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="${ant.java.version}" arg2="9"/>
 108     </condition>
 109     <!-- Java 10 JVM args -->
 110     <condition property="java10">
 111       <equals arg1="${ant.java.version}" arg2="10"/>
 112     </condition>
 113     <!-- Java 11 JVM args -->
 114     <condition property="java11">
 115       <equals arg1="${ant.java.version}" arg2="11"/>
 116     </condition>
 117     <echo message="java version is ${ant.java.version}"/>
 118
 119     <!-- Don't change anything below here unless you know what you are doing! -->
 120     <!-- Url path for WebStart in JNLP file -->
 121     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
 122     <!-- Webstart Image - looked for in resources/images -->
 123     <property name="WebStartImage" value="JalviewLogo_big.png" />
 124     <!-- J2SE version needed for webstart launch -->
 125     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
 126     <property name="j2sev" value="1.7+" />
 127     <!-- Java Compilation settings - source and target javac version -->
 128     <property name="javac.source" value="1.8" />
 129     <property name="javac.target" value="1.8" />
 130
 131     <!-- Permissions for running Java applets and applications. -->
 132     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 133     <property name="application.codebase" value="*.jalview.org" />
 134     <!-- and allowing the applet to be deployed from any URL -->
 135     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
 136     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 137     <property name="applet.caller-codebase" value="${applet.codebase}" />
 138
 139     <!-- build directory configuration -->
 140     <property name="libDir" value="lib" />
 141     <property name="j11libDir" value="j11lib" />
 142     <property name="resourceDir" value="resources" />
 143     <property name="helpDir" value="help" />
 144     <property name="docDir" value="doc" />
 145     <property name="sourceDir" value="src" />
 146     <property name="schemaDir" value="schemas" />
 147     <property name="outputDir" value="classes" unless:set="clover.jar"/>
 148     <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
 149     <property name="packageDir" value="dist" />
 150     <property name="outputJar" value="jalview.jar" />
 151     <!-- Jalview Applet JMol Jar Dependency -->
 152     <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
 153     <property name="varnaJar" value="VARNAv3-93.jar" />
 154     <property name="jsoup" value="jsoup-1.8.1.jar" />
 155     <property name="jsonSimple" value="json_simple-1.1.jar" />
 156     <property name="javaJson" value="java-json.jar" />
 157     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 158     <property name="reportDir" value="test-reports" />
 159     <property name="testDir" value="test" />
 160     <property name="testOutputDir" value="tests" />
 161     <!-- switch to indicate if we should obfuscate jalviewLite -->
 162     <!-- <property name="donotobfuscate" value="true"/> -->
 163     <!-- switch to exclude associations from generated jnlp files -->
 164     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 165
 166     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 167     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 168     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 169     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 170     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 171     <property name="WSInterf" value="MsaWS" />
 172     <property name="wsdl.Namespace" value="vamsas" />
 173     <property name="wsdl.ClientNS" value="ext.vamsas" />
 174     <!-- the class path for building the application -->
 175     <path id="build.classpath">
 176       <fileset dir="utils">
 177         <include name="*.jar" />
 178         <include name="**/*.jar" />
 179       </fileset>
 180       <fileset dir="${j11libDir}">
 181         <include name="*.jar" />
 182         <include name="**/*.jar" />
 183       </fileset>
 184       <fileset dir="${libDir}">
 185         <include name="*.jar" />
 186         <include name="**/*.jar" />
 187       </fileset>
 188       <fileset dir="${java.home}/lib">
 189         <include name="plugin.jar" />
 190       </fileset>
 191       <fileset dir="appletlib">
 192         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 193                                 -->
 194         <include name="${jmolJar}" />
 195         <include name="${varnaJar}" />
 196       </fileset>
 197     </path>
 198     <path id="test.classpath">
 199       <pathelement path="${outputDir}" />
 200       <path refid="build.classpath" />
 201     </path>
 202     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 203     <!-- The Location of the java 1.1.8 jdk -->
 204     <property name="java118.home" value="${java.home}" />
 205     <!-- jre for 1.4 version -->
 206     <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
 207
 208     <!-- the classpath for building the 1.1 applet -->
 209     <path id="jalviewlite.deps">
 210       <fileset dir="${java118.home}">
 211         <include name="lib/rt.jar" />
 212       </fileset>
 213       <fileset dir="${java.home}/lib">
 214         <include name="plugin.jar" />
 215       </fileset>
 216       <pathelement location="appletlib/${jmolJar}" />
