build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <project name="jalviewX" default="usage" basedir="."
  21  xmlns:if="ant:if"
  22     xmlns:unless="ant:unless">
  23   <taskdef classpath="${clover.jar}" resource="cloverlib.xml" if:set="clover.jar"/>
  24   <clover-env if:set="clover.jar"/>
  25
  26   <target name="help" depends="usage" />
  27   <target name="usage" depends="init">
  28     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  29     <echo message="Targets include:" />
  30     <echo message="usage - default target, displays this message" />
  31     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  32     <echo message="build - compiles all necessary files for Application" />
  33     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  34     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  35     <echo message="              this needs a keystore and key."/>
  36     <echo message="              Add -Dtimestamp to timestamp signed jars"/>
  37     <echo message="              -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
  38     <echo message="              See docs/building.html for more information." />
  39     <echo message="compileApplet - compiles all necessary files for Applet" />
  40     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  41     <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
  42     <echo message="      you can specify particular test groups as a list via -Dtestng-groups=" />
  43     <echo message="See docs/building.html and the comments in build file for other targets." />
  44     <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 " />
  45     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  46     <echo message="Useful -D flags: -Dclover.jar to specify path to openclover for testng coverage report" />
  47   </target>
  48
  49
  50   <!-- utils is a class path to additional utilities needed for
  51     building docs, jars and webstart stuff -->
  52   <!--
  53         Userdefined build property defaults
  54
  55         wsdl.server list (plus namespace mapping info ???)  - also want
  56                 ... to make this a dynamically generatable property
  57         WebStart Location
  58         Build location - provide a temporary root for speed
  59         jarsigner keystore and info
  60         Jakarta and axis classpath ?
  61         Default argument for starting Jalview (if it exists).
  62
  63 -->
  64
  65   <target name="init">
  66     <path id="axis.classpath">
  67       <!-->
  68       <fileset dir="/usr/local/axis/lib">
  69         <include name="**/*.jar" />
  70       </fileset>
  71       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  72         <include name="**/*.jar"/>
  73         <include name="*.jar"/>
  74       </fileset> -->
  75       </path>
  76
  77     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  78     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  79
  80     <property name="INSTALLATION" value="Source" />
  81
  82     <!-- 2.4 (VAMSAS)" -->
  83     <!-- Include debugging information in javac true or false -->
  84     <property name="javac.debug" value="true" />
  85
  86     <!-- JarSigner Key Store for Webstart Distribution -->
  87     <property name="jalview.keystore" value="./keys/.keystore" />
  88     <!-- Keystore Password -->
  89     <property name="jalview.keystore.pass" value="alignmentisfun" />
  90     <!-- Key Name -->
  91     <property name="jalview.key" value="jalview" />
  92     <!-- Key Password -->
  93     <property name="jalview.key.pass" value="alignmentisfun" />
  94     <!-- time stamp server URL -->
  95     <property name="jalview.tsaurl" value="" />
  96     <!-- locally valid proxy for signing with external time server -->
  97     <property name="proxyPort" value="80"/>
  98     <property name="proxyHost" value="sqid"/>
  99     <!-- key sign/digest algorithms -->
 100     <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
 101     <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
 102
 103     <!-- default TestNG groups to run -->
 104     <property name="testng-groups" value="Functional" />
 105     <!-- Java 9 JVM args -->
 106     <condition property="java9">
 107       <equals arg1="${ant.java.version}" arg2="9"/>
 108     </condition>
 109
 110     <!-- Don't change anything below here unless you know what you are doing! -->
 111     <!-- Url path for WebStart in JNLP file -->
 112     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
 113     <!-- Webstart Image - looked for in resources/images -->
 114     <property name="WebStartImage" value="JalviewLogo_big.png" />
 115     <!-- J2SE version needed for webstart launch -->
 116     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
 117     <property name="j2sev" value="1.7+" />
 118     <!-- Java Compilation settings - source and target javac version -->
 119     <property name="javac.source" value="1.8" />
 120     <property name="javac.target" value="1.8" />
 121
 122     <!-- Permissions for running Java applets and applications. -->
 123     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 124     <property name="application.codebase" value="*.jalview.org" />
 125     <!-- and allowing the applet to be deployed from any URL -->
 126     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
 127     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 128     <property name="applet.caller-codebase" value="${applet.codebase}" />
 129
