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     <echo message="Useful -D flags: -Ddeprecation=true to add -Xlint:deprecation to the java compiler" />
  48   </target>
  49
  50
  51   <!-- utils is a class path to additional utilities needed for
  52     building docs, jars and webstart stuff -->
  53   <!--
  54         Userdefined build property defaults
  55
  56         wsdl.server list (plus namespace mapping info ???)  - also want
  57                 ... to make this a dynamically generatable property
  58         WebStart Location
  59         Build location - provide a temporary root for speed
  60         jarsigner keystore and info
  61         Jakarta and axis classpath ?
  62         Default argument for starting Jalview (if it exists).
  63
  64 -->
  65
  66   <target name="init">
  67     <path id="axis.classpath">
  68       <!-->
  69       <fileset dir="/usr/local/axis/lib">
  70         <include name="**/*.jar" />
  71       </fileset>
  72       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  73         <include name="**/*.jar"/>
  74         <include name="*.jar"/>
  75       </fileset> -->
  76       </path>
  77
  78     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  79     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  80
  81     <property name="INSTALLATION" value="Source" />
  82
  83     <!-- 2.4 (VAMSAS)" -->
  84     <!-- Include debugging information in javac true or false -->
  85     <property name="javac.debug" value="true" />
  86
  87     <!-- JarSigner Key Store for Webstart Distribution -->
  88     <property name="jalview.keystore" value="./keys/.keystore" />
  89     <!-- Keystore Password -->
  90     <property name="jalview.keystore.pass" value="alignmentisfun" />
  91     <!-- Key Name -->
  92     <property name="jalview.key" value="jalview" />
  93     <!-- Key Password -->
  94     <property name="jalview.key.pass" value="alignmentisfun" />
  95     <!-- time stamp server URL -->
  96     <property name="jalview.tsaurl" value="" />
  97     <!-- locally valid proxy for signing with external time server -->
  98     <property name="proxyPort" value="80"/>
  99     <property name="proxyHost" value="sqid"/>
 100     <!-- key sign/digest algorithms -->
 101     <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
 102     <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
 103
 104     <!-- default TestNG groups to run -->
 105     <property name="testng-groups" value="Functional" />
 106     <!-- Java 9 JVM args -->
 107     <condition property="java9">
 108       <equals arg1="${ant.java.version}" arg2="9"/>
 109     </condition>
 110     <!-- Java 10 JVM args -->
 111     <condition property="java10">
 112       <equals arg1="${ant.java.version}" arg2="10"/>
 113     </condition>
 114     <!-- Java 11 JVM args -->
 115     <condition property="java11">
 116       <equals arg1="${ant.java.version}" arg2="11"/>
 117     </condition>
 118     <echo message="ant.java.version is ${ant.java.version}"/>
 119
 120     <!-- Don't change anything below here unless you know what you are doing! -->
 121     <!-- Url path for WebStart in JNLP file -->
 122     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
 123     <!-- Webstart Image - looked for in resources/images -->
 124     <property name="WebStartImage" value="JalviewLogo_big.png" />
 125     <!-- J2SE version needed for webstart launch -->
 126     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
 127     <property name="j2sev" value="1.7+" />
 128     <!-- Java Compilation settings - source and target javac version -->
 129     <property name="javac.source" value="11" if:set="java11" />
 130     <property name="javac.target" value="11" if:set="java11" />
 131     <property name="javac.source" value="1.8" unless:set="java11" />
 132     <property name="javac.target" value="1.8" unless:set="java11" />
 133     <echo message="javac.source is ${javac.source}"/>
 134     <echo message="javac.target is ${javac.target}"/>
 135
 136     <!-- Permissions for running Java applets and applications. -->
 137     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 138     <property name="application.codebase" value="*.jalview.org" />
 139     <!-- and allowing the applet to be deployed from any URL -->
 140     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
 141     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 142     <property name="applet.caller-codebase" value="${applet.codebase}" />
 143
 144     <!-- build directory configuration -->
 145     <property name="libDir" value="lib" />
 146     <property name="j11libDir" value="j11lib" />
 147     <property name="resourceDir" value="resources" />
 148     <property name="helpDir" value="help" />
 149     <property name="docDir" value="doc" />
 150     <property name="sourceDir" value="src" />
 151     <property name="schemaDir" value="schemas" />
 152     <property name="outputDir" value="classes" unless:set="clover.jar"/>
 153     <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
 154     <property name="packageDir" value="dist" />
 155     <property name="outputJar" value="jalview.jar" />
 156     <!-- Jalview Applet JMol Jar Dependency -->
 157     <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
 158     <property name="varnaJar" value="VARNAv3-93.jar" />
 159     <property name="jsoup" value="jsoup-1.8.1.jar" />
