build.Bob-Windows.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     <!-- default verbosity for TestNG -->
 106     <property name="testng-verbosity" value="2"/>
 107     <!-- Java 9 JVM args -->
 108     <condition property="java9">
 109       <equals arg1="${ant.java.version}" arg2="9"/>
 110     </condition>
 111
 112     <!-- Don't change anything below here unless you know what you are doing! -->
 113     <!-- Url path for WebStart in JNLP file -->
 114     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
 115     <!-- Webstart Image - looked for in resources/images -->
 116     <property name="WebStartImage" value="JalviewLogo_big.png" />
 117     <!-- J2SE version needed for webstart launch -->
 118     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
 119     <property name="j2sev" value="1.7+" />
 120     <!-- Java Compilation settings - source and target javac version -->
 121     <property name="javac.source" value="1.8" />
 122     <property name="javac.target" value="1.8" />
 123
 124     <!-- Permissions for running Java applets and applications. -->
 125     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 126     <property name="application.codebase" value="*.jalview.org" />
 127     <!-- and allowing the applet to be deployed from any URL -->
 128     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
 129     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 130     <property name="applet.caller-codebase" value="${applet.codebase}" />
 131
 132     <!-- build directory configuration -->
 133     <property name="libDir" value="lib" />
 134     <property name="resourceDir" value="resources" />
 135     <property name="helpDir" value="help" />
 136     <property name="docDir" value="doc" />
 137     <property name="sourceDir" value="src" />
 138     <property name="schemaDir" value="schemas" />
 139     <property name="outputDir" value="classes" unless:set="clover.jar"/>
 140     <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
 141     <property name="packageDir" value="dist" />
 142     <property name="outputJar" value="jalview.jar" />
 143     <!-- Jalview Applet JMol Jar Dependency -->
 144     <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
 145     <property name="varnaJar" value="VARNAv3-93.jar" />
 146     <property name="jsoup" value="jsoup-1.8.1.jar" />
 147     <property name="jsonSimple" value="json_simple-1.1.jar" />
 148     <property name="javaJson" value="java-json.jar" />
 149     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 150     <property name="reportDir" value="test-reports" />
 151     <property name="testDir" value="test" />
 152     <property name="testOutputDir" value="tests" />
 153         <property name="cloverOutputDir" value="clover" if:set="clover.jar" />
 154     <!-- switch to indicate if we should obfuscate jalviewLite -->
 155     <!-- <property name="donotobfuscate" value="true"/> -->
 156     <!-- switch to exclude associations from generated jnlp files -->
 157     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 158
 159     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 160     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 161     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 162     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 163     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 164     <property name="WSInterf" value="MsaWS" />
 165     <property name="wsdl.Namespace" value="vamsas" />
 166     <property name="wsdl.ClientNS" value="ext.vamsas" />
 167     <!-- the class path for building the application -->
 168     <path id="build.classpath">
 169       <fileset dir="utils">
 170         <include name="*.jar" />
 171         <include name="**/*.jar" />
 172       </fileset>
 173       <fileset dir="${libDir}">
 174         <include name="*.jar" />
 175         <include name="**/*.jar" />
 176       </fileset>
 177       <fileset dir="${java.home}/lib">
 178         <include name="plugin.jar" />
 179       </fileset>
 180       <fileset dir="appletlib">
 181         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 182                                 -->
 183         <include name="${jmolJar}" />
 184         <include name="${varnaJar}" />
 185       </fileset>
 186     </path>
 187     <path id="test.classpath">
 188       <pathelement path="${outputDir}" />
 189       <path refid="build.classpath" />
 190     </path>
 191     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 192     <!-- The Location of the java 1.1.8 jdk -->
 193     <property name="java118.home" value="${java.home}" />
 194     <!-- jre for 1.4 version -->
 195     <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
 196
 197     <!-- the classpath for building the 1.1 applet -->
 198     <path id="jalviewlite.deps">
 199       <fileset dir="${java118.home}">
 200         <include name="lib/rt.jar" />
 201       </fileset>
 202       <fileset dir="${java.home}/lib">
 203         <include name="plugin.jar" />
 204       </fileset>
 205       <pathelement location="appletlib/${jmolJar}" />
 206       <pathelement location="lib/${varnaJar}" />
 207       <pathelement location="appletlib/${jsoup}" />
 208       <pathelement location="appletlib/${jsonSimple}" />
 209       <pathelement location="appletlib/${javaJson}" />
 210
 211     </path>
