* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<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
+ <!-- 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
-->
- <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> -->
+ <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" />
- <!-- 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+"/>
+ <!-- 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" />
+ <!-- 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+"/>
<!-- Permissions for running Java applets and applications. -->
<!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
<property name="applet.codebase" value="*" />
<property name="applet.caller-codebase" value="${applet.codebase}" />
- <!-- build directory configuration -->
- <property name="libDir" value="lib" />
- <property name="resourceDir" value="resources" />
- <property name="helpDir" value="help" />
- <property name="docDir" value="doc" />
- <property name="sourceDir" value="src" />
- <property name="schemaDir" value="schemas" />
- <property name="outputDir" value="classes" />
- <property name="packageDir" value="dist" />
- <property name="outputJar" value="jalview.jar" />
- <!-- Jalview Applet JMol Jar Dependency -->
- <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
- <property name="jalviewLiteJar" value="jalviewApplet.jar" />
- <!-- switch to indicate if we should obfuscate jalviewLite -->
- <!--<property name="donotobfuscate" value="true"/> -->
-
- <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
- <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
- <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
- <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
- <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
- <property name="WSInterf" value="MsaWS" />
- <property name="wsdl.Namespace" value="vamsas" />
- <property name="wsdl.ClientNS" value="ext.vamsas" />
- <!-- the class path for building the application -->
- <path id="build.classpath">
- <fileset dir="utils">
- <include name="*.jar" />
- <include name="**/*.jar" />
- </fileset>
- <fileset dir="${libDir}">
- <include name="*.jar" />
- <include name="**/*.jar" />
- </fileset>
- <fileset dir="${java.home}/lib">
- <include name="plugin.jar"/>
- </fileset>
- <fileset dir="appletlib">
- <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
+ <!-- build directory configuration -->
+ <property name="libDir" value="lib" />
+ <property name="resourceDir" value="resources" />
+ <property name="helpDir" value="help" />
+ <property name="docDir" value="doc" />
+ <property name="sourceDir" value="src" />
+ <property name="schemaDir" value="schemas" />
+ <property name="outputDir" value="classes" />
+ <property name="packageDir" value="dist" />
+ <property name="outputJar" value="jalview.jar" />
+ <!-- Jalview Applet JMol Jar Dependency -->
+ <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
+ <property name="jalviewLiteJar" value="jalviewApplet.jar" />
+ <!-- switch to indicate if we should obfuscate jalviewLite -->
+ <!--<property name="donotobfuscate" value="true"/> -->
+
+ <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
+ <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
+ <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
+ <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
+ <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
+ <property name="WSInterf" value="MsaWS" />
+ <property name="wsdl.Namespace" value="vamsas" />
+ <property name="wsdl.ClientNS" value="ext.vamsas" />
+ <!-- the class path for building the application -->
+ <path id="build.classpath">
+ <fileset dir="utils">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="${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>
+ <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" />
+ </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/${jmolJar}" />
- </path>
+ <property name="java118.home" value="${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>
+ </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="${outputDir}/.build_properties">
- <header>
+ <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
+ <target name="buildPropertiesFile" depends="init">
+ <tstamp prefix="build">
+ <format property="date" pattern="dd MMMM yyyy" />
+ </tstamp>
+ <properties file="${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}/${helpDir}">
- <arg line="html" />
- </java>
- </target>
-
- <target name="makefulldist" depends="makedist">
- <copy todir="${packageDir}">