 160     <property name="jsonSimple" value="json_simple-1.1.jar" />
 161     <property name="javaJson" value="java-json.jar" />
 162     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 163     <property name="reportDir" value="test-reports" />
 164     <property name="testDir" value="test" />
 165     <property name="testOutputDir" value="tests" />
 166     <!-- switch to indicate if we should obfuscate jalviewLite -->
 167     <!-- <property name="donotobfuscate" value="true"/> -->
 168     <!-- switch to exclude associations from generated jnlp files -->
 169     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 170
 171     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 172     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 173     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 174     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 175     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 176     <property name="WSInterf" value="MsaWS" />
 177     <property name="wsdl.Namespace" value="vamsas" />
 178     <property name="wsdl.ClientNS" value="ext.vamsas" />
 179     <!-- the class path for building the application -->
 180     <path id="build.classpath">
 181       <fileset dir="utils">
 182         <include name="*.jar" />
 183         <include name="**/*.jar" />
 184       </fileset>
 185       <fileset dir="${j11libDir}">
 186         <include name="*.jar" />
 187         <include name="**/*.jar" />
 188       </fileset>
 189       <fileset dir="${libDir}">
 190         <include name="*.jar" />
 191         <include name="**/*.jar" />
 192       </fileset>
 193       <fileset dir="${java.home}/lib">
 194         <include name="plugin.jar" />
 195       </fileset>
 196       <fileset dir="appletlib">
 197         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 198                                 -->
 199         <include name="${jmolJar}" />
 200         <include name="${varnaJar}" />
 201       </fileset>
 202       <pathelement location="${clover.jar}" if:set="clover.jar"/>
 203     </path>
 204     <path id="test.classpath">
 205       <pathelement path="${outputDir}" />
 206       <path refid="build.classpath" />
 207     </path>
 208     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 209     <!-- The Location of the java 1.1.8 jdk -->
 210     <property name="java118.home" value="${java.home}" />
 211     <!-- jre for 1.4 version -->
 212     <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
 213
 214     <!-- the classpath for building the 1.1 applet -->
 215     <path id="jalviewlite.deps">
 216       <fileset dir="${java118.home}">
 217         <include name="lib/rt.jar" />
 218       </fileset>
 219       <fileset dir="${java.home}/lib">
 220         <include name="plugin.jar" />
 221       </fileset>
 222       <pathelement location="appletlib/${jmolJar}" />
 223       <pathelement location="lib/${varnaJar}" />
 224       <pathelement location="appletlib/${jsoup}" />
 225       <pathelement location="appletlib/${jsonSimple}" />
 226       <pathelement location="appletlib/${javaJson}" />
 227
 228     </path>
 229     <!-- default location for outputting javadoc -->
 230     <property name="javadocDir" value="${packageDir}/javadoc" />
 231   </target>
 232
 233
 234   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 235   <target name="buildPropertiesFile" depends="init">
 236     <tstamp prefix="build">
 237       <format property="date" pattern="dd MMMM yyyy" />
 238     </tstamp>
 239     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 240       <arg value="rev-parse" />
 241       <arg value="--short" />
 242       <arg value="HEAD" />
 243     </exec>
 244     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 245       <arg value="rev-parse" />
 246       <arg value="--abbrev-ref" />
 247       <arg value="HEAD" />
 248     </exec>
 249     <properties file="${outputDir}/.build_properties">
 250       <header>
 251           ---Jalview Build Details---
 252         </header>
 253       <property name="VERSION" value="${JALVIEW_VERSION}" />
 254       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 255       <property name="BUILD_DATE" value="${build.date}" />
 256     </properties>
 257   </target>
 258
 259
 260   <target name="clean" depends="init">
 261     <!-- not efficient yet. -->
 262     <delete dir="${outputDir}" includes="*,**/*" />
 263   </target>
 264
 265   <target name="distclean" depends="init, clean">
 266
 267     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 268     <delete>
 269       <fileset dir=".">
 270         <include name="${outputJar}" />
 271         <include name="#*#" />
 272         <include name="#*.*#" />
 273         <include name="**/#*#" />
 274         <include name="**/#*.*#" />
 275         <include name="*~" />
 276         <include name="*.*~" />
 277         <include name="**/*~" />
 278         <include name="**/*.*~" />
 279       </fileset>
 280     </delete>
 281   </target>
 282
 283   <target name="prepare" depends="init">
 284     <mkdir dir="${outputDir}" />
 285     <copy todir="${outputDir}">
 286       <fileset dir=".">
 287         <include name="${docDir}/**/*.*" />
 288         <include name="${helpDir}/**/*.*" />
 289         <include name="${libDir}/*.jar" />
 290       </fileset>
 291       <fileset dir="${resourceDir}">
 292         <include name="**/*.*" />
