build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <project name="jalviewX" default="usage" basedir="."
  21  xmlns:if="ant:if"
  22     xmlns:unless="ant:unless">
  23   <taskdef classpath="${clover.jar}" resource="cloverlib.xml" if:set="clover.jar"/>
  24   <clover-env if:set="clover.jar"/>
  25
  26   <target name="help" depends="usage" />
  27   <target name="usage" depends="init">
  28     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  29     <echo message="Targets include:" />
  30     <echo message="usage - default target, displays this message" />
  31     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  32     <echo message="build - compiles all necessary files for Application" />
  33     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  34     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  35     <echo message="              this needs a keystore and key."/>
  36     <echo message="              Add -Dtimestamp to timestamp signed jars"/>
  37     <echo message="              -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
  38     <echo message="              See docs/building.html for more information." />
  39     <echo message="compileApplet - compiles all necessary files for Applet" />
  40     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  41     <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
  42     <echo message="      you can specify particular test groups as a list via -Dtestng-groups=" />
  43     <echo message="See docs/building.html and the comments in build file for other targets." />
  44     <echo message="note: compile and makeApplet optionally compile/obfuscate applet against a different Java version by specifying -Djava118.home=PathtoJDK/lib which is the lib directory in the JDK install that contains rt.jar " />
  45     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  46     <echo message="Useful -D flags: -Dclover.jar to specify path to openclover for testng coverage report" />
  47   </target>
  48
  49
  50   <!-- utils is a class path to additional utilities needed for
  51     building docs, jars and webstart stuff -->
  52   <!--
  53         Userdefined build property defaults
  54
  55         wsdl.server list (plus namespace mapping info ???)  - also want
  56                 ... to make this a dynamically generatable property
  57         WebStart Location
  58         Build location - provide a temporary root for speed
  59         jarsigner keystore and info
  60         Jakarta and axis classpath ?
  61         Default argument for starting Jalview (if it exists).
  62
  63 -->
  64
  65   <target name="init">
  66     <path id="axis.classpath">
  67       <!-->
  68       <fileset dir="/usr/local/axis/lib">
  69         <include name="**/*.jar" />
  70       </fileset>
  71       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  72         <include name="**/*.jar"/>
  73         <include name="*.jar"/>
  74       </fileset> -->
  75       </path>
  76
  77     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  78     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  79
  80     <property name="INSTALLATION" value="Source" />
  81
  82     <!-- 2.4 (VAMSAS)" -->
  83     <!-- Include debugging information in javac true or false -->
  84     <property name="javac.debug" value="true" />
  85
  86     <!-- JarSigner Key Store for Webstart Distribution -->
  87     <property name="jalview.keystore" value="./keys/.keystore" />
  88     <!-- Keystore Password -->
  89     <property name="jalview.keystore.pass" value="alignmentisfun" />
  90     <!-- Key Name -->
  91     <property name="jalview.key" value="jalview" />
  92     <!-- Key Password -->
  93     <property name="jalview.key.pass" value="alignmentisfun" />
  94     <!-- time stamp server URL -->
  95     <property name="jalview.tsaurl" value="" />
  96     <!-- locally valid proxy for signing with external time server -->
  97     <property name="proxyPort" value="80"/>
  98     <property name="proxyHost" value="sqid"/>
  99     <!-- key sign/digest algorithms -->
 100     <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
 101     <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
 102
 103     <!-- default TestNG groups to run -->
 104     <property name="testng-groups" value="Functional" />
 105     <!-- Java 9 JVM args -->
 106     <condition property="java9">
 107       <equals arg1="${ant.java.version}" arg2="9"/>
 108     </condition>
 109
 110     <!-- Don't change anything below here unless you know what you are doing! -->
 111     <!-- Url path for WebStart in JNLP file -->
 112     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
 113     <!-- Webstart Image - looked for in resources/images -->
 114     <property name="WebStartImage" value="JalviewLogo_big.png" />
 115     <!-- J2SE version needed for webstart launch -->
 116     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
 117     <property name="j2sev" value="1.7+" />