 130     <!-- build directory configuration -->
 131     <property name="libDir" value="lib" />
 132     <property name="resourceDir" value="resources" />
 133     <property name="helpDir" value="help" />
 134     <property name="docDir" value="doc" />
 135     <property name="sourceDir" value="src" />
 136     <property name="schemaDir" value="schemas" />
 137     <property name="outputDir" value="classes" unless:set="clover.jar"/>
 138     <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
 139     <property name="packageDir" value="dist" />
 140     <property name="outputJar" value="jalview.jar" />
 141     <!-- Jalview Applet JMol Jar Dependency -->
 142     <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
 143     <property name="varnaJar" value="VARNAv3-93.jar" />
 144     <property name="jsoup" value="jsoup-1.8.1.jar" />
 145     <property name="jsonSimple" value="json_simple-1.1.jar" />
 146     <property name="javaJson" value="java-json.jar" />
 147     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 148     <property name="reportDir" value="test-reports" />
 149     <property name="testDir" value="test" />
 150     <property name="testOutputDir" value="tests" />
 151     <!-- switch to indicate if we should obfuscate jalviewLite -->
 152     <!-- <property name="donotobfuscate" value="true"/> -->
 153     <!-- switch to exclude associations from generated jnlp files -->
 154     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 155
 156     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 157     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 158     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 159     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 160     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 161     <property name="WSInterf" value="MsaWS" />
 162     <property name="wsdl.Namespace" value="vamsas" />
 163     <property name="wsdl.ClientNS" value="ext.vamsas" />
 164     <!-- the class path for building the application -->
 165     <path id="build.classpath">
 166       <fileset dir="utils">
 167         <include name="*.jar" />
 168         <include name="**/*.jar" />
 169       </fileset>
 170       <fileset dir="${libDir}">
 171         <include name="*.jar" />
 172         <include name="**/*.jar" />
 173       </fileset>
 174       <fileset dir="${java.home}/lib">
 175         <include name="plugin.jar" />
 176       </fileset>
 177       <fileset dir="appletlib">
 178         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 179                                 -->
 180         <include name="${jmolJar}" />
 181         <include name="${varnaJar}" />
 182       </fileset>
 183     </path>
 184     <path id="test.classpath">
 185       <pathelement path="${outputDir}" />
 186       <path refid="build.classpath" />
 187     </path>
 188     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 189     <!-- The Location of the java 1.1.8 jdk -->
 190     <property name="java118.home" value="${java.home}" />
 191     <!-- jre for 1.4 version -->
 192     <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
 193
 194     <!-- the classpath for building the 1.1 applet -->
 195     <path id="jalviewlite.deps">
 196       <fileset dir="${java118.home}">
 197         <include name="lib/rt.jar" />
 198       </fileset>
 199       <fileset dir="${java.home}/lib">
 200         <include name="plugin.jar" />
 201       </fileset>
 202       <pathelement location="appletlib/${jmolJar}" />
 203       <pathelement location="lib/${varnaJar}" />
 204       <pathelement location="appletlib/${jsoup}" />
 205       <pathelement location="appletlib/${jsonSimple}" />
 206       <pathelement location="appletlib/${javaJson}" />
 207
 208     </path>
 209     <!-- default location for outputting javadoc -->
 210     <property name="javadocDir" value="${packageDir}/javadoc" />
 211   </target>
 212
 213
 214   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 215   <target name="buildPropertiesFile" depends="init">
 216     <tstamp prefix="build">
 217       <format property="date" pattern="dd MMMM yyyy" />
 218     </tstamp>
 219     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 220       <arg value="rev-parse" />
 221       <arg value="--short" />
 222       <arg value="HEAD" />
 223     </exec>
 224     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 225       <arg value="rev-parse" />
 226       <arg value="--abbrev-ref" />
 227       <arg value="HEAD" />
 228     </exec>
 229     <properties file="${outputDir}/.build_properties">
 230       <header>
 231           ---Jalview Build Details---
 232         </header>
 233       <property name="VERSION" value="${JALVIEW_VERSION}" />
 234       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 235       <property name="BUILD_DATE" value="${build.date}" />
 236     </properties>
 237   </target>
 238
 239
 240   <target name="clean" depends="init">
 241     <!-- not efficient yet. -->
 242     <delete dir="${outputDir}" includes="*,**/*" />
 243   </target>
 244
 245   <target name="distclean" depends="init, clean">
 246
 247     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 248     <delete>
 249       <fileset dir=".">
 250         <include name="${outputJar}" />
 251         <include name="#*#" />
 252         <include name="#*.*#" />
 253         <include name="**/#*#" />
 254         <include name="**/#*.*#" />
 255         <include name="*~" />
 256         <include name="*.*~" />
 257         <include name="**/*~" />