 212     <!-- default location for outputting javadoc -->
 213     <property name="javadocDir" value="${packageDir}/javadoc" />
 214   </target>
 215
 216
 217   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 218   <target name="buildPropertiesFile" depends="init">
 219     <tstamp prefix="build">
 220       <format property="date" pattern="dd MMMM yyyy" />
 221     </tstamp>
 222     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 223       <arg value="rev-parse" />
 224       <arg value="--short" />
 225       <arg value="HEAD" />
 226     </exec>
 227     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 228       <arg value="rev-parse" />
 229       <arg value="--abbrev-ref" />
 230       <arg value="HEAD" />
 231     </exec>
 232     <properties file="${outputDir}/.build_properties">
 233       <header>
 234           ---Jalview Build Details---
 235         </header>
 236       <property name="VERSION" value="${JALVIEW_VERSION}" />
 237       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 238       <property name="BUILD_DATE" value="${build.date}" />
 239     </properties>
 240   </target>
 241
 242
 243   <target name="clean" depends="init">
 244     <!-- not efficient yet. -->
 245     <delete dir="${outputDir}" includes="*,**/*" />
 246   </target>
 247
 248   <target name="distclean" depends="init, clean">
 249
 250     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 251     <delete>
 252       <fileset dir=".">
 253         <include name="${outputJar}" />
 254         <include name="#*#" />
 255         <include name="#*.*#" />
 256         <include name="**/#*#" />
 257         <include name="**/#*.*#" />
 258         <include name="*~" />
 259         <include name="*.*~" />
 260         <include name="**/*~" />
 261         <include name="**/*.*~" />
 262       </fileset>
 263     </delete>
 264   </target>
 265
 266   <target name="prepare" depends="init">
 267     <mkdir dir="${outputDir}" />
 268     <copy todir="${outputDir}">
 269       <fileset dir=".">
 270         <include name="${docDir}/**/*.*" />
 271         <include name="${helpDir}/**/*.*" />
 272         <include name="${libDir}/*.jar" />
 273       </fileset>
 274       <fileset dir="${resourceDir}">
 275         <include name="**/*.*" />
 276       </fileset>
 277     </copy>
 278         <mkdir dir="${cloverOutputDir}" if:set="clover.jar"/>
 279   </target>
 280
 281   <target name="build" depends="prepare">
 282     <!-- not efficient yet. -->
 283     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 284       <exclude name="jalview/*applet*" />
 285       <exclude name="jalview/appletgui/**" />
 286       <exclude name="com/stevesoft/**" />
 287     </javac>
 288   </target>
 289
 290
 291   <target name="testclean" depends="init">
 292     <delete dir="${testOutputDir}" includes="*,**/*" />
 293   </target>
 294
 295   <target name="prepareTests" depends="init,testclean">
 296     <mkdir dir="${testOutputDir}" />
 297   </target>
 298
 299   <target name="buildTests" depends="build,buildindices,prepareTests">
 300     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 301     </javac>
 302   </target>
 303
 304   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 305
 306   <target name="testng" depends="buildTests">
 307     <testng workingDir="c:/users/hansonr/git/jalview1" outputDir="${reportDir}" haltOnFailure="true" groups="${testng-groups}" mode="testng"
 308       verbose="${testng-verbosity}">
 309       <classpath>
 310         <pathelement location="${testOutputDir}" />
 311         <pathelement location="${clover.jar}" if:set="clover.jar"/>
 312         <path refid="test.classpath" />
 313       </classpath>
 314       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 315       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 316       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 317     </testng>
 318   </target>
 319
 320   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 321     <replace value="${JALVIEW_VERSION}">
 322       <replacetoken>
 323         <![CDATA[$$Version-Rel$$]]>
 324       </replacetoken>
 325       <fileset dir="${outputDir}/${helpDir}">
 326         <include name="help.jhm" />
 327       </fileset>
 328     </replace>
 329
 330     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 331       <arg line="html" />
 332     </java>
 333   </target>
 334
 335   <target name="preparejnlp" depends="makedist">
 336     <copy todir="${packageDir}">
 337       <fileset dir="${resourceDir}/images">
 338         <include name="${WebStartImage}" />
 339       </fileset>
 340     </copy>
 341
 342     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 343
 344     <!-- create a dummy jar which will eventually contain the jnlp template -->
 345     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 346       <fileset dir="${packageDir}">
 347         <include name="jalview.jar" />
 348       </fileset>
 349     </jar>
 350
 351     <mkdir dir="${packageDir}/JNLP-INF" />
 352     <antcall target="writejnlpf">
 353       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 354       <param name="inih" value="*" />
 355       <param name="maxh" value="*" />
 356     </antcall>
 357
 358     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 359       <fileset dir="${packageDir}">