- <fileset dir="${resourceDir}/images">
- <include name="${WebStartImage}"/>
- </fileset>
- </copy>
-
- <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
+ <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}/${helpDir}">
+ <arg line="html" />
+ </java>
+ </target>
+
+ <target name="makefulldist" depends="makedist">
+ <copy todir="${packageDir}">
+ <fileset dir="${resourceDir}/images">
+ <include name="${WebStartImage}"/>
+ </fileset>
+ </copy>
+
+ <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
<!-- create a dummy jar which will eventually contain the jnlp template -->
<jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
- <fileset dir="${packageDir}">
- <include name="jalview.jar" />
- </fileset>
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
+ </jar>
+
+ <mkdir dir="${packageDir}/JNLP-INF"/>
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+ <param name="inih" value="*" />
+ <param name="maxh" value="*"/>
+ </antcall>
+
+ <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+ <fileset dir="${packageDir}">
+ <include name="JNLP-INF"/>
+ </fileset>
</jar>
-
- <mkdir dir="${packageDir}/JNLP-INF"/>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
+ <param name="inih" value="10M" />
+ <param name="maxh" value="256M"/>
+ </antcall>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
+ <param name="inih" value="128M" />
+ <param name="maxh" value="512M"/>
+ </antcall>
+
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
- <param name="inih" value="*" />
- <param name="maxh" value="*"/>
+ <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
+ <param name="inih" value="256M" />
+ <param name="maxh" value="1024M"/>
</antcall>
-
- <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
- <fileset dir="${packageDir}">
- <include name="JNLP-INF"/>
- </fileset>
- </jar>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
- <param name="inih" value="10M" />
- <param name="maxh" value="256M"/>
- </antcall>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
- <param name="inih" value="128M" />
- <param name="maxh" value="512M"/>
- </antcall>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
- <param name="inih" value="256M" />
- <param name="maxh" value="1024M"/>
- </antcall>
-
- <!-- finally, need to postprocess to add in associations at end of 'information' element
+
+ <!-- finally, need to postprocess to add in associations at end of 'information' element
<xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
<!-- and sign the jars -->
<!-- the default keystore details might need to be edited here -->
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ </fileset>
</signjar>
- </target>
-
- <target name="runenv" depends="init">
- <path id="run.classpath">
- <pathelement location="${outputDir}" />
- <fileset dir="${outputDir}">
- <include name="${libDir}/*.jar" />
- </fileset>
- </path>
- <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
-
- <echo>java -classpath ${run.classpath} jalview.bin.Jalview
+ </target>
+
+ <target name="runenv" depends="init">
+ <path id="run.classpath">
+ <pathelement location="${outputDir}" />
+ <fileset dir="${outputDir}">
+ <include name="${libDir}/*.jar" />
+ </fileset>
+ </path>
+ <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
+
+ <echo>java -classpath ${run.classpath} jalview.bin.Jalview
</echo>
- </target>
+ </target>
<target name="writejnlpf">
<presetdef name="jnlpf">
<jnlp codebase="${WebStartLocation}">
<jnlpf toFile="${jnlpFile}"/>
</target>
- <target name="buildextclients" depends="init">
- <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
- <condition property="dontextbuild">
- <equals arg1="n" arg2="${doextbuild.response}" />
- </condition>
- <condition property="dontextbuild">
- <equals arg1="N" arg2="${doextbuild.response}" />
- </condition>
- <fail if="dontextbuild">
+ <target name="buildextclients" depends="init">
+ <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
+ <condition property="dontextbuild">
+ <equals arg1="n" arg2="${doextbuild.response}" />
+ </condition>
+ <condition property="dontextbuild">
+ <equals arg1="N" arg2="${doextbuild.response}" />
+ </condition>
+ <fail if="dontextbuild">
Build External Client Code process aborted by user. Jalview source is unchanged.
</fail>
- <!-- Currently, this doesn't happen automatically.
+ <!-- Currently, this doesn't happen automatically.
1. Run WSDL2Java as below, which generates an ext.vamsas +
vamsas.<datapackages> fileset.
2. refactor ext.vamsas.SpecificserviceWS* to
might be using.
