<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* 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=".">
+<project name="jalviewX" default="usage" basedir="."
+ xmlns:if="ant:if"
+ xmlns:unless="ant:unless">
+ <taskdef classpath="${clover.jar}" resource="cloverlib.xml" if:set="clover.jar"/>
+ <clover-env if:set="clover.jar"/>
+
<target name="help" depends="usage" />
<target name="usage" depends="init">
<echo message="~~~Jalview Ant build.xml Usage~~~~" />
<echo message="build - compiles all necessary files for Application" />
<echo message="makedist - compiles and places all necessary jar files into directory dist" />
<echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
- <echo message=" this needs a keystore and key. Add -Dtimestamp to timestamp signed jars"/>
+ <echo message=" this needs a keystore and key."/>
+ <echo message=" Add -Dtimestamp to timestamp signed jars"/>
+ <echo message=" -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
<echo message=" See docs/building.html for more information." />
<echo message="compileApplet - compiles all necessary files for Applet" />
<echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
<echo message="testng - run jalview's tests via testNG. Default group is '${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 require the property java118.home to be set to point to a java 1.1.8 jdk." />
+ <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>
<!-- 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="${ant.java.version}" arg2="9"/>
+ </condition>
<!-- Don't change anything below here unless you know what you are doing! -->
<!-- Url path for WebStart in JNLP file -->
<!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
<property name="j2sev" value="1.7+" />
<!-- Java Compilation settings - source and target javac version -->
- <property name="javac.source" value="1.7" />
- <property name="javac.target" value="1.7" />
+ <property name="javac.source" value="1.8" />
+ <property name="javac.target" value="1.8" />
<!-- Permissions for running Java applets and applications. -->
<!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
<property name="docDir" value="doc" />
<property name="sourceDir" value="src" />
<property name="schemaDir" value="schemas" />
- <property name="outputDir" value="classes" />
+ <property name="outputDir" value="classes" unless:set="clover.jar"/>
+ <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
<property name="packageDir" value="dist" />
<property name="outputJar" value="jalview.jar" />
<!-- Jalview Applet JMol Jar Dependency -->
- <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
+ <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
<property name="varnaJar" value="VARNAv3-93.jar" />
<property name="jsoup" value="jsoup-1.8.1.jar" />
<property name="jsonSimple" value="json_simple-1.1.jar" />
</path>
<property name="source.dist.name" value="${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="${java.home}/lib/rt.jar" />
+ <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
<!-- the classpath for building the 1.1 applet -->
<path id="jalviewlite.deps">
<fileset dir="${java118.home}">
- <include name="lib/classes.zip" />
+ <include name="lib/rt.jar" />
</fileset>
<fileset dir="${java.home}/lib">
<include name="plugin.jar" />
</fileset>
<pathelement location="appletlib/${jmolJar}" />
<pathelement location="lib/${varnaJar}" />
- <pathelement location="lib/${jsoup}" />
- <pathelement location="lib/${jsonSimple}" />
- <pathelement location="lib/${javaJson}" />
+ <pathelement location="appletlib/${jsoup}" />
+ <pathelement location="appletlib/${jsonSimple}" />
+ <pathelement location="appletlib/${javaJson}" />
</path>
<!-- default location for outputting javadoc -->
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>
</jar>
<antcall target="writejnlpf">
- <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
+ <param name="jnlpFile" value="${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" />
<antcall target="writejnlpf">
<param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
- <param name="inih" value="256M" />
+ <param name="inih" value="800M" />
<param name="maxh" value="1024M" />
</antcall>
<association mime-type="application-x/ext-file" extensions="jar"/>-->
</target>
- <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA"
+ <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
+ <signjar storepass="${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="${packageDir}">
<include name="*.jar" />
</fileset>
</signjar>
</target>
- <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
+ <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
+ <signjar storepass="${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>
<offline_allowed />
</information>
<resources>
- <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
- <fileset dir="${packageDir}">
- <include name="jalview.jar" />
- </fileset>
+ <j2se version="1.8+" />
+ <jar main="true" href="jalview.jar"/>
<fileset dir="${packageDir}">
+ <exclude name="jalview.jar" />
<include name="*.jar" />
<include name="*_*.jar" />
- <exclude name="jalview.jar" />
- <exclude name="*jnilib.jar" />
+ <exclude name="*quaqua*.jar" />
</fileset>
<property name="jalview.version" value="${JALVIEW_VERSION}" />
</resources>
<resources os="Mac OS X">
<fileset dir="${packageDir}">
