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     <echo message="java9 is ${java9}"/>
 119     <echo message="java10 is ${java10}"/>
 120     <echo message="java11 is ${java11}"/>
 121
 122     <!-- Don't change anything below here unless you know what you are doing! -->
 123     <!-- Url path for WebStart in JNLP file -->
 124     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
 125     <!-- Webstart Image - looked for in resources/images -->
 126     <property name="WebStartImage" value="JalviewLogo_big.png" />
 127     <!-- J2SE version needed for webstart launch -->
 128     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
 129     <property name="j2sev" value="1.7+" />
 130     <!-- Java Compilation settings - source and target javac version -->
 131     <property name="javac.source" value="1.8" />
 132     <property name="javac.target" value="1.8" />
 133
 134     <!-- Permissions for running Java applets and applications. -->
 135     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 136     <property name="application.codebase" value="*.jalview.org" />
 137     <!-- and allowing the applet to be deployed from any URL -->
 138     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
 139     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 140     <property name="applet.caller-codebase" value="${applet.codebase}" />
 141
 142     <!-- build directory configuration -->
 143     <property name="libDir" value="lib" />
 144     <property name="j11libDir" value="j11lib" />
 145     <property name="resourceDir" value="resources" />
 146     <property name="helpDir" value="help" />
 147     <property name="docDir" value="doc" />
 148     <property name="sourceDir" value="src" />
 149     <property name="schemaDir" value="schemas" />
 150     <property name="outputDir" value="classes" unless:set="clover.jar"/>
 151     <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
 152     <property name="packageDir" value="dist" />
 153     <property name="outputJar" value="jalview.jar" />
 154     <!-- Jalview Applet JMol Jar Dependency -->
 155     <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
 156     <property name="varnaJar" value="VARNAv3-93.jar" />
 157     <property name="jsoup" value="jsoup-1.8.1.jar" />
 158     <property name="jsonSimple" value="json_simple-1.1.jar" />
 159     <property name="javaJson" value="java-json.jar" />
 160     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 161     <property name="reportDir" value="test-reports" />
 162     <property name="testDir" value="test" />
 163     <property name="testOutputDir" value="tests" />
 164     <!-- switch to indicate if we should obfuscate jalviewLite -->
 165     <!-- <property name="donotobfuscate" value="true"/> -->
 166     <!-- switch to exclude associations from generated jnlp files -->
 167     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 168
 169     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 170     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 171     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 172     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 173     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 174     <property name="WSInterf" value="MsaWS" />
 175     <property name="wsdl.Namespace" value="vamsas" />
 176     <property name="wsdl.ClientNS" value="ext.vamsas" />
 177     <!-- the class path for building the application -->
 178     <path id="build.classpath">
 179       <fileset dir="utils">
 180         <include name="*.jar" />
 181         <include name="**/*.jar" />
 182       </fileset>
 183       <fileset dir="${j11libDir}">
 184         <include name="*.jar" />
 185         <include name="**/*.jar" />
 186       </fileset>
 187       <fileset dir="${libDir}">
 188         <include name="*.jar" />
 189         <include name="**/*.jar" />
 190       </fileset>
 191       <fileset dir="${java.home}/lib">
 192         <include name="plugin.jar" />
 193       </fileset>
 194       <fileset dir="appletlib">
 195         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 196                                 -->
 197         <include name="${jmolJar}" />
 198         <include name="${varnaJar}" />
 199       </fileset>
 200     </path>
 201     <path id="test.classpath">
 202       <pathelement path="${outputDir}" />
 203       <path refid="build.classpath" />
 204     </path>
 205     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 206     <!-- The Location of the java 1.1.8 jdk -->
 207     <property name="java118.home" value="${java.home}" />
 208     <!-- jre for 1.4 version -->
 209     <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
 210
 211     <!-- the classpath for building the 1.1 applet -->
 212     <path id="jalviewlite.deps">
 213       <fileset dir="${java118.home}">
 214         <include name="lib/rt.jar" />
 215       </fileset>
 216       <fileset dir="${java.home}/lib">
 217         <include name="plugin.jar" />
 218       </fileset>
 219       <pathelement location="appletlib/${jmolJar}" />
 220       <pathelement location="lib/${varnaJar}" />
 221       <pathelement location="appletlib/${jsoup}" />
 222       <pathelement location="appletlib/${jsonSimple}" />
 223       <pathelement location="appletlib/${javaJson}" />
 224
 225     </path>
