build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <project name="jalviewX" default="usage" basedir="."
  21  xmlns:if="ant:if"
  22     xmlns:unless="ant:unless">
  23   <taskdef classpath="${clover.jar}" resource="cloverlib.xml" if:set="clover.jar"/>
  24   <clover-env if:set="clover.jar"/>
  25
  26   <target name="help" depends="usage" />
  27   <target name="usage" depends="init">
  28     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  29     <echo message="Targets include:" />
  30     <echo message="usage - default target, displays this message" />
  31     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  32     <echo message="build - compiles all necessary files for Application" />
  33     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  34     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  35     <echo message="              this needs a keystore and key."/>
  36     <echo message="              Add -Dtimestamp to timestamp signed jars"/>
  37     <echo message="              -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
  38     <echo message="              See docs/building.html for more information." />
  39     <echo message="compileApplet - compiles all necessary files for Applet" />
  40     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  41     <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
  42     <echo message="      you can specify particular test groups as a list via -Dtestng-groups=" />
  43     <echo message="See docs/building.html and the comments in build file for other targets." />
  44     <echo message="note: compile and makeApplet optionally compile/obfuscate applet against a different Java version by specifying -Djava118.home=PathtoJDK/lib which is the lib directory in the JDK install that contains rt.jar " />
  45     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  46     <echo message="Useful -D flags: -Dclover.jar to specify path to openclover for testng coverage report" />
  47   </target>
  48
  49
  50   <!-- utils is a class path to additional utilities needed for
  51     building docs, jars and webstart stuff -->
  52   <!--
  53         Userdefined build property defaults
  54
  55         wsdl.server list (plus namespace mapping info ???)  - also want
  56                 ... to make this a dynamically generatable property
  57         WebStart Location
  58         Build location - provide a temporary root for speed
  59         jarsigner keystore and info
  60         Jakarta and axis classpath ?
  61         Default argument for starting Jalview (if it exists).
  62
  63 -->
  64
  65   <target name="init">
  66     <path id="axis.classpath">
  67       <!-->
  68       <fileset dir="/usr/local/axis/lib">
  69         <include name="**/*.jar" />
  70       </fileset>
  71       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  72         <include name="**/*.jar"/>
  73         <include name="*.jar"/>
  74       </fileset> -->
  75       </path>
  76
  77     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  78     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  79
  80     <property name="INSTALLATION" value="Source" />
  81
  82     <!-- 2.4 (VAMSAS)" -->
  83     <!-- Include debugging information in javac true or false -->
  84     <property name="javac.debug" value="true" />
  85
  86     <!-- JarSigner Key Store for Webstart Distribution -->
  87     <property name="jalview.keystore" value="./keys/.keystore" />
  88     <!-- Keystore Password -->
  89     <property name="jalview.keystore.pass" value="alignmentisfun" />
  90     <!-- Key Name -->
  91     <property name="jalview.key" value="jalview" />
  92     <!-- Key Password -->
  93     <property name="jalview.key.pass" value="alignmentisfun" />
  94     <!-- time stamp server URL -->
  95     <property name="jalview.tsaurl" value="" />
  96     <!-- locally valid proxy for signing with external time server -->
  97     <property name="proxyPort" value="80"/>
  98     <property name="proxyHost" value="sqid"/>
  99     <!-- key sign/digest algorithms -->
 100     <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
 101     <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
 102
 103     <!-- default TestNG groups to run -->
 104     <property name="testng-groups" value="Functional" />
 105     <!-- Java 9 JVM args -->
 106     <condition property="java9">
 107       <equals arg1="${ant.java.version}" arg2="9"/>
 108     </condition>
 109
 110     <!-- Don't change anything below here unless you know what you are doing! -->
 111     <!-- Url path for WebStart in JNLP file -->
 112     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
 113     <!-- Webstart Image - looked for in resources/images -->
 114     <property name="WebStartImage" value="JalviewLogo_big.png" />
 115     <!-- J2SE version needed for webstart launch -->
 116     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
 117     <property name="j2sev" value="1.7+" />
 118     <!-- Java Compilation settings - source and target javac version -->
 119     <property name="javac.source" value="1.8" />
 120     <property name="javac.target" value="1.8" />
 121
 122     <!-- Permissions for running Java applets and applications. -->
 123     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 124     <property name="application.codebase" value="*.jalview.org" />
 125     <!-- and allowing the applet to be deployed from any URL -->
 126     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