 258         <include name="**/*.*~" />
 259       </fileset>
 260     </delete>
 261   </target>
 262
 263   <target name="prepare" depends="init">
 264     <mkdir dir="${outputDir}" />
 265     <copy todir="${outputDir}">
 266       <fileset dir=".">
 267         <include name="${docDir}/**/*.*" />
 268         <include name="${helpDir}/**/*.*" />
 269         <include name="${libDir}/*.jar" />
 270       </fileset>
 271       <fileset dir="${resourceDir}">
 272         <include name="**/*.*" />
 273       </fileset>
 274     </copy>
 275   </target>
 276
 277   <target name="build" depends="prepare">
 278     <!-- not efficient yet. -->
 279     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 280       <exclude name="jalview/*applet*" />
 281       <exclude name="jalview/appletgui/**" />
 282       <exclude name="com/stevesoft/**" />
 283     </javac>
 284   </target>
 285
 286
 287   <target name="testclean" depends="init">
 288     <delete dir="${testOutputDir}" includes="*,**/*" />
 289   </target>
 290
 291   <target name="prepareTests" depends="init,testclean">
 292     <mkdir dir="${testOutputDir}" />
 293   </target>
 294
 295   <target name="buildTests" depends="build,buildindices,prepareTests">
 296     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 297     </javac>
 298   </target>
 299
 300   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 301
 302   <target name="testng" depends="buildTests">
 303     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 304       verbose="2">
 305       <classpath>
 306         <pathelement location="${testOutputDir}" />
 307         <pathelement location="${clover.jar}" if:set="clover.jar"/>
 308         <path refid="test.classpath" />
 309       </classpath>
 310       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 311       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 312       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 313     </testng>
 314   </target>
 315
 316   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 317     <replace value="${JALVIEW_VERSION}">
 318       <replacetoken>
 319         <![CDATA[$$Version-Rel$$]]>
 320       </replacetoken>
 321       <fileset dir="${outputDir}/${helpDir}">
 322         <include name="help.jhm" />
 323       </fileset>
 324     </replace>
 325
 326     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 327       <arg line="html" />
 328     </java>
 329   </target>
 330
 331   <target name="preparejnlp" depends="makedist">
 332     <copy todir="${packageDir}">
 333       <fileset dir="${resourceDir}/images">
 334         <include name="${WebStartImage}" />
 335       </fileset>
 336     </copy>
 337
 338     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 339
 340     <!-- create a dummy jar which will eventually contain the jnlp template -->
 341     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 342       <fileset dir="${packageDir}">
 343         <include name="jalview.jar" />
 344       </fileset>
 345     </jar>
 346
 347     <mkdir dir="${packageDir}/JNLP-INF" />
 348     <antcall target="writejnlpf">
 349       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 350       <param name="inih" value="*" />
 351       <param name="maxh" value="*" />
 352     </antcall>
 353
 354     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 355       <fileset dir="${packageDir}">
 356         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 357       </fileset>
 358     </jar>
 359
 360     <antcall target="writejnlpf">
 361       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 362       <param name="inih" value="10M" />
 363       <param name="maxh" value="256M" />
 364     </antcall>
 365
 366     <antcall target="writejnlpf">
 367       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 368       <param name="inih" value="128M" />
 369       <param name="maxh" value="512M" />
 370     </antcall>
 371
 372     <antcall target="writejnlpf">
 373       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 374       <param name="inih" value="256M" />
 375       <param name="maxh" value="1024M" />
 376     </antcall>
 377
 378     <!-- finally, need to postprocess to add in associations at end of 'information' element
 379
 380                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 381
 382                 </xslt>
 383
 384
 385                         -->
 386     <!--
 387                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 388         <association mime-type="application-x/ext-file" extensions="fasta"/>
 389         <association mime-type="application-x/ext-file" extensions="mfa"/>
 390         <association mime-type="application-x/ext-file" extensions="fastq"/>
 391         <association mime-type="application-x/ext-file" extensions="blc"/>
 392         <association mime-type="application-x/ext-file" extensions="msf"/>
 393         <association mime-type="application-x/ext-file" extensions="pfam"/>
 394         <association mime-type="application-x/ext-file" extensions="aln"/>
 395         <association mime-type="application-x/ext-file" extensions="pir"/>
 396         <association mime-type="application-x/ext-file" extensions="amsa"/>
 397         <association mime-type="application-x/ext-file" extensions="stk"/>
 398         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 399   </target>
 400
 401   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
 402     <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}"