 360         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 361       </fileset>
 362     </jar>
 363
 364     <antcall target="writejnlpf">
 365       <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
 366       <param name="inih" value="10M" />
 367       <param name="maxh" value="256M" />
 368     </antcall>
 369     <antcall target="writejnlpf">
 370       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 371       <param name="inih" value="800M" />
 372       <param name="maxh" value="1024M" />
 373     </antcall>
 374
 375     <antcall target="writejnlpf">
 376       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 377       <param name="inih" value="128M" />
 378       <param name="maxh" value="512M" />
 379     </antcall>
 380
 381     <antcall target="writejnlpf">
 382       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 383       <param name="inih" value="800M" />
 384       <param name="maxh" value="1024M" />
 385     </antcall>
 386
 387     <!-- finally, need to postprocess to add in associations at end of 'information' element
 388
 389                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 390
 391                 </xslt>
 392
 393
 394                         -->
 395     <!--
 396                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 397         <association mime-type="application-x/ext-file" extensions="fasta"/>
 398         <association mime-type="application-x/ext-file" extensions="mfa"/>
 399         <association mime-type="application-x/ext-file" extensions="fastq"/>
 400         <association mime-type="application-x/ext-file" extensions="blc"/>
 401         <association mime-type="application-x/ext-file" extensions="msf"/>
 402         <association mime-type="application-x/ext-file" extensions="pfam"/>
 403         <association mime-type="application-x/ext-file" extensions="aln"/>
 404         <association mime-type="application-x/ext-file" extensions="pir"/>
 405         <association mime-type="application-x/ext-file" extensions="amsa"/>
 406         <association mime-type="application-x/ext-file" extensions="stk"/>
 407         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 408   </target>
 409
 410   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
 411     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
 412       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 413       <fileset dir="${packageDir}">
 414         <include name="*.jar" />
 415       </fileset>
 416     </signjar>
 417   </target>
 418   <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
 419     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
 420       <fileset dir="${packageDir}">
 421         <include name="*.jar" />
 422       </fileset>
 423     </signjar>
 424   </target>
 425
 426   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 427     <!-- and sign the jars -->
 428     <!-- the default keystore details might need to be edited here -->
 429   </target>
 430
 431   <target name="runenv" depends="init">
 432     <path id="run.classpath">
 433       <pathelement location="${outputDir}" />
 434       <fileset dir="${outputDir}">
 435         <include name="${libDir}/*.jar" />
 436       </fileset>
 437     </path>
 438     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 439
 440     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 441       </echo>
 442   </target>
 443
 444   <target name="-generatejnlpf">
 445     <presetdef name="jnlpf">
 446       <jnlp codebase="${WebStartLocation}">
 447         <information>
 448           <title>Jalview</title>
 449           <vendor>The Barton Group</vendor>
 450           <homepage href="http://www.jalview.org" />
 451           <description>Jalview Multiple Alignment Editor</description>
 452           <description kind="short">Jalview</description>
 453           <icon href="${WebStartImage}" />
 454           <offline_allowed />
 455         </information>
 456         <resources>
 457           <j2se version="1.8+" />
 458           <jar main="true" href="jalview.jar"/>
 459           <fileset dir="${packageDir}">
 460             <exclude name="jalview.jar" />
 461             <include name="*.jar" />
 462             <include name="*_*.jar" />
 463             <exclude name="*quaqua*.jar" />
 464           </fileset>
 465           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 466         </resources>
 467         <resources os="Mac OS X">
 468           <fileset dir="${packageDir}">
 469             <include name="quaqua-filechooser-only-8.0.jar"/>
 470             <include name="*quaqua64*.jnilib.jar" />
 471           </fileset>
 472         </resources>
 473
 474         <application_desc main_class="jalview.bin.Jalview">
 475         </application_desc>
 476         <security>
 477           <all_permissions />
 478         </security>
 479       </jnlp>
 480     </presetdef>
 481
 482     <jnlpf toFile="${jnlpFile}" />
 483     <!-- add the add-modules j2se attribute for java 9 -->
 484     <replace file="${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;">
 485       <replacetoken>j2se version="1.8+"</replacetoken>
 486     </replace>
 487   </target>
 488
 489   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 490     <echo message="Not adding JNLP File Associations" />
 491   </target>
 492