 127     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 128     <property name="applet.caller-codebase" value="${applet.codebase}" />
 129
 130     <!-- build directory configuration -->
 131     <property name="libDir" value="lib" />
 132     <property name="resourceDir" value="resources" />
 133     <property name="helpDir" value="help" />
 134     <property name="docDir" value="doc" />
 135     <property name="sourceDir" value="src" />
 136     <property name="schemaDir" value="schemas" />
 137     <property name="outputDir" value="classes" unless:set="clover.jar"/>
 138     <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
 139     <property name="outputDir" value="classes" />
 140     <property name="packageDir" value="dist" />
 141     <property name="outputJar" value="jalview.jar" />
 142     <!-- Jalview Applet JMol Jar Dependency -->
 143     <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
 144     <property name="varnaJar" value="VARNAv3-93.jar" />
 145     <property name="jsoup" value="jsoup-1.8.1.jar" />
 146     <property name="jsonSimple" value="json_simple-1.1.jar" />
 147     <property name="javaJson" value="java-json.jar" />
 148     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 149     <property name="reportDir" value="test-reports" />
 150     <property name="testDir" value="test" />
 151     <property name="testOutputDir" value="tests" />
 152     <!-- switch to indicate if we should obfuscate jalviewLite -->
 153     <!-- <property name="donotobfuscate" value="true"/> -->
 154     <!-- switch to exclude associations from generated jnlp files -->
 155     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 156
 157     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 158     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 159     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 160     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 161     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 162     <property name="WSInterf" value="MsaWS" />
 163     <property name="wsdl.Namespace" value="vamsas" />
 164     <property name="wsdl.ClientNS" value="ext.vamsas" />
 165     <!-- the class path for building the application -->
 166     <path id="build.classpath">
 167       <fileset dir="utils">
 168         <include name="*.jar" />
 169         <include name="**/*.jar" />
 170       </fileset>
 171       <fileset dir="${libDir}">
 172         <include name="*.jar" />
 173         <include name="**/*.jar" />
 174       </fileset>
 175       <fileset dir="${java.home}/lib">
 176         <include name="plugin.jar" />
 177       </fileset>
 178       <fileset dir="appletlib">
 179         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 180                                 -->
 181         <include name="${jmolJar}" />
 182         <include name="${varnaJar}" />
 183       </fileset>
 184     </path>
 185     <path id="test.classpath">
 186       <pathelement path="${outputDir}" />
 187       <path refid="build.classpath" />
 188     </path>
 189     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 190     <!-- The Location of the java 1.1.8 jdk -->
 191     <property name="java118.home" value="${java.home}" />
 192     <!-- jre for 1.4 version -->
 193     <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
 194
 195     <!-- the classpath for building the 1.1 applet -->
 196     <path id="jalviewlite.deps">
 197       <fileset dir="${java118.home}">
 198         <include name="lib/rt.jar" />
 199       </fileset>
 200       <fileset dir="${java.home}/lib">
 201         <include name="plugin.jar" />
 202       </fileset>
 203       <pathelement location="appletlib/${jmolJar}" />
 204       <pathelement location="lib/${varnaJar}" />
 205       <pathelement location="appletlib/${jsoup}" />
 206       <pathelement location="appletlib/${jsonSimple}" />
 207       <pathelement location="appletlib/${javaJson}" />
 208
 209     </path>
 210     <!-- default location for outputting javadoc -->
 211     <property name="javadocDir" value="${packageDir}/javadoc" />
 212   </target>
 213
 214
 215   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 216   <target name="buildPropertiesFile" depends="init">
 217     <tstamp prefix="build">
 218       <format property="date" pattern="dd MMMM yyyy" />
 219     </tstamp>
 220     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 221       <arg value="rev-parse" />
 222       <arg value="--short" />
 223       <arg value="HEAD" />
 224     </exec>
 225     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 226       <arg value="rev-parse" />
 227       <arg value="--abbrev-ref" />
 228       <arg value="HEAD" />
 229     </exec>
 230     <properties file="${outputDir}/.build_properties">
 231       <header>
 232           ---Jalview Build Details---
 233         </header>
 234       <property name="VERSION" value="${JALVIEW_VERSION}" />
 235       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 236       <property name="BUILD_DATE" value="${build.date}" />
 237     </properties>
 238   </target>
 239
 240
 241   <target name="clean" depends="init">
 242     <!-- not efficient yet. -->
 243     <delete dir="${outputDir}" includes="*,**/*" />
 244   </target>
 245
 246   <target name="distclean" depends="init, clean">
 247
 248     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 249     <delete>
 250       <fileset dir=".">
 251         <include name="${outputJar}" />
 252         <include name="#*#" />
 253         <include name="#*.*#" />