 293       </fileset>
 294     </copy>
 295   </target>
 296
 297   <target name="build" depends="prepare">
 298     <!-- not efficient yet. -->
 299     <!-- Echo the build.classpath
 300     <pathconvert property="echoClasspath" refid="build.classpath" />
 301     <echo message="build.classpath is '${echoClasspath}'" />
 302     -->
 303     <echo message="javac.target is '${javac.target}'" />
 304     <echo message="adding -Xlint:deprecation to javac" if:set="deprecation"/>
 305     <javac includeantruntime="false" source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 306       <compilerarg value="-Xlint:deprecation" if:set="deprecation" />
 307       <exclude name="jalview/*applet*" />
 308       <exclude name="jalview/appletgui/**" />
 309       <exclude name="com/stevesoft/**" />
 310     </javac>
 311   </target>
 312
 313
 314   <target name="testclean" depends="init">
 315     <delete dir="${testOutputDir}" includes="*,**/*" />
 316   </target>
 317
 318   <target name="prepareTests" depends="init,testclean">
 319     <mkdir dir="${testOutputDir}" />
 320   </target>
 321
 322   <target name="buildTests" depends="build,buildindices,prepareTests">
 323     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 324     </javac>
 325   </target>
 326
 327   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 328
 329   <target name="testng" depends="buildTests">
 330     <loadfile property="j11modules" srcFile="modules">
 331       <filterchain>
 332         <striplinebreaks/>
 333       </filterchain>
 334     </loadfile>
 335     <echo message="j11libDir is '${j11libDir}'" />
 336     <echo message="j11modules is '${j11modules}'" />
 337     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 338       verbose="2">
 339       <classpath>
 340         <pathelement location="${testOutputDir}" />
 341         <pathelement location="${clover.jar}" if:set="clover.jar"/>
 342         <path refid="test.classpath" />
 343       </classpath>
 344       <!--
 345       <jvmarg value="DASH_DASH_module-path=${j11libDir}:${java.home}/jmods" if:set="java11"/>
 346       -->
 347       <jvmarg value="--module-path=${j11libDir}" if:set="java11"/>
 348       <jvmarg value="--add-modules=${j11modules}" if:set="java11"/>
 349       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 350       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 351       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 352     </testng>
 353   </target>
 354
 355   <target name="testngclass" depends="buildTests">
 356     <condition property="propsSpecified">
 357       <isset property="class.name" />
 358     </condition>
 359     <fail unless="propsSpecified" message="class.name property not specified."/>
 360     <echo message="testng-groups is '${testng-groups}'" />
 361     <loadfile property="j11modules" srcFile="modules"/>
 362     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng" verbose="2">
 363       <classpath>
 364         <pathelement location="${testOutputDir}" />
 365         <pathelement location="${clover.jar}" if:set="clover.jar"/>
 366         <path refid="test.classpath" />
 367       </classpath>
 368       <jvmarg value="--module-path=${j11libDir}:${java.home}/jmods" if:set="java11"/>
 369       <jvmarg value="--add-modules=${j11modules}" if:set="java11"/>
 370       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 371       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 372       <classfileset dir="${testOutputDir}" includes="${class.name}" />
 373     </testng>
 374   </target>
 375
 376   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 377     <replace value="${JALVIEW_VERSION}">
 378       <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 379       <fileset dir="${outputDir}/${helpDir}">
 380         <include name="help.jhm" />
 381       </fileset>
 382     </replace>
 383
 384     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 385       <arg line="html" />
 386     </java>
 387   </target>
 388
 389   <target name="preparejnlp" depends="makedist">
 390     <copy todir="${packageDir}">
 391       <fileset dir="${resourceDir}/images">
 392         <include name="${WebStartImage}" />
 393       </fileset>
 394     </copy>
 395
 396     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 397
 398     <!-- create a dummy jar which will eventually contain the jnlp template -->
 399     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 400       <fileset dir="${packageDir}">
 401         <include name="jalview.jar" />
 402       </fileset>
 403     </jar>
 404
 405     <mkdir dir="${packageDir}/JNLP-INF" />
 406     <antcall target="writejnlpf">
 407       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 408       <param name="inih" value="*" />
 409       <param name="maxh" value="*" />
 410     </antcall>
 411
 412     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 413       <fileset dir="${packageDir}">
 414         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 415       </fileset>
 416     </jar>
 417
 418     <antcall target="writejnlpf">
 419       <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
 420       <param name="inih" value="10M" />
 421       <param name="maxh" value="256M" />
 422     </antcall>
 423     <antcall target="writejnlpf">
 424       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 425       <param name="inih" value="800M" />
