build-j11.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="ant.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="11" if:set="java11" />
 129     <property name="javac.target" value="11" if:set="java11" />
 130     <property name="javac.source" value="1.8" unless:set="java11" />
 131     <property name="javac.target" value="1.8" unless:set="java11" />
 132     <echo message="javac.source is ${javac.source}"/>
 133     <echo message="javac.target is ${javac.target}"/>
 134
 135     <!-- Permissions for running Java applets and applications. -->
 136     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 137     <property name="application.codebase" value="*.jalview.org" />
 138     <!-- and allowing the applet to be deployed from any URL -->
 139     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
 140     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 141     <property name="applet.caller-codebase" value="${applet.codebase}" />
 142
 143     <!-- build directory configuration -->
 144     <property name="libDir" value="lib" />
 145     <property name="j11libDir" value="j11lib" />
 146     <property name="resourceDir" value="resources" />
 147     <property name="helpDir" value="help" />
 148     <property name="docDir" value="doc" />
 149     <property name="sourceDir" value="src" />
 150     <property name="schemaDir" value="schemas" />
 151     <property name="outputDir" value="classes" unless:set="clover.jar"/>
 152     <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
 153     <property name="packageDir" value="dist" />
 154     <property name="outputJar" value="jalview.jar" />
 155     <!-- Jalview Applet JMol Jar Dependency -->
 156     <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
 157     <property name="varnaJar" value="VARNAv3-93.jar" />
 158     <property name="jsoup" value="jsoup-1.8.1.jar" />
 159     <property name="jsonSimple" value="json_simple-1.1.jar" />
 160     <property name="javaJson" value="java-json.jar" />
 161     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 162     <property name="reportDir" value="test-reports" />
 163     <property name="testDir" value="test" />
 164     <property name="testOutputDir" value="tests" />
 165     <!-- switch to indicate if we should obfuscate jalviewLite -->
 166     <!-- <property name="donotobfuscate" value="true"/> -->
 167     <!-- switch to exclude associations from generated jnlp files -->
 168     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 169
 170     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 171     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 172     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 173     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 174     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 175     <property name="WSInterf" value="MsaWS" />
 176     <property name="wsdl.Namespace" value="vamsas" />
 177     <property name="wsdl.ClientNS" value="ext.vamsas" />
 178     <!-- the class path for building the application -->
 179     <path id="build.classpath">
 180       <fileset dir="utils">
 181         <include name="*.jar" />
 182         <include name="**/*.jar" />
 183       </fileset>
 184       <fileset dir="${j11libDir}">
 185         <include name="*.jar" />
 186         <include name="**/*.jar" />
 187       </fileset>
 188       <fileset dir="${libDir}">
 189         <include name="*.jar" />
 190         <include name="**/*.jar" />
 191       </fileset>
 192       <fileset dir="${java.home}/lib">
 193         <include name="plugin.jar" />
 194       </fileset>
 195       <fileset dir="appletlib">
 196         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 197                                 -->
 198         <include name="${jmolJar}" />
 199         <include name="${varnaJar}" />
 200       </fileset>
 201       <pathelement location="${clover.jar}" if:set="clover.jar"/>
 202     </path>
 203     <path id="test.classpath">
 204       <pathelement path="${outputDir}" />
 205       <path refid="build.classpath" />
 206     </path>
 207     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 208     <!-- The Location of the java 1.1.8 jdk -->
 209     <property name="java118.home" value="${java.home}" />
 210     <!-- jre for 1.4 version -->
 211     <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
 212
 213     <!-- the classpath for building the 1.1 applet -->
 214     <path id="jalviewlite.deps">
 215       <fileset dir="${java118.home}">
 216         <include name="lib/rt.jar" />
 217       </fileset>
 218       <fileset dir="${java.home}/lib">
 219         <include name="plugin.jar" />
 220       </fileset>
 221       <pathelement location="appletlib/${jmolJar}" />
 222       <pathelement location="lib/${varnaJar}" />
 223       <pathelement location="appletlib/${jsoup}" />
 224       <pathelement location="appletlib/${jsonSimple}" />