 254         <include name="**/#*#" />
 255         <include name="**/#*.*#" />
 256         <include name="*~" />
 257         <include name="*.*~" />
 258         <include name="**/*~" />
 259         <include name="**/*.*~" />
 260       </fileset>
 261     </delete>
 262   </target>
 263
 264   <target name="prepare" depends="init">
 265     <mkdir dir="${outputDir}" />
 266     <copy todir="${outputDir}">
 267       <fileset dir=".">
 268         <include name="${docDir}/**/*.*" />
 269         <include name="${helpDir}/**/*.*" />
 270         <include name="${libDir}/*.jar" />
 271       </fileset>
 272       <fileset dir="${resourceDir}">
 273         <include name="**/*.*" />
 274       </fileset>
 275     </copy>
 276   </target>
 277
 278   <target name="build" depends="prepare">
 279     <!-- not efficient yet. -->
 280     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 281       <exclude name="jalview/*applet*" />
 282       <exclude name="jalview/appletgui/**" />
 283       <exclude name="com/stevesoft/**" />
 284     </javac>
 285   </target>
 286
 287
 288   <target name="testclean" depends="init">
 289     <delete dir="${testOutputDir}" includes="*,**/*" />
 290   </target>
 291
 292   <target name="prepareTests" depends="init,testclean">
 293     <mkdir dir="${testOutputDir}" />
 294   </target>
 295
 296   <target name="buildTests" depends="build,buildindices,prepareTests">
 297     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 298     </javac>
 299   </target>
 300
 301   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 302
 303   <target name="testng" depends="buildTests">
 304     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 305       verbose="2">
 306       <classpath>
 307         <pathelement location="${testOutputDir}" />
 308         <pathelement location="${clover.jar}" if:set="clover.jar"/>
 309         <path refid="test.classpath" />
 310       </classpath>
 311       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 312       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 313       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 314     </testng>
 315   </target>
 316
 317   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 318     <replace value="${JALVIEW_VERSION}">
 319       <replacetoken>
 320         <![CDATA[$$Version-Rel$$]]>
 321       </replacetoken>
 322       <fileset dir="${outputDir}/${helpDir}">
 323         <include name="help.jhm" />
 324       </fileset>
 325     </replace>
 326
 327     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 328       <arg line="html" />
 329     </java>
 330   </target>
 331
 332   <target name="preparejnlp" depends="makedist">
 333     <copy todir="${packageDir}">
 334       <fileset dir="${resourceDir}/images">
 335         <include name="${WebStartImage}" />
 336       </fileset>
 337     </copy>
 338
 339     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 340
 341     <!-- create a dummy jar which will eventually contain the jnlp template -->
 342     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 343       <fileset dir="${packageDir}">
 344         <include name="jalview.jar" />
 345       </fileset>
 346     </jar>
 347
 348     <mkdir dir="${packageDir}/JNLP-INF" />
 349     <antcall target="writejnlpf">
 350       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 351       <param name="inih" value="*" />
 352       <param name="maxh" value="*" />
 353     </antcall>
 354
 355     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 356       <fileset dir="${packageDir}">
 357         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 358       </fileset>
 359     </jar>
 360
 361     <antcall target="writejnlpf">
 362       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 363       <param name="inih" value="10M" />
 364       <param name="maxh" value="256M" />
 365     </antcall>
 366
 367     <antcall target="writejnlpf">
 368       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 369       <param name="inih" value="128M" />
 370       <param name="maxh" value="512M" />
 371     </antcall>
 372
 373     <antcall target="writejnlpf">
 374       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 375       <param name="inih" value="256M" />
 376       <param name="maxh" value="1024M" />
 377     </antcall>
 378
 379     <!-- finally, need to postprocess to add in associations at end of 'information' element
 380
 381                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 382
 383                 </xslt>
 384
 385
 386                         -->
 387     <!--
 388                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 389         <association mime-type="application-x/ext-file" extensions="fasta"/>
 390         <association mime-type="application-x/ext-file" extensions="mfa"/>
 391         <association mime-type="application-x/ext-file" extensions="fastq"/>
 392         <association mime-type="application-x/ext-file" extensions="blc"/>
 393         <association mime-type="application-x/ext-file" extensions="msf"/>
 394         <association mime-type="application-x/ext-file" extensions="pfam"/>
 395         <association mime-type="application-x/ext-file" extensions="aln"/>
 396         <association mime-type="application-x/ext-file" extensions="pir"/>
 397         <association mime-type="application-x/ext-file" extensions="amsa"/>
 398         <association mime-type="application-x/ext-file" extensions="stk"/>
 399         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 400   </target>