 118     <!-- Java Compilation settings - source and target javac version -->
 119     <property name="javac.source" value="1.8" />
 120     <property name="javac.target" value="1.8" />
 121
 122     <!-- Permissions for running Java applets and applications. -->
 123     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 124     <property name="application.codebase" value="*.jalview.org" />
 125     <!-- and allowing the applet to be deployed from any URL -->
 126     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
 127     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 128     <property name="applet.caller-codebase" value="${applet.codebase}" />
 129
 130     <!-- build directory configuration -->
 131     <property name="libDir" value="lib" />
 132     <property name="resourceDir" value="resources" />
 133     <property name="helpDir" value="help" />
 134     <property name="docDir" value="doc" />
 135     <property name="sourceDir" value="src" />
 136     <property name="schemaDir" value="schemas" />
 137     <property name="outputDir" value="classes" unless:set="clover.jar"/>
 138     <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
 139     <property name="packageDir" value="dist" />
 140     <property name="outputJar" value="jalview.jar" />
 141     <!-- Jalview Applet JMol Jar Dependency -->
 142     <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
 143     <property name="varnaJar" value="VARNAv3-93.jar" />
 144     <property name="jsoup" value="jsoup-1.8.1.jar" />
 145     <property name="jsonSimple" value="json_simple-1.1.jar" />
 146     <property name="javaJson" value="java-json.jar" />
 147     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 148     <property name="reportDir" value="test-reports" />
 149     <property name="testDir" value="test" />
 150     <property name="testOutputDir" value="tests" />
 151     <!-- switch to indicate if we should obfuscate jalviewLite -->
 152     <!-- <property name="donotobfuscate" value="true"/> -->
 153     <!-- switch to exclude associations from generated jnlp files -->
 154     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 155
 156     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 157     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 158     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 159     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 160     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 161     <property name="WSInterf" value="MsaWS" />
 162     <property name="wsdl.Namespace" value="vamsas" />
 163     <property name="wsdl.ClientNS" value="ext.vamsas" />
 164     <!-- the class path for building the application -->
 165     <path id="build.classpath">
 166       <fileset dir="utils">
 167         <include name="*.jar" />
 168         <include name="**/*.jar" />
 169       </fileset>
 170       <fileset dir="${libDir}">
 171         <include name="*.jar" />
 172         <include name="**/*.jar" />
 173       </fileset>
 174       <fileset dir="${java.home}/lib">
 175         <include name="plugin.jar" />
 176       </fileset>
 177       <fileset dir="appletlib">
 178         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 179                                 -->
 180         <include name="${jmolJar}" />
 181         <include name="${varnaJar}" />
 182       </fileset>
 183     </path>
 184     <path id="test.classpath">
 185       <pathelement path="${outputDir}" />
 186       <path refid="build.classpath" />
 187     </path>
 188     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 189     <!-- The Location of the java 1.1.8 jdk -->
 190     <property name="java118.home" value="${java.home}" />
 191     <!-- jre for 1.4 version -->
 192     <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
 193
 194     <!-- the classpath for building the 1.1 applet -->
 195     <path id="jalviewlite.deps">
 196       <fileset dir="${java118.home}">
 197         <include name="lib/rt.jar" />
 198       </fileset>
 199       <fileset dir="${java.home}/lib">
 200         <include name="plugin.jar" />
 201       </fileset>
 202       <pathelement location="appletlib/${jmolJar}" />
 203       <pathelement location="lib/${varnaJar}" />
 204       <pathelement location="appletlib/${jsoup}" />
 205       <pathelement location="appletlib/${jsonSimple}" />
 206       <pathelement location="appletlib/${javaJson}" />
 207
 208     </path>
 209     <!-- default location for outputting javadoc -->
 210     <property name="javadocDir" value="${packageDir}/javadoc" />
 211   </target>
 212
 213
 214   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 215   <target name="buildPropertiesFile" depends="init">
 216     <tstamp prefix="build">
 217       <format property="date" pattern="dd MMMM yyyy" />
 218     </tstamp>
 219     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 220       <arg value="rev-parse" />
 221       <arg value="--short" />
 222       <arg value="HEAD" />
 223     </exec>
 224     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 225       <arg value="rev-parse" />