 403       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 404       <fileset dir="${packageDir}">
 405         <include name="*.jar" />
 406       </fileset>
 407     </signjar>
 408   </target>
 409   <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
 410     <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}">
 411       <fileset dir="${packageDir}">
 412         <include name="*.jar" />
 413       </fileset>
 414     </signjar>
 415   </target>
 416
 417   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 418     <!-- and sign the jars -->
 419     <!-- the default keystore details might need to be edited here -->
 420   </target>
 421
 422   <target name="runenv" depends="init">
 423     <path id="run.classpath">
 424       <pathelement location="${outputDir}" />
 425       <fileset dir="${outputDir}">
 426         <include name="${libDir}/*.jar" />
 427       </fileset>
 428     </path>
 429     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 430
 431     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 432       </echo>
 433   </target>
 434
 435   <target name="-generatejnlpf">
 436     <presetdef name="jnlpf">
 437       <jnlp codebase="${WebStartLocation}">
 438         <information>
 439           <title>Jalview</title>
 440           <vendor>The Barton Group</vendor>
 441           <homepage href="http://www.jalview.org" />
 442           <description>Jalview Multiple Alignment Editor</description>
 443           <description kind="short">Jalview</description>
 444           <icon href="${WebStartImage}" />
 445           <offline_allowed />
 446         </information>
 447         <resources>
 448           <j2se version="1.8+" />
 449           <jar main="true" href="jalview.jar"/>
 450           <fileset dir="${packageDir}">
 451             <exclude name="jalview.jar" />
 452             <include name="*.jar" />
 453             <include name="*_*.jar" />
 454             <exclude name="*quaqua*.jar" />
 455           </fileset>
 456           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 457         </resources>
 458         <resources os="Mac OS X">
 459           <fileset dir="${packageDir}">
 460             <include name="quaqua-filechooser-only-8.0.jar"/>
 461             <include name="*quaqua64*.jnilib.jar" />
 462           </fileset>
 463         </resources>
 464
 465         <application_desc main_class="jalview.bin.Jalview">
 466         </application_desc>
 467         <security>
 468           <all_permissions />
 469         </security>
 470       </jnlp>
 471     </presetdef>
 472
 473     <jnlpf toFile="${jnlpFile}" />
 474     <!-- add the add-modules j2se attribute for java 9 -->
 475     <replace file="${jnlpFile}" value="j2se version=&quot;1.8+&quot; initial-heap-size=&quot;${inih}&quot; max-heap-size=&quot;${maxh}&quot; java-vm-args=&quot;--add-modules=java.se.ee --illegal-access=warn&quot;">
 476       <replacetoken>j2se version="1.8+"</replacetoken>
 477     </replace>
 478   </target>
 479
 480   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 481     <echo message="Not adding JNLP File Associations" />
 482   </target>
 483
 484   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 485     <replace file="${jnlpFile}">
 486       <replacetoken>
 487         <![CDATA[</information>]]></replacetoken>
 488       <replacevalue>
 489         <![CDATA[
 490           <association mime-type="application-x/ext-file" extensions="fa" />
 491         <association mime-type="application-x/ext-file" extensions="fasta" />
 492         <association mime-type="application-x/ext-file" extensions="mfa" />
 493         <association mime-type="application-x/ext-file" extensions="fastq" />
 494         <association mime-type="application-x/ext-file" extensions="blc" />
 495         <association mime-type="application-x/ext-file" extensions="msf" />
 496         <association mime-type="application-x/ext-file" extensions="pfam" />
 497         <association mime-type="application-x/ext-file" extensions="aln"/>
 498         <association mime-type="application-x/ext-file" extensions="pir"/>
 499         <association mime-type="application-x/ext-file" extensions="amsa"/>
 500         <association mime-type="application-x/ext-file" extensions="stk"/>
 501         <association mime-type="application-x/ext-file" extensions="jvp"/>
 502       </information>]]></replacevalue>
 503   </replace>
 504   <echo message="Added file associations to JNLP file" />
 505 </target>
 506 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 507 </target>
 508
 509 <target name="buildextclients" depends="init">
 510   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 511   <condition property="dontextbuild">
 512     <equals arg1="n" arg2="${doextbuild.response}" />
 513   </condition>
 514   <condition property="dontextbuild">
 515     <equals arg1="N" arg2="${doextbuild.response}" />
 516   </condition>
 517   <fail if="dontextbuild">
 518         Build External Client Code process aborted by user. Jalview source is unchanged.
 519       </fail>
 520   <!-- Currently, this doesn't happen automatically.
 521      1. Run WSDL2Java as below, which generates an ext.vamsas +
 522      vamsas.<datapackages> fileset.
 523      2. refactor ext.vamsas.SpecificserviceWS* to
 524      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 525      3. Update the jalview.ws.*WServices classes to reflect the
 526      interface type, and all locations of this wsdl type that Jalview
 527      might be using.