 217       <pathelement location="lib/${varnaJar}" />
 218       <pathelement location="appletlib/${jsoup}" />
 219       <pathelement location="appletlib/${jsonSimple}" />
 220       <pathelement location="appletlib/${javaJson}" />
 221
 222     </path>
 223     <!-- default location for outputting javadoc -->
 224     <property name="javadocDir" value="${packageDir}/javadoc" />
 225   </target>
 226
 227
 228   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 229   <target name="buildPropertiesFile" depends="init">
 230     <tstamp prefix="build">
 231       <format property="date" pattern="dd MMMM yyyy" />
 232     </tstamp>
 233     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 234       <arg value="rev-parse" />
 235       <arg value="--short" />
 236       <arg value="HEAD" />
 237     </exec>
 238     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 239       <arg value="rev-parse" />
 240       <arg value="--abbrev-ref" />
 241       <arg value="HEAD" />
 242     </exec>
 243     <properties file="${outputDir}/.build_properties">
 244       <header>
 245           ---Jalview Build Details---
 246         </header>
 247       <property name="VERSION" value="${JALVIEW_VERSION}" />
 248       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 249       <property name="BUILD_DATE" value="${build.date}" />
 250     </properties>
 251   </target>
 252
 253
 254   <target name="clean" depends="init">
 255     <!-- not efficient yet. -->
 256     <delete dir="${outputDir}" includes="*,**/*" />
 257   </target>
 258
 259   <target name="distclean" depends="init, clean">
 260
 261     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 262     <delete>
 263       <fileset dir=".">
 264         <include name="${outputJar}" />
 265         <include name="#*#" />
 266         <include name="#*.*#" />
 267         <include name="**/#*#" />
 268         <include name="**/#*.*#" />
 269         <include name="*~" />
 270         <include name="*.*~" />
 271         <include name="**/*~" />
 272         <include name="**/*.*~" />
 273       </fileset>
 274     </delete>
 275   </target>
 276
 277   <target name="prepare" depends="init">
 278     <mkdir dir="${outputDir}" />
 279     <copy todir="${outputDir}">
 280       <fileset dir=".">
 281         <include name="${docDir}/**/*.*" />
 282         <include name="${helpDir}/**/*.*" />
 283         <include name="${libDir}/*.jar" />
 284       </fileset>
 285       <fileset dir="${resourceDir}">
 286         <include name="**/*.*" />
 287       </fileset>
 288     </copy>
 289   </target>
 290
 291   <target name="build" depends="prepare">
 292     <!-- not efficient yet. -->
 293     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 294       <exclude name="jalview/*applet*" />
 295       <exclude name="jalview/appletgui/**" />
 296       <exclude name="com/stevesoft/**" />
 297     </javac>
 298   </target>
 299
 300
 301   <target name="testclean" depends="init">
 302     <delete dir="${testOutputDir}" includes="*,**/*" />
 303   </target>
 304
 305   <target name="prepareTests" depends="init,testclean">
 306     <mkdir dir="${testOutputDir}" />
 307   </target>
 308
 309   <target name="buildTests" depends="build,buildindices,prepareTests">
 310     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 311     </javac>
 312   </target>
 313
 314   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 315
 316   <target name="testng" depends="buildTests">
 317     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 318       verbose="2">
 319       <classpath>
 320         <pathelement location="${testOutputDir}" />
 321         <pathelement location="${clover.jar}" if:set="clover.jar"/>
 322         <path refid="test.classpath" />
 323       </classpath>
 324       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 325       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 326       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 327     </testng>
 328   </target>
 329
 330   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 331     <replace value="${JALVIEW_VERSION}">
 332       <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 333       <fileset dir="${outputDir}/${helpDir}">
 334         <include name="help.jhm" />
 335       </fileset>
 336     </replace>
 337
 338     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 339       <arg line="html" />
 340     </java>
 341   </target>
 342
 343   <target name="preparejnlp" depends="makedist">
 344     <copy todir="${packageDir}">
 345       <fileset dir="${resourceDir}/images">
 346         <include name="${WebStartImage}" />
 347       </fileset>
 348     </copy>
 349
 350     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 351
 352     <!-- create a dummy jar which will eventually contain the jnlp template -->
 353     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 354       <fileset dir="${packageDir}">
 355         <include name="jalview.jar" />
 356       </fileset>
 357     </jar>
 358
 359     <mkdir dir="${packageDir}/JNLP-INF" />
 360     <antcall target="writejnlpf">
 361       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 362       <param name="inih" value="*" />
 363       <param name="maxh" value="*" />
 364     </antcall>
 365
 366     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 367       <fileset dir="${packageDir}">