 226       <arg value="--abbrev-ref" />
 227       <arg value="HEAD" />
 228     </exec>
 229     <properties file="${outputDir}/.build_properties">
 230       <header>
 231           ---Jalview Build Details---
 232         </header>
 233       <property name="VERSION" value="${JALVIEW_VERSION}" />
 234       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 235       <property name="BUILD_DATE" value="${build.date}" />
 236     </properties>
 237   </target>
 238
 239
 240   <target name="clean" depends="init">
 241     <!-- not efficient yet. -->
 242     <delete dir="${outputDir}" includes="*,**/*" />
 243   </target>
 244
 245   <target name="distclean" depends="init, clean">
 246
 247     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 248     <delete>
 249       <fileset dir=".">
 250         <include name="${outputJar}" />
 251         <include name="#*#" />
 252         <include name="#*.*#" />
 253         <include name="**/#*#" />
 254         <include name="**/#*.*#" />
 255         <include name="*~" />
 256         <include name="*.*~" />
 257         <include name="**/*~" />
 258         <include name="**/*.*~" />
 259       </fileset>
 260     </delete>
 261   </target>
 262
 263   <target name="prepare" depends="init">
 264     <mkdir dir="${outputDir}" />
 265     <copy todir="${outputDir}">
 266       <fileset dir=".">
 267         <include name="${docDir}/**/*.*" />
 268         <include name="${helpDir}/**/*.*" />
 269         <include name="${libDir}/*.jar" />
 270       </fileset>
 271       <fileset dir="${resourceDir}">
 272         <include name="**/*.*" />
 273       </fileset>
 274     </copy>
 275   </target>
 276
 277   <target name="build" depends="prepare">
 278     <!-- not efficient yet. -->
 279     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 280       <exclude name="jalview/*applet*" />
 281       <exclude name="jalview/appletgui/**" />
 282       <exclude name="com/stevesoft/**" />
 283     </javac>
 284   </target>
 285
 286
 287   <target name="testclean" depends="init">
 288     <delete dir="${testOutputDir}" includes="*,**/*" />
 289   </target>
 290
 291   <target name="prepareTests" depends="init,testclean">
 292     <mkdir dir="${testOutputDir}" />
 293   </target>
 294
 295   <target name="buildTests" depends="build,buildindices,prepareTests">
 296     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 297     </javac>
 298   </target>
 299
 300   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 301
 302   <target name="testng" depends="buildTests">
 303     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 304       verbose="2">
 305       <classpath>
 306         <pathelement location="${testOutputDir}" />
 307         <pathelement location="${clover.jar}" if:set="clover.jar"/>
 308         <path refid="test.classpath" />
 309       </classpath>
 310       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 311       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 312       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 313     </testng>
 314   </target>
 315
 316   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 317     <replace value="${JALVIEW_VERSION}">
 318       <replacetoken><![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_256M.jnlp" />
 360       <param name="inih" value="10M" />
 361       <param name="maxh" value="256M" />
 362     </antcall>
 363     <antcall target="writejnlpf">
 364       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 365       <param name="inih" value="800M" />
 366       <param name="maxh" value="1024M" />
 367     </antcall>
 368
 369     <antcall target="writejnlpf">
 370       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 371       <param name="inih" value="128M" />
 372       <param name="maxh" value="512M" />
 373     </antcall>
 374
 375     <antcall target="writejnlpf">
 376       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 377       <param name="inih" value="800M" />
 378       <param name="maxh" value="1024M" />
 379     </antcall>
 380
 381     <!-- finally, need to postprocess to add in associations at end of 'information' element
 382
 383                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 384
 385                 </xslt>
 386
 387
 388                         -->
 389     <!--
 390                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 391         <association mime-type="application-x/ext-file" extensions="fasta"/>
 392         <association mime-type="application-x/ext-file" extensions="mfa"/>
 393         <association mime-type="application-x/ext-file" extensions="fastq"/>
 394         <association mime-type="application-x/ext-file" extensions="blc"/>
 395         <association mime-type="application-x/ext-file" extensions="msf"/>
 396         <association mime-type="application-x/ext-file" extensions="pfam"/>
 397         <association mime-type="application-x/ext-file" extensions="aln"/>