 401
 402   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
 403     <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}"
 404       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 405       <fileset dir="${packageDir}">
 406         <include name="*.jar" />
 407       </fileset>
 408     </signjar>
 409   </target>
 410   <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
 411     <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}">
 412       <fileset dir="${packageDir}">
 413         <include name="*.jar" />
 414       </fileset>
 415     </signjar>
 416   </target>
 417
 418   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 419     <!-- and sign the jars -->
 420     <!-- the default keystore details might need to be edited here -->
 421   </target>
 422
 423   <target name="runenv" depends="init">
 424     <path id="run.classpath">
 425       <pathelement location="${outputDir}" />
 426       <fileset dir="${outputDir}">
 427         <include name="${libDir}/*.jar" />
 428       </fileset>
 429     </path>
 430     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 431
 432     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 433       </echo>
 434   </target>
 435
 436   <target name="-generatejnlpf">
 437     <presetdef name="jnlpf">
 438       <jnlp codebase="${WebStartLocation}">
 439         <information>
 440           <title>Jalview</title>
 441           <vendor>The Barton Group</vendor>
 442           <homepage href="http://www.jalview.org" />
 443           <description>Jalview Multiple Alignment Editor</description>
 444           <description kind="short">Jalview</description>
 445           <icon href="${WebStartImage}" />
 446           <offline_allowed />
 447         </information>
 448         <resources>
 449           <j2se version="1.8+" />
 450           <jar main="true" href="jalview.jar"/>
 451           <fileset dir="${packageDir}">
 452             <exclude name="jalview.jar" />
 453             <include name="*.jar" />
 454             <include name="*_*.jar" />
 455             <exclude name="*quaqua*.jar" />
 456           </fileset>
 457           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 458         </resources>
 459         <resources os="Mac OS X">
 460           <fileset dir="${packageDir}">
 461             <include name="quaqua-filechooser-only-8.0.jar"/>
 462             <include name="*quaqua64*.jnilib.jar" />
 463           </fileset>
 464         </resources>
 465
 466         <application_desc main_class="jalview.bin.Jalview">
 467         </application_desc>
 468         <security>
 469           <all_permissions />
 470         </security>
 471       </jnlp>
 472     </presetdef>
 473
 474     <jnlpf toFile="${jnlpFile}" />
 475     <!-- add the add-modules j2se attribute for java 9 -->
 476     <replace file="${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;">
 477       <replacetoken>j2se version="1.8+"</replacetoken>
 478     </replace>
 479   </target>
 480
 481   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 482     <echo message="Not adding JNLP File Associations" />
 483   </target>
 484
 485   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 486     <replace file="${jnlpFile}">
 487       <replacetoken>
 488         <![CDATA[</information>]]></replacetoken>
 489       <replacevalue>
 490         <![CDATA[
 491           <association mime-type="application-x/ext-file" extensions="fa" />
 492         <association mime-type="application-x/ext-file" extensions="fasta" />
 493         <association mime-type="application-x/ext-file" extensions="mfa" />
 494         <association mime-type="application-x/ext-file" extensions="fastq" />
 495         <association mime-type="application-x/ext-file" extensions="blc" />
 496         <association mime-type="application-x/ext-file" extensions="msf" />
 497         <association mime-type="application-x/ext-file" extensions="pfam" />
 498         <association mime-type="application-x/ext-file" extensions="aln"/>
 499         <association mime-type="application-x/ext-file" extensions="pir"/>
 500         <association mime-type="application-x/ext-file" extensions="amsa"/>
 501         <association mime-type="application-x/ext-file" extensions="stk"/>
 502         <association mime-type="application-x/ext-file" extensions="jvp"/>
 503       </information>]]></replacevalue>
 504   </replace>
 505   <echo message="Added file associations to JNLP file" />
 506 </target>
 507 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 508 </target>
 509
 510 <target name="buildextclients" depends="init">
 511   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 512   <condition property="dontextbuild">
 513     <equals arg1="n" arg2="${doextbuild.response}" />
 514   </condition>
 515   <condition property="dontextbuild">
 516     <equals arg1="N" arg2="${doextbuild.response}" />
 517   </condition>
 518   <fail if="dontextbuild">
 519         Build External Client Code process aborted by user. Jalview source is unchanged.
 520       </fail>
 521   <!-- Currently, this doesn't happen automatically.
 522      1. Run WSDL2Java as below, which generates an ext.vamsas +
 523      vamsas.<datapackages> fileset.
 524      2. refactor ext.vamsas.SpecificserviceWS* to
 525      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 526      3. Update the jalview.ws.*WServices classes to reflect the
 527      interface type, and all locations of this wsdl type that Jalview
 528      might be using.