 426       <param name="maxh" value="1024M" />
 427     </antcall>
 428
 429     <antcall target="writejnlpf">
 430       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 431       <param name="inih" value="128M" />
 432       <param name="maxh" value="512M" />
 433     </antcall>
 434
 435     <antcall target="writejnlpf">
 436       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 437       <param name="inih" value="800M" />
 438       <param name="maxh" value="1024M" />
 439     </antcall>
 440
 441     <!-- finally, need to postprocess to add in associations at end of 'information' element
 442
 443                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 444
 445                 </xslt>
 446
 447
 448                         -->
 449     <!--
 450                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 451         <association mime-type="application-x/ext-file" extensions="fasta"/>
 452         <association mime-type="application-x/ext-file" extensions="mfa"/>
 453         <association mime-type="application-x/ext-file" extensions="fastq"/>
 454         <association mime-type="application-x/ext-file" extensions="blc"/>
 455         <association mime-type="application-x/ext-file" extensions="msf"/>
 456         <association mime-type="application-x/ext-file" extensions="pfam"/>
 457         <association mime-type="application-x/ext-file" extensions="aln"/>
 458         <association mime-type="application-x/ext-file" extensions="pir"/>
 459         <association mime-type="application-x/ext-file" extensions="amsa"/>
 460         <association mime-type="application-x/ext-file" extensions="stk"/>
 461         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 462   </target>
 463
 464   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
 465     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
 466       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 467       <fileset dir="${packageDir}">
 468         <include name="*.jar" />
 469       </fileset>
 470     </signjar>
 471   </target>
 472   <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
 473     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
 474       <fileset dir="${packageDir}">
 475         <include name="*.jar" />
 476       </fileset>
 477     </signjar>
 478   </target>
 479
 480   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 481     <!-- and sign the jars -->
 482     <!-- the default keystore details might need to be edited here -->
 483   </target>
 484
 485   <target name="runenv" depends="init">
 486     <path id="run.classpath">
 487       <pathelement location="${outputDir}" />
 488       <fileset dir="${outputDir}">
 489         <include name="${libDir}/*.jar" />
 490       </fileset>
 491     </path>
 492     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 493
 494     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 495       </echo>
 496   </target>
 497
 498   <target name="-generatejnlpf">
 499     <presetdef name="jnlpf">
 500       <jnlp codebase="${WebStartLocation}">
 501         <information>
 502           <title>Jalview</title>
 503           <vendor>The Barton Group</vendor>
 504           <homepage href="http://www.jalview.org" />
 505           <description>Jalview Multiple Alignment Editor</description>
 506           <description kind="short">Jalview</description>
 507           <icon href="${WebStartImage}" />
 508           <offline_allowed />
 509         </information>
 510         <resources>
 511           <j2se version="1.8+" />
 512           <jar main="true" href="jalview.jar"/>
 513           <fileset dir="${packageDir}">
 514             <exclude name="jalview.jar" />
 515             <include name="*.jar" />
 516             <include name="*_*.jar" />
 517             <exclude name="*quaqua*.jar" />
 518           </fileset>
 519           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 520         </resources>
 521         <resources os="Mac OS X">
 522           <fileset dir="${packageDir}">
 523                  <include name="quaqua-filechooser-only-8.0.jar"/>
 524             <include name="*quaqua64*.jnilib.jar" />
 525           </fileset>
 526         </resources>
 527
 528         <application_desc main_class="jalview.bin.Jalview">
 529         </application_desc>
 530         <security>
 531           <all_permissions />
 532         </security>
 533       </jnlp>
 534     </presetdef>
 535
 536     <jnlpf toFile="${jnlpFile}" />
 537     <!-- add the add-modules j2se attribute for java 9 -->
 538     <replace file="${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;">
 539           <replacetoken>j2se version="1.8+"</replacetoken>
 540     </replace>
 541   </target>
 542
 543   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 544     <echo message="Not adding JNLP File Associations" />
 545   </target>
 546
 547   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 548     <replace file="${jnlpFile}">
 549       <replacetoken>
 550         <![CDATA[</information>]]></replacetoken>
 551       <replacevalue>
 552         <![CDATA[
 553           <association mime-type="application-x/ext-file" extensions="fa" />
 554         <association mime-type="application-x/ext-file" extensions="fasta" />
 555         <association mime-type="application-x/ext-file" extensions="mfa" />
 556         <association mime-type="application-x/ext-file" extensions="fastq" />