 398         <association mime-type="application-x/ext-file" extensions="pir"/>
 399         <association mime-type="application-x/ext-file" extensions="amsa"/>
 400         <association mime-type="application-x/ext-file" extensions="stk"/>
 401         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 402   </target>
 403
 404   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
 405     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
 406       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 407       <fileset dir="${packageDir}">
 408         <include name="*.jar" />
 409       </fileset>
 410     </signjar>
 411   </target>
 412   <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
 413     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
 414       <fileset dir="${packageDir}">
 415         <include name="*.jar" />
 416       </fileset>
 417     </signjar>
 418   </target>
 419
 420   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 421     <!-- and sign the jars -->
 422     <!-- the default keystore details might need to be edited here -->
 423   </target>
 424
 425   <target name="runenv" depends="init">
 426     <path id="run.classpath">
 427       <pathelement location="${outputDir}" />
 428       <fileset dir="${outputDir}">
 429         <include name="${libDir}/*.jar" />
 430       </fileset>
 431     </path>
 432     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 433
 434     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 435       </echo>
 436   </target>
 437
 438   <target name="-generatejnlpf">
 439     <presetdef name="jnlpf">
 440       <jnlp codebase="${WebStartLocation}">
 441         <information>
 442           <title>Jalview</title>
 443           <vendor>The Barton Group</vendor>
 444           <homepage href="http://www.jalview.org" />
 445           <description>Jalview Multiple Alignment Editor</description>
 446           <description kind="short">Jalview</description>
 447           <icon href="${WebStartImage}" />
 448           <offline_allowed />
 449         </information>
 450         <resources>
 451           <j2se version="1.8+" />
 452           <jar main="true" href="jalview.jar"/>
 453           <fileset dir="${packageDir}">
 454             <exclude name="jalview.jar" />
 455             <include name="*.jar" />
 456             <include name="*_*.jar" />
 457             <exclude name="*quaqua*.jar" />
 458           </fileset>
 459           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 460         </resources>
 461         <resources os="Mac OS X">
 462           <fileset dir="${packageDir}">
 463                  <include name="quaqua-filechooser-only-8.0.jar"/>
 464             <include name="*quaqua64*.jnilib.jar" />
 465           </fileset>
 466         </resources>
 467
 468         <application_desc main_class="jalview.bin.Jalview">
 469         </application_desc>
 470         <security>
 471           <all_permissions />
 472         </security>
 473       </jnlp>
 474     </presetdef>
 475
 476     <jnlpf toFile="${jnlpFile}" />
 477     <!-- add the add-modules j2se attribute for java 9 -->
 478     <replace file="${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;">
 479           <replacetoken>j2se version="1.8+"</replacetoken>
 480     </replace>
 481   </target>
 482
 483   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 484     <echo message="Not adding JNLP File Associations" />
 485   </target>
 486
 487   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 488     <replace file="${jnlpFile}">
 489       <replacetoken>
 490         <![CDATA[</information>]]></replacetoken>
 491       <replacevalue>
 492         <![CDATA[
 493           <association mime-type="application-x/ext-file" extensions="fa" />
 494         <association mime-type="application-x/ext-file" extensions="fasta" />
 495         <association mime-type="application-x/ext-file" extensions="mfa" />
 496         <association mime-type="application-x/ext-file" extensions="fastq" />
 497         <association mime-type="application-x/ext-file" extensions="blc" />
 498         <association mime-type="application-x/ext-file" extensions="msf" />
 499         <association mime-type="application-x/ext-file" extensions="pfam" />
 500         <association mime-type="application-x/ext-file" extensions="aln"/>
 501         <association mime-type="application-x/ext-file" extensions="pir"/>
 502         <association mime-type="application-x/ext-file" extensions="amsa"/>
 503         <association mime-type="application-x/ext-file" extensions="stk"/>
 504         <association mime-type="application-x/ext-file" extensions="jvp"/>
 505       </information>]]></replacevalue>
 506   </replace>
 507   <echo message="Added file associations to JNLP file" />
 508 </target>
 509 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 510 </target>
 511
 512 <target name="buildextclients" depends="init">
 513   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 514   <condition property="dontextbuild">
