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