 557         <association mime-type="application-x/ext-file" extensions="blc" />
 558         <association mime-type="application-x/ext-file" extensions="msf" />
 559         <association mime-type="application-x/ext-file" extensions="pfam" />
 560         <association mime-type="application-x/ext-file" extensions="aln"/>
 561         <association mime-type="application-x/ext-file" extensions="pir"/>
 562         <association mime-type="application-x/ext-file" extensions="amsa"/>
 563         <association mime-type="application-x/ext-file" extensions="stk"/>
 564         <association mime-type="application-x/ext-file" extensions="jvp"/>
 565       </information>]]></replacevalue>
 566   </replace>
 567   <echo message="Added file associations to JNLP file" />
 568 </target>
 569 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 570 </target>
 571
 572 <target name="buildextclients" depends="init">
 573   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 574   <condition property="dontextbuild">
 575     <equals arg1="n" arg2="${doextbuild.response}" />
 576   </condition>
 577   <condition property="dontextbuild">
 578     <equals arg1="N" arg2="${doextbuild.response}" />
 579   </condition>
 580   <fail if="dontextbuild">
 581         Build External Client Code process aborted by user. Jalview source is unchanged.
 582       </fail>
 583   <!-- Currently, this doesn't happen automatically.
 584      1. Run WSDL2Java as below, which generates an ext.vamsas +
 585      vamsas.<datapackages> fileset.
 586      2. refactor ext.vamsas.SpecificserviceWS* to
 587      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 588      3. Update the jalview.ws.*WServices classes to reflect the
 589      interface type, and all locations of this wsdl type that Jalview
 590      might be using.
 591
 592 -->
 593   <path id="axisbuild">
 594     <path refid="build.classpath" />
 595   </path>
 596   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 597   <move todir="./bak">
 598     <fileset dir="${sourceDir}" id="client">
 599       <include name="${wsdl.ClientNS}/*.*" />
 600     </fileset>
 601   </move>
 602
 603   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 604     <mappingSet>
 605       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 606       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 607     </mappingSet>
 608   </axis-wsdl2java>
 609 </target>
 610
 611 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
 612   <fail if="clover.jar">
 613     Ignoring request to build jalview distribution with clover-instrumented classes
 614   </fail>
 615   <!-- make the package jar if not already existing -->
 616   <mkdir dir="${packageDir}" />
 617   <!-- clean dir if it already existed -->
 618   <delete>
 619     <fileset dir="${packageDir}">
 620       <include name="*.jar" />
 621     </fileset>
 622   </delete>
 623   <jar destfile="${packageDir}/${outputJar}" index="true">
 624     <manifest>
 625       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 626       <attribute name="Permissions" value="all-permissions" />
 627       <attribute name="Application-Name" value="Jalview Desktop" />
 628       <attribute name="Codebase" value="${application.codebase}" />
 629     </manifest>
 630     <fileset dir="${outputDir}/">
 631       <exclude name="cache*/**" />
 632       <exclude name="*.jar" />
 633       <exclude name="*.jar.*" />
 634       <exclude name="**/*.jar" />
 635       <exclude name="**/*.jar.*" />
 636     </fileset>
 637   </jar>
 638
 639   <copy toDir="${packageDir}" flatten="true">
 640     <fileset dir="${outputDir}">
 641       <include name="*.jar" />
 642       <include name="**/*.jar" />
 643     </fileset>
 644   </copy>
 645 </target>
 646
 647
 648 <!-- jalopy code reformatter -->
 649 <target name="sourcescrub" depends="init,build">
 650   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 651     <fileset dir="${sourceDir}">
 652       <include name="*.java" />
 653       <include name="**/*.java" />
 654       <include name="**/**/*.java" />
 655     </fileset>
 656   </jalopy>
 657 </target>
 658
 659
 660
 661 <!-- Compile, package and obfuscate Jalview Applet -->
 662 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 663
 664 <target name="compileApplet" depends="init,clean">
 665   <mkdir dir="${outputDir}" />
 666   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 667 </target>
 668
 669 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 670   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 671   <copy todir="${outputDir}/lang">
 672     <fileset dir="${resourceDir}/lang">
 673       <include name="**.*" />
 674     </fileset>
 675   </copy>
 676   <jar destfile="in.jar" index="true">
 677     <manifest>
 678       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 679       <attribute name="Application-Name" value="JalviewLite" />
 680       <attribute name="Codebase" value="${applet.codebase}" />
 681     </manifest>
 682     <fileset dir="${outputDir}">
 683       <include name="com/**" />
 684       <include name="MCview/**" />
 685       <include name="jalview/**" />
 686       <include name=".build_properties" />
 687       <include name="images/link.gif" />
 688       <include name="lang/**" />
 689     </fileset>
 690   </jar>
 691 </target>
 692 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 693 </target>