 515     <equals arg1="n" arg2="${doextbuild.response}" />
 516   </condition>
 517   <condition property="dontextbuild">
 518     <equals arg1="N" arg2="${doextbuild.response}" />
 519   </condition>
 520   <fail if="dontextbuild">
 521         Build External Client Code process aborted by user. Jalview source is unchanged.
 522       </fail>
 523   <!-- Currently, this doesn't happen automatically.
 524      1. Run WSDL2Java as below, which generates an ext.vamsas +
 525      vamsas.<datapackages> fileset.
 526      2. refactor ext.vamsas.SpecificserviceWS* to
 527      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 528      3. Update the jalview.ws.*WServices classes to reflect the
 529      interface type, and all locations of this wsdl type that Jalview
 530      might be using.
 531
 532 -->
 533   <path id="axisbuild">
 534     <path refid="build.classpath" />
 535   </path>
 536   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 537   <move todir="./bak">
 538     <fileset dir="${sourceDir}" id="client">
 539       <include name="${wsdl.ClientNS}/*.*" />
 540     </fileset>
 541   </move>
 542
 543   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 544     <mappingSet>
 545       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 546       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 547     </mappingSet>
 548   </axis-wsdl2java>
 549 </target>
 550
 551 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
 552   <fail if="clover.jar">
 553     Ignoring request to build jalview distribution with clover-instrumented classes
 554   </fail>
 555   <!-- make the package jar if not already existing -->
 556   <mkdir dir="${packageDir}" />
 557   <!-- clean dir if it already existed -->
 558   <delete>
 559     <fileset dir="${packageDir}">
 560       <include name="*.jar" />
 561     </fileset>
 562   </delete>
 563   <jar destfile="${packageDir}/${outputJar}" index="true">
 564     <manifest>
 565       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 566       <attribute name="Permissions" value="all-permissions" />
 567       <attribute name="Application-Name" value="Jalview Desktop" />
 568       <attribute name="Codebase" value="${application.codebase}" />
 569     </manifest>
 570     <fileset dir="${outputDir}/">
 571       <exclude name="cache*/**" />
 572       <exclude name="*.jar" />
 573       <exclude name="*.jar.*" />
 574       <exclude name="**/*.jar" />
 575       <exclude name="**/*.jar.*" />
 576     </fileset>
 577   </jar>
 578
 579   <copy toDir="${packageDir}" flatten="true">
 580     <fileset dir="${outputDir}">
 581       <include name="*.jar" />
 582       <include name="**/*.jar" />
 583     </fileset>
 584   </copy>
 585 </target>
 586
 587
 588 <!-- jalopy code reformatter -->
 589 <target name="sourcescrub" depends="init,build">
 590   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 591     <fileset dir="${sourceDir}">
 592       <include name="*.java" />
 593       <include name="**/*.java" />
 594       <include name="**/**/*.java" />
 595     </fileset>
 596   </jalopy>
 597 </target>
 598
 599
 600
 601 <!-- Compile, package and obfuscate Jalview Applet -->
 602 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 603
 604 <target name="compileApplet" depends="init,clean">
 605   <mkdir dir="${outputDir}" />
 606   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 607 </target>
 608
 609 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 610   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 611   <copy todir="${outputDir}/lang">
 612     <fileset dir="${resourceDir}/lang">
 613       <include name="**.*" />
 614     </fileset>
 615   </copy>
 616   <jar destfile="in.jar" index="true">
 617     <manifest>
 618       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 619       <attribute name="Application-Name" value="JalviewLite" />
 620       <attribute name="Codebase" value="${applet.codebase}" />
 621     </manifest>
 622     <fileset dir="${outputDir}">
 623       <include name="com/**" />
 624       <include name="MCview/**" />
 625       <include name="jalview/**" />
 626       <include name=".build_properties" />
 627       <include name="images/link.gif" />
 628       <include name="lang/**" />
 629     </fileset>
 630   </jar>
 631 </target>
 632 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 633 </target>
 634 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 635   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 636   <delete file="in.jar" />
 637 </target>
 638 <target name="-obfuscatereally" unless="donotobfuscate">
 639
 640   <path id="obfuscateDeps.path">
 641     <pathelement location="${applet.jre.tools}" />
 642     <pathelement location="appletlib/${jmolJar}" />
 643     <pathelement location="lib/${varnaJar}" />
 644     <pathelement location="appletlib/${jsoup}" />
 645     <pathelement location="appletlib/${jsonSimple}" />
 646     <pathelement location="appletlib/${javaJson}" />