 529
 530 -->
 531   <path id="axisbuild">
 532     <path refid="build.classpath" />
 533   </path>
 534   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 535   <move todir="./bak">
 536     <fileset dir="${sourceDir}" id="client">
 537       <include name="${wsdl.ClientNS}/*.*" />
 538     </fileset>
 539   </move>
 540
 541   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 542     <mappingSet>
 543       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 544       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 545     </mappingSet>
 546   </axis-wsdl2java>
 547 </target>
 548
 549 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
 550   <fail if="clover.jar">
 551     Ignoring request to build jalview distribution with clover-instrumented classes
 552   </fail>
 553   <!-- make the package jar if not already existing -->
 554   <mkdir dir="${packageDir}" />
 555   <!-- clean dir if it already existed -->
 556   <delete>
 557     <fileset dir="${packageDir}">
 558       <include name="*.jar" />
 559     </fileset>
 560   </delete>
 561   <jar destfile="${packageDir}/${outputJar}" index="true">
 562     <manifest>
 563       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 564       <attribute name="Permissions" value="all-permissions" />
 565       <attribute name="Application-Name" value="Jalview Desktop" />
 566       <attribute name="Codebase" value="${application.codebase}" />
 567     </manifest>
 568     <fileset dir="${outputDir}/">
 569       <exclude name="cache*/**" />
 570       <exclude name="*.jar" />
 571       <exclude name="*.jar.*" />
 572       <exclude name="**/*.jar" />
 573       <exclude name="**/*.jar.*" />
 574     </fileset>
 575   </jar>
 576
 577   <copy toDir="${packageDir}" flatten="true">
 578     <fileset dir="${outputDir}">
 579       <include name="*.jar" />
 580       <include name="**/*.jar" />
 581     </fileset>
 582   </copy>
 583 </target>
 584
 585
 586 <!-- jalopy code reformatter -->
 587 <target name="sourcescrub" depends="init,build">
 588   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 589     <fileset dir="${sourceDir}">
 590       <include name="*.java" />
 591       <include name="**/*.java" />
 592       <include name="**/**/*.java" />
 593     </fileset>
 594   </jalopy>
 595 </target>
 596
 597
 598
 599 <!-- Compile, package and obfuscate Jalview Applet -->
 600 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 601
 602 <target name="compileApplet" depends="init,clean">
 603   <mkdir dir="${outputDir}" />
 604   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 605 </target>
 606
 607 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 608   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 609   <copy todir="${outputDir}/lang">
 610     <fileset dir="${resourceDir}/lang">
 611       <include name="**.*" />
 612     </fileset>
 613   </copy>
 614   <jar destfile="in.jar" index="true">
 615     <manifest>
 616       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 617       <attribute name="Application-Name" value="JalviewLite" />
 618       <attribute name="Codebase" value="${applet.codebase}" />
 619     </manifest>
 620     <fileset dir="${outputDir}">
 621       <include name="com/**" />
 622       <include name="MCview/**" />
 623       <include name="jalview/**" />
 624       <include name=".build_properties" />
 625       <include name="images/link.gif" />
 626       <include name="lang/**" />
 627     </fileset>
 628   </jar>
 629 </target>
 630 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 631 </target>
 632 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 633   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 634   <delete file="in.jar" />
 635 </target>
 636 <target name="-obfuscatereally" unless="donotobfuscate">
 637
 638   <path id="obfuscateDeps.path">
 639     <pathelement location="${applet.jre.tools}" />
 640     <pathelement location="appletlib/${jmolJar}" />
 641     <pathelement location="lib/${varnaJar}" />
 642     <pathelement location="appletlib/${jsoup}" />
 643     <pathelement location="appletlib/${jsonSimple}" />
 644     <pathelement location="appletlib/${javaJson}" />
 645     <fileset dir="${java.home}/lib">
 646       <include name="plugin.jar" />
 647     </fileset>
 648   </path>
 649   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
 650
 651   <proguard verbose="true" >
 652     <injar file="in.jar" />
 653     <outjar file="${jalviewLiteJar}" />
 654     <libraryjar refid="obfuscateDeps.path" />
 655     <dontwarn />
 656     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 657       <field access="public" />
 658       <method access="public" />
 659       <constructor access="public" />
 660     </keep>
 661     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 662       <field access="public" />
 663       <method access="public" />
 664       <constructor access="public" />
 665     </keep>
 666
 667     <keep name="jalview.json.binding**">
 668       <constructor/>
 669       <method name="*"/>
 670     </keep>
 671
 672     <keep access="public" type="class" name="MCview.PDBfile">
 673       <field access="public" />
 674       <method access="public" />
 675       <constructor access="public" />
 676     </keep>
 677
 678     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 679       <field access="public" />
 680       <method access="public" />
 681       <constructor access="public" />
 682     </keep>
 683
 684     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 685       <field access="public" />
 686       <method access="public" />
 687       <constructor access="public" />
 688     </keep>
 689
 690
 691     <!--      -libraryjars "${obfuscateDeps}"
 692       -injars      in.jar
 693       -outjars     jalviewApplet.jar
 694       -keep public class jalview.bin.JalviewLite
 695        { public * ; } -->
 696   </proguard>
 697   <delete file="in.jar" />
 698 </target>
 699
 700 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 701   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 702   <delete>
 703     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 704       <include name="*.java" />