 493   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 494     <replace file="${jnlpFile}">
 495       <replacetoken>
 496         <![CDATA[</information>]]></replacetoken>
 497       <replacevalue>
 498         <![CDATA[
 499           <association mime-type="application-x/ext-file" extensions="fa" />
 500         <association mime-type="application-x/ext-file" extensions="fasta" />
 501         <association mime-type="application-x/ext-file" extensions="mfa" />
 502         <association mime-type="application-x/ext-file" extensions="fastq" />
 503         <association mime-type="application-x/ext-file" extensions="blc" />
 504         <association mime-type="application-x/ext-file" extensions="msf" />
 505         <association mime-type="application-x/ext-file" extensions="pfam" />
 506         <association mime-type="application-x/ext-file" extensions="aln"/>
 507         <association mime-type="application-x/ext-file" extensions="pir"/>
 508         <association mime-type="application-x/ext-file" extensions="amsa"/>
 509         <association mime-type="application-x/ext-file" extensions="stk"/>
 510         <association mime-type="application-x/ext-file" extensions="jvp"/>
 511       </information>]]></replacevalue>
 512   </replace>
 513   <echo message="Added file associations to JNLP file" />
 514 </target>
 515 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 516 </target>
 517
 518 <target name="buildextclients" depends="init">
 519   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 520   <condition property="dontextbuild">
 521     <equals arg1="n" arg2="${doextbuild.response}" />
 522   </condition>
 523   <condition property="dontextbuild">
 524     <equals arg1="N" arg2="${doextbuild.response}" />
 525   </condition>
 526   <fail if="dontextbuild">
 527         Build External Client Code process aborted by user. Jalview source is unchanged.
 528       </fail>
 529   <!-- Currently, this doesn't happen automatically.
 530      1. Run WSDL2Java as below, which generates an ext.vamsas +
 531      vamsas.<datapackages> fileset.
 532      2. refactor ext.vamsas.SpecificserviceWS* to
 533      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 534      3. Update the jalview.ws.*WServices classes to reflect the
 535      interface type, and all locations of this wsdl type that Jalview
 536      might be using.
 537
 538 -->
 539   <path id="axisbuild">
 540     <path refid="build.classpath" />
 541   </path>
 542   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 543   <move todir="./bak">
 544     <fileset dir="${sourceDir}" id="client">
 545       <include name="${wsdl.ClientNS}/*.*" />
 546     </fileset>
 547   </move>
 548
 549   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 550     <mappingSet>
 551       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 552       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 553     </mappingSet>
 554   </axis-wsdl2java>
 555 </target>
 556
 557 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
 558   <fail if="clover.jar">
 559     Ignoring request to build jalview distribution with clover-instrumented classes
 560   </fail>
 561   <!-- make the package jar if not already existing -->
 562   <mkdir dir="${packageDir}" />
 563   <!-- clean dir if it already existed -->
 564   <delete>
 565     <fileset dir="${packageDir}">
 566       <include name="*.jar" />
 567     </fileset>
 568   </delete>
 569   <jar destfile="${packageDir}/${outputJar}" index="true">
 570     <manifest>
 571       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 572       <attribute name="Permissions" value="all-permissions" />
 573       <attribute name="Application-Name" value="Jalview Desktop" />
 574       <attribute name="Codebase" value="${application.codebase}" />
 575     </manifest>
 576     <fileset dir="${outputDir}/">
 577       <exclude name="cache*/**" />
 578       <exclude name="*.jar" />
 579       <exclude name="*.jar.*" />
 580       <exclude name="**/*.jar" />
 581       <exclude name="**/*.jar.*" />
 582     </fileset>
 583   </jar>
 584
 585   <copy toDir="${packageDir}" flatten="true">
 586     <fileset dir="${outputDir}">
 587       <include name="*.jar" />
 588       <include name="**/*.jar" />
 589     </fileset>
 590   </copy>
 591 </target>
 592
 593
 594 <!-- jalopy code reformatter -->
 595 <target name="sourcescrub" depends="init,build">
 596   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 597     <fileset dir="${sourceDir}">
 598       <include name="*.java" />
 599       <include name="**/*.java" />
 600       <include name="**/**/*.java" />
 601     </fileset>
 602   </jalopy>
 603 </target>
 604
 605
 606
 607 <!-- Compile, package and obfuscate Jalview Applet -->
 608 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 609
 610 <target name="compileApplet" depends="init,clean">
 611   <mkdir dir="${outputDir}" />
 612   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 613 </target>
 614
 615 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 616   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 617   <copy todir="${outputDir}/lang">
 618     <fileset dir="${resourceDir}/lang">
 619       <include name="**.*" />
 620     </fileset>
 621   </copy>
 622   <jar destfile="in.jar" index="true">
 623     <manifest>
 624       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 625       <attribute name="Application-Name" value="JalviewLite" />