 528
 529 -->
 530   <path id="axisbuild">
 531     <path refid="build.classpath" />
 532   </path>
 533   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 534   <move todir="./bak">
 535     <fileset dir="${sourceDir}" id="client">
 536       <include name="${wsdl.ClientNS}/*.*" />
 537     </fileset>
 538   </move>
 539
 540   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 541     <mappingSet>
 542       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 543       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 544     </mappingSet>
 545   </axis-wsdl2java>
 546 </target>
 547
 548 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
 549   <fail if="clover.jar">
 550     Ignoring request to build jalview distribution with clover-instrumented classes
 551   </fail>
 552   <!-- make the package jar if not already existing -->
 553   <mkdir dir="${packageDir}" />
 554   <!-- clean dir if it already existed -->
 555   <delete>
 556     <fileset dir="${packageDir}">
 557       <include name="*.jar" />
 558     </fileset>
 559   </delete>
 560   <jar destfile="${packageDir}/${outputJar}" index="true">
 561     <manifest>
 562       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 563       <attribute name="Permissions" value="all-permissions" />
 564       <attribute name="Application-Name" value="Jalview Desktop" />
 565       <attribute name="Codebase" value="${application.codebase}" />
 566     </manifest>
 567     <fileset dir="${outputDir}/">
 568       <exclude name="cache*/**" />
 569       <exclude name="*.jar" />
 570       <exclude name="*.jar.*" />
 571       <exclude name="**/*.jar" />
 572       <exclude name="**/*.jar.*" />
 573     </fileset>
 574   </jar>
 575
 576   <copy toDir="${packageDir}" flatten="true">
 577     <fileset dir="${outputDir}">
 578       <include name="*.jar" />
 579       <include name="**/*.jar" />
 580     </fileset>
 581   </copy>
 582 </target>
 583
 584
 585 <!-- jalopy code reformatter -->
 586 <target name="sourcescrub" depends="init,build">
 587   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 588     <fileset dir="${sourceDir}">
 589       <include name="*.java" />
 590       <include name="**/*.java" />
 591       <include name="**/**/*.java" />
 592     </fileset>
 593   </jalopy>
 594 </target>
 595
 596
 597
 598 <!-- Compile, package and obfuscate Jalview Applet -->
 599 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 600
 601 <target name="compileApplet" depends="init,clean">
 602   <mkdir dir="${outputDir}" />
 603   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 604 </target>
 605
 606 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 607   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 608   <copy todir="${outputDir}/lang">
 609     <fileset dir="${resourceDir}/lang">
 610       <include name="**.*" />
 611     </fileset>
 612   </copy>
 613   <jar destfile="in.jar" index="true">
 614     <manifest>
 615       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 616       <attribute name="Application-Name" value="JalviewLite" />
 617       <attribute name="Codebase" value="${applet.codebase}" />
 618     </manifest>
 619     <fileset dir="${outputDir}">
 620       <include name="com/**" />
 621       <include name="MCview/**" />
 622       <include name="jalview/**" />
 623       <include name=".build_properties" />
 624       <include name="images/link.gif" />
 625       <include name="lang/**" />
 626     </fileset>
 627   </jar>
 628 </target>
 629 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 630 </target>
 631 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 632   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 633   <delete file="in.jar" />
 634 </target>
 635 <target name="-obfuscatereally" unless="donotobfuscate">
 636
 637   <path id="obfuscateDeps.path">
 638     <pathelement location="${applet.jre.tools}" />
 639     <pathelement location="appletlib/${jmolJar}" />
 640     <pathelement location="lib/${varnaJar}" />
 641     <pathelement location="appletlib/${jsoup}" />
 642     <pathelement location="appletlib/${jsonSimple}" />
 643     <pathelement location="appletlib/${javaJson}" />
 644     <fileset dir="${java.home}/lib">
 645       <include name="plugin.jar" />
 646     </fileset>
 647   </path>
 648   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
 649
 650   <proguard verbose="true" >
 651     <injar file="in.jar" />
 652     <outjar file="${jalviewLiteJar}" />
 653     <libraryjar refid="obfuscateDeps.path" />
 654     <dontwarn />
 655     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 656       <field access="public" />
 657       <method access="public" />
 658       <constructor access="public" />
 659     </keep>
 660     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 661       <field access="public" />
 662       <method access="public" />
 663       <constructor access="public" />
 664     </keep>
 665
 666     <keep name="jalview.json.binding**">
 667       <constructor/>
 668       <method name="*"/>
 669     </keep>
 670
 671     <keep access="public" type="class" name="MCview.PDBfile">
 672       <field access="public" />
 673       <method access="public" />
 674       <constructor access="public" />
 675     </keep>
 676
 677     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 678       <field access="public" />
 679       <method access="public" />
 680       <constructor access="public" />
 681     </keep>
 682
 683     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 684       <field access="public" />
 685       <method access="public" />
 686       <constructor access="public" />
 687     </keep>
 688
 689
 690     <!--      -libraryjars "${obfuscateDeps}"
 691       -injars      in.jar
 692       -outjars     jalviewApplet.jar
 693       -keep public class jalview.bin.JalviewLite
 694        { public * ; } -->
 695   </proguard>
 696   <delete file="in.jar" />
 697 </target>
 698
 699 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 700   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 701   <delete>
 702     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 703       <include name="*.java" />