 705       <include name="descriptors/*.java" />
 706     </fileset>
 707   </delete>
 708   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 709   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 710   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 711   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 712   <!--
 713                 now build the jalview.binding package with the old schema set
 714                 -->
 715   <delete>
 716     <fileset dir="${sourceDir}/jalview/binding/">
 717       <include name="**" />
 718     </fileset>
 719   </delete>
 720   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 721   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 722   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 723 </target>
 724 <target name="sourcedist" description="create jalview source distribution" depends="init">
 725   <delete file="${source.dist.name}" />
 726   <!-- temporary copy of source to update timestamps -->
 727   <copy todir="_sourcedist">
 728     <fileset dir=".">
 729       <exclude name=".*" />
 730       <exclude name="**/.*" />
 731       <exclude name="*.class" />
 732       <exclude name="**/*.class" />
 733       <include name="LICENSE" />
 734       <include name="README" />
 735       <include name="build.xml" />
 736       <include name="jalview-jalopy.xml" />
 737       <include name="JalviewApplet.jpx" />
 738       <include name="JalviewX.jpx" />
 739       <include name="nbbuild.xml" />
 740       <include name="nbproject/genfiles.properties" />
 741       <include name="nbproject/project.properties" />
 742       <include name="nbproject/project.xml" />
 743       <include name="${sourceDir}/*.java" />
 744       <include name="${sourceDir}/**/*.java" />
 745       <include name="${sourceDir}/**/*.cdr" />
 746       <include name="${libDir}/**/*" />
 747       <include name="${resourceDir}/**/*" />
 748       <include name="${helpDir}/**/*" />
 749       <include name="appletlib/${jmolJar}" />
 750       <include name="appletlib/${jsonSimple}" />
 751       <include name="appletlib/${javaJson}" />
 752       <exclude name="**/*locales" />
 753       <exclude name="*locales/**" />
 754       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 755       <exclude name="utils/InstallAnywhere/**Build*/**" />
 756       <exclude name="utils/InstallAnywhere/**Build*/**" />
 757       <exclude name="utils/InstallAnywhere/.build*.*/**" />
 758       <exclude name="utils/InstallAnywhere/**locale*" />
 759       <exclude name="utils/InstallAnywhere/**locale*/**" />
 760       <exclude name="utils/InstallAnywhere/**locale*/**" />
 761       <include name="${schemaDir}/**/*" />
 762       <include name="utils/**/*" />
 763       <include name="${docDir}/**/*" />
 764       <include name="examples/**/*" />
 765     </fileset>
 766   </copy>
 767
 768   <tstamp prefix="build">
 769     <format property="year" pattern="yyyy" />
 770   </tstamp>
 771   <!-- each replacetoken CDATA body must be on one line -
 772        otherwise the pattern doesn't match -->
 773   <replace value="${JALVIEW_VERSION}">
 774     <replacetoken>
 775       <![CDATA[$$Version-Rel$$]]>
 776     </replacetoken>
 777     <fileset dir="_sourcedist">
 778       <include name="**/*" />
 779     </fileset>
 780   </replace>
 781   <replace dir="_sourcedist" value="${build.year}">
 782     <replacetoken>
 783       <![CDATA[$$Year-Rel$$]]>
 784     </replacetoken>
 785     <fileset dir="_sourcedist">
 786       <include name="**/*" />
 787     </fileset>
 788   </replace>
 789
 790   <tar destfile="${source.dist.name}" compression="gzip">
 791     <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
 792     </tarfileset>
 793   </tar>
 794
 795   <delete dir="_sourcedist" />
 796 </target>
 797 <target name="prepubapplet_1" depends="makeApplet">
 798   <copy todir="${packageDir}/examples">
 799     <fileset dir="examples">
 800       <include name="**/*" />
 801       <include name="javascript/*" />
 802       <include name="jmol/*" />
 803     </fileset>
 804     <fileset dir=".">
 805       <include name="${jalviewLiteJar}" />
 806     </fileset>
 807     <fileset dir="appletlib">
 808       <include name="**/*" />
 809     </fileset>
 810   </copy>
 811   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 812   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 813   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 814   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 815     <manifest>
 816       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 817       <!--          <attribute name="Permissions" value="sandbox" /> -->
 818       <!--<attribute name="Trusted-Lib" value="true" /> -->
 819       <attribute name="Codebase" value="${applet.codebase}" />
 820       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 821     </manifest>
 822   </jar>
 823
 824   <presetdef name="ap_applet.jar">
 825     <!-- build a signed applet with 'all-permissions' -
 826                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 827                           JalviewLite+JmolApplet linked sequence/structure fails
 828                           Mixed code warnings are raised
 829                           -->
 830     <jar update="true" index="true">
 831       <manifest>
 832         <attribute name="Application-Name" value="JalviewLite" />
 833         <attribute name="Permissions" value="all-permissions" />
 834         <attribute name="Codebase" value="${applet.codebase}" />
 835         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 836         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 837       </manifest>
 838     </jar>
 839   </presetdef>
 840   <presetdef name="applet.jar">
 841     <!-- build signed applet with sandbox permissions -
 842                           Needs 'param name="permissions' value="sandbox"' in applet tag
 843                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 844                         -->
 845
 846     <jar update="true" index="true">
 847       <manifest>
 848         <attribute name="Application-Name" value="JalviewLite" />