-->
- <path id="axisbuild">
- <path refid="build.classpath" />
- </path>
- <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
- <move todir="./bak">
- <fileset dir="${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 if not already existing -->
- <mkdir dir="${packageDir}" />
- <!-- clean dir if it already existed -->
- <delete>
- <fileset dir="${packageDir}">
- <include name="*.jar"/>
- </fileset>
- </delete>
- <jar destfile="${packageDir}/${outputJar}" index="true">
- <manifest>
- <attribute name="Main-Class" value="jalview.bin.Jalview" />
+ <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="${wsdl.ClientNS}" />
+ </mappingSet>
+ </axis-wsdl2java>
+ </target>
+
+ <target name="makedist" depends="build, buildPropertiesFile, buildindices">
+ <!-- make the package jar if not already existing -->
+ <mkdir dir="${packageDir}" />
+ <!-- clean dir if it already existed -->
+ <delete>
+ <fileset dir="${packageDir}">
+ <include name="*.jar"/>
+ </fileset>
+ </delete>
+ <jar destfile="${packageDir}/${outputJar}" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.Jalview" />
<attribute name="Permissions" value="all-permissions" />
<attribute name="Application-Name" value="Jalview Desktop" />
<attribute name="Codebase" value="${application.codebase}" />
- </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" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
-
- <target name="compileApplet" depends="init,clean">
- <mkdir dir="${outputDir}" />
- <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
+ </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" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
+
+ <target name="compileApplet" depends="init,clean">
+ <mkdir dir="${outputDir}" />
+ <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
classpathref="jalviewlite.deps" 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" />
- <copy todir="${outputDir}/lang">
- <fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
- <jar destfile="in.jar" index="true">
- <manifest>
- <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Codebase" value="${applet.codebase}" />
- </manifest>
- <fileset dir="${outputDir}">
- <include name="com/**" />
- <include name="MCview/**" />
- <include name="jalview/**" />
- <include name=".build_properties" />
- <include name="images/idwidth.gif" />
- <include name="images/link.gif" />
- <include name="lang/**" />
- </fileset>
- </jar>
- </target>
- <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
- </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" />
- <dontwarn/>
- <keep access="public" type="class" name="jalview.bin.JalviewLite">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
- <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
- <!-- -libraryjars "${obfuscateDeps}"
+ </target>
+
+ <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+ <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
+ <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
+ <copy todir="${outputDir}/lang">
+ <fileset dir="${resourceDir}/lang">
+ <include name="**.*"/>
+ </fileset>
+ </copy>
+ <jar destfile="in.jar" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ </manifest>
+ <fileset dir="${outputDir}">
+ <include name="com/**" />
+ <include name="MCview/**" />
+ <include name="jalview/**" />
+ <include name=".build_properties" />
+ <include name="images/idwidth.gif" />
+ <include name="images/link.gif" />
+ <include name="lang/**" />
+ </fileset>
+ </jar>
+ </target>
+ <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
+ </target>
+ <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+ <copy file="in.jar" tofile="${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="${jalviewLiteJar}" />
+ <libraryjar refid="obfuscateDeps.path" />
+ <dontwarn/>
+ <keep access="public" type="class" name="jalview.bin.JalviewLite">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+ <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+ <!-- -libraryjars "${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="${schemaDir}/jalview.properties" />
- <!--
+ </proguard>
+ <delete file="in.jar" />
+ </target>
+
+ <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
+ <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
+ <delete>
+ <fileset dir="${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="nbbuild.xml"/>
- <include name="nbproject/genfiles.properties"/>
+ <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="nbbuild.xml"/>
+ <include name="nbproject/genfiles.properties"/>
<include name="nbproject/project.properties"/>
<include name="nbproject/project.xml"/>
- <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}/**/*" />
- <include name="examples/**/*" />
- </tarfileset>
- </tar>
- </target>
- <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
- <copy todir="${packageDir}/examples">
- <fileset dir="examples">
- <include name="**/*"/>
- <include name="javascript/*"/>
- <include name="jmol/*"/>
- </fileset>
- <fileset dir=".">
+ <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}/**/*" />
+ <include name="examples/**/*" />
+ </tarfileset>
+ </tar>
+ </target>
+ <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
+ <copy todir="${packageDir}/examples">
+ <fileset dir="examples">
+ <include name="**/*"/>
+ <include name="javascript/*"/>
+ <include name="jmol/*"/>
+ </fileset>
+ <fileset dir=".">
<include name="${jalviewLiteJar}" />
- </fileset>
- <fileset dir="appletlib">
- <include name="**/*"/>
- </fileset>
- </copy>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
- <manifest>
- <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
- <!-- <attribute name="Permissions" value="sandbox" /> -->
- <!--<attribute name="Trusted-Lib" value="true" /> -->
- <attribute name="Codebase" value="${applet.codebase}"/>
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
- </manifest>
- </jar>
+ </fileset>
+ <fileset dir="appletlib">
+ <include name="**/*"/>
+ </fileset>
+ </copy>
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
+ <manifest>
+ <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
+ <!-- <attribute name="Permissions" value="sandbox" /> -->
+ <!--<attribute name="Trusted-Lib" value="true" /> -->
+ <attribute name="Codebase" value="${applet.codebase}"/>
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+ </manifest>
+ </jar>
<signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
<fileset dir="${packageDir}/examples">
<include name="*.jar" />
git://source.jalview.org / jalview.git / commitdiff