<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* 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~~~~" />
<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" />
<!-- 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+"/>
-
+ <!-- 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="1.7"/>
+ <property name="javac.target" value="1.7"/>
+
<!-- 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" />
<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="jmolJar" value="JmolApplet-14.2.14_2015.06.11.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 -->
<!-- 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>
<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
<!-- The Location of the java 1.1.8 jdk -->
- <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
- -->
+ <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
<property name="java118.home" value="${java.home}" />
- <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
+ <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
-->
<!-- jre for 1.4 version -->
<property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
<include name="plugin.jar"/>
</fileset>
<pathelement location="appletlib/${jmolJar}" />
+ <pathelement location="lib/${varnaJar}" />
+ <pathelement location="lib/${jsoup}" />
+ <pathelement location="lib/${jsonSimple}" />
+ <pathelement location="lib/${javaJson}" />
+
</path>
<!-- default location for outputting javadoc -->
<property name="javadocDir" value="${packageDir}/javadoc"/>
<tstamp prefix="build">
<format property="date" pattern="dd MMMM yyyy" />
</tstamp>
+ <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
+ <arg value="rev-parse"/>
+ <arg value="--short"/>
+ <arg value="HEAD"/>
+ </exec>
+ <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
+ <arg value="rev-parse"/>
+ <arg value="--abbrev-ref"/>
+ <arg value="HEAD"/>
+ </exec>
<properties file="${outputDir}/.build_properties">
<header>
---Jalview Build Details---
- </header>
+ </header>
<property name="VERSION" value="${JALVIEW_VERSION}" />
+ <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
<property name="BUILD_DATE" value="${build.date}" />
</properties>
</target>
<target name="build" depends="prepare">
<!-- not efficient yet. -->
- <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
+ <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">
+ <mkdir dir="${testOutputDir}" />
+ <copy todir="${testOutputDir}">
+ <fileset dir=".">
+ <include name="${docDir}/**/*.*" />
+ <include name="${helpDir}/**/*.*" />
+ <include name="${libDir}/*.jar" />
+ </fileset>
+ <fileset dir="${resourceDir}">
+ <include name="**/*.*" />
+ </fileset>
+ </copy>
+ </target>
+
+ <target name="buildTests" depends="prepareTests">
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${testOutputDir}"
+ debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
+ </javac>
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}"
+ debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
+ </javac>
+ </target>
+
+ <taskdef name="testng" classname="org.testng.TestNGAntTask" >
+ <classpath location="utils/testnglibs/testng.jar" />
+ </taskdef>
+
+ <target name="testng" depends="buildTests">
+ <testng classpathref="build.classpath" outputDir="${reportDir}"
+ haltOnFailure="false">
+ <classpath location="${testOutputDir}" />
+ <xmlfileset dir="utils" includes="jalview_testng.xml" />
+ </testng>
+ </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" />
<include name="*.jar" />
<include name="*_*.jar" />
<exclude name="jalview.jar" />
+ <exclude name="*jnilib.jar"/>
</fileset>
+ </resources>
+ <resources os="Mac OS X">
<property name="jalview.version" value="${JALVIEW_VERSION}" />
+ <fileset dir="${packageDir}">
+ <include name="*quaqua*.jnilib.jar"/>
+ </fileset>
</resources>
+
<application_desc main_class="jalview.bin.Jalview">
</application_desc>
<security>
</presetdef>
<jnlpf toFile="${jnlpFile}"/>
-
+
</target>
-
+
<target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
<echo message="Not adding JNLP File Associations"/>
</target>
-
+
<target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
<replace file="${jnlpFile}">
<replacetoken>
<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>
+ </replace>
+ <echo message="Added file associations to JNLP file"/>
+</target>
<target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
</target>
<target name="compileApplet" depends="init,clean">
<mkdir dir="${outputDir}" />
- <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
- excludes="ext/**,MCview/**,org/**,vamsas/**" />
+ excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
</target>
<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
<path id="obfuscateDeps.path">
<pathelement location="${applet.jre.tools}" />
<pathelement location="appletlib/${jmolJar}" />
+ <pathelement location="appletlib/${jsonSimple}" />
+ <pathelement location="appletlib/${javaJson}" />
</path>
<taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
</fileset>
</copy>
<jar update="true" index="true" jarfile="${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/${jmolJar}">
<manifest>
<attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
<!-- create differently privileged artefacts -->
<copy file="${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/${jsonSimple}" />
<!-- todo - write examples/downloads for alternate versions of the applet -->
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
<exclude name="u_*.jar"/>
<include name="${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_${jsonSimple}" />
</fileset>
</signjar>
<!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
<copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+ <!-- 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}">
git://source.jalview.org / jalview.git / blobdiff