 225       <pathelement location="appletlib/${javaJson}" />
 226
 227     </path>
 228     <!-- default location for outputting javadoc -->
 229     <property name="javadocDir" value="${packageDir}/javadoc" />
 230   </target>
 231
 232
 233   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 234   <target name="buildPropertiesFile" depends="init">
 235     <tstamp prefix="build">
 236       <format property="date" pattern="dd MMMM yyyy" />
 237     </tstamp>
 238     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 239       <arg value="rev-parse" />
 240       <arg value="--short" />
 241       <arg value="HEAD" />
 242     </exec>
 243     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 244       <arg value="rev-parse" />
 245       <arg value="--abbrev-ref" />
 246       <arg value="HEAD" />
 247     </exec>
 248     <properties file="${outputDir}/.build_properties">
 249       <header>
 250           ---Jalview Build Details---
 251         </header>
 252       <property name="VERSION" value="${JALVIEW_VERSION}" />
 253       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 254       <property name="BUILD_DATE" value="${build.date}" />
 255     </properties>
 256   </target>
 257
 258
 259   <target name="clean" depends="init">
 260     <!-- not efficient yet. -->
 261     <delete dir="${outputDir}" includes="*,**/*" />
 262   </target>
 263
 264   <target name="distclean" depends="init, clean">
 265
 266     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 267     <delete>
 268       <fileset dir=".">
 269         <include name="${outputJar}" />
 270         <include name="#*#" />
 271         <include name="#*.*#" />
 272         <include name="**/#*#" />
 273         <include name="**/#*.*#" />
 274         <include name="*~" />
 275         <include name="*.*~" />
 276         <include name="**/*~" />
 277         <include name="**/*.*~" />
 278       </fileset>
 279     </delete>
 280   </target>
 281
 282   <target name="prepare" depends="init">
 283     <mkdir dir="${outputDir}" />
 284     <copy todir="${outputDir}">
 285       <fileset dir=".">
 286         <include name="${docDir}/**/*.*" />
 287         <include name="${helpDir}/**/*.*" />
 288         <include name="${libDir}/*.jar" />
 289       </fileset>
 290       <fileset dir="${resourceDir}">
 291         <include name="**/*.*" />
 292       </fileset>
 293     </copy>
 294   </target>
 295
 296   <target name="build" depends="prepare">
 297     <!-- not efficient yet. -->
 298     <!-- Echo the build.classpath
 299     <pathconvert property="echoClasspath" refid="build.classpath" />
 300     <echo message="build.classpath is '${echoClasspath}'" />
 301     -->
 302     <echo message="javac.target is '${javac.target}'" />
 303     <javac includeantruntime="false" source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 304       <exclude name="jalview/*applet*" />
 305       <exclude name="jalview/appletgui/**" />
 306       <exclude name="com/stevesoft/**" />
 307     </javac>
 308   </target>
 309
 310
 311   <target name="testclean" depends="init">
 312     <delete dir="${testOutputDir}" includes="*,**/*" />
 313   </target>
 314
 315   <target name="prepareTests" depends="init,testclean">
 316     <mkdir dir="${testOutputDir}" />
 317   </target>
 318
 319   <target name="buildTests" depends="build,buildindices,prepareTests">
 320     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 321     </javac>
 322   </target>
 323
 324   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 325
 326   <target name="testng" depends="buildTests">
 327     <loadfile property="j11modules" srcFile="modules"/>
 328     <echo message="j11libDir is '${j11libDir}'" />
 329     <echo message="j11modules is '${j11modules}'" />
 330     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 331       verbose="2">
 332       <classpath>
 333         <pathelement location="${testOutputDir}" />
 334         <pathelement location="${clover.jar}" if:set="clover.jar"/>
 335         <path refid="test.classpath" />
 336       </classpath>
 337       <jvmarg value="--module-path=${j11libDir}:${java.home}/jmods" if:set="java11"/>
 338       <jvmarg value="--add-modules=${j11modules}" if:set="java11"/>
 339       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 340       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 341       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 342     </testng>
 343   </target>
 344
 345   <target name="testngclass" depends="buildTests">
 346     <condition property="propsSpecified">
 347       <isset property="class.name" />
 348     </condition>
 349     <fail unless="propsSpecified" message="class.name property not specified."/>
 350     <echo message="testng-groups is '${testng-groups}'" />
 351     <loadfile property="j11modules" srcFile="modules"/>