 626       <attribute name="Codebase" value="${applet.codebase}" />
 627     </manifest>
 628     <fileset dir="${outputDir}">
 629       <include name="com/**" />
 630       <include name="MCview/**" />
 631       <include name="jalview/**" />
 632       <include name=".build_properties" />
 633       <include name="images/link.gif" />
 634       <include name="lang/**" />
 635     </fileset>
 636   </jar>
 637 </target>
 638 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 639 </target>
 640 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 641   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 642   <delete file="in.jar" />
 643 </target>
 644 <target name="-obfuscatereally" unless="donotobfuscate">
 645
 646   <path id="obfuscateDeps.path">
 647     <pathelement location="${applet.jre.tools}" />
 648     <pathelement location="appletlib/${jmolJar}" />
 649     <pathelement location="lib/${varnaJar}" />
 650     <pathelement location="appletlib/${jsoup}" />
 651     <pathelement location="appletlib/${jsonSimple}" />
 652     <pathelement location="appletlib/${javaJson}" />
 653     <fileset dir="${java.home}/lib">
 654       <include name="plugin.jar" />
 655     </fileset>
 656   </path>
 657   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
 658
 659   <proguard verbose="true" >
 660     <injar file="in.jar" />
 661     <outjar file="${jalviewLiteJar}" />
 662     <libraryjar refid="obfuscateDeps.path" />
 663     <dontwarn />
 664     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 665       <field access="public" />
 666       <method access="public" />
 667       <constructor access="public" />
 668     </keep>
 669     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 670       <field access="public" />
 671       <method access="public" />
 672       <constructor access="public" />
 673     </keep>
 674
 675     <keep name="jalview.json.binding**">
 676       <constructor/>
 677       <method name="*"/>
 678     </keep>
 679
 680     <keep access="public" type="class" name="MCview.PDBfile">
 681       <field access="public" />
 682       <method access="public" />
 683       <constructor access="public" />
 684     </keep>
 685
 686     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 687       <field access="public" />
 688       <method access="public" />
 689       <constructor access="public" />
 690     </keep>
 691
 692     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 693       <field access="public" />
 694       <method access="public" />
 695       <constructor access="public" />
 696     </keep>
 697
 698
 699     <!--      -libraryjars "${obfuscateDeps}"
 700       -injars      in.jar
 701       -outjars     jalviewApplet.jar
 702       -keep public class jalview.bin.JalviewLite
 703        { public * ; } -->
 704   </proguard>
 705   <delete file="in.jar" />
 706 </target>
 707
 708 <target name="jaxb-bindings" depends="init" description="Generates JAXB bindings for supported Jalview XML models (needs xjc on the path)">
 709   <delete>
 710     <fileset dir="${sourceDir}/jalview/xml/binding/jalview">
 711       <include name="*.java" />
 712     </fileset>
 713   </delete>
 714   <exec executable="xjc">
 715     <arg value="${schemaDir}/jalview.xsd"/>
 716     <arg value="-d"/>
 717     <arg value="${sourceDir}"/>
 718     <arg value="-p"/>
 719     <arg value="jalview.xml.binding.jalview"/>
 720   </exec>
 721   <delete>
 722     <fileset dir="${sourceDir}/jalview/xml/binding/embl">
 723       <include name="*.java" />
 724     </fileset>
 725   </delete>
 726
 727   <exec executable="xjc">
 728     <arg value="${schemaDir}/embl.xsd"/>
 729     <arg value="-d"/>
 730     <arg value="${sourceDir}"/>
 731     <arg value="-b"/>
 732     <arg value="${schemaDir}/embl_bindings.xml"/>
 733     <arg value="-p"/>
 734     <arg value="jalview.xml.binding.embl"/>
 735   </exec>
 736
 737   <delete>
 738     <fileset dir="${sourceDir}/jalview/xml/binding/uniprot">
 739       <include name="*.java" />
 740     </fileset>
 741   </delete>
 742
 743   <exec executable="xjc">
 744     <arg value="${schemaDir}/uniprot.xsd"/>
 745     <arg value="-d"/>
 746     <arg value="${sourceDir}"/>
 747     <arg value="-p"/>
 748     <arg value="jalview.xml.binding.uniprot"/>
 749   </exec>
 750 </target>
 751
 752 <target name="sourcedist" description="create jalview source distribution" depends="init">
 753   <delete file="${source.dist.name}" />
 754   <!-- temporary copy of source to update timestamps -->
 755   <copy todir="_sourcedist">
 756     <fileset dir=".">
 757       <exclude name=".*" />
 758       <exclude name="**/.*" />
 759       <exclude name="*.class" />
 760       <exclude name="**/*.class" />
 761       <include name="LICENSE" />
 762       <include name="README" />
 763       <include name="build.xml" />
 764       <include name="jalview-jalopy.xml" />
 765       <include name="JalviewApplet.jpx" />
 766       <include name="JalviewX.jpx" />
 767       <include name="nbbuild.xml" />
 768       <include name="nbproject/genfiles.properties" />
 769       <include name="nbproject/project.properties" />
 770       <include name="nbproject/project.xml" />
 771       <include name="${sourceDir}/*.java" />
 772       <include name="${sourceDir}/**/*.java" />