 704       <include name="descriptors/*.java" />
 705     </fileset>
 706   </delete>
 707   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 708   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 709   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 710   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 711   <!--
 712                 now build the jalview.binding package with the old schema set
 713                 -->
 714   <delete>
 715     <fileset dir="${sourceDir}/jalview/binding/">
 716       <include name="**" />
 717     </fileset>
 718   </delete>
 719   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 720   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 721   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 722 </target>
 723 <target name="sourcedist" description="create jalview source distribution" depends="init">
 724   <delete file="${source.dist.name}" />
 725   <!-- temporary copy of source to update timestamps -->
 726   <copy todir="_sourcedist">
 727     <fileset dir=".">
 728       <exclude name=".*" />
 729       <exclude name="**/.*" />
 730       <exclude name="*.class" />
 731       <exclude name="**/*.class" />
 732       <include name="LICENSE" />
 733       <include name="README" />
 734       <include name="build.xml" />
 735       <include name="jalview-jalopy.xml" />
 736       <include name="JalviewApplet.jpx" />
 737       <include name="JalviewX.jpx" />
 738       <include name="nbbuild.xml" />
 739       <include name="nbproject/genfiles.properties" />
 740       <include name="nbproject/project.properties" />
 741       <include name="nbproject/project.xml" />
 742       <include name="${sourceDir}/*.java" />
 743       <include name="${sourceDir}/**/*.java" />
 744       <include name="${sourceDir}/**/*.cdr" />
 745       <include name="${libDir}/**/*" />
 746       <include name="${resourceDir}/**/*" />
 747       <include name="${helpDir}/**/*" />
 748       <include name="appletlib/${jmolJar}" />
 749       <include name="appletlib/${jsonSimple}" />
 750       <include name="appletlib/${javaJson}" />
 751       <exclude name="**/*locales" />
 752       <exclude name="*locales/**" />
 753       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 754       <exclude name="utils/InstallAnywhere/**Build*/**" />
 755       <exclude name="utils/InstallAnywhere/**Build*/**" />
 756       <exclude name="utils/InstallAnywhere/.build*.*/**" />
 757       <exclude name="utils/InstallAnywhere/**locale*" />
 758       <exclude name="utils/InstallAnywhere/**locale*/**" />
 759       <exclude name="utils/InstallAnywhere/**locale*/**" />
 760       <include name="${schemaDir}/**/*" />
 761       <include name="utils/**/*" />
 762       <include name="${docDir}/**/*" />
 763       <include name="examples/**/*" />
 764     </fileset>
 765   </copy>
 766
 767   <tstamp prefix="build">
 768     <format property="year" pattern="yyyy" />
 769   </tstamp>
 770   <!-- each replacetoken CDATA body must be on one line -
 771        otherwise the pattern doesn't match -->
 772   <replace value="${JALVIEW_VERSION}">
 773     <replacetoken>
 774       <![CDATA[$$Version-Rel$$]]>
 775     </replacetoken>
 776     <fileset dir="_sourcedist">
 777       <include name="**/*" />
 778     </fileset>
 779   </replace>
 780   <replace dir="_sourcedist" value="${build.year}">
 781     <replacetoken>
 782       <![CDATA[$$Year-Rel$$]]>
 783     </replacetoken>
 784     <fileset dir="_sourcedist">
 785       <include name="**/*" />
 786     </fileset>
 787   </replace>
 788
 789   <tar destfile="${source.dist.name}" compression="gzip">
 790     <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
 791     </tarfileset>
 792   </tar>
 793
 794   <delete dir="_sourcedist" />
 795 </target>
 796 <target name="prepubapplet_1" depends="makeApplet">
 797   <copy todir="${packageDir}/examples">
 798     <fileset dir="examples">
 799       <include name="**/*" />
 800       <include name="javascript/*" />
 801       <include name="jmol/*" />
 802     </fileset>
 803     <fileset dir=".">
 804       <include name="${jalviewLiteJar}" />
 805     </fileset>
 806     <fileset dir="appletlib">
 807       <include name="**/*" />
 808     </fileset>
 809   </copy>
 810   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 811   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 812   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 813   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 814     <manifest>
 815       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 816       <!--          <attribute name="Permissions" value="sandbox" /> -->
 817       <!--<attribute name="Trusted-Lib" value="true" /> -->
 818       <attribute name="Codebase" value="${applet.codebase}" />
 819       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 820     </manifest>
 821   </jar>
 822
 823   <presetdef name="ap_applet.jar">
 824     <!-- build a signed applet with 'all-permissions' -
 825                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 826                           JalviewLite+JmolApplet linked sequence/structure fails
 827                           Mixed code warnings are raised
 828                           -->
 829     <jar update="true" index="true">
 830       <manifest>
 831         <attribute name="Application-Name" value="JalviewLite" />
 832         <attribute name="Permissions" value="all-permissions" />
 833         <attribute name="Codebase" value="${applet.codebase}" />
 834         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 835         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 836       </manifest>
 837     </jar>
 838   </presetdef>
 839   <presetdef name="applet.jar">
 840     <!-- build signed applet with sandbox permissions -
 841                           Needs 'param name="permissions' value="sandbox"' in applet tag
 842                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 843                         -->
 844
 845     <jar update="true" index="true">
 846       <manifest>
 847         <attribute name="Application-Name" value="JalviewLite" />