 226     <!-- default location for outputting javadoc -->
 227     <property name="javadocDir" value="${packageDir}/javadoc" />
 228   </target>
 229
 230
 231   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 232   <target name="buildPropertiesFile" depends="init">
 233     <tstamp prefix="build">
 234       <format property="date" pattern="dd MMMM yyyy" />
 235     </tstamp>
 236     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 237       <arg value="rev-parse" />
 238       <arg value="--short" />
 239       <arg value="HEAD" />
 240     </exec>
 241     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 242       <arg value="rev-parse" />
 243       <arg value="--abbrev-ref" />
 244       <arg value="HEAD" />
 245     </exec>
 246     <properties file="${outputDir}/.build_properties">
 247       <header>
 248           ---Jalview Build Details---
 249         </header>
 250       <property name="VERSION" value="${JALVIEW_VERSION}" />
 251       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 252       <property name="BUILD_DATE" value="${build.date}" />
 253     </properties>
 254   </target>
 255
 256
 257   <target name="clean" depends="init">
 258     <!-- not efficient yet. -->
 259     <delete dir="${outputDir}" includes="*,**/*" />
 260   </target>
 261
 262   <target name="distclean" depends="init, clean">
 263
 264     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 265     <delete>
 266       <fileset dir=".">
 267         <include name="${outputJar}" />
 268         <include name="#*#" />
 269         <include name="#*.*#" />
 270         <include name="**/#*#" />
 271         <include name="**/#*.*#" />
 272         <include name="*~" />
 273         <include name="*.*~" />
 274         <include name="**/*~" />
 275         <include name="**/*.*~" />
 276       </fileset>
 277     </delete>
 278   </target>
 279
 280   <target name="prepare" depends="init">
 281     <mkdir dir="${outputDir}" />
 282     <copy todir="${outputDir}">
 283       <fileset dir=".">
 284         <include name="${docDir}/**/*.*" />
 285         <include name="${helpDir}/**/*.*" />
 286         <include name="${libDir}/*.jar" />
 287       </fileset>
 288       <fileset dir="${resourceDir}">
 289         <include name="**/*.*" />
 290       </fileset>
 291     </copy>
 292   </target>
 293
 294   <target name="build" depends="prepare">
 295     <!-- not efficient yet. -->
 296     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 297       <exclude name="jalview/*applet*" />
 298       <exclude name="jalview/appletgui/**" />
 299       <exclude name="com/stevesoft/**" />
 300     </javac>
 301   </target>
 302
 303
 304   <target name="testclean" depends="init">
 305     <delete dir="${testOutputDir}" includes="*,**/*" />
 306   </target>
 307
 308   <target name="prepareTests" depends="init,testclean">
 309     <mkdir dir="${testOutputDir}" />
 310   </target>
 311
 312   <target name="buildTests" depends="build,buildindices,prepareTests">
 313     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 314     </javac>
 315   </target>
 316
 317   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 318
 319   <target name="testng" depends="buildTests">
 320     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 321       verbose="2">
 322       <classpath>
 323         <pathelement location="${testOutputDir}" />
 324         <pathelement location="${clover.jar}" if:set="clover.jar"/>
 325         <path refid="test.classpath" />
 326       </classpath>
 327       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 328       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 329       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 330     </testng>
 331   </target>
 332
 333   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 334     <replace value="${JALVIEW_VERSION}">
 335       <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 336       <fileset dir="${outputDir}/${helpDir}">
 337         <include name="help.jhm" />
 338       </fileset>
 339     </replace>
 340
 341     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 342       <arg line="html" />
 343     </java>
 344   </target>
 345
 346   <target name="preparejnlp" depends="makedist">
 347     <copy todir="${packageDir}">
 348       <fileset dir="${resourceDir}/images">
 349         <include name="${WebStartImage}" />
 350       </fileset>
 351     </copy>
 352
 353     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 354
 355     <!-- create a dummy jar which will eventually contain the jnlp template -->
 356     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 357       <fileset dir="${packageDir}">
 358         <include name="jalview.jar" />
 359       </fileset>
 360     </jar>
 361
 362     <mkdir dir="${packageDir}/JNLP-INF" />
 363     <antcall target="writejnlpf">
 364       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 365       <param name="inih" value="*" />
 366       <param name="maxh" value="*" />
 367     </antcall>
 368
 369     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 370       <fileset dir="${packageDir}">
 371         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 372       </fileset>
 373     </jar>
 374
 375     <antcall target="writejnlpf">
 376       <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