 773       <include name="${sourceDir}/**/*.cdr" />
 774       <include name="${libDir}/**/*" />
 775       <include name="${resourceDir}/**/*" />
 776       <include name="${helpDir}/**/*" />
 777       <include name="appletlib/${jmolJar}" />
 778       <include name="appletlib/${jsonSimple}" />
 779       <include name="appletlib/${javaJson}" />
 780       <exclude name="**/*locales" />
 781       <exclude name="*locales/**" />
 782       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 783       <exclude name="utils/InstallAnywhere/**Build*/**" />
 784       <exclude name="utils/InstallAnywhere/**Build*/**" />
 785       <exclude name="utils/InstallAnywhere/.build*.*/**" />
 786       <exclude name="utils/InstallAnywhere/**locale*" />
 787       <exclude name="utils/InstallAnywhere/**locale*/**" />
 788       <exclude name="utils/InstallAnywhere/**locale*/**" />
 789       <include name="${schemaDir}/**/*" />
 790       <include name="utils/**/*" />
 791       <include name="${docDir}/**/*" />
 792       <include name="examples/**/*" />
 793     </fileset>
 794   </copy>
 795
 796   <tstamp prefix="build">
 797     <format property="year" pattern="yyyy" />
 798   </tstamp>
 799   <!-- each replacetoken CDATA body must be on one line -
 800        otherwise the pattern doesn't match -->
 801   <replace value="${JALVIEW_VERSION}">
 802     <replacetoken>
 803       <![CDATA[$$Version-Rel$$]]>
 804     </replacetoken>
 805     <fileset dir="_sourcedist">
 806       <include name="**/*" />
 807     </fileset>
 808   </replace>
 809   <replace dir="_sourcedist" value="${build.year}">
 810     <replacetoken>
 811       <![CDATA[$$Year-Rel$$]]>
 812     </replacetoken>
 813     <fileset dir="_sourcedist">
 814       <include name="**/*" />
 815     </fileset>
 816   </replace>
 817
 818   <tar destfile="${source.dist.name}" compression="gzip">
 819     <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
 820     </tarfileset>
 821   </tar>
 822
 823   <delete dir="_sourcedist" />
 824 </target>
 825 <target name="prepubapplet_1" depends="makeApplet">
 826   <copy todir="${packageDir}/examples">
 827     <fileset dir="examples">
 828       <include name="**/*" />
 829       <include name="javascript/*" />
 830       <include name="jmol/*" />
 831     </fileset>
 832     <fileset dir=".">
 833       <include name="${jalviewLiteJar}" />
 834     </fileset>
 835     <fileset dir="appletlib">
 836       <include name="**/*" />
 837     </fileset>
 838   </copy>
 839   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 840   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 841   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 842   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 843     <manifest>
 844       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 845       <!--          <attribute name="Permissions" value="sandbox" /> -->
 846       <!--<attribute name="Trusted-Lib" value="true" /> -->
 847       <attribute name="Codebase" value="${applet.codebase}" />
 848       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 849     </manifest>
 850   </jar>
 851
 852   <presetdef name="ap_applet.jar">
 853     <!-- build a signed applet with 'all-permissions' -
 854                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 855                           JalviewLite+JmolApplet linked sequence/structure fails
 856                           Mixed code warnings are raised
 857                           -->
 858     <jar update="true" index="true">
 859       <manifest>
 860         <attribute name="Application-Name" value="JalviewLite" />
 861         <attribute name="Permissions" value="all-permissions" />
 862         <attribute name="Codebase" value="${applet.codebase}" />
 863         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 864         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 865       </manifest>
 866     </jar>
 867   </presetdef>
 868   <presetdef name="applet.jar">
 869     <!-- build signed applet with sandbox permissions -
 870                           Needs 'param name="permissions' value="sandbox"' in applet tag
 871                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 872                         -->
 873
 874     <jar update="true" index="true">
 875       <manifest>
 876         <attribute name="Application-Name" value="JalviewLite" />
 877         <attribute name="Permissions" value="sandbox" />
 878         <attribute name="Codebase" value="${applet.codebase}" />
 879         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 880         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 881       </manifest>
 882     </jar>
 883   </presetdef>
 884   <presetdef name="tl_applet.jar">
 885     <!-- build signed applet with trusted library/trusted permissions -
 886                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 887                                j1.7_45:
 888                                No mixed code warnings raised
 889                                Jmol/JalviewLite sequence/structure example doesn't link structures
 890                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 891
 892                               -->
 893
 894     <jar update="true" index="true">
 895       <manifest>
 896         <attribute name="Application-Name" value="JalviewLite" />