 368         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 369       </fileset>
 370     </jar>
 371
 372     <antcall target="writejnlpf">
 373       <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
 374       <param name="inih" value="10M" />
 375       <param name="maxh" value="256M" />
 376     </antcall>
 377     <antcall target="writejnlpf">
 378       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 379       <param name="inih" value="800M" />
 380       <param name="maxh" value="1024M" />
 381     </antcall>
 382
 383     <antcall target="writejnlpf">
 384       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 385       <param name="inih" value="128M" />
 386       <param name="maxh" value="512M" />
 387     </antcall>
 388
 389     <antcall target="writejnlpf">
 390       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 391       <param name="inih" value="800M" />
 392       <param name="maxh" value="1024M" />
 393     </antcall>
 394
 395     <!-- finally, need to postprocess to add in associations at end of 'information' element
 396
 397                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 398
 399                 </xslt>
 400
 401
 402                         -->
 403     <!--
 404                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 405         <association mime-type="application-x/ext-file" extensions="fasta"/>
 406         <association mime-type="application-x/ext-file" extensions="mfa"/>
 407         <association mime-type="application-x/ext-file" extensions="fastq"/>
 408         <association mime-type="application-x/ext-file" extensions="blc"/>
 409         <association mime-type="application-x/ext-file" extensions="msf"/>
 410         <association mime-type="application-x/ext-file" extensions="pfam"/>
 411         <association mime-type="application-x/ext-file" extensions="aln"/>
 412         <association mime-type="application-x/ext-file" extensions="pir"/>
 413         <association mime-type="application-x/ext-file" extensions="amsa"/>
 414         <association mime-type="application-x/ext-file" extensions="stk"/>
 415         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 416   </target>
 417
 418   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
 419     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
 420       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 421       <fileset dir="${packageDir}">
 422         <include name="*.jar" />
 423       </fileset>
 424     </signjar>
 425   </target>
 426   <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
 427     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
 428       <fileset dir="${packageDir}">
 429         <include name="*.jar" />
 430       </fileset>
 431     </signjar>
 432   </target>
 433
 434   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 435     <!-- and sign the jars -->
 436     <!-- the default keystore details might need to be edited here -->
 437   </target>
 438
 439   <target name="runenv" depends="init">
 440     <path id="run.classpath">
 441       <pathelement location="${outputDir}" />
 442       <fileset dir="${outputDir}">
 443         <include name="${libDir}/*.jar" />
 444       </fileset>
 445     </path>
 446     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 447
 448     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 449       </echo>
 450   </target>
 451
 452   <target name="-generatejnlpf">
 453     <presetdef name="jnlpf">
 454       <jnlp codebase="${WebStartLocation}">
 455         <information>
 456           <title>Jalview</title>
 457           <vendor>The Barton Group</vendor>
 458           <homepage href="http://www.jalview.org" />
 459           <description>Jalview Multiple Alignment Editor</description>
 460           <description kind="short">Jalview</description>
 461           <icon href="${WebStartImage}" />
 462           <offline_allowed />
 463         </information>
 464         <resources>
 465           <j2se version="1.8+" />
 466           <jar main="true" href="jalview.jar"/>
 467           <fileset dir="${packageDir}">
 468             <exclude name="jalview.jar" />
 469             <include name="*.jar" />
 470             <include name="*_*.jar" />
 471             <exclude name="*quaqua*.jar" />
 472           </fileset>
 473           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 474         </resources>
 475         <resources os="Mac OS X">
 476           <fileset dir="${packageDir}">
 477                  <include name="quaqua-filechooser-only-8.0.jar"/>
 478             <include name="*quaqua64*.jnilib.jar" />
 479           </fileset>
 480         </resources>
 481
 482         <application_desc main_class="jalview.bin.Jalview">
 483         </application_desc>
 484         <security>
 485           <all_permissions />
 486         </security>
 487       </jnlp>
 488     </presetdef>
 489
 490     <jnlpf toFile="${jnlpFile}" />
 491     <!-- add the add-modules j2se attribute for java 9 -->
 492     <replace file="${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;">
 493           <replacetoken>j2se version="1.8+"</replacetoken>
 494     </replace>
 495   </target>
 496
 497   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 498     <echo message="Not adding JNLP File Associations" />
 499   </target>
 500