 377       <param name="inih" value="10M" />
 378       <param name="maxh" value="256M" />
 379     </antcall>
 380     <antcall target="writejnlpf">
 381       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 382       <param name="inih" value="800M" />
 383       <param name="maxh" value="1024M" />
 384     </antcall>
 385
 386     <antcall target="writejnlpf">
 387       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 388       <param name="inih" value="128M" />
 389       <param name="maxh" value="512M" />
 390     </antcall>
 391
 392     <antcall target="writejnlpf">
 393       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 394       <param name="inih" value="800M" />
 395       <param name="maxh" value="1024M" />
 396     </antcall>
 397
 398     <!-- finally, need to postprocess to add in associations at end of 'information' element
 399
 400                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 401
 402                 </xslt>
 403
 404
 405                         -->
 406     <!--
 407                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 408         <association mime-type="application-x/ext-file" extensions="fasta"/>
 409         <association mime-type="application-x/ext-file" extensions="mfa"/>
 410         <association mime-type="application-x/ext-file" extensions="fastq"/>
 411         <association mime-type="application-x/ext-file" extensions="blc"/>
 412         <association mime-type="application-x/ext-file" extensions="msf"/>
 413         <association mime-type="application-x/ext-file" extensions="pfam"/>
 414         <association mime-type="application-x/ext-file" extensions="aln"/>
 415         <association mime-type="application-x/ext-file" extensions="pir"/>
 416         <association mime-type="application-x/ext-file" extensions="amsa"/>
 417         <association mime-type="application-x/ext-file" extensions="stk"/>
 418         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 419   </target>
 420
 421   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
 422     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
 423       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 424       <fileset dir="${packageDir}">
 425         <include name="*.jar" />
 426       </fileset>
 427     </signjar>
 428   </target>
 429   <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
 430     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
 431       <fileset dir="${packageDir}">
 432         <include name="*.jar" />
 433       </fileset>
 434     </signjar>
 435   </target>
 436
 437   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 438     <!-- and sign the jars -->
 439     <!-- the default keystore details might need to be edited here -->
 440   </target>
 441
 442   <target name="runenv" depends="init">
 443     <path id="run.classpath">
 444       <pathelement location="${outputDir}" />
 445       <fileset dir="${outputDir}">
 446         <include name="${libDir}/*.jar" />
 447       </fileset>
 448     </path>
 449     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 450
 451     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 452       </echo>
 453   </target>
 454
 455   <target name="-generatejnlpf">
 456     <presetdef name="jnlpf">
 457       <jnlp codebase="${WebStartLocation}">
 458         <information>
 459           <title>Jalview</title>
 460           <vendor>The Barton Group</vendor>
 461           <homepage href="http://www.jalview.org" />
 462           <description>Jalview Multiple Alignment Editor</description>
 463           <description kind="short">Jalview</description>
 464           <icon href="${WebStartImage}" />
 465           <offline_allowed />
 466         </information>
 467         <resources>
 468           <j2se version="1.8+" />
 469           <jar main="true" href="jalview.jar"/>
 470           <fileset dir="${packageDir}">
 471             <exclude name="jalview.jar" />
 472             <include name="*.jar" />
 473             <include name="*_*.jar" />
 474             <exclude name="*quaqua*.jar" />
 475           </fileset>
 476           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 477         </resources>
 478         <resources os="Mac OS X">
 479           <fileset dir="${packageDir}">
 480                  <include name="quaqua-filechooser-only-8.0.jar"/>
 481             <include name="*quaqua64*.jnilib.jar" />
 482           </fileset>
 483         </resources>
 484
 485         <application_desc main_class="jalview.bin.Jalview">
 486         </application_desc>
 487         <security>
 488           <all_permissions />
 489         </security>
 490       </jnlp>
 491     </presetdef>
 492
 493     <jnlpf toFile="${jnlpFile}" />
 494     <!-- add the add-modules j2se attribute for java 9 -->
 495     <replace file="${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;">
 496           <replacetoken>j2se version="1.8+"</replacetoken>
 497     </replace>
 498   </target>
 499
 500   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 501     <echo message="Not adding JNLP File Associations" />
 502   </target>
 503
 504   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 505     <replace file="${jnlpFile}">
 506       <replacetoken>
 507         <![CDATA[</information>]]></replacetoken>
 508       <replacevalue>