 694 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 695   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 696   <delete file="in.jar" />
 697 </target>
 698 <target name="-obfuscatereally" unless="donotobfuscate">
 699
 700   <path id="obfuscateDeps.path">
 701     <pathelement location="${applet.jre.tools}" />
 702     <pathelement location="appletlib/${jmolJar}" />
 703     <pathelement location="lib/${varnaJar}" />
 704     <pathelement location="appletlib/${jsoup}" />
 705     <pathelement location="appletlib/${jsonSimple}" />
 706     <pathelement location="appletlib/${javaJson}" />
 707     <fileset dir="${java.home}/lib">
 708       <include name="plugin.jar" />
 709     </fileset>
 710   </path>
 711   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
 712
 713   <proguard verbose="true" >
 714     <injar file="in.jar" />
 715     <outjar file="${jalviewLiteJar}" />
 716     <libraryjar refid="obfuscateDeps.path" />
 717     <dontwarn />
 718     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 719       <field access="public" />
 720       <method access="public" />
 721       <constructor access="public" />
 722     </keep>
 723     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 724       <field access="public" />
 725       <method access="public" />
 726       <constructor access="public" />
 727     </keep>
 728
 729     <keep name="jalview.json.binding**">
 730       <constructor/>
 731       <method name="*"/>
 732     </keep>
 733
 734     <keep access="public" type="class" name="MCview.PDBfile">
 735       <field access="public" />
 736       <method access="public" />
 737       <constructor access="public" />
 738     </keep>
 739
 740     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 741       <field access="public" />
 742       <method access="public" />
 743       <constructor access="public" />
 744     </keep>
 745
 746     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 747       <field access="public" />
 748       <method access="public" />
 749       <constructor access="public" />
 750     </keep>
 751
 752
 753     <!--      -libraryjars "${obfuscateDeps}"
 754       -injars      in.jar
 755       -outjars     jalviewApplet.jar
 756       -keep public class jalview.bin.JalviewLite
 757        { public * ; } -->
 758   </proguard>
 759   <delete file="in.jar" />
 760 </target>
 761
 762 <target name="jaxb-bindings" depends="init" description="Generates JAXB bindings for supported Jalview XML models (needs xjc on the path)">
 763   <delete>
 764     <fileset dir="${sourceDir}/jalview/xml/binding/jalview">
 765       <include name="*.java" />
 766     </fileset>
 767   </delete>
 768   <exec executable="xjc">
 769     <arg value="${schemaDir}/jalview.xsd"/>
 770     <arg value="-d"/>
 771     <arg value="${sourceDir}"/>
 772     <arg value="-p"/>
 773     <arg value="jalview.xml.binding.jalview"/>
 774   </exec>
 775   <delete>
 776     <fileset dir="${sourceDir}/jalview/xml/binding/embl">
 777       <include name="*.java" />
 778     </fileset>
 779   </delete>
 780
 781   <exec executable="xjc">
 782     <arg value="${schemaDir}/embl.xsd"/>
 783     <arg value="-d"/>
 784     <arg value="${sourceDir}"/>
 785     <arg value="-b"/>
 786     <arg value="${schemaDir}/embl_bindings.xml"/>
 787     <arg value="-p"/>
 788     <arg value="jalview.xml.binding.embl"/>
 789   </exec>
 790
 791   <delete>
 792     <fileset dir="${sourceDir}/jalview/xml/binding/uniprot">
 793       <include name="*.java" />
 794     </fileset>
 795   </delete>
 796
 797   <exec executable="xjc">
 798     <arg value="${schemaDir}/uniprot.xsd"/>
 799     <arg value="-d"/>
 800     <arg value="${sourceDir}"/>
 801     <arg value="-p"/>
 802     <arg value="jalview.xml.binding.uniprot"/>
 803   </exec>
 804 </target>
 805
 806 <target name="sourcedist" description="create jalview source distribution" depends="init">
 807   <delete file="${source.dist.name}" />
 808   <!-- temporary copy of source to update timestamps -->
 809   <copy todir="_sourcedist">
 810     <fileset dir=".">
 811       <exclude name=".*" />
 812       <exclude name="**/.*" />
 813       <exclude name="*.class" />
 814       <exclude name="**/*.class" />
 815       <include name="LICENSE" />
 816       <include name="README" />
 817       <include name="build.xml" />
 818       <include name="jalview-jalopy.xml" />
 819       <include name="JalviewApplet.jpx" />
 820       <include name="JalviewX.jpx" />
 821       <include name="nbbuild.xml" />
 822       <include name="nbproject/genfiles.properties" />
 823       <include name="nbproject/project.properties" />
 824       <include name="nbproject/project.xml" />
 825       <include name="${sourceDir}/*.java" />
 826       <include name="${sourceDir}/**/*.java" />
 827       <include name="${sourceDir}/**/*.cdr" />
 828       <include name="${libDir}/**/*" />
 829       <include name="${resourceDir}/**/*" />
 830       <include name="${helpDir}/**/*" />
 831       <include name="appletlib/${jmolJar}" />
 832       <include name="appletlib/${jsonSimple}" />
 833       <include name="appletlib/${javaJson}" />
 834       <exclude name="**/*locales" />
 835       <exclude name="*locales/**" />
 836       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 837       <exclude name="utils/InstallAnywhere/**Build*/**" />
