+++ /dev/null
-<?xml version="1.0"?>
-<!--
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
--->
-<project name="jalviewX" default="usage" basedir="."
- xmlns:if="ant:if"
- xmlns:unless="ant:unless">
- <taskdef classpath="${clover.jar}" resource="cloverlib.xml" if:set="clover.jar"/>
- <clover-env if:set="clover.jar"/>
-
- <target name="help" depends="usage" />
- <target name="usage" depends="init">
- <echo message="~~~Jalview Ant build.xml Usage~~~~" />
- <echo message="Targets include:" />
- <echo message="usage - default target, displays this message" />
- <echo message="buildindices - generates JavaHelpSearch from the help files" />
- <echo message="build - compiles all necessary files for Application" />
- <echo message="makedist - compiles and places all necessary jar files into directory dist" />
- <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
- <echo message=" this needs a keystore and key."/>
- <echo message=" Add -Dtimestamp to timestamp signed jars"/>
- <echo message=" -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
- <echo message=" See docs/building.html for more information." />
- <echo message="compileApplet - compiles all necessary files for Applet" />
- <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
- <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
- <echo message=" you can specify particular test groups as a list via -Dtestng-groups=" />
- <echo message="See docs/building.html and the comments in build file for other targets." />
- <echo message="note: compile and makeApplet optionally compile/obfuscate applet against a different Java version by specifying -Djava118.home=PathtoJDK/lib which is the lib directory in the JDK install that contains rt.jar " />
- <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
- <echo message="Useful -D flags: -Dclover.jar to specify path to openclover for testng coverage report" />
- </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" />
-
- <property name="INSTALLATION" value="Source" />
-
- <!-- 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" />
- <!-- time stamp server URL -->
- <property name="jalview.tsaurl" value="" />
- <!-- locally valid proxy for signing with external time server -->
- <property name="proxyPort" value="80"/>
- <property name="proxyHost" value="sqid"/>
- <!-- key sign/digest algorithms -->
- <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
- <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
-
- <!-- default TestNG groups to run -->
- <property name="testng-groups" value="Functional" />
- <!-- Java 9 JVM args -->
- <condition property="java9">
- <equals arg1="${ant.java.version}" arg2="9"/>
- </condition>
-
- <!-- Don't change anything below here unless you know what you are doing! -->
- <!-- Url path for WebStart in JNLP file -->
- <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
- <!-- Webstart Image - looked for in resources/images -->
- <property name="WebStartImage" value="JalviewLogo_big.png" />
- <!-- J2SE version needed for webstart launch -->
- <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
- <property name="j2sev" value="1.7+" />
- <!-- Java Compilation settings - source and target javac version -->
- <property name="javac.source" value="1.8" />
- <property name="javac.target" value="1.8" />
-
- <!-- Permissions for running Java applets and applications. -->
- <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
- <property name="application.codebase" value="*.jalview.org" />
- <!-- and allowing the applet to be deployed from any URL -->
- <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
- <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
- <property name="applet.caller-codebase" value="${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" unless:set="clover.jar"/>
- <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
- <property name="packageDir" value="dist" />
- <property name="outputJar" value="jalview.jar" />
- <!-- Jalview Applet JMol Jar Dependency -->
- <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
- <property name="varnaJar" value="VARNAv3-93.jar" />
- <property name="jsoup" value="jsoup-1.8.1.jar" />
- <property name="jsonSimple" value="json_simple-1.1.jar" />
- <property name="javaJson" value="java-json.jar" />
- <property name="jalviewLiteJar" value="jalviewApplet.jar" />
- <property name="reportDir" value="test-reports" />
- <property name="testDir" value="test" />
- <property name="testOutputDir" value="tests" />
- <!-- switch to indicate if we should obfuscate jalviewLite -->
- <!-- <property name="donotobfuscate" value="true"/> -->
- <!-- switch to exclude associations from generated jnlp files -->
- <!-- <property name="nojnlpfileassocs" 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="${jmolJar}" />
- <include name="${varnaJar}" />
- </fileset>
- </path>
- <path id="test.classpath">
- <pathelement path="${outputDir}" />
- <path refid="build.classpath" />
- </path>