 509         <![CDATA[
 510           <association mime-type="application-x/ext-file" extensions="fa" />
 511         <association mime-type="application-x/ext-file" extensions="fasta" />
 512         <association mime-type="application-x/ext-file" extensions="mfa" />
 513         <association mime-type="application-x/ext-file" extensions="fastq" />
 514         <association mime-type="application-x/ext-file" extensions="blc" />
 515         <association mime-type="application-x/ext-file" extensions="msf" />
 516         <association mime-type="application-x/ext-file" extensions="pfam" />
 517         <association mime-type="application-x/ext-file" extensions="aln"/>
 518         <association mime-type="application-x/ext-file" extensions="pir"/>
 519         <association mime-type="application-x/ext-file" extensions="amsa"/>
 520         <association mime-type="application-x/ext-file" extensions="stk"/>
 521         <association mime-type="application-x/ext-file" extensions="jvp"/>
 522       </information>]]></replacevalue>
 523   </replace>
 524   <echo message="Added file associations to JNLP file" />
 525 </target>
 526 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 527 </target>
 528
 529 <target name="buildextclients" depends="init">
 530   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 531   <condition property="dontextbuild">
 532     <equals arg1="n" arg2="${doextbuild.response}" />
 533   </condition>
 534   <condition property="dontextbuild">
 535     <equals arg1="N" arg2="${doextbuild.response}" />
 536   </condition>
 537   <fail if="dontextbuild">
 538         Build External Client Code process aborted by user. Jalview source is unchanged.
 539       </fail>
 540   <!-- Currently, this doesn't happen automatically.
 541      1. Run WSDL2Java as below, which generates an ext.vamsas +
 542      vamsas.<datapackages> fileset.
 543      2. refactor ext.vamsas.SpecificserviceWS* to
 544      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 545      3. Update the jalview.ws.*WServices classes to reflect the
 546      interface type, and all locations of this wsdl type that Jalview
 547      might be using.
 548
 549 -->
 550   <path id="axisbuild">
 551     <path refid="build.classpath" />
 552   </path>
 553   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 554   <move todir="./bak">
 555     <fileset dir="${sourceDir}" id="client">
 556       <include name="${wsdl.ClientNS}/*.*" />
 557     </fileset>
 558   </move>
 559
 560   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 561     <mappingSet>
 562       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 563       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 564     </mappingSet>
 565   </axis-wsdl2java>
 566 </target>
 567
 568 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
 569   <fail if="clover.jar">
 570     Ignoring request to build jalview distribution with clover-instrumented classes
 571   </fail>
 572   <!-- make the package jar if not already existing -->
 573   <mkdir dir="${packageDir}" />
 574   <!-- clean dir if it already existed -->
 575   <delete>
 576     <fileset dir="${packageDir}">
 577       <include name="*.jar" />
 578     </fileset>
 579   </delete>
 580   <jar destfile="${packageDir}/${outputJar}" index="true">
 581     <manifest>
 582       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 583       <attribute name="Permissions" value="all-permissions" />
 584       <attribute name="Application-Name" value="Jalview Desktop" />
 585       <attribute name="Codebase" value="${application.codebase}" />
 586     </manifest>
 587     <fileset dir="${outputDir}/">
 588       <exclude name="cache*/**" />
 589       <exclude name="*.jar" />
 590       <exclude name="*.jar.*" />
 591       <exclude name="**/*.jar" />
 592       <exclude name="**/*.jar.*" />
 593     </fileset>
 594   </jar>
 595
 596   <copy toDir="${packageDir}" flatten="true">
 597     <fileset dir="${outputDir}">
 598       <include name="*.jar" />
 599       <include name="**/*.jar" />
 600     </fileset>
 601   </copy>
 602 </target>
 603
 604
 605 <!-- jalopy code reformatter -->
 606 <target name="sourcescrub" depends="init,build">
 607   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 608     <fileset dir="${sourceDir}">
 609       <include name="*.java" />
 610       <include name="**/*.java" />
 611       <include name="**/**/*.java" />
 612     </fileset>
 613   </jalopy>
 614 </target>
 615
 616
 617
 618 <!-- Compile, package and obfuscate Jalview Applet -->
 619 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 620
 621 <target name="compileApplet" depends="init,clean">
 622   <mkdir dir="${outputDir}" />
 623   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 624 </target>
 625
 626 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 627   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 628   <copy todir="${outputDir}/lang">
 629     <fileset dir="${resourceDir}/lang">
 630       <include name="**.*" />
 631     </fileset>
 632   </copy>
 633   <jar destfile="in.jar" index="true">
 634     <manifest>
 635       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 636       <attribute name="Application-Name" value="JalviewLite" />
 637       <attribute name="Codebase" value="${applet.codebase}" />
 638     </manifest>