 647     <fileset dir="${java.home}/lib">
 648       <include name="plugin.jar" />
 649     </fileset>
 650   </path>
 651   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
 652
 653   <proguard verbose="true" >
 654     <injar file="in.jar" />
 655     <outjar file="${jalviewLiteJar}" />
 656     <libraryjar refid="obfuscateDeps.path" />
 657     <dontwarn />
 658     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 659       <field access="public" />
 660       <method access="public" />
 661       <constructor access="public" />
 662     </keep>
 663     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 664       <field access="public" />
 665       <method access="public" />
 666       <constructor access="public" />
 667     </keep>
 668
 669     <keep name="jalview.json.binding**">
 670       <constructor/>
 671       <method name="*"/>
 672     </keep>
 673
 674     <keep access="public" type="class" name="MCview.PDBfile">
 675       <field access="public" />
 676       <method access="public" />
 677       <constructor access="public" />
 678     </keep>
 679
 680     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 681       <field access="public" />
 682       <method access="public" />
 683       <constructor access="public" />
 684     </keep>
 685
 686     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 687       <field access="public" />
 688       <method access="public" />
 689       <constructor access="public" />
 690     </keep>
 691
 692
 693     <!--      -libraryjars "${obfuscateDeps}"
 694       -injars      in.jar
 695       -outjars     jalviewApplet.jar
 696       -keep public class jalview.bin.JalviewLite
 697        { public * ; } -->
 698   </proguard>
 699   <delete file="in.jar" />
 700 </target>
 701
 702 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 703   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 704   <delete>
 705     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 706       <include name="*.java" />
 707       <include name="descriptors/*.java" />
 708     </fileset>
 709   </delete>
 710   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 711   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 712   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 713   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 714   <!--
 715                 now build the jalview.binding package with the old schema set
 716                 -->
 717   <delete>
 718     <fileset dir="${sourceDir}/jalview/binding/">
 719       <include name="**" />
 720     </fileset>
 721   </delete>
 722   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 723   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 724   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 725 </target>
 726 <target name="sourcedist" description="create jalview source distribution" depends="init">
 727   <delete file="${source.dist.name}" />
 728   <!-- temporary copy of source to update timestamps -->
 729   <copy todir="_sourcedist">
 730     <fileset dir=".">
 731       <exclude name=".*" />
 732       <exclude name="**/.*" />
 733       <exclude name="*.class" />
 734       <exclude name="**/*.class" />
 735       <include name="LICENSE" />
 736       <include name="README" />
 737       <include name="build.xml" />
 738       <include name="jalview-jalopy.xml" />
 739       <include name="JalviewApplet.jpx" />
 740       <include name="JalviewX.jpx" />
 741       <include name="nbbuild.xml" />
 742       <include name="nbproject/genfiles.properties" />
 743       <include name="nbproject/project.properties" />
 744       <include name="nbproject/project.xml" />
 745       <include name="${sourceDir}/*.java" />
 746       <include name="${sourceDir}/**/*.java" />
 747       <include name="${sourceDir}/**/*.cdr" />
 748       <include name="${libDir}/**/*" />
 749       <include name="${resourceDir}/**/*" />
 750       <include name="${helpDir}/**/*" />
 751       <include name="appletlib/${jmolJar}" />
 752       <include name="appletlib/${jsonSimple}" />
 753       <include name="appletlib/${javaJson}" />
 754       <exclude name="**/*locales" />
 755       <exclude name="*locales/**" />
 756       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 757       <exclude name="utils/InstallAnywhere/**Build*/**" />
 758       <exclude name="utils/InstallAnywhere/**Build*/**" />
 759       <exclude name="utils/InstallAnywhere/.build*.*/**" />
 760       <exclude name="utils/InstallAnywhere/**locale*" />
 761       <exclude name="utils/InstallAnywhere/**locale*/**" />
 762       <exclude name="utils/InstallAnywhere/**locale*/**" />
 763       <include name="${schemaDir}/**/*" />
 764       <include name="utils/**/*" />
 765       <include name="${docDir}/**/*" />
 766       <include name="examples/**/*" />
 767     </fileset>
 768   </copy>
 769
 770   <tstamp prefix="build">
 771     <format property="year" pattern="yyyy" />
 772   </tstamp>
 773   <!-- each replacetoken CDATA body must be on one line -