- <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
- <!-- The Location of the java 1.1.8 jdk -->
- <property name="java118.home" value="${java.home}" />
- <!-- jre for 1.4 version -->
- <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
-
- <!-- the classpath for building the 1.1 applet -->
- <path id="jalviewlite.deps">
- <fileset dir="${java118.home}">
- <include name="lib/rt.jar" />
- </fileset>
- <fileset dir="${java.home}/lib">
- <include name="plugin.jar" />
- </fileset>
- <pathelement location="appletlib/${jmolJar}" />
- <pathelement location="lib/${varnaJar}" />
- <pathelement location="appletlib/${jsoup}" />
- <pathelement location="appletlib/${jsonSimple}" />
- <pathelement location="appletlib/${javaJson}" />
-
- </path>
- <!-- default location for outputting javadoc -->
- <property name="javadocDir" value="${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>
- <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
- <arg value="rev-parse" />
- <arg value="--short" />
- <arg value="HEAD" />
- </exec>
- <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
- <arg value="rev-parse" />
- <arg value="--abbrev-ref" />
- <arg value="HEAD" />
- </exec>
- <properties file="${outputDir}/.build_properties">
- <header>
- ---Jalview Build Details---
- </header>
- <property name="VERSION" value="${JALVIEW_VERSION}" />
- <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
- <property name="BUILD_DATE" value="${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="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
- <exclude name="jalview/*applet*" />
- <exclude name="jalview/appletgui/**" />
- <exclude name="com/stevesoft/**" />
- </javac>
- </target>
-
-
- <target name="testclean" depends="init">
- <delete dir="${testOutputDir}" includes="*,**/*" />
- </target>
-
- <target name="prepareTests" depends="init,testclean">
- <mkdir dir="${testOutputDir}" />
- </target>
-
- <target name="buildTests" depends="build,buildindices,prepareTests">
- <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
- </javac>
- </target>
-
- <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
-
- <target name="testng" depends="buildTests">
- <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
- verbose="2">
- <classpath>
- <pathelement location="${testOutputDir}" />
- <pathelement location="${clover.jar}" if:set="clover.jar"/>
- <path refid="test.classpath" />
- </classpath>
- <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
- <jvmarg value="--illegal-access=warn" if:set="java9"/>
- <classfileset dir="${testOutputDir}" includes="**/*.class" />
- </testng>
- </target>
-
- <target name="buildindices" depends="init, prepare" unless="help.uptodate">
- <replace value="${JALVIEW_VERSION}">
- <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
- <fileset dir="${outputDir}/${helpDir}">
- <include name="help.jhm" />
- </fileset>
- </replace>
-
- <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
- <arg line="html" />
- </java>
- </target>
-
- <target name="preparejnlp" 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="${packageDir}">
- <include name="jalview.jar" />
- </fileset>
- </jar>
-
- <mkdir dir="${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="${packageDir}">
- <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
- </fileset>
- </jar>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
- <param name="inih" value="10M" />
- <param name="maxh" value="256M" />
- </antcall>
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
- <param name="inih" value="800M" />
- <param name="maxh" value="1024M" />
- </antcall>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
- <param name="inih" value="128M" />
- <param name="maxh" value="512M" />
- </antcall>
-
- <antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
- <param name="inih" value="800M" />
- <param name="maxh" value="1024M" />
- </antcall>
-
- <!-- finally, need to postprocess to add in associations at end of 'information' element
-
- <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
-
- </xslt>
-
-
- -->
- <!--
- <association mime-type="application-x/ext-file" extensions="fa"/>
- <association mime-type="application-x/ext-file" extensions="fasta"/>
- <association mime-type="application-x/ext-file" extensions="mfa"/>
- <association mime-type="application-x/ext-file" extensions="fastq"/>
- <association mime-type="application-x/ext-file" extensions="blc"/>
- <association mime-type="application-x/ext-file" extensions="msf"/>
- <association mime-type="application-x/ext-file" extensions="pfam"/>
- <association mime-type="application-x/ext-file" extensions="aln"/>
- <association mime-type="application-x/ext-file" extensions="pir"/>
- <association mime-type="application-x/ext-file" extensions="amsa"/>
- <association mime-type="application-x/ext-file" extensions="stk"/>
- <association mime-type="application-x/ext-file" extensions="jar"/>-->
- </target>
-
- <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
- tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- </fileset>
- </signjar>
- </target>
- <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- </fileset>
- </signjar>
- </target>
-
- <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
- <!-- and sign the jars -->
- <!-- the default keystore details might need to be edited here -->
- </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 ${run.classpath} jalview.bin.Jalview
- </echo>
- </target>
-
- <target name="-generatejnlpf">
- <presetdef name="jnlpf">
- <jnlp codebase="${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="${WebStartImage}" />
- <offline_allowed />
- </information>
- <resources>
- <j2se version="1.8+" />
- <jar main="true" href="jalview.jar"/>
- <fileset dir="${packageDir}">
- <exclude name="jalview.jar" />
- <include name="*.jar" />
- <include name="*_*.jar" />
- <exclude name="*quaqua*.jar" />
- </fileset>
- <property name="jalview.version" value="${JALVIEW_VERSION}" />
- </resources>
- <resources os="Mac OS X">
- <fileset dir="${packageDir}">
- <include name="quaqua-filechooser-only-8.0.jar"/>
- <include name="*quaqua64*.jnilib.jar" />
- </fileset>
- </resources>
-
- <application_desc main_class="jalview.bin.Jalview">
- </application_desc>
- <security>
- <all_permissions />
- </security>
- </jnlp>
- </presetdef>
-
- <jnlpf toFile="${jnlpFile}" />
- <!-- add the add-modules j2se attribute for java 9 -->
- <replace file="${jnlpFile}" value="j2se version="1.8+" initial-heap-size="${inih}" max-heap-size="${maxh}" java-vm-args="--add-modules=java.se.ee --illegal-access=warn"">
- <replacetoken>j2se version="1.8+"</replacetoken>
- </replace>
- </target>
-
- <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
- <echo message="Not adding JNLP File Associations" />
- </target>
-
- <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
- <replace file="${jnlpFile}">
- <replacetoken>
- <![CDATA[</information>]]></replacetoken>
- <replacevalue>
- <![CDATA[
- <association mime-type="application-x/ext-file" extensions="fa" />
- <association mime-type="application-x/ext-file" extensions="fasta" />
- <association mime-type="application-x/ext-file" extensions="mfa" />
- <association mime-type="application-x/ext-file" extensions="fastq" />
- <association mime-type="application-x/ext-file" extensions="blc" />
- <association mime-type="application-x/ext-file" extensions="msf" />
- <association mime-type="application-x/ext-file" extensions="pfam" />
- <association mime-type="application-x/ext-file" extensions="aln"/>
- <association mime-type="application-x/ext-file" extensions="pir"/>
- <association mime-type="application-x/ext-file" extensions="amsa"/>
- <association mime-type="application-x/ext-file" extensions="stk"/>
- <association mime-type="application-x/ext-file" extensions="jvp"/>
- </information>]]></replacevalue>
- </replace>
- <echo message="Added file associations to JNLP file" />
-</target>
-<target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
-</target>
-
-<target name="buildextclients" depends="init">
- <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
- <condition property="dontextbuild">
- <equals arg1="n" arg2="${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, linkcheck, buildindices">
- <fail if="clover.jar">
- Ignoring request to build jalview distribution with clover-instrumented classes
- </fail>
- <!-- 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="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
-</target>
-
-<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
- <copy file="${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="${outputDir}">
- <include name="com/**" />
- <include name="MCview/**" />
- <include name="jalview/**" />
- <include name=".build_properties" />
- <include name="images/link.gif" />
- <include name="lang/**" />
- </fileset>
- </jar>
-</target>
-<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
-</target>
-<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
- <copy file="in.jar" tofile="${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}" />
- <pathelement location="lib/${varnaJar}" />
- <pathelement location="appletlib/${jsoup}" />
- <pathelement location="appletlib/${jsonSimple}" />
- <pathelement location="appletlib/${javaJson}" />
- <fileset dir="${java.home}/lib">
- <include name="plugin.jar" />
- </fileset>
- </path>
- <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
-
- <proguard verbose="true" >
- <injar file="in.jar" />
- <outjar file="${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>
-
- <keep name="jalview.json.binding**">
- <constructor/>
- <method name="*"/>
- </keep>
-
- <keep access="public" type="class" name="MCview.PDBfile">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
-
- <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
-
- <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
-
-
- <!-- -libraryjars "${obfuscateDeps}"
- -injars in.jar
- -outjars jalviewApplet.jar