 838       <exclude name="utils/InstallAnywhere/**Build*/**" />
 839       <exclude name="utils/InstallAnywhere/.build*.*/**" />
 840       <exclude name="utils/InstallAnywhere/**locale*" />
 841       <exclude name="utils/InstallAnywhere/**locale*/**" />
 842       <exclude name="utils/InstallAnywhere/**locale*/**" />
 843       <include name="${schemaDir}/**/*" />
 844       <include name="utils/**/*" />
 845       <include name="${docDir}/**/*" />
 846       <include name="examples/**/*" />
 847     </fileset>
 848   </copy>
 849
 850   <tstamp prefix="build">
 851     <format property="year" pattern="yyyy" />
 852   </tstamp>
 853   <!-- each replacetoken CDATA body must be on one line -
 854        otherwise the pattern doesn't match -->
 855   <replace value="${JALVIEW_VERSION}">
 856     <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 857     <fileset dir="_sourcedist">
 858       <include name="**/*" />
 859     </fileset>
 860   </replace>
 861   <replace dir="_sourcedist" value="${build.year}">
 862     <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
 863     <fileset dir="_sourcedist">
 864       <include name="**/*" />
 865     </fileset>
 866   </replace>
 867
 868   <tar destfile="${source.dist.name}" compression="gzip">
 869     <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
 870     </tarfileset>
 871   </tar>
 872
 873   <delete dir="_sourcedist" />
 874 </target>
 875 <target name="prepubapplet_1" depends="makeApplet">
 876   <copy todir="${packageDir}/examples">
 877     <fileset dir="examples">
 878       <include name="**/*" />
 879       <include name="javascript/*" />
 880       <include name="jmol/*" />
 881     </fileset>
 882     <fileset dir=".">
 883       <include name="${jalviewLiteJar}" />
 884     </fileset>
 885     <fileset dir="appletlib">
 886       <include name="**/*" />
 887     </fileset>
 888   </copy>
 889   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 890   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 891   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 892   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 893     <manifest>
 894       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 895       <!--          <attribute name="Permissions" value="sandbox" /> -->
 896       <!--<attribute name="Trusted-Lib" value="true" /> -->
 897       <attribute name="Codebase" value="${applet.codebase}" />
 898       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 899     </manifest>
 900   </jar>
 901
 902   <presetdef name="ap_applet.jar">
 903     <!-- build a signed applet with 'all-permissions' -
 904                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 905                           JalviewLite+JmolApplet linked sequence/structure fails
 906                           Mixed code warnings are raised
 907                           -->
 908     <jar update="true" index="true">
 909       <manifest>
 910         <attribute name="Application-Name" value="JalviewLite" />
 911         <attribute name="Permissions" value="all-permissions" />
 912         <attribute name="Codebase" value="${applet.codebase}" />
 913         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 914         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 915       </manifest>
 916     </jar>
 917   </presetdef>
 918   <presetdef name="applet.jar">
 919     <!-- build signed applet with sandbox permissions -
 920                           Needs 'param name="permissions' value="sandbox"' in applet tag
 921                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 922                         -->
 923
 924     <jar update="true" index="true">
 925       <manifest>
 926         <attribute name="Application-Name" value="JalviewLite" />
 927         <attribute name="Permissions" value="sandbox" />
 928         <attribute name="Codebase" value="${applet.codebase}" />
 929         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 930         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 931       </manifest>
 932     </jar>
 933   </presetdef>
 934   <presetdef name="tl_applet.jar">
 935     <!-- build signed applet with trusted library/trusted permissions -
 936                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 937                                j1.7_45:
 938                                No mixed code warnings raised
 939                                Jmol/JalviewLite sequence/structure example doesn't link structures
 940                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 941
 942                               -->
 943
 944     <jar update="true" index="true">
 945       <manifest>
 946         <attribute name="Application-Name" value="JalviewLite" />
 947         <attribute name="Permissions" value="all-permissions" />
 948         <attribute name="Codebase" value="${applet.codebase}" />
 949         <attribute name="Trusted-Only" value="true" />
 950         <attribute name="Trusted-Library" value="true" />
 951       </manifest>
 952     </jar>
 953   </presetdef>
 954   <presetdef name="to_applet.jar">
 955     <!-- not fully test variant (yet) -->
 956     <jar update="true" index="true">
 957       <manifest>
 958         <attribute name="Application-Name" value="JalviewLite" />
 959         <attribute name="Permissions" value="all-permissions" />
 960         <attribute name="Codebase" value="${applet.codebase}" />