 501   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 502     <replace file="${jnlpFile}">
 503       <replacetoken>
 504         <![CDATA[</information>]]></replacetoken>
 505       <replacevalue>
 506         <![CDATA[
 507           <association mime-type="application-x/ext-file" extensions="fa" />
 508         <association mime-type="application-x/ext-file" extensions="fasta" />
 509         <association mime-type="application-x/ext-file" extensions="mfa" />
 510         <association mime-type="application-x/ext-file" extensions="fastq" />
 511         <association mime-type="application-x/ext-file" extensions="blc" />
 512         <association mime-type="application-x/ext-file" extensions="msf" />
 513         <association mime-type="application-x/ext-file" extensions="pfam" />
 514         <association mime-type="application-x/ext-file" extensions="aln"/>
 515         <association mime-type="application-x/ext-file" extensions="pir"/>
 516         <association mime-type="application-x/ext-file" extensions="amsa"/>
 517         <association mime-type="application-x/ext-file" extensions="stk"/>
 518         <association mime-type="application-x/ext-file" extensions="jvp"/>
 519       </information>]]></replacevalue>
 520   </replace>
 521   <echo message="Added file associations to JNLP file" />
 522 </target>
 523 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 524 </target>
 525
 526 <target name="buildextclients" depends="init">
 527   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 528   <condition property="dontextbuild">
 529     <equals arg1="n" arg2="${doextbuild.response}" />
 530   </condition>
 531   <condition property="dontextbuild">
 532     <equals arg1="N" arg2="${doextbuild.response}" />
 533   </condition>
 534   <fail if="dontextbuild">
 535         Build External Client Code process aborted by user. Jalview source is unchanged.
 536       </fail>
 537   <!-- Currently, this doesn't happen automatically.
 538      1. Run WSDL2Java as below, which generates an ext.vamsas +
 539      vamsas.<datapackages> fileset.
 540      2. refactor ext.vamsas.SpecificserviceWS* to
 541      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 542      3. Update the jalview.ws.*WServices classes to reflect the
 543      interface type, and all locations of this wsdl type that Jalview
 544      might be using.
 545
 546 -->
 547   <path id="axisbuild">
 548     <path refid="build.classpath" />
 549   </path>
 550   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 551   <move todir="./bak">
 552     <fileset dir="${sourceDir}" id="client">
 553       <include name="${wsdl.ClientNS}/*.*" />
 554     </fileset>
 555   </move>
 556
 557   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 558     <mappingSet>
 559       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 560       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 561     </mappingSet>
 562   </axis-wsdl2java>
 563 </target>
 564
 565 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
 566   <fail if="clover.jar">
 567     Ignoring request to build jalview distribution with clover-instrumented classes
 568   </fail>
 569   <!-- make the package jar if not already existing -->
 570   <mkdir dir="${packageDir}" />
 571   <!-- clean dir if it already existed -->
 572   <delete>
 573     <fileset dir="${packageDir}">
 574       <include name="*.jar" />
 575     </fileset>
 576   </delete>
 577   <jar destfile="${packageDir}/${outputJar}" index="true">
 578     <manifest>
 579       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 580       <attribute name="Permissions" value="all-permissions" />
 581       <attribute name="Application-Name" value="Jalview Desktop" />
 582       <attribute name="Codebase" value="${application.codebase}" />
 583     </manifest>
 584     <fileset dir="${outputDir}/">
 585       <exclude name="cache*/**" />
 586       <exclude name="*.jar" />
 587       <exclude name="*.jar.*" />
 588       <exclude name="**/*.jar" />
 589       <exclude name="**/*.jar.*" />
 590     </fileset>
 591   </jar>
 592
 593   <copy toDir="${packageDir}" flatten="true">
 594     <fileset dir="${outputDir}">
 595       <include name="*.jar" />
 596       <include name="**/*.jar" />
 597     </fileset>
 598   </copy>
 599 </target>
 600
 601
 602 <!-- jalopy code reformatter -->
 603 <target name="sourcescrub" depends="init,build">
 604   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 605     <fileset dir="${sourceDir}">
 606       <include name="*.java" />
 607       <include name="**/*.java" />
 608       <include name="**/**/*.java" />
 609     </fileset>
 610   </jalopy>
 611 </target>
 612
 613
 614
 615 <!-- Compile, package and obfuscate Jalview Applet -->
 616 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 617
 618 <target name="compileApplet" depends="init,clean">
 619   <mkdir dir="${outputDir}" />
 620   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 621 </target>
 622
 623 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 624   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 625   <copy todir="${outputDir}/lang">
 626     <fileset dir="${resourceDir}/lang">
 627       <include name="**.*" />
 628     </fileset>
 629   </copy>
 630   <jar destfile="in.jar" index="true">
 631     <manifest>
 632       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 633       <attribute name="Application-Name" value="JalviewLite" />