 849         <attribute name="Permissions" value="sandbox" />
 850         <attribute name="Codebase" value="${applet.codebase}" />
 851         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 852         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 853       </manifest>
 854     </jar>
 855   </presetdef>
 856   <presetdef name="tl_applet.jar">
 857     <!-- build signed applet with trusted library/trusted permissions -
 858                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 859                                j1.7_45:
 860                                No mixed code warnings raised
 861                                Jmol/JalviewLite sequence/structure example doesn't link structures
 862                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 863
 864                               -->
 865
 866     <jar update="true" index="true">
 867       <manifest>
 868         <attribute name="Application-Name" value="JalviewLite" />
 869         <attribute name="Permissions" value="all-permissions" />
 870         <attribute name="Codebase" value="${applet.codebase}" />
 871         <attribute name="Trusted-Only" value="true" />
 872         <attribute name="Trusted-Library" value="true" />
 873       </manifest>
 874     </jar>
 875   </presetdef>
 876   <presetdef name="to_applet.jar">
 877     <!-- not fully test variant (yet) -->
 878     <jar update="true" index="true">
 879       <manifest>
 880         <attribute name="Application-Name" value="JalviewLite" />
 881         <attribute name="Permissions" value="all-permissions" />
 882         <attribute name="Codebase" value="${applet.codebase}" />
 883         <attribute name="Trusted-Only" value="true" />
 884       </manifest>
 885     </jar>
 886   </presetdef>
 887   <!-- create differently privileged artefacts -->
 888   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 889   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 890   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 891   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 892   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 893   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 894   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 895   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 896   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 897   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 898   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 899   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 900   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 901   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 902   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 903   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 904   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 905   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 906   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 907   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 908   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 909   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 910   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 911   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 912   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 913   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 914   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 915   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 916   <!-- finally, create manifest for original jars -->
 917   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 918   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 919   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 920   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 921
 922   <!-- todo - write examples/downloads for alternate versions of the applet
 923     probably don't need to do this now since we don't have alternate versions anymore !-->
 924 </target>
 925 <target name="-signapplet" depends="prepubapplet_1">
 926   <fileset id="signappletjarset" dir="${packageDir}/examples">
 927     <exclude name="u_*.jar" />
 928     <include name="${jalviewLiteJar}" />
 929     <include name="${jmolJar}" />
 930     <include name="${javaJson}" />
 931     <include name="${jsonSimple}" />
 932     <include name="to_${jalviewLiteJar}" />
 933     <include name="to_${jmolJar}" />
 934     <include name="to_${javaJson}" />
 935     <include name="to_${jsonSimple}" />
 936     <include name="tl_${jalviewLiteJar}" />
 937     <include name="tl_${jmolJar}" />
 938     <include name="tl_${javaJson}" />
 939     <include name="tl_${jsonSimple}" />
 940     <include name="ap_${jalviewLiteJar}" />
 941     <include name="ap_${jmolJar}" />
 942     <include name="ap_${javaJson}" />
 943     <include name="ap_${jsonSimple}" />
 944   </fileset>
 945 </target>
 946 <target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
 947   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 948     <fileset refid="signappletjarset" />
 949   </signjar>
 950 </target>
 951
 952 <target name="-signapplettsa" if="timestamp" depends="-signapplet">
 953   <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}">
 954     <fileset refid="signappletjarset" />
 955   </signjar>
 956 </target>
 957
 958 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
 959
 960 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 961
 962   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 963   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 964   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 965   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 966   <!-- finally, replace any launchApp servlet tags with a version specification -->
 967   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 968     <replacetoken>
 969       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 970     </replacetoken>
 971     <fileset dir="${packageDir}/examples">
 972       <include name="**/*.html" />
 973     </fileset>
 974   </replace>
 975   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 976     <replacetoken>
 977       <![CDATA[http://www.jalview.org/services/launchApp']]>
