name="${helpDir}/**/*"/>
+ <include name="appletlib/${jmolJar}"/>
+ <exclude name="**/*locales"/>
+ <exclude name="*locales/**"/>
+ <exclude name="utils/InstallAnywhere/**Build.iap_xml"/>
+ <exclude name="utils/InstallAnywhere/**Build*/**"/>
+ <exclude name="utils/InstallAnywhere/**Build*/**"/>
+ <exclude name="utils/InstallAnywhere/**locale*"/>
+ <exclude name="utils/InstallAnywhere/**locale*/**"/>
+ <include name="${schemaDir}/**/*"/>
+ <include name="utils/**/*"/>
+ <include name="${docDir}/**/*"/>
+ </tarfileset>
+ </tar>
+ </target>
+ </project>
git://source.jalview.org / jalview.git / blobdiff