 634       <attribute name="Codebase" value="${applet.codebase}" />
 635     </manifest>
 636     <fileset dir="${outputDir}">
 637       <include name="com/**" />
 638       <include name="MCview/**" />
 639       <include name="jalview/**" />
 640       <include name=".build_properties" />
 641       <include name="images/link.gif" />
 642       <include name="lang/**" />
 643     </fileset>
 644   </jar>
 645 </target>
 646 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 647 </target>
 648 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 649   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 650   <delete file="in.jar" />
 651 </target>
 652 <target name="-obfuscatereally" unless="donotobfuscate">
 653
 654   <path id="obfuscateDeps.path">
 655     <pathelement location="${applet.jre.tools}" />
 656     <pathelement location="appletlib/${jmolJar}" />
 657     <pathelement location="lib/${varnaJar}" />
 658     <pathelement location="appletlib/${jsoup}" />
 659     <pathelement location="appletlib/${jsonSimple}" />
 660     <pathelement location="appletlib/${javaJson}" />
 661     <fileset dir="${java.home}/lib">
 662       <include name="plugin.jar" />
 663     </fileset>
 664   </path>
 665   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
 666
 667   <proguard verbose="true" >
 668     <injar file="in.jar" />
 669     <outjar file="${jalviewLiteJar}" />
 670     <libraryjar refid="obfuscateDeps.path" />
 671     <dontwarn />
 672     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 673       <field access="public" />
 674       <method access="public" />
 675       <constructor access="public" />
 676     </keep>
 677     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 678       <field access="public" />
 679       <method access="public" />
 680       <constructor access="public" />
 681     </keep>
 682
 683     <keep name="jalview.json.binding**">
 684       <constructor/>
 685       <method name="*"/>
 686     </keep>
 687
 688     <keep access="public" type="class" name="MCview.PDBfile">
 689       <field access="public" />
 690       <method access="public" />
 691       <constructor access="public" />
 692     </keep>
 693
 694     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 695       <field access="public" />
 696       <method access="public" />
 697       <constructor access="public" />
 698     </keep>
 699
 700     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 701       <field access="public" />
 702       <method access="public" />
 703       <constructor access="public" />
 704     </keep>
 705
 706
 707     <!--      -libraryjars "${obfuscateDeps}"
 708       -injars      in.jar
 709       -outjars     jalviewApplet.jar
 710       -keep public class jalview.bin.JalviewLite
 711        { public * ; } -->
 712   </proguard>
 713   <delete file="in.jar" />
 714 </target>
 715
 716 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 717   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 718   <delete>
 719     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 720       <include name="*.java" />
 721       <include name="descriptors/*.java" />
 722     </fileset>
 723   </delete>
 724   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 725   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 726   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 727   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 728   <!--
 729                 now build the jalview.binding package with the old schema set
 730                 -->
 731   <delete>
 732     <fileset dir="${sourceDir}/jalview/binding/">
 733       <include name="**" />
 734     </fileset>
 735   </delete>
 736   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 737   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 738   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 739 </target>
 740 <target name="sourcedist" description="create jalview source distribution" depends="init">
 741   <delete file="${source.dist.name}" />
 742   <!-- temporary copy of source to update timestamps -->
 743   <copy todir="_sourcedist">
 744     <fileset dir=".">
 745       <exclude name=".*" />
 746       <exclude name="**/.*" />
 747       <exclude name="*.class" />
 748       <exclude name="**/*.class" />
 749       <include name="LICENSE" />
 750       <include name="README" />
 751       <include name="build.xml" />
 752       <include name="jalview-jalopy.xml" />
 753       <include name="JalviewApplet.jpx" />
 754       <include name="JalviewX.jpx" />
 755       <include name="nbbuild.xml" />
 756       <include name="nbproject/genfiles.properties" />
 757       <include name="nbproject/project.properties" />
 758       <include name="nbproject/project.xml" />
 759       <include name="${sourceDir}/*.java" />
 760       <include name="${sourceDir}/**/*.java" />
 761       <include name="${sourceDir}/**/*.cdr" />
 762       <include name="${libDir}/**/*" />
 763       <include name="${resourceDir}/**/*" />
 764       <include name="${helpDir}/**/*" />
 765       <include name="appletlib/${jmolJar}" />
 766       <include name="appletlib/${jsonSimple}" />
 767       <include name="appletlib/${javaJson}" />
 768       <exclude name="**/*locales" />
 769       <exclude name="*locales/**" />