 848         <attribute name="Permissions" value="sandbox" />
 849         <attribute name="Codebase" value="${applet.codebase}" />
 850         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 851         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 852       </manifest>
 853     </jar>
 854   </presetdef>
 855   <presetdef name="tl_applet.jar">
 856     <!-- build signed applet with trusted library/trusted permissions -
 857                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 858                                j1.7_45:
 859                                No mixed code warnings raised
 860                                Jmol/JalviewLite sequence/structure example doesn't link structures
 861                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 862
 863                               -->
 864
 865     <jar update="true" index="true">
 866       <manifest>
 867         <attribute name="Application-Name" value="JalviewLite" />
 868         <attribute name="Permissions" value="all-permissions" />
 869         <attribute name="Codebase" value="${applet.codebase}" />
 870         <attribute name="Trusted-Only" value="true" />
 871         <attribute name="Trusted-Library" value="true" />
 872       </manifest>
 873     </jar>
 874   </presetdef>
 875   <presetdef name="to_applet.jar">
 876     <!-- not fully test variant (yet) -->
 877     <jar update="true" index="true">
 878       <manifest>
 879         <attribute name="Application-Name" value="JalviewLite" />
 880         <attribute name="Permissions" value="all-permissions" />
 881         <attribute name="Codebase" value="${applet.codebase}" />
 882         <attribute name="Trusted-Only" value="true" />
 883       </manifest>
 884     </jar>
 885   </presetdef>
 886   <!-- create differently privileged artefacts -->
 887   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 888   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 889   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 890   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 891   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 892   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 893   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 894   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 895   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 896   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 897   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 898   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 899   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 900   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 901   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 902   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 903   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 904   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 905   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 906   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 907   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 908   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 909   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 910   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 911   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 912   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 913   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 914   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 915   <!-- finally, create manifest for original jars -->
 916   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 917   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 918   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 919   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 920
 921   <!-- todo - write examples/downloads for alternate versions of the applet
 922     probably don't need to do this now since we don't have alternate versions anymore !-->
 923 </target>
 924 <target name="-signapplet" depends="prepubapplet_1">
 925   <fileset id="signappletjarset" dir="${packageDir}/examples">
 926     <exclude name="u_*.jar" />
 927     <include name="${jalviewLiteJar}" />
 928     <include name="${jmolJar}" />
 929     <include name="${javaJson}" />
 930     <include name="${jsonSimple}" />
 931     <include name="to_${jalviewLiteJar}" />
 932     <include name="to_${jmolJar}" />
 933     <include name="to_${javaJson}" />
 934     <include name="to_${jsonSimple}" />
 935     <include name="tl_${jalviewLiteJar}" />
 936     <include name="tl_${jmolJar}" />
 937     <include name="tl_${javaJson}" />
 938     <include name="tl_${jsonSimple}" />
 939     <include name="ap_${jalviewLiteJar}" />
 940     <include name="ap_${jmolJar}" />
 941     <include name="ap_${javaJson}" />
 942     <include name="ap_${jsonSimple}" />
 943   </fileset>
 944 </target>
 945 <target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
 946   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 947     <fileset refid="signappletjarset" />
 948   </signjar>
 949 </target>
 950
 951 <target name="-signapplettsa" if="timestamp" depends="-signapplet">
 952   <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}">
 953     <fileset refid="signappletjarset" />
 954   </signjar>
 955 </target>
 956
 957 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
 958
 959 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 960
 961   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 962   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 963   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 964   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 965   <!-- finally, replace any launchApp servlet tags with a version specification -->
 966   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 967     <replacetoken>
 968       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 969     </replacetoken>
 970     <fileset dir="${packageDir}/examples">
 971       <include name="**/*.html" />
 972     </fileset>
 973   </replace>
 974   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 975     <replacetoken>
 976       <![CDATA[http://www.jalview.org/services/launchApp']]>
