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