 897         <attribute name="Permissions" value="all-permissions" />
 898         <attribute name="Codebase" value="${applet.codebase}" />
 899         <attribute name="Trusted-Only" value="true" />
 900         <attribute name="Trusted-Library" value="true" />
 901       </manifest>
 902     </jar>
 903   </presetdef>
 904   <presetdef name="to_applet.jar">
 905     <!-- not fully test variant (yet) -->
 906     <jar update="true" index="true">
 907       <manifest>
 908         <attribute name="Application-Name" value="JalviewLite" />
 909         <attribute name="Permissions" value="all-permissions" />
 910         <attribute name="Codebase" value="${applet.codebase}" />
 911         <attribute name="Trusted-Only" value="true" />
 912       </manifest>
 913     </jar>
 914   </presetdef>
 915   <!-- create differently privileged artefacts -->
 916   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 917   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 918   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 919   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 920   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 921   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 922   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 923   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 924   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 925   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 926   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 927   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 928   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 929   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 930   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 931   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 932   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 933   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 934   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 935   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 936   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 937   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 938   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 939   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 940   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 941   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 942   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 943   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 944   <!-- finally, create manifest for original jars -->
 945   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 946   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 947   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 948   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 949
 950   <!-- todo - write examples/downloads for alternate versions of the applet
 951     probably don't need to do this now since we don't have alternate versions anymore !-->
 952 </target>
 953 <target name="-signapplet" depends="prepubapplet_1">
 954   <fileset id="signappletjarset" dir="${packageDir}/examples">
 955     <exclude name="u_*.jar" />
 956     <include name="${jalviewLiteJar}" />
 957     <include name="${jmolJar}" />
 958     <include name="${javaJson}" />
 959     <include name="${jsonSimple}" />
 960     <include name="to_${jalviewLiteJar}" />
 961     <include name="to_${jmolJar}" />
 962     <include name="to_${javaJson}" />
 963     <include name="to_${jsonSimple}" />
 964     <include name="tl_${jalviewLiteJar}" />
 965     <include name="tl_${jmolJar}" />
 966     <include name="tl_${javaJson}" />
 967     <include name="tl_${jsonSimple}" />
 968     <include name="ap_${jalviewLiteJar}" />
 969     <include name="ap_${jmolJar}" />
 970     <include name="ap_${javaJson}" />
 971     <include name="ap_${jsonSimple}" />
 972   </fileset>
 973 </target>
 974 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
 975   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 976     <fileset refid="signappletjarset" />
 977   </signjar>
 978 </target>
 979
 980 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
 981   <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}">
 982     <fileset refid="signappletjarset" />
 983   </signjar>
 984 </target>
 985
 986 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
 987 <target name="pubapplet" description="Dummy target to keep legacy Jalview build system happy. We don't actually publish the applet anymore."/>
 988
 989 <target name="_pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 990
 991   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 992   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 993   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 994   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 995   <!-- finally, replace any launchApp servlet tags with a version specification -->
 996   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 997     <replacetoken>
 998       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 999     </replacetoken>
1000     <fileset dir="${packageDir}/examples">
1001       <include name="**/*.html" />
1002     </fileset>
1003   </replace>
1004   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
1005     <replacetoken>