- -keep public class jalview.bin.JalviewLite
- { public * ; } -->
- </proguard>
- <delete file="in.jar" />
-</target>
-
-<target name="jaxb-bindings" depends="init" description="Generates JAXB bindings for supported Jalview XML models (needs xjc on the path)">
- <delete>
- <fileset dir="${sourceDir}/jalview/xml/binding/jalview">
- <include name="*.java" />
- </fileset>
- </delete>
- <exec executable="xjc">
- <arg value="${schemaDir}/jalview.xsd"/>
- <arg value="-d"/>
- <arg value="${sourceDir}"/>
- <arg value="-p"/>
- <arg value="jalview.xml.binding.jalview"/>
- </exec>
- <delete>
- <fileset dir="${sourceDir}/jalview/xml/binding/embl">
- <include name="*.java" />
- </fileset>
- </delete>
-
- <exec executable="xjc">
- <arg value="${schemaDir}/embl.xsd"/>
- <arg value="-d"/>
- <arg value="${sourceDir}"/>
- <arg value="-b"/>
- <arg value="${schemaDir}/embl_bindings.xml"/>
- <arg value="-p"/>
- <arg value="jalview.xml.binding.embl"/>
- </exec>
-
- <delete>
- <fileset dir="${sourceDir}/jalview/xml/binding/uniprot">
- <include name="*.java" />
- </fileset>
- </delete>
-
- <exec executable="xjc">
- <arg value="${schemaDir}/uniprot.xsd"/>
- <arg value="-d"/>
- <arg value="${sourceDir}"/>
- <arg value="-p"/>
- <arg value="jalview.xml.binding.uniprot"/>
- </exec>
-</target>
-
-<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
- <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
- <delete>
- <fileset dir="${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="${source.dist.name}" />
- <!-- temporary copy of source to update timestamps -->
- <copy todir="_sourcedist">
- <fileset dir=".">
- <exclude name=".*" />
- <exclude name="**/.*" />
- <exclude name="*.class" />
- <exclude name="**/*.class" />
- <include name="LICENSE" />
- <include name="README" />
- <include name="build.xml" />
- <include name="jalview-jalopy.xml" />
- <include name="JalviewApplet.jpx" />
- <include name="JalviewX.jpx" />
- <include name="nbbuild.xml" />
- <include name="nbproject/genfiles.properties" />
- <include name="nbproject/project.properties" />
- <include name="nbproject/project.xml" />
- <include name="${sourceDir}/*.java" />
- <include name="${sourceDir}/**/*.java" />
- <include name="${sourceDir}/**/*.cdr" />
- <include name="${libDir}/**/*" />
- <include name="${resourceDir}/**/*" />
- <include name="${helpDir}/**/*" />
- <include name="appletlib/${jmolJar}" />
- <include name="appletlib/${jsonSimple}" />
- <include name="appletlib/${javaJson}" />
- <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/.build*.*/**" />
- <exclude name="utils/InstallAnywhere/**locale*" />
- <exclude name="utils/InstallAnywhere/**locale*/**" />
- <exclude name="utils/InstallAnywhere/**locale*/**" />
- <include name="${schemaDir}/**/*" />
- <include name="utils/**/*" />
- <include name="${docDir}/**/*" />
- <include name="examples/**/*" />
- </fileset>
- </copy>
-
- <tstamp prefix="build">
- <format property="year" pattern="yyyy" />
- </tstamp>
- <!-- each replacetoken CDATA body must be on one line -
- otherwise the pattern doesn't match -->
- <replace value="${JALVIEW_VERSION}">
- <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
- <fileset dir="_sourcedist">
- <include name="**/*" />
- </fileset>
- </replace>
- <replace dir="_sourcedist" value="${build.year}">
- <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
- <fileset dir="_sourcedist">
- <include name="**/*" />
- </fileset>
- </replace>
-
- <tar destfile="${source.dist.name}" compression="gzip">
- <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
- </tarfileset>
- </tar>
-
- <delete dir="_sourcedist" />
-</target>
-<target name="prepubapplet_1" depends="makeApplet">
- <copy todir="${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/${javaJson}" />
- <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
- <jar update="true" index="true" jarfile="${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="${applet.caller-codebase}" />
- </manifest>
- </jar>
-
- <presetdef name="ap_applet.jar">
- <!-- build a signed applet with 'all-permissions' -
- Needs 'param name="permissions' value="all-permissions"' in applet tag
- JalviewLite+JmolApplet linked sequence/structure fails
- Mixed code warnings are raised
- -->
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
- <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
- </manifest>
- </jar>
- </presetdef>
- <presetdef name="applet.jar">
- <!-- build signed applet with sandbox permissions -
- Needs 'param name="permissions' value="sandbox"' in applet tag
- Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
- -->
-
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="sandbox" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
- <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
- </manifest>
- </jar>
- </presetdef>
- <presetdef name="tl_applet.jar">
- <!-- build signed applet with trusted library/trusted permissions -
- Needs 'param name="permissions' value="all-permissions"' in applet tag