 352     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng" verbose="2">
 353       <classpath>
 354         <pathelement location="${testOutputDir}" />
 355         <pathelement location="${clover.jar}" if:set="clover.jar"/>
 356         <path refid="test.classpath" />
 357       </classpath>
 358       <jvmarg value="--module-path=${j11libDir}:${java.home}/jmods" if:set="java11"/>
 359       <jvmarg value="--add-modules=${j11modules}" if:set="java11"/>
 360       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 361       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 362       <classfileset dir="${testOutputDir}" includes="${class.name}" />
 363     </testng>
 364   </target>
 365
 366   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 367     <replace value="${JALVIEW_VERSION}">
 368       <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 369       <fileset dir="${outputDir}/${helpDir}">
 370         <include name="help.jhm" />
 371       </fileset>
 372     </replace>
 373
 374     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 375       <arg line="html" />
 376     </java>
 377   </target>
 378
 379   <target name="preparejnlp" depends="makedist">
 380     <copy todir="${packageDir}">
 381       <fileset dir="${resourceDir}/images">
 382         <include name="${WebStartImage}" />
 383       </fileset>
 384     </copy>
 385
 386     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 387
 388     <!-- create a dummy jar which will eventually contain the jnlp template -->
 389     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 390       <fileset dir="${packageDir}">
 391         <include name="jalview.jar" />
 392       </fileset>
 393     </jar>
 394
 395     <mkdir dir="${packageDir}/JNLP-INF" />
 396     <antcall target="writejnlpf">
 397       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 398       <param name="inih" value="*" />
 399       <param name="maxh" value="*" />
 400     </antcall>
 401
 402     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 403       <fileset dir="${packageDir}">
 404         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 405       </fileset>
 406     </jar>
 407
 408     <antcall target="writejnlpf">
 409       <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
 410       <param name="inih" value="10M" />
 411       <param name="maxh" value="256M" />
 412     </antcall>
 413     <antcall target="writejnlpf">
 414       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 415       <param name="inih" value="800M" />
 416       <param name="maxh" value="1024M" />
 417     </antcall>
 418
 419     <antcall target="writejnlpf">
 420       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 421       <param name="inih" value="128M" />
 422       <param name="maxh" value="512M" />
 423     </antcall>
 424
 425     <antcall target="writejnlpf">
 426       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 427       <param name="inih" value="800M" />
 428       <param name="maxh" value="1024M" />
 429     </antcall>
 430
 431     <!-- finally, need to postprocess to add in associations at end of 'information' element
 432
 433                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 434
 435                 </xslt>
 436
 437
 438                         -->
 439     <!--
 440                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 441         <association mime-type="application-x/ext-file" extensions="fasta"/>
 442         <association mime-type="application-x/ext-file" extensions="mfa"/>
 443         <association mime-type="application-x/ext-file" extensions="fastq"/>
 444         <association mime-type="application-x/ext-file" extensions="blc"/>
 445         <association mime-type="application-x/ext-file" extensions="msf"/>
 446         <association mime-type="application-x/ext-file" extensions="pfam"/>
 447         <association mime-type="application-x/ext-file" extensions="aln"/>
 448         <association mime-type="application-x/ext-file" extensions="pir"/>
 449         <association mime-type="application-x/ext-file" extensions="amsa"/>
 450         <association mime-type="application-x/ext-file" extensions="stk"/>
 451         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 452   </target>
 453
 454   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
 455     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
 456       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 457       <fileset dir="${packageDir}">
 458         <include name="*.jar" />
 459       </fileset>
 460     </signjar>
 461   </target>
 462   <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
 463     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
 464       <fileset dir="${packageDir}">
 465         <include name="*.jar" />
 466       </fileset>
 467     </signjar>
 468   </target>
 469