1006       <![CDATA[http://www.jalview.org/services/launchApp']]>
1007     </replacetoken>
1008     <fileset dir="${packageDir}/examples">
1009       <include name="**/*.html" />
1010     </fileset>
1011   </replace>
1012
1013 </target>
1014 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
1015   <javadoc destdir="${javadocDir}">
1016     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
1017     </packageset>
1018   </javadoc>
1019 </target>
1020 <target name="linkcheck" depends="init,prepare">
1021   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
1022   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
1023     <arg file="${helpDir}"/>
1024     <arg value="-nointernet" />
1025   </java>
1026 </target>
1027
1028 <target name="eclipse-install" depends="init,prepare">
1029
1030   <property name="eclipseTempFile" value="eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
1031   <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"/>
1032   <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"/>
1033
1034   <get url="${eclipseInstallURL}" dest="${eclipseTempFile}"/>
1035   <untar compression="gzip" src="${eclipseTempFile}" dest="${eclipse-inst}"/>
1036
1037   <!-- not needed since we ship transpiler with source
1038     <get url="${java2scriptURL}" dest="eclipse-inst/dropins/net.sf.j2s.core.jar" /> -->
1039
1040 </target>
1041
1042 <target name="build-site" depends="init,prepare,compile-site,unzip-to-site,make-j2s-cores">
1043   <!-- tarball -->
1044   <tar compression="gzip" destfile="site.tar.gz">
1045     <tarfileset dir="site" />
1046   </tar>
1047 </target>
1048 <target name="prepare-site" depends="init,prepare">
1049   <property name="swingjsdir" value="swingjs"/>
1050   <property name="eclipse-inst" value="/home/bamboo/buildtools/eclipse/eclipse-js"/>
1051   <property name="eclipse-exec" value="${eclipse-inst}/eclipse"/>
1052   <property name="site" value="site"/>
1053   <!-- where the eclipse js workspace has been initialised -->
1054   <property name="eclipse-work" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace"/>
1055   <!-- git repository linked to project in workspace -->
1056   <property name="eclipse-workrepo" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace/jalview-js"/>
1057 </target>
1058   <target name="clean-site" depends="prepare-site">
1059     <delete dir="${eclipse-workrepo}/${site}"/>
1060     <mkdir dir="${eclipse-workrepo}/${site}"/>
1061   </target>
1062 <target name="compile-site" depends="prepare-site,clean-site">
1063   <!-- update transpiler -->
1064   <copy file="${swingjsdir}/net.sf.j2s.core.jar" todir="${eclipse-inst}/dropins" overwrite="true" failonerror="true"/>
1065   <!-- update the git repo linked to the eclipse workspace -->
1066   <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="true">
1067     <arg value="rev-parse" />
1068     <arg value="--short" />
1069     <arg value="HEAD" />
1070   </exec>
1071   <!-- update and checkout the same commit in the workspace project -->
1072   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1073     <arg value="reset" />
1074     <arg value="--hard" />
1075   </exec>
1076   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1077       <arg value="pull" />
1078   </exec>
1079   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1080     <arg value="checkout" />
1081     <arg value="${git.commit}" />
1082   </exec>
1083   <!-- custom classpath for .js builds -->
1084   <copy file=".classpath.js" tofile="${eclipse-workrepo}/.classpath" overwrite="true"/>
1085   <!-- clean eclipse log -->
1086   <delete file="${eclipse-work}/.metadata/.log"/>
1087
1088   <!-- execute the eclipse build - the build may fail but valid javascript may still be produced, so we ignore return codes -->
1089   <exec executable="${eclipse-exec}" failonerror="no">
1090     <arg value="-nosplash"/>
1091     <arg value="--launcher.suppressErrors"/>
1092     <arg value="-application"/>
1093     <arg value="org.eclipse.jdt.apt.core.aptBuild"/>
1094     <arg value="-data"/>
1095     <arg value="${eclipse-work}"/>
1096   </exec>
1097   <!-- report log -->
1098   <exec executable="/bin/cat">
1099     <arg value="${eclipse-work}/.metadata/.log"/>
1100   </exec>
1101   <!-- TODO: run jslint and something else here to check we have a complete set of .js files for java -->
1102   <!-- possibly compare timestamps between .js files and their mate in source - any newer or not present triggers a new build -->
1103   <!-- <mkdir dir="${packageDir}/${site}" /> -->
1104   <!--   <property name="swingjs.zipurl" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.java.core/dist/SwingJS-site.zip?raw=true" /> -->
1105
1106   <!-- and reset the .classpath -->
1107   <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1108     <arg value="checkout" />
1109     <arg value="${git.commit}"/>
1110     <arg value="--"/>
1111     <arg value=".classpath" />
1112   </exec>
1113
1114   <!-- finally copy artefacts from eclipse project checkout to the build site -->
1115   <copy todir="${site}">
1116     <fileset dir="${eclipse-workrepo}/site"/>
1117   </copy>
1118 </target>
1119 <target name="unzip-to-site" depends="prepare-site">
1120   <ant antfile="build-site.xml"/>
1121 </target>
1122
1123   <target name="make-j2s-cores" depends="">
1124     <ant antfile="buildcore.xml" target="build-all-cores"/>
1125   </target>
1126 </project>