 770       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 771       <exclude name="utils/InstallAnywhere/**Build*/**" />
 772       <exclude name="utils/InstallAnywhere/**Build*/**" />
 773       <exclude name="utils/InstallAnywhere/.build*.*/**" />
 774       <exclude name="utils/InstallAnywhere/**locale*" />
 775       <exclude name="utils/InstallAnywhere/**locale*/**" />
 776       <exclude name="utils/InstallAnywhere/**locale*/**" />
 777       <include name="${schemaDir}/**/*" />
 778       <include name="utils/**/*" />
 779       <include name="${docDir}/**/*" />
 780       <include name="examples/**/*" />
 781     </fileset>
 782   </copy>
 783
 784   <tstamp prefix="build">
 785     <format property="year" pattern="yyyy" />
 786   </tstamp>
 787   <!-- each replacetoken CDATA body must be on one line -
 788        otherwise the pattern doesn't match -->
 789   <replace value="${JALVIEW_VERSION}">
 790     <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 791     <fileset dir="_sourcedist">
 792       <include name="**/*" />
 793     </fileset>
 794   </replace>
 795   <replace dir="_sourcedist" value="${build.year}">
 796     <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
 797     <fileset dir="_sourcedist">
 798       <include name="**/*" />
 799     </fileset>
 800   </replace>
 801
 802   <tar destfile="${source.dist.name}" compression="gzip">
 803     <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
 804     </tarfileset>
 805   </tar>
 806
 807   <delete dir="_sourcedist" />
 808 </target>
 809 <target name="prepubapplet_1" depends="makeApplet">
 810   <copy todir="${packageDir}/examples">
 811     <fileset dir="examples">
 812       <include name="**/*" />
 813       <include name="javascript/*" />
 814       <include name="jmol/*" />
 815     </fileset>
 816     <fileset dir=".">
 817       <include name="${jalviewLiteJar}" />
 818     </fileset>
 819     <fileset dir="appletlib">
 820       <include name="**/*" />
 821     </fileset>
 822   </copy>
 823   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 824   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 825   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 826   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 827     <manifest>
 828       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 829       <!--          <attribute name="Permissions" value="sandbox" /> -->
 830       <!--<attribute name="Trusted-Lib" value="true" /> -->
 831       <attribute name="Codebase" value="${applet.codebase}" />
 832       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 833     </manifest>
 834   </jar>
 835
 836   <presetdef name="ap_applet.jar">
 837     <!-- build a signed applet with 'all-permissions' -
 838                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 839                           JalviewLite+JmolApplet linked sequence/structure fails
 840                           Mixed code warnings are raised
 841                           -->
 842     <jar update="true" index="true">
 843       <manifest>
 844         <attribute name="Application-Name" value="JalviewLite" />
 845         <attribute name="Permissions" value="all-permissions" />
 846         <attribute name="Codebase" value="${applet.codebase}" />
 847         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 848         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 849       </manifest>
 850     </jar>
 851   </presetdef>
 852   <presetdef name="applet.jar">
 853     <!-- build signed applet with sandbox permissions -
 854                           Needs 'param name="permissions' value="sandbox"' in applet tag
 855                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 856                         -->
 857
 858     <jar update="true" index="true">
 859       <manifest>
 860         <attribute name="Application-Name" value="JalviewLite" />
 861         <attribute name="Permissions" value="sandbox" />
 862         <attribute name="Codebase" value="${applet.codebase}" />
 863         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 864         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 865       </manifest>
 866     </jar>
 867   </presetdef>
 868   <presetdef name="tl_applet.jar">
 869     <!-- build signed applet with trusted library/trusted permissions -
 870                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 871                                j1.7_45:
 872                                No mixed code warnings raised
 873                                Jmol/JalviewLite sequence/structure example doesn't link structures
 874                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 875
 876                               -->
 877
 878     <jar update="true" index="true">
 879       <manifest>
 880         <attribute name="Application-Name" value="JalviewLite" />
 881         <attribute name="Permissions" value="all-permissions" />
 882         <attribute name="Codebase" value="${applet.codebase}" />
 883         <attribute name="Trusted-Only" value="true" />
 884         <attribute name="Trusted-Library" value="true" />
 885       </manifest>
 886     </jar>
 887   </presetdef>
 888   <presetdef name="to_applet.jar">
 889     <!-- not fully test variant (yet) -->
 890     <jar update="true" index="true">
 891       <manifest>
 892         <attribute name="Application-Name" value="JalviewLite" />