- j1.7_45:
- No mixed code warnings raised
- Jmol/JalviewLite sequence/structure example doesn't link structures
- Raises dialog asking user to allow page to control applet via LiveConnect javascript
-
- -->
-
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Trusted-Only" value="true" />
- <attribute name="Trusted-Library" value="true" />
- </manifest>
- </jar>
- </presetdef>
- <presetdef name="to_applet.jar">
- <!-- not fully test variant (yet) -->
- <jar update="true" index="true">
- <manifest>
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Codebase" value="${applet.codebase}" />
- <attribute name="Trusted-Only" value="true" />
- </manifest>
- </jar>
- </presetdef>
- <!-- create differently privileged artefacts -->
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
- <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
- <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
- <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
- <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
- <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
- <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
- <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
- <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
- <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
- <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
- <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
- <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
- <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
- <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
- <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
- <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
- <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
- <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
- <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
- <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
- <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
- <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
- <!-- finally, create manifest for original jars -->
- <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
- <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
- <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
- <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
-
- <!-- todo - write examples/downloads for alternate versions of the applet
- probably don't need to do this now since we don't have alternate versions anymore !-->
-</target>
-<target name="-signapplet" depends="prepubapplet_1">
- <fileset id="signappletjarset" dir="${packageDir}/examples">
- <exclude name="u_*.jar" />
- <include name="${jalviewLiteJar}" />
- <include name="${jmolJar}" />
- <include name="${javaJson}" />
- <include name="${jsonSimple}" />
- <include name="to_${jalviewLiteJar}" />
- <include name="to_${jmolJar}" />
- <include name="to_${javaJson}" />
- <include name="to_${jsonSimple}" />
- <include name="tl_${jalviewLiteJar}" />
- <include name="tl_${jmolJar}" />
- <include name="tl_${javaJson}" />
- <include name="tl_${jsonSimple}" />
- <include name="ap_${jalviewLiteJar}" />
- <include name="ap_${jmolJar}" />
- <include name="ap_${javaJson}" />
- <include name="ap_${jsonSimple}" />
- </fileset>
-</target>
-<target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
- <fileset refid="signappletjarset" />
- </signjar>
-</target>
-
-<target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
- <fileset refid="signappletjarset" />
- </signjar>
-</target>
-
-<target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
-
-<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
-
- <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
- <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
- <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
- <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
- <!-- finally, replace any launchApp servlet tags with a version specification -->
- <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
- <replacetoken>
- <![CDATA[http://www.jalview.org/services/launchApp"]]>
- </replacetoken>
- <fileset dir="${packageDir}/examples">
- <include name="**/*.html" />
- </fileset>
- </replace>
- <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
- <replacetoken>
- <![CDATA[http://www.jalview.org/services/launchApp']]>
- </replacetoken>
- <fileset dir="${packageDir}/examples">
- <include name="**/*.html" />
- </fileset>
- </replace>
-
-</target>
-<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
- <javadoc destdir="${javadocDir}">
- <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
- </packageset>
- </javadoc>
-</target>
-<target name="linkcheck" depends="init,prepare">
- <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
- <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
- <arg file="${helpDir}"/>
- <arg value="-nointernet"/>
- </java>
-</target>
-</project>
git://source.jalview.org / jalview.git / blobdiff