 978     </replacetoken>
 979     <fileset dir="${packageDir}/examples">
 980       <include name="**/*.html" />
 981     </fileset>
 982   </replace>
 983
 984 </target>
 985 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 986   <javadoc destdir="${javadocDir}">
 987     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 988     </packageset>
 989   </javadoc>
 990 </target>
 991 <target name="linkcheck" depends="init,prepare">
 992   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
 993   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
 994     <arg file="${helpDir}"/>
 995     <arg value="-nointernet" />
 996   </java>
 997 </target>
 998
 999 <target name="eclipse-install" depends="init,prepare">
1000
1001   <property name="eclipseTempFile" value="eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
1002   <property name="eclipseInstallURL" value="http://mirror.csclub.uwaterloo.ca/eclipse/technology/epp/downloads/release/oxygen/R/eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
1003   <property name="java2scriptURL" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.core/dist/dropins/net.sf.j2s.core.jar?raw=true"/>
1004
1005   <get url="${eclipseInstallURL}" dest="${eclipseTempFile}"/>
1006   <untar compression="gzip" src="${eclipseTempFile}" dest="${eclipse-inst}"/>
1007
1008   <!-- not needed since we ship transpiler with source
1009     <get url="${java2scriptURL}" dest="eclipse-inst/dropins/net.sf.j2s.core.jar" /> -->
1010
1011 </target>
1012
1013 <target name="build-site" depends="init,prepare,compile-site,unzip-to-site">
1014   <!-- closure compile -->
1015   <!-- tarball -->
1016   <tar compression="gzip" destfile="site.tar.gz">
1017     <tarfileset dir="site" />
1018   </tar>
1019 </target>
1020 <target name="prepare-site" depends="init,prepare">
1021   <property name="swingjsdir" value="swingjs"/>
1022   <property name="eclipse-inst" value="/home/bamboo/buildtools/eclipse/eclipse-js"/>
1023   <property name="eclipse-exec" value="${eclipse-inst}/eclipse"/>
1024   <property name="site" value="site"/>
1025   <!-- where the eclipse js workspace has been initialised -->
1026   <property name="eclipse-work" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace"/>
1027   <!-- git repository linked to project in workspace -->
1028   <property name="eclipse-workrepo" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace/jalview-js"/>
1029 </target>
1030   <target name="clean-site" depends="prepare-site">
1031     <delete dir="${eclipse-workrepo}/${site}"/>
1032     <mkdir dir="${eclipse-workrepo}/${site}"/>
1033   </target>
1034 <target name="compile-site" depends="prepare-site,clean-site">
1035   <!-- update transpiler -->
1036   <copy file="${swingjsdir}/net.sf.j2s.core.jar" todir="${eclipse-inst}/dropins" overwrite="true" failonerror="true"/>
1037   <!-- update the git repo linked to the eclipse workspace -->
1038   <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="true">
1039     <arg value="rev-parse" />
1040     <arg value="--short" />
1041     <arg value="HEAD" />
1042   </exec>
1043   <!-- update and checkout the same commit in the workspace project -->
1044   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1045     <arg value="reset" />
1046     <arg value="--hard" />
1047   </exec>
1048   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1049       <arg value="pull" />
1050   </exec>
1051   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1052     <arg value="checkout" />
1053     <arg value="${git.commit}" />
1054   </exec>
1055   <!-- custom classpath for .js builds -->
1056   <copy file=".classpath.js" tofile="${eclipse-workrepo}/.classpath" overwrite="true"/>
1057   <!-- clean eclipse log -->
1058   <delete file="${eclipse-work}/.metadata/.log"/>
1059
1060   <!-- execute the eclipse build - the build may fail but valid javascript may still be produced, so we ignore return codes -->
1061   <exec executable="${eclipse-exec}" failonerror="no">
1062     <arg value="-nosplash"/>
1063     <arg value="--launcher.suppressErrors"/>
1064     <arg value="-application"/>
1065     <arg value="org.eclipse.jdt.apt.core.aptBuild"/>
1066     <arg value="-data"/>
1067     <arg value="${eclipse-work}"/>
1068   </exec>
1069   <!-- report log -->
1070   <exec executable="/bin/cat">
1071     <arg value="${eclipse-work}/.metadata/.log"/>
1072   </exec>
1073   <!-- TODO: run jslint and something else here to check we have a complete set of .js files for java -->
1074   <!-- possibly compare timestamps between .js files and their mate in source - any newer or not present triggers a new build -->
1075   <!-- <mkdir dir="${packageDir}/${site}" /> -->
1076   <!--   <property name="swingjs.zipurl" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.java.core/dist/SwingJS-site.zip?raw=true" /> -->
1077
1078   <!-- and reset the .classpath -->
1079   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1080     <arg value="checkout" />
1081     <arg value="${git.commit}"/>
1082     <arg value="--"/>
1083     <arg value=".classpath" />
1084   </exec>
1085
1086   <!-- finally copy artefacts from eclipse project checkout to the build site -->
1087   <copy todir="${site}">
1088     <fileset dir="${eclipse-workrepo}/site"/>
1089   </copy>
1090 </target>
1091 <target name="unzip-to-site" depends="prepare-site">
1092   <property name="swingjs.zip" value="${swingjsdir}/SwingJS-site.zip" />
1093   <unzip dest="${site}/" overwrite="true">
1094     <fileset dir="libjs">
1095       <include name="*.zip" />
1096     </fileset>
1097   </unzip>
1098   <copy overwrite="true" todir="${site}/swingjs/j2s/">
1099     <fileset dir="${resourceDir}">
1100       <include name="**"/>
1101     </fileset>
1102   </copy>
1103
1104   <!-- copy test files into place in site -->
1105   <copy todir="${site}/examples">
1106     <fileset dir="examples">
1107       <include name="*.*"/>
1108     </fileset>
1109   </copy>
1110   <!-- lastly, update SwingJS -->
1111   <unzip dest="${site}/" overwrite="true">
1112     <fileset dir="${swingjsdir}">
1113       <include name="SwingJS-site.zip"/>
1114     </fileset>
1115   </unzip>
1116 </target>
1117 </project>