 893         <attribute name="Permissions" value="all-permissions" />
 894         <attribute name="Codebase" value="${applet.codebase}" />
 895         <attribute name="Trusted-Only" value="true" />
 896       </manifest>
 897     </jar>
 898   </presetdef>
 899   <!-- create differently privileged artefacts -->
 900   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 901   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 902   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 903   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 904   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 905   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 906   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 907   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 908   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 909   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 910   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 911   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 912   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 913   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 914   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 915   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 916   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 917   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 918   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 919   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 920   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 921   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 922   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 923   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 924   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 925   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 926   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 927   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 928   <!-- finally, create manifest for original jars -->
 929   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 930   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 931   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 932   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 933
 934   <!-- todo - write examples/downloads for alternate versions of the applet
 935     probably don't need to do this now since we don't have alternate versions anymore !-->
 936 </target>
 937 <target name="-signapplet" depends="prepubapplet_1">
 938   <fileset id="signappletjarset" dir="${packageDir}/examples">
 939     <exclude name="u_*.jar" />
 940     <include name="${jalviewLiteJar}" />
 941     <include name="${jmolJar}" />
 942     <include name="${javaJson}" />
 943     <include name="${jsonSimple}" />
 944     <include name="to_${jalviewLiteJar}" />
 945     <include name="to_${jmolJar}" />
 946     <include name="to_${javaJson}" />
 947     <include name="to_${jsonSimple}" />
 948     <include name="tl_${jalviewLiteJar}" />
 949     <include name="tl_${jmolJar}" />
 950     <include name="tl_${javaJson}" />
 951     <include name="tl_${jsonSimple}" />
 952     <include name="ap_${jalviewLiteJar}" />
 953     <include name="ap_${jmolJar}" />
 954     <include name="ap_${javaJson}" />
 955     <include name="ap_${jsonSimple}" />
 956   </fileset>
 957 </target>
 958 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
 959   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 960     <fileset refid="signappletjarset" />
 961   </signjar>
 962 </target>
 963
 964 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
 965   <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}">
 966     <fileset refid="signappletjarset" />
 967   </signjar>
 968 </target>
 969
 970 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
 971
 972 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 973
 974   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 975   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 976   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 977   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 978   <!-- finally, replace any launchApp servlet tags with a version specification -->
 979   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 980     <replacetoken>
 981       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 982     </replacetoken>
 983     <fileset dir="${packageDir}/examples">
 984       <include name="**/*.html" />
 985     </fileset>
 986   </replace>
 987   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 988     <replacetoken>
 989       <![CDATA[http://www.jalview.org/services/launchApp']]>
 990     </replacetoken>
 991     <fileset dir="${packageDir}/examples">
 992       <include name="**/*.html" />
 993     </fileset>
 994   </replace>
 995
 996 </target>
 997 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 998   <javadoc destdir="${javadocDir}">
 999     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
1000     </packageset>
1001   </javadoc>
1002 </target>
1003 <target name="linkcheck" depends="init,prepare">
1004   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
1005   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
1006     <arg file="${helpDir}"/>
1007     <arg value="-nointernet"/>
1008   </java>
1009 </target>
1010 </project>