 774        otherwise the pattern doesn't match -->
 775   <replace value="${JALVIEW_VERSION}">
 776     <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 777     <fileset dir="_sourcedist">
 778       <include name="**/*" />
 779     </fileset>
 780   </replace>
 781   <replace dir="_sourcedist" value="${build.year}">
 782     <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
 783     <fileset dir="_sourcedist">
 784       <include name="**/*" />
 785     </fileset>
 786   </replace>
 787
 788   <tar destfile="${source.dist.name}" compression="gzip">
 789     <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
 790     </tarfileset>
 791   </tar>
 792
 793   <delete dir="_sourcedist" />
 794 </target>
 795 <target name="prepubapplet_1" depends="makeApplet">
 796   <copy todir="${packageDir}/examples">
 797     <fileset dir="examples">
 798       <include name="**/*" />
 799       <include name="javascript/*" />
 800       <include name="jmol/*" />
 801     </fileset>
 802     <fileset dir=".">
 803       <include name="${jalviewLiteJar}" />
 804     </fileset>
 805     <fileset dir="appletlib">
 806       <include name="**/*" />
 807     </fileset>
 808   </copy>
 809   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 810   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 811   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 812   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 813     <manifest>
 814       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 815       <!--          <attribute name="Permissions" value="sandbox" /> -->
 816       <!--<attribute name="Trusted-Lib" value="true" /> -->
 817       <attribute name="Codebase" value="${applet.codebase}" />
 818       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 819     </manifest>
 820   </jar>
 821
 822   <presetdef name="ap_applet.jar">
 823     <!-- build a signed applet with 'all-permissions' -
 824                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 825                           JalviewLite+JmolApplet linked sequence/structure fails
 826                           Mixed code warnings are raised
 827                           -->
 828     <jar update="true" index="true">
 829       <manifest>
 830         <attribute name="Application-Name" value="JalviewLite" />
 831         <attribute name="Permissions" value="all-permissions" />
 832         <attribute name="Codebase" value="${applet.codebase}" />
 833         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 834         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 835       </manifest>
 836     </jar>
 837   </presetdef>
 838   <presetdef name="applet.jar">
 839     <!-- build signed applet with sandbox permissions -
 840                           Needs 'param name="permissions' value="sandbox"' in applet tag
 841                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 842                         -->
 843
 844     <jar update="true" index="true">
 845       <manifest>
 846         <attribute name="Application-Name" value="JalviewLite" />
 847         <attribute name="Permissions" value="sandbox" />
 848         <attribute name="Codebase" value="${applet.codebase}" />
 849         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 850         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 851       </manifest>
 852     </jar>
 853   </presetdef>
 854   <presetdef name="tl_applet.jar">
 855     <!-- build signed applet with trusted library/trusted permissions -
 856                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 857                                j1.7_45:
 858                                No mixed code warnings raised
 859                                Jmol/JalviewLite sequence/structure example doesn't link structures
 860                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 861
 862                               -->
 863
 864     <jar update="true" index="true">
 865       <manifest>
 866         <attribute name="Application-Name" value="JalviewLite" />
 867         <attribute name="Permissions" value="all-permissions" />
 868         <attribute name="Codebase" value="${applet.codebase}" />
 869         <attribute name="Trusted-Only" value="true" />
 870         <attribute name="Trusted-Library" value="true" />
 871       </manifest>
 872     </jar>
 873   </presetdef>
 874   <presetdef name="to_applet.jar">
 875     <!-- not fully test variant (yet) -->
 876     <jar update="true" index="true">
 877       <manifest>
 878         <attribute name="Application-Name" value="JalviewLite" />
 879         <attribute name="Permissions" value="all-permissions" />
 880         <attribute name="Codebase" value="${applet.codebase}" />
 881         <attribute name="Trusted-Only" value="true" />
 882       </manifest>
 883     </jar>
 884   </presetdef>
 885   <!-- create differently privileged artefacts -->