 470   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 471     <!-- and sign the jars -->
 472     <!-- the default keystore details might need to be edited here -->
 473   </target>
 474
 475   <target name="runenv" depends="init">
 476     <path id="run.classpath">
 477       <pathelement location="${outputDir}" />
 478       <fileset dir="${outputDir}">
 479         <include name="${libDir}/*.jar" />
 480       </fileset>
 481     </path>
 482     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 483
 484     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 485       </echo>
 486   </target>
 487
 488   <target name="-generatejnlpf">
 489     <presetdef name="jnlpf">
 490       <jnlp codebase="${WebStartLocation}">
 491         <information>
 492           <title>Jalview</title>
 493           <vendor>The Barton Group</vendor>
 494           <homepage href="http://www.jalview.org" />
 495           <description>Jalview Multiple Alignment Editor</description>
 496           <description kind="short">Jalview</description>
 497           <icon href="${WebStartImage}" />
 498           <offline_allowed />
 499         </information>
 500         <resources>
 501           <j2se version="1.8+" />
 502           <jar main="true" href="jalview.jar"/>
 503           <fileset dir="${packageDir}">
 504             <exclude name="jalview.jar" />
 505             <include name="*.jar" />
 506             <include name="*_*.jar" />
 507             <exclude name="*quaqua*.jar" />
 508           </fileset>
 509           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 510         </resources>
 511         <resources os="Mac OS X">
 512           <fileset dir="${packageDir}">
 513                  <include name="quaqua-filechooser-only-8.0.jar"/>
 514             <include name="*quaqua64*.jnilib.jar" />
 515           </fileset>
 516         </resources>
 517
 518         <application_desc main_class="jalview.bin.Jalview">
 519         </application_desc>
 520         <security>
 521           <all_permissions />
 522         </security>
 523       </jnlp>
 524     </presetdef>
 525
 526     <jnlpf toFile="${jnlpFile}" />
 527     <!-- add the add-modules j2se attribute for java 9 -->
 528     <replace file="${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;">
 529           <replacetoken>j2se version="1.8+"</replacetoken>
 530     </replace>
 531   </target>
 532
 533   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 534     <echo message="Not adding JNLP File Associations" />
 535   </target>
 536
 537   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 538     <replace file="${jnlpFile}">
 539       <replacetoken>
 540         <![CDATA[</information>]]></replacetoken>
 541       <replacevalue>
 542         <![CDATA[
 543           <association mime-type="application-x/ext-file" extensions="fa" />
 544         <association mime-type="application-x/ext-file" extensions="fasta" />
 545         <association mime-type="application-x/ext-file" extensions="mfa" />
 546         <association mime-type="application-x/ext-file" extensions="fastq" />
 547         <association mime-type="application-x/ext-file" extensions="blc" />
 548         <association mime-type="application-x/ext-file" extensions="msf" />
 549         <association mime-type="application-x/ext-file" extensions="pfam" />
 550         <association mime-type="application-x/ext-file" extensions="aln"/>
 551         <association mime-type="application-x/ext-file" extensions="pir"/>
 552         <association mime-type="application-x/ext-file" extensions="amsa"/>
 553         <association mime-type="application-x/ext-file" extensions="stk"/>
 554         <association mime-type="application-x/ext-file" extensions="jvp"/>
 555       </information>]]></replacevalue>
 556   </replace>
 557   <echo message="Added file associations to JNLP file" />
 558 </target>
 559 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 560 </target>
 561
 562 <target name="buildextclients" depends="init">
 563   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 564   <condition property="dontextbuild">
 565     <equals arg1="n" arg2="${doextbuild.response}" />
 566   </condition>
 567   <condition property="dontextbuild">
 568     <equals arg1="N" arg2="${doextbuild.response}" />
 569   </condition>
 570   <fail if="dontextbuild">
 571         Build External Client Code process aborted by user. Jalview source is unchanged.
 572       </fail>
 573   <!-- Currently, this doesn't happen automatically.
 574      1. Run WSDL2Java as below, which generates an ext.vamsas +
 575      vamsas.<datapackages> fileset.
 576      2. refactor ext.vamsas.SpecificserviceWS* to
 577      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 578      3. Update the jalview.ws.*WServices classes to reflect the
 579      interface type, and all locations of this wsdl type that Jalview
 580      might be using.