 639     <fileset dir="${outputDir}">
 640       <include name="com/**" />
 641       <include name="MCview/**" />
 642       <include name="jalview/**" />
 643       <include name=".build_properties" />
 644       <include name="images/link.gif" />
 645       <include name="lang/**" />
 646     </fileset>
 647   </jar>
 648 </target>
 649 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 650 </target>
 651 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 652   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 653   <delete file="in.jar" />
 654 </target>
 655 <target name="-obfuscatereally" unless="donotobfuscate">
 656
 657   <path id="obfuscateDeps.path">
 658     <pathelement location="${applet.jre.tools}" />
 659     <pathelement location="appletlib/${jmolJar}" />
 660     <pathelement location="lib/${varnaJar}" />
 661     <pathelement location="appletlib/${jsoup}" />
 662     <pathelement location="appletlib/${jsonSimple}" />
 663     <pathelement location="appletlib/${javaJson}" />
 664     <fileset dir="${java.home}/lib">
 665       <include name="plugin.jar" />
 666     </fileset>
 667   </path>
 668   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
 669
 670   <proguard verbose="true" >
 671     <injar file="in.jar" />
 672     <outjar file="${jalviewLiteJar}" />
 673     <libraryjar refid="obfuscateDeps.path" />
 674     <dontwarn />
 675     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 676       <field access="public" />
 677       <method access="public" />
 678       <constructor access="public" />
 679     </keep>
 680     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 681       <field access="public" />
 682       <method access="public" />
 683       <constructor access="public" />
 684     </keep>
 685
 686     <keep name="jalview.json.binding**">
 687       <constructor/>
 688       <method name="*"/>
 689     </keep>
 690
 691     <keep access="public" type="class" name="MCview.PDBfile">
 692       <field access="public" />
 693       <method access="public" />
 694       <constructor access="public" />
 695     </keep>
 696
 697     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 698       <field access="public" />
 699       <method access="public" />
 700       <constructor access="public" />
 701     </keep>
 702
 703     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 704       <field access="public" />
 705       <method access="public" />
 706       <constructor access="public" />
 707     </keep>
 708
 709
 710     <!--      -libraryjars "${obfuscateDeps}"
 711       -injars      in.jar
 712       -outjars     jalviewApplet.jar
 713       -keep public class jalview.bin.JalviewLite
 714        { public * ; } -->
 715   </proguard>
 716   <delete file="in.jar" />
 717 </target>
 718
 719 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 720   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 721   <delete>
 722     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 723       <include name="*.java" />
 724       <include name="descriptors/*.java" />
 725     </fileset>
 726   </delete>
 727   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 728   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 729   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 730   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 731   <!--
 732                 now build the jalview.binding package with the old schema set
 733                 -->
 734   <delete>
 735     <fileset dir="${sourceDir}/jalview/binding/">
 736       <include name="**" />
 737     </fileset>
 738   </delete>
 739   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 740   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 741   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 742 </target>
 743 <target name="sourcedist" description="create jalview source distribution" depends="init">
 744   <delete file="${source.dist.name}" />
 745   <!-- temporary copy of source to update timestamps -->
 746   <copy todir="_sourcedist">
 747     <fileset dir=".">
 748       <exclude name=".*" />
 749       <exclude name="**/.*" />
 750       <exclude name="*.class" />
 751       <exclude name="**/*.class" />
 752       <include name="LICENSE" />
 753       <include name="README" />
 754       <include name="build.xml" />
 755       <include name="jalview-jalopy.xml" />
 756       <include name="JalviewApplet.jpx" />
 757       <include name="JalviewX.jpx" />
 758       <include name="nbbuild.xml" />
 759       <include name="nbproject/genfiles.properties" />
 760       <include name="nbproject/project.properties" />
 761       <include name="nbproject/project.xml" />
 762       <include name="${sourceDir}/*.java" />
 763       <include name="${sourceDir}/**/*.java" />
 764       <include name="${sourceDir}/**/*.cdr" />
 765       <include name="${libDir}/**/*" />
 766       <include name="${resourceDir}/**/*" />
 767       <include name="${helpDir}/**/*" />
 768       <include name="appletlib/${jmolJar}" />
 769       <include name="appletlib/${jsonSimple}" />
 770       <include name="appletlib/${javaJson}" />
 771       <exclude name="**/*locales" />
 772       <exclude name="*locales/**" />
 773       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 774       <exclude name="utils/InstallAnywhere/**Build*/**" />