- <include name="*quaqua*.jnilib.jar" />
+ <include name="quaqua-filechooser-only-8.0.jar"/>
+ <include name="*quaqua64*.jnilib.jar" />
</fileset>
</resources>
</presetdef>
<jnlpf toFile="${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="${maxh}" java-vm-args="--add-modules=java.se.ee --illegal-access=warn"">
+ <replacetoken>j2se version="1.8+"</replacetoken>
+ </replace>
</target>
<target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
</axis-wsdl2java>
</target>
-<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+<target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
+ <fail if="clover.jar">
+ Ignoring request to build jalview distribution with clover-instrumented classes
+ </fail>
<!-- make the package jar if not already existing -->
<mkdir dir="${packageDir}" />
<!-- clean dir if it already existed -->
<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/**" />
+ <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/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
<copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
<copy todir="${outputDir}/lang">
<fileset dir="${resourceDir}/lang">
<include name="MCview/**" />
<include name="jalview/**" />
<include name=".build_properties" />
- <include name="images/idwidth.gif" />
<include name="images/link.gif" />
<include name="lang/**" />
</fileset>
<path id="obfuscateDeps.path">
<pathelement location="${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.jar" />
+ <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
- <proguard>
+ <proguard verbose="true" >
<injar file="in.jar" />
<outjar file="${jalviewLiteJar}" />
<libraryjar refid="obfuscateDeps.path" />
<method access="public" />
<constructor access="public" />
</keep>
+
+ <keep name="jalview.json.binding**">
+ <constructor/>
+ <method name="*"/>
+ </keep>
+
+ <keep access="public" type="class" name="MCview.PDBfile">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+
+ <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+
+ <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+
+
<!-- -libraryjars "${obfuscateDeps}"
-injars in.jar
-outjars jalviewApplet.jar
<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" />
+<target name="jaxb-bindings" depends="init" description="Generates JAXB bindings for supported Jalview XML models (needs xjc on the path)">
<delete>
- <fileset dir="${sourceDir}/jalview/schemabinding/version2">
+ <fileset dir="${sourceDir}/jalview/xml/binding/jalview">
<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
- -->
+ <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="${sourceDir}/jalview/binding/">
- <include name="**" />
+ <fileset dir="${sourceDir}/jalview/xml/binding/embl">
+ <include name="*.java" />
</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="${schemaDir}/jalview.nodesc.properties" />
+
+ <exec executable="xjc">
+ <arg value="${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="${sourceDir}"/>
+ <arg value="-p"/>
+ <arg value="jalview.xml.binding.uniprot"/>
+ </exec>
</target>
+
<target name="sourcedist" description="create jalview source distribution" depends="init">
<delete file="${source.dist.name}" />
- <tar destfile="${source.dist.name}" compression="gzip">
- <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+ <!-- temporary copy of source to update timestamps -->
+ <copy todir="_sourcedist">
+ <fileset dir=".">
+ <exclude name=".*" />
+ <exclude name="**/.*" />
+ <exclude name="*.class" />
+ <exclude name="**/*.class" />
<include name="LICENSE" />
<include name="README" />
<include name="build.xml" />
<include name="${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">
<attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
</manifest>
</jar>
-</target>
-<target name="-signexdirsnotsa" depends="prepubapplet_1" unless="timestamp">
- <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
- <fileset dir="${packageDir}/examples">
- <include name="*.jar" />
- </fileset>
- </signjar>
-</target>
-<target name="-signexdirstsa" depends="prepubapplet_1" if="timestamp">
- <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
- <fileset dir="${packageDir}/examples">
- <include name="*.jar" />
- </fileset>
- </signjar>
-</target>
-<target name="prepubapplet_2" depends="-signexdirsnotsa,-signexdirstsa">
<presetdef name="ap_applet.jar">
<!-- build a signed applet with 'all-permissions' -
Needs 'param name="permissions' value="all-permissions"' in applet tag
<!-- 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_2">
- <fileset name="signappletjarset" dir="${packageDir}/examples">
+<target name="-signapplet" depends="prepubapplet_1">
+ <fileset id="signappletjarset" dir="${packageDir}/examples">
<exclude name="u_*.jar" />
<include name="${jalviewLiteJar}" />
<include name="${jmolJar}" />
<include name="ap_${jsonSimple}" />
</fileset>
</target>
-<target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
+<target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
<fileset refid="signappletjarset" />
</signjar>
</target>
-<target name="-signapplettsa" if="timestamp" depends="-signapplet">
+<target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
<signjar storepass="${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>
<!-- 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>
</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