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