 775       <exclude name="utils/InstallAnywhere/**Build*/**" />
 776       <exclude name="utils/InstallAnywhere/.build*.*/**" />
 777       <exclude name="utils/InstallAnywhere/**locale*" />
 778       <exclude name="utils/InstallAnywhere/**locale*/**" />
 779       <exclude name="utils/InstallAnywhere/**locale*/**" />
 780       <include name="${schemaDir}/**/*" />
 781       <include name="utils/**/*" />
 782       <include name="${docDir}/**/*" />
 783       <include name="examples/**/*" />
 784     </fileset>
 785   </copy>
 786
 787   <tstamp prefix="build">
 788     <format property="year" pattern="yyyy" />
 789   </tstamp>
 790   <!-- each replacetoken CDATA body must be on one line -
 791        otherwise the pattern doesn't match -->
 792   <replace value="${JALVIEW_VERSION}">
 793     <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 794     <fileset dir="_sourcedist">
 795       <include name="**/*" />
 796     </fileset>
 797   </replace>
 798   <replace dir="_sourcedist" value="${build.year}">
 799     <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
 800     <fileset dir="_sourcedist">
 801       <include name="**/*" />
 802     </fileset>
 803   </replace>
 804
 805   <tar destfile="${source.dist.name}" compression="gzip">
 806     <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
 807     </tarfileset>
 808   </tar>
 809
 810   <delete dir="_sourcedist" />
 811 </target>
 812 <target name="prepubapplet_1" depends="makeApplet">
 813   <copy todir="${packageDir}/examples">
 814     <fileset dir="examples">
 815       <include name="**/*" />
 816       <include name="javascript/*" />
 817       <include name="jmol/*" />
 818     </fileset>
 819     <fileset dir=".">
 820       <include name="${jalviewLiteJar}" />
 821     </fileset>
 822     <fileset dir="appletlib">
 823       <include name="**/*" />
 824     </fileset>
 825   </copy>
 826   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 827   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 828   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 829   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 830     <manifest>
 831       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 832       <!--          <attribute name="Permissions" value="sandbox" /> -->
 833       <!--<attribute name="Trusted-Lib" value="true" /> -->
 834       <attribute name="Codebase" value="${applet.codebase}" />
 835       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 836     </manifest>
 837   </jar>
 838
 839   <presetdef name="ap_applet.jar">
 840     <!-- build a signed applet with 'all-permissions' -
 841                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 842                           JalviewLite+JmolApplet linked sequence/structure fails
 843                           Mixed code warnings are raised
 844                           -->
 845     <jar update="true" index="true">
 846       <manifest>
 847         <attribute name="Application-Name" value="JalviewLite" />
 848         <attribute name="Permissions" value="all-permissions" />
 849         <attribute name="Codebase" value="${applet.codebase}" />
 850         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 851         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 852       </manifest>
 853     </jar>
 854   </presetdef>
 855   <presetdef name="applet.jar">
 856     <!-- build signed applet with sandbox permissions -
 857                           Needs 'param name="permissions' value="sandbox"' in applet tag
 858                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 859                         -->
 860
 861     <jar update="true" index="true">
 862       <manifest>
 863         <attribute name="Application-Name" value="JalviewLite" />
 864         <attribute name="Permissions" value="sandbox" />
 865         <attribute name="Codebase" value="${applet.codebase}" />
 866         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 867         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 868       </manifest>
 869     </jar>
 870   </presetdef>
 871   <presetdef name="tl_applet.jar">
 872     <!-- build signed applet with trusted library/trusted permissions -
 873                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 874                                j1.7_45:
 875                                No mixed code warnings raised
 876                                Jmol/JalviewLite sequence/structure example doesn't link structures
 877                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 878
 879                               -->
 880
 881     <jar update="true" index="true">
 882       <manifest>
 883         <attribute name="Application-Name" value="JalviewLite" />
 884         <attribute name="Permissions" value="all-permissions" />
 885         <attribute name="Codebase" value="${applet.codebase}" />
 886         <attribute name="Trusted-Only" value="true" />
 887         <attribute name="Trusted-Library" value="true" />
 888       </manifest>
 889     </jar>
 890   </presetdef>
 891   <presetdef name="to_applet.jar">
 892     <!-- not fully test variant (yet) -->
 893     <jar update="true" index="true">
 894       <manifest>
 895         <attribute name="Application-Name" value="JalviewLite" />