 581
 582 -->
 583   <path id="axisbuild">
 584     <path refid="build.classpath" />
 585   </path>
 586   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 587   <move todir="./bak">
 588     <fileset dir="${sourceDir}" id="client">
 589       <include name="${wsdl.ClientNS}/*.*" />
 590     </fileset>
 591   </move>
 592
 593   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 594     <mappingSet>
 595       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 596       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 597     </mappingSet>
 598   </axis-wsdl2java>
 599 </target>
 600
 601 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
 602   <fail if="clover.jar">
 603     Ignoring request to build jalview distribution with clover-instrumented classes
 604   </fail>
 605   <!-- make the package jar if not already existing -->
 606   <mkdir dir="${packageDir}" />
 607   <!-- clean dir if it already existed -->
 608   <delete>
 609     <fileset dir="${packageDir}">
 610       <include name="*.jar" />
 611     </fileset>
 612   </delete>
 613   <jar destfile="${packageDir}/${outputJar}" index="true">
 614     <manifest>
 615       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 616       <attribute name="Permissions" value="all-permissions" />
 617       <attribute name="Application-Name" value="Jalview Desktop" />
 618       <attribute name="Codebase" value="${application.codebase}" />
 619     </manifest>
 620     <fileset dir="${outputDir}/">
 621       <exclude name="cache*/**" />
 622       <exclude name="*.jar" />
 623       <exclude name="*.jar.*" />
 624       <exclude name="**/*.jar" />
 625       <exclude name="**/*.jar.*" />
 626     </fileset>
 627   </jar>
 628
 629   <copy toDir="${packageDir}" flatten="true">
 630     <fileset dir="${outputDir}">
 631       <include name="*.jar" />
 632       <include name="**/*.jar" />
 633     </fileset>
 634   </copy>
 635 </target>
 636
 637
 638 <!-- jalopy code reformatter -->
 639 <target name="sourcescrub" depends="init,build">
 640   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 641     <fileset dir="${sourceDir}">
 642       <include name="*.java" />
 643       <include name="**/*.java" />
 644       <include name="**/**/*.java" />
 645     </fileset>
 646   </jalopy>
 647 </target>
 648
 649
 650
 651 <!-- Compile, package and obfuscate Jalview Applet -->
 652 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 653
 654 <target name="compileApplet" depends="init,clean">
 655   <mkdir dir="${outputDir}" />
 656   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 657 </target>
 658
 659 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 660   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 661   <copy todir="${outputDir}/lang">
 662     <fileset dir="${resourceDir}/lang">
 663       <include name="**.*" />
 664     </fileset>
 665   </copy>
 666   <jar destfile="in.jar" index="true">
 667     <manifest>
 668       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 669       <attribute name="Application-Name" value="JalviewLite" />
 670       <attribute name="Codebase" value="${applet.codebase}" />
 671     </manifest>
 672     <fileset dir="${outputDir}">
 673       <include name="com/**" />
 674       <include name="MCview/**" />
 675       <include name="jalview/**" />
 676       <include name=".build_properties" />
 677       <include name="images/link.gif" />
 678       <include name="lang/**" />
 679     </fileset>
 680   </jar>
 681 </target>
 682 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 683 </target>
 684 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 685   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 686   <delete file="in.jar" />
 687 </target>
 688 <target name="-obfuscatereally" unless="donotobfuscate">
 689
 690   <path id="obfuscateDeps.path">
 691     <pathelement location="${applet.jre.tools}" />
 692     <pathelement location="appletlib/${jmolJar}" />
 693     <pathelement location="lib/${varnaJar}" />
 694     <pathelement location="appletlib/${jsoup}" />
 695     <pathelement location="appletlib/${jsonSimple}" />
 696     <pathelement location="appletlib/${javaJson}" />
 697     <fileset dir="${java.home}/lib">
 698       <include name="plugin.jar" />
 699     </fileset>
 700   </path>
 701   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
 702
 703   <proguard verbose="true" >
 704     <injar file="in.jar" />
 705     <outjar file="${jalviewLiteJar}" />
 706     <libraryjar refid="obfuscateDeps.path" />
 707     <dontwarn />
 708     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 709       <field access="public" />
 710       <method access="public" />
 711       <constructor access="public" />
 712     </keep>
 713     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 714       <field access="public" />
 715       <method access="public" />
 716       <constructor access="public" />
 717     </keep>
 718
 719     <keep name="jalview.json.binding**">
 720       <constructor/>
 721       <method name="*"/>
 722     </keep>
 723
 724     <keep access="public" type="class" name="MCview.PDBfile">
 725       <field access="public" />
 726       <method access="public" />
 727       <constructor access="public" />
 728     </keep>
 729
 730     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 731       <field access="public" />
 732       <method access="public" />
 733       <constructor access="public" />
 734     </keep>
 735
 736     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 737       <field access="public" />
 738       <method access="public" />
 739       <constructor access="public" />
 740     </keep>
 741
 742
 743     <!--      -libraryjars "${obfuscateDeps}"
 744       -injars      in.jar
 745       -outjars     jalviewApplet.jar
 746       -keep public class jalview.bin.JalviewLite
 747        { public * ; } -->
 748   </proguard>
 749   <delete file="in.jar" />
 750 </target>
 751
 752 <target name="sourcedist" description="create jalview source distribution" depends="init">