 961         <attribute name="Trusted-Only" value="true" />
 962       </manifest>
 963     </jar>
 964   </presetdef>
 965   <!-- create differently privileged artefacts -->
 966   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 967   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 968   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 969   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 970   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 971   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 972   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 973   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 974   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 975   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 976   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 977   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 978   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 979   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 980   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 981   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 982   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 983   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 984   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 985   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 986   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 987   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 988   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 989   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 990   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 991   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 992   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 993   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 994   <!-- finally, create manifest for original jars -->
 995   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 996   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 997   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 998   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 999
1000   <!-- todo - write examples/downloads for alternate versions of the applet
1001     probably don't need to do this now since we don't have alternate versions anymore !-->
1002 </target>
1003 <target name="-signapplet" depends="prepubapplet_1">
1004   <fileset id="signappletjarset" dir="${packageDir}/examples">
1005     <exclude name="u_*.jar" />
1006     <include name="${jalviewLiteJar}" />
1007     <include name="${jmolJar}" />
1008     <include name="${javaJson}" />
1009     <include name="${jsonSimple}" />
1010     <include name="to_${jalviewLiteJar}" />
1011     <include name="to_${jmolJar}" />
1012     <include name="to_${javaJson}" />
1013     <include name="to_${jsonSimple}" />
1014     <include name="tl_${jalviewLiteJar}" />
1015     <include name="tl_${jmolJar}" />
1016     <include name="tl_${javaJson}" />
1017     <include name="tl_${jsonSimple}" />
1018     <include name="ap_${jalviewLiteJar}" />
1019     <include name="ap_${jmolJar}" />
1020     <include name="ap_${javaJson}" />
1021     <include name="ap_${jsonSimple}" />
1022   </fileset>
1023 </target>
1024 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
1025   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
1026     <fileset refid="signappletjarset" />
1027   </signjar>
1028 </target>
1029
1030 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
1031   <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}">
1032     <fileset refid="signappletjarset" />
1033   </signjar>
1034 </target>
1035
1036 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
1037 <target name="pubapplet" description="Dummy target to keep legacy Jalview build system happy. We don't actually publish the applet anymore."/>
1038
1039 <target name="_pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
1040
1041   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
1042   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
1043   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
1044   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
1045   <!-- finally, replace any launchApp servlet tags with a version specification -->
1046   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
1047     <replacetoken>
1048       <![CDATA[http://www.jalview.org/services/launchApp"]]>
1049     </replacetoken>
1050     <fileset dir="${packageDir}/examples">
1051       <include name="**/*.html" />
1052     </fileset>
1053   </replace>
1054   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
1055     <replacetoken>
1056       <![CDATA[http://www.jalview.org/services/launchApp']]>
1057     </replacetoken>
1058     <fileset dir="${packageDir}/examples">
1059       <include name="**/*.html" />
1060     </fileset>
1061   </replace>
1062
1063 </target>
1064 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
1065   <javadoc destdir="${javadocDir}">
1066     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
1067     </packageset>
1068   </javadoc>
1069 </target>
1070 <target name="linkcheck" depends="init,prepare">
1071   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
1072   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
1073     <arg file="${helpDir}"/>
1074     <arg value="-nointernet"/>
1075   </java>
1076 </target>
1077 </project>