 896         <attribute name="Permissions" value="all-permissions" />
 897         <attribute name="Codebase" value="${applet.codebase}" />
 898         <attribute name="Trusted-Only" value="true" />
 899       </manifest>
 900     </jar>
 901   </presetdef>
 902   <!-- create differently privileged artefacts -->
 903   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 904   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 905   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 906   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 907   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 908   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 909   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 910   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 911   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 912   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 913   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 914   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 915   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 916   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 917   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 918   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 919   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 920   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 921   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 922   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 923   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 924   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 925   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 926   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 927   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 928   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 929   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 930   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 931   <!-- finally, create manifest for original jars -->
 932   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 933   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 934   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 935   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 936
 937   <!-- todo - write examples/downloads for alternate versions of the applet
 938     probably don't need to do this now since we don't have alternate versions anymore !-->
 939 </target>
 940 <target name="-signapplet" depends="prepubapplet_1">
 941   <fileset id="signappletjarset" dir="${packageDir}/examples">
 942     <exclude name="u_*.jar" />
 943     <include name="${jalviewLiteJar}" />
 944     <include name="${jmolJar}" />
 945     <include name="${javaJson}" />
 946     <include name="${jsonSimple}" />
 947     <include name="to_${jalviewLiteJar}" />
 948     <include name="to_${jmolJar}" />
 949     <include name="to_${javaJson}" />
 950     <include name="to_${jsonSimple}" />
 951     <include name="tl_${jalviewLiteJar}" />
 952     <include name="tl_${jmolJar}" />
 953     <include name="tl_${javaJson}" />
 954     <include name="tl_${jsonSimple}" />
 955     <include name="ap_${jalviewLiteJar}" />
 956     <include name="ap_${jmolJar}" />
 957     <include name="ap_${javaJson}" />
 958     <include name="ap_${jsonSimple}" />
 959   </fileset>
 960 </target>
 961 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
 962   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 963     <fileset refid="signappletjarset" />
 964   </signjar>
 965 </target>
 966
 967 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
 968   <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}">
 969     <fileset refid="signappletjarset" />
 970   </signjar>
 971 </target>
 972
 973 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
 974
 975 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 976
 977   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 978   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 979   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 980   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 981   <!-- finally, replace any launchApp servlet tags with a version specification -->
 982   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 983     <replacetoken>
 984       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 985     </replacetoken>
 986     <fileset dir="${packageDir}/examples">
 987       <include name="**/*.html" />
 988     </fileset>
 989   </replace>
 990   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 991     <replacetoken>
 992       <![CDATA[http://www.jalview.org/services/launchApp']]>
 993     </replacetoken>
 994     <fileset dir="${packageDir}/examples">
 995       <include name="**/*.html" />
 996     </fileset>
 997   </replace>
 998
 999 </target>
1000 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
1001   <javadoc destdir="${javadocDir}">
1002     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
1003     </packageset>
1004   </javadoc>
1005 </target>
1006 <target name="linkcheck" depends="init,prepare">
1007   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
1008   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
1009     <arg file="${helpDir}"/>
1010     <arg value="-nointernet"/>
1011   </java>
1012 </target>
1013 </project>