 753   <delete file="${source.dist.name}" />
 754   <!-- temporary copy of source to update timestamps -->
 755   <copy todir="_sourcedist">
 756     <fileset dir=".">
 757       <exclude name=".*" />
 758       <exclude name="**/.*" />
 759       <exclude name="*.class" />
 760       <exclude name="**/*.class" />
 761       <include name="LICENSE" />
 762       <include name="README" />
 763       <include name="build.xml" />
 764       <include name="jalview-jalopy.xml" />
 765       <include name="JalviewApplet.jpx" />
 766       <include name="JalviewX.jpx" />
 767       <include name="nbbuild.xml" />
 768       <include name="nbproject/genfiles.properties" />
 769       <include name="nbproject/project.properties" />
 770       <include name="nbproject/project.xml" />
 771       <include name="${sourceDir}/*.java" />
 772       <include name="${sourceDir}/**/*.java" />
 773       <include name="${sourceDir}/**/*.cdr" />
 774       <include name="${libDir}/**/*" />
 775       <include name="${resourceDir}/**/*" />
 776       <include name="${helpDir}/**/*" />
 777       <include name="appletlib/${jmolJar}" />
 778       <include name="appletlib/${jsonSimple}" />
 779       <include name="appletlib/${javaJson}" />
 780       <exclude name="**/*locales" />
 781       <exclude name="*locales/**" />
 782       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 783       <exclude name="utils/InstallAnywhere/**Build*/**" />
 784       <exclude name="utils/InstallAnywhere/**Build*/**" />
 785       <exclude name="utils/InstallAnywhere/.build*.*/**" />
 786       <exclude name="utils/InstallAnywhere/**locale*" />
 787       <exclude name="utils/InstallAnywhere/**locale*/**" />
 788       <exclude name="utils/InstallAnywhere/**locale*/**" />
 789       <include name="${schemaDir}/**/*" />
 790       <include name="utils/**/*" />
 791       <include name="${docDir}/**/*" />
 792       <include name="examples/**/*" />
 793     </fileset>
 794   </copy>
 795
 796   <tstamp prefix="build">
 797     <format property="year" pattern="yyyy" />
 798   </tstamp>
 799   <!-- each replacetoken CDATA body must be on one line -
 800        otherwise the pattern doesn't match -->
 801   <replace value="${JALVIEW_VERSION}">
 802     <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 803     <fileset dir="_sourcedist">
 804       <include name="**/*" />
 805     </fileset>
 806   </replace>
 807   <replace dir="_sourcedist" value="${build.year}">
 808     <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
 809     <fileset dir="_sourcedist">
 810       <include name="**/*" />
 811     </fileset>
 812   </replace>
 813
 814   <tar destfile="${source.dist.name}" compression="gzip">
 815     <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
 816     </tarfileset>
 817   </tar>
 818
 819   <delete dir="_sourcedist" />
 820 </target>
 821 <target name="prepubapplet_1" depends="makeApplet">
 822   <copy todir="${packageDir}/examples">
 823     <fileset dir="examples">
 824       <include name="**/*" />
 825       <include name="javascript/*" />
 826       <include name="jmol/*" />
 827     </fileset>
 828     <fileset dir=".">
 829       <include name="${jalviewLiteJar}" />
 830     </fileset>
 831     <fileset dir="appletlib">
 832       <include name="**/*" />
 833     </fileset>
 834   </copy>
 835   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 836   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 837   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 838   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 839     <manifest>
 840       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 841       <!--          <attribute name="Permissions" value="sandbox" /> -->
 842       <!--<attribute name="Trusted-Lib" value="true" /> -->
 843       <attribute name="Codebase" value="${applet.codebase}" />
 844       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 845     </manifest>
 846   </jar>
 847
 848   <presetdef name="ap_applet.jar">
 849     <!-- build a signed applet with 'all-permissions' -
 850                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 851                           JalviewLite+JmolApplet linked sequence/structure fails
 852                           Mixed code warnings are raised
 853                           -->
 854     <jar update="true" index="true">
 855       <manifest>
 856         <attribute name="Application-Name" value="JalviewLite" />
 857         <attribute name="Permissions" value="all-permissions" />
 858         <attribute name="Codebase" value="${applet.codebase}" />
 859         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 860         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 861       </manifest>
 862     </jar>
 863   </presetdef>
 864   <presetdef name="applet.jar">
 865     <!-- build signed applet with sandbox permissions -
 866                           Needs 'param name="permissions' value="sandbox"' in applet tag
 867                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 868                         -->
 869
 870     <jar update="true" index="true">
 871       <manifest>
 872         <attribute name="Application-Name" value="JalviewLite" />
 873         <attribute name="Permissions" value="sandbox" />
 874         <attribute name="Codebase" value="${applet.codebase}" />
 875         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 876         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 877       </manifest>
 878     </jar>
 879   </presetdef>
 880   <presetdef name="tl_applet.jar">
 881     <!-- build signed applet with trusted library/trusted permissions -
 882                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 883                                j1.7_45:
 884                                No mixed code warnings raised
 885                                Jmol/JalviewLite sequence/structure example doesn't link structures
 886                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 887
 888                               -->