 886   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 887   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 888   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 889   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 890   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 891   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 892   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 893   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 894   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 895   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 896   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 897   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 898   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 899   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 900   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 901   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 902   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 903   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 904   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 905   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 906   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 907   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 908   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 909   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 910   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 911   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 912   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 913   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 914   <!-- finally, create manifest for original jars -->
 915   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 916   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 917   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 918   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 919
 920   <!-- todo - write examples/downloads for alternate versions of the applet
 921     probably don't need to do this now since we don't have alternate versions anymore !-->
 922 </target>
 923 <target name="-signapplet" depends="prepubapplet_1">
 924   <fileset id="signappletjarset" dir="${packageDir}/examples">
 925     <exclude name="u_*.jar" />
 926     <include name="${jalviewLiteJar}" />
 927     <include name="${jmolJar}" />
 928     <include name="${javaJson}" />
 929     <include name="${jsonSimple}" />
 930     <include name="to_${jalviewLiteJar}" />
 931     <include name="to_${jmolJar}" />
 932     <include name="to_${javaJson}" />
 933     <include name="to_${jsonSimple}" />
 934     <include name="tl_${jalviewLiteJar}" />
 935     <include name="tl_${jmolJar}" />
 936     <include name="tl_${javaJson}" />
 937     <include name="tl_${jsonSimple}" />
 938     <include name="ap_${jalviewLiteJar}" />
 939     <include name="ap_${jmolJar}" />
 940     <include name="ap_${javaJson}" />
 941     <include name="ap_${jsonSimple}" />
 942   </fileset>
 943 </target>
 944 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
 945   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 946     <fileset refid="signappletjarset" />
 947   </signjar>
 948 </target>
 949
 950 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
 951   <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}">
 952     <fileset refid="signappletjarset" />
 953   </signjar>
 954 </target>
 955
 956 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
 957
 958 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 959
 960   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 961   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 962   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 963   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 964   <!-- finally, replace any launchApp servlet tags with a version specification -->
 965   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 966     <replacetoken>
 967       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 968     </replacetoken>
 969     <fileset dir="${packageDir}/examples">
 970       <include name="**/*.html" />
 971     </fileset>
 972   </replace>
 973   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 974     <replacetoken>
 975       <![CDATA[http://www.jalview.org/services/launchApp']]>
 976     </replacetoken>
 977     <fileset dir="${packageDir}/examples">
 978       <include name="**/*.html" />
 979     </fileset>
 980   </replace>
 981
 982 </target>
 983 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 984   <javadoc destdir="${javadocDir}">
 985     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 986     </packageset>
 987   </javadoc>
 988 </target>
 989 <target name="linkcheck" depends="init,prepare">
 990   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
 991   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
 992     <arg file="${helpDir}"/>
 993     <arg value="-nointernet"/>
 994   </java>
 995 </target>
 996 </project>