 977     </replacetoken>
 978     <fileset dir="${packageDir}/examples">
 979       <include name="**/*.html" />
 980     </fileset>
 981   </replace>
 982
 983 </target>
 984 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 985   <javadoc destdir="${javadocDir}">
 986     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 987     </packageset>
 988   </javadoc>
 989 </target>
 990 <target name="linkcheck" depends="init,prepare">
 991   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
 992   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
 993     <arg file="${helpDir}"/>
 994     <arg value="-nointernet" />
 995   </java>
 996 </target>
 997
 998 <target name="eclipse-install" depends="init,prepare">
 999
1000   <property name="eclipseTempFile" value="eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
1001   <property name="eclipseInstallURL" value="http://mirror.csclub.uwaterloo.ca/eclipse/technology/epp/downloads/release/oxygen/R/eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
1002   <property name="java2scriptURL" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.core/dist/dropins/net.sf.j2s.core.jar?raw=true"/>
1003
1004   <get url="${eclipseInstallURL}" dest="${eclipseTempFile}"/>
1005   <untar compression="gzip" src="${eclipseTempFile}" dest="${eclipse-inst}"/>
1006
1007   <!-- not needed since we ship transpiler with source
1008     <get url="${java2scriptURL}" dest="eclipse-inst/dropins/net.sf.j2s.core.jar" /> -->
1009
1010 </target>
1011
1012 <target name="build-site" depends="init,prepare,compile-site,unzip-to-site">
1013   <!-- closure compile -->
1014   <!-- tarball -->
1015   <tar compression="gzip" destfile="site.tar.gz">
1016     <tarfileset dir="site" />
1017   </tar>
1018 </target>
1019 <target name="prepare-site" depends="init,prepare">
1020   <property name="swingjsdir" value="swingjs"/>
1021   <property name="eclipse-inst" value="/home/bamboo/buildtools/eclipse/eclipse-js"/>
1022   <property name="eclipse-exec" value="${eclipse-inst}/eclipse"/>
1023   <property name="site" value="site"/>
1024   <!-- where the eclipse js workspace has been initialised -->
1025   <property name="eclipse-work" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace"/>
1026   <!-- git repository linked to project in workspace -->
1027   <property name="eclipse-workrepo" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace/jalview-js"/>
1028 </target>
1029   <target name="clean-site" depends="prepare-site">
1030     <delete dir="${eclipse-workrepo}/${site}"/>
1031     <mkdir dir="${eclipse-workrepo}/${site}"/>
1032   </target>
1033 <target name="compile-site" depends="prepare-site,clean-site">
1034   <!-- update transpiler -->
1035   <copy file="${swingjsdir}/net.sf.j2s.core.jar" todir="${eclipse-inst}/dropins" overwrite="true" failonerror="true"/>
1036   <!-- update the git repo linked to the eclipse workspace -->
1037   <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="true">
1038     <arg value="rev-parse" />
1039     <arg value="--short" />
1040     <arg value="HEAD" />
1041   </exec>
1042   <!-- update and checkout the same commit in the workspace project -->
1043   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1044     <arg value="reset" />
1045     <arg value="--hard" />
1046   </exec>
1047   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1048       <arg value="pull" />
1049   </exec>
1050   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1051     <arg value="checkout" />
1052     <arg value="${git.commit}" />
1053   </exec>
1054   <!-- custom classpath for .js builds -->
1055   <copy file=".classpath.js" tofile="${eclipse-workrepo}/.classpath" overwrite="true"/>
1056   <!-- clean eclipse log -->
1057   <delete file="${eclipse-work}/.metadata/.log"/>
1058
1059   <!-- execute the eclipse build - the build may fail but valid javascript may still be produced, so we ignore return codes -->
1060   <exec executable="${eclipse-exec}" failonerror="no">
1061     <arg value="-nosplash"/>
1062     <arg value="--launcher.suppressErrors"/>
1063     <arg value="-application"/>
1064     <arg value="org.eclipse.jdt.apt.core.aptBuild"/>
1065     <arg value="-data"/>
1066     <arg value="${eclipse-work}"/>
1067   </exec>
1068   <!-- report log -->
1069   <exec executable="/bin/cat">
1070     <arg value="${eclipse-work}/.metadata/.log"/>
1071   </exec>
1072   <!-- TODO: run jslint and something else here to check we have a complete set of .js files for java -->
1073   <!-- possibly compare timestamps between .js files and their mate in source - any newer or not present triggers a new build -->
1074   <!-- <mkdir dir="${packageDir}/${site}" /> -->
1075   <!--   <property name="swingjs.zipurl" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.java.core/dist/SwingJS-site.zip?raw=true" /> -->
1076
1077   <!-- and reset the .classpath -->
1078   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1079     <arg value="checkout" />
1080     <arg value="${git.commit}"/>
1081     <arg value="--"/>
1082     <arg value=".classpath" />
1083   </exec>
1084
1085   <!-- finally copy artefacts from eclipse project checkout to the build site -->
1086   <copy todir="${site}">
1087     <fileset dir="${eclipse-workrepo}/site"/>
1088   </copy>
1089 </target>
1090 <target name="unzip-to-site" depends="prepare-site">
1091   <property name="swingjs.zip" value="${swingjsdir}/SwingJS-site.zip" />
1092   <unzip dest="${site}/" overwrite="true">
1093     <fileset dir="libjs">
1094       <include name="*.zip" />
1095     </fileset>
1096   </unzip>
1097   <copy overwrite="true" todir="${site}/swingjs/j2s/">
1098     <fileset dir="${resourceDir}">
1099       <include name="**"/>
1100     </fileset>
1101   </copy>
1102
1103   <!-- copy test files into place in site -->
1104   <copy todir="${site}/examples">
1105     <fileset dir="examples">
1106       <include name="*.*"/>
1107     </fileset>
1108   </copy>
1109   <!-- lastly, update SwingJS -->
1110   <unzip dest="${site}/" overwrite="true">
1111     <fileset dir="${swingjsdir}">
1112       <include name="SwingJS-site.zip"/>
1113     </fileset>
1114   </unzip>
1115 </target>
1116 </project>