 889
 890     <jar update="true" index="true">
 891       <manifest>
 892         <attribute name="Application-Name" value="JalviewLite" />
 893         <attribute name="Permissions" value="all-permissions" />
 894         <attribute name="Codebase" value="${applet.codebase}" />
 895         <attribute name="Trusted-Only" value="true" />
 896         <attribute name="Trusted-Library" value="true" />
 897       </manifest>
 898     </jar>
 899   </presetdef>
 900   <presetdef name="to_applet.jar">
 901     <!-- not fully test variant (yet) -->
 902     <jar update="true" index="true">
 903       <manifest>
 904         <attribute name="Application-Name" value="JalviewLite" />
 905         <attribute name="Permissions" value="all-permissions" />
 906         <attribute name="Codebase" value="${applet.codebase}" />
 907         <attribute name="Trusted-Only" value="true" />
 908       </manifest>
 909     </jar>
 910   </presetdef>
 911   <!-- create differently privileged artefacts -->
 912   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 913   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 914   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 915   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 916   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 917   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 918   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 919   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 920   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 921   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 922   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 923   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 924   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 925   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 926   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 927   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 928   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 929   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 930   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 931   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 932   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 933   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 934   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 935   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 936   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 937   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 938   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 939   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 940   <!-- finally, create manifest for original jars -->
 941   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 942   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 943   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 944   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 945
 946   <!-- todo - write examples/downloads for alternate versions of the applet
 947     probably don't need to do this now since we don't have alternate versions anymore !-->
 948 </target>
 949 <target name="-signapplet" depends="prepubapplet_1">
 950   <fileset id="signappletjarset" dir="${packageDir}/examples">
 951     <exclude name="u_*.jar" />
 952     <include name="${jalviewLiteJar}" />
 953     <include name="${jmolJar}" />
 954     <include name="${javaJson}" />
 955     <include name="${jsonSimple}" />
 956     <include name="to_${jalviewLiteJar}" />
 957     <include name="to_${jmolJar}" />
 958     <include name="to_${javaJson}" />
 959     <include name="to_${jsonSimple}" />
 960     <include name="tl_${jalviewLiteJar}" />
 961     <include name="tl_${jmolJar}" />
 962     <include name="tl_${javaJson}" />
 963     <include name="tl_${jsonSimple}" />
 964     <include name="ap_${jalviewLiteJar}" />
 965     <include name="ap_${jmolJar}" />
 966     <include name="ap_${javaJson}" />
 967     <include name="ap_${jsonSimple}" />
 968   </fileset>
 969 </target>
 970 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
 971   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 972     <fileset refid="signappletjarset" />
 973   </signjar>
 974 </target>
 975
 976 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
 977   <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}">
 978     <fileset refid="signappletjarset" />
 979   </signjar>
 980 </target>
 981
 982 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
 983
 984 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 985
 986   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 987   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 988   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 989   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 990   <!-- finally, replace any launchApp servlet tags with a version specification -->
 991   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 992     <replacetoken>
 993       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 994     </replacetoken>
 995     <fileset dir="${packageDir}/examples">
 996       <include name="**/*.html" />
 997     </fileset>
 998   </replace>
 999   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
1000     <replacetoken>
1001       <![CDATA[http://www.jalview.org/services/launchApp']]>
1002     </replacetoken>
1003     <fileset dir="${packageDir}/examples">
1004       <include name="**/*.html" />
1005     </fileset>
1006   </replace>
1007
1008 </target>
1009 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
1010   <javadoc destdir="${javadocDir}">
1011     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
1012     </packageset>
1013   </javadoc>
1014 </target>
1015 <target name="linkcheck" depends="init,prepare">
1016   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
1017   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
1018     <arg file="${helpDir}"/>
1019     <arg value="-nointernet"/>
1020   </java>
1021 </target>
1022 </project>