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