build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
   4  * Copyright (C) 2015 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   <target name="help" depends="usage" />
  22   <target name="usage" depends="init">
  23     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  24     <echo message="Targets include:" />
  25     <echo message="usage - default target, displays this message" />
  26     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  27     <echo message="build - compiles all necessary files for Application" />
  28     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  29     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  30     <echo message="              this needs a keystore and key. See docs/building.html for more information." />
  31     <echo message="compileApplet - compiles all necessary files for Applet" />
  32     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  33     <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
  34     <echo message="      you can specify particular test groups as a list via -Dtestng-groups=" />
  35     <echo message="See docs/building.html and the comments in build file for other targets." />
  36     <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  37     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  38   </target>
  39
  40
  41   <!-- utils is a class path to additional utilities needed for
  42     building docs, jars and webstart stuff -->
  43   <!--
  44         Userdefined build property defaults
  45
  46         wsdl.server list (plus namespace mapping info ???)  - also want
  47                 ... to make this a dynamically generatable property
  48         WebStart Location
  49         Build location - provide a temporary root for speed
  50         jarsigner keystore and info
  51         Jakarta and axis classpath ?
  52         Default argument for starting Jalview (if it exists).
  53
  54 -->
  55
  56   <target name="init">
  57     <path id="axis.classpath">
  58       <!-->
  59       <fileset dir="/usr/local/axis/lib">
  60         <include name="**/*.jar" />
  61       </fileset>
  62       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  63         <include name="**/*.jar"/>
  64         <include name="*.jar"/>
  65       </fileset> -->
  66       </path>
  67
  68     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  69     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  70
  71     <property name="INSTALLATION" value="Source" />
  72
  73     <!-- 2.4 (VAMSAS)" -->
  74     <!-- Include debugging information in javac true or false -->
  75     <property name="javac.debug" value="true" />
  76
  77     <!-- JarSigner Key Store for Webstart Distribution -->
  78     <property name="jalview.keystore" value="./keys/.keystore" />
  79     <!-- Keystore Password -->
  80     <property name="jalview.keystore.pass" value="alignmentisfun" />
  81     <!-- Key Name -->
  82     <property name="jalview.key" value="jalview" />
  83     <!-- Key Password -->
  84     <property name="jalview.key.pass" value="alignmentisfun" />
  85         <!-- time stamp server URL -->
  86     <property name="jalview.tsaurl" value="" />
  87
  88     <property name="testng-groups" value="Functional" />
  89
  90     <!-- Don't change anything below here unless you know what you are doing! -->
  91     <!-- Url path for WebStart in JNLP file -->
  92     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  93     <!-- Webstart Image - looked for in resources/images -->
  94     <property name="WebStartImage" value="JalviewLogo_big.png" />
  95     <!-- J2SE version needed for webstart launch -->
  96     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  97     <property name="j2sev" value="1.7+" />
  98     <!-- Java Compilation settings - source and target javac version -->
  99     <property name="javac.source" value="1.7" />
 100     <property name="javac.target" value="1.7" />
 101
 102     <!-- Permissions for running Java applets and applications. -->
 103     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 104     <property name="application.codebase" value="*.jalview.org" />
 105     <!-- and allowing the applet to be deployed from any URL -->
 106     <!-- 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 -->
 107     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 108     <property name="applet.caller-codebase" value="${applet.codebase}" />
 109
 110     <!-- build directory configuration -->
 111     <property name="libDir" value="lib" />
 112     <property name="resourceDir" value="resources" />
 113     <property name="helpDir" value="help" />
 114     <property name="docDir" value="doc" />
 115     <property name="sourceDir" value="src" />
 116     <property name="schemaDir" value="schemas" />
 117     <property name="outputDir" value="classes" />
 118     <property name="packageDir" value="dist" />
 119     <property name="outputJar" value="jalview.jar" />
 120     <!-- Jalview Applet JMol Jar Dependency -->
 121     <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
 122     <property name="varnaJar" value="VARNAv3-93.jar" />
 123     <property name="jsoup" value="jsoup-1.8.1.jar" />
 124     <property name="jsonSimple" value="json_simple-1.1.jar" />
 125     <property name="javaJson" value="java-json.jar" />
 126     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 127     <property name="reportDir" value="test-reports" />
 128     <property name="testDir" value="test" />
 129     <property name="testOutputDir" value="tests" />
 130     <!-- switch to indicate if we should obfuscate jalviewLite -->
 131     <!-- <property name="donotobfuscate" value="true"/> -->
 132     <!-- switch to exclude associations from generated jnlp files -->
 133     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 134
 135     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 136     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 137     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 138     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 139     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 140     <property name="WSInterf" value="MsaWS" />
 141     <property name="wsdl.Namespace" value="vamsas" />
 142     <property name="wsdl.ClientNS" value="ext.vamsas" />
 143     <!-- the class path for building the application -->
 144     <path id="build.classpath">
 145       <fileset dir="utils">
 146         <include name="*.jar" />
 147         <include name="**/*.jar" />
 148       </fileset>
 149       <fileset dir="${libDir}">
 150         <include name="*.jar" />
 151         <include name="**/*.jar" />
 152       </fileset>
 153       <fileset dir="${java.home}/lib">
 154         <include name="plugin.jar" />
 155       </fileset>
 156       <fileset dir="appletlib">
 157         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 158                                 -->
 159         <include name="${jmolJar}" />
 160         <include name="${varnaJar}" />
 161       </fileset>
 162     </path>
 163     <path id="test.classpath">
 164       <pathelement path="${outputDir}" />
 165       <path refid="build.classpath" />
 166     </path>
 167     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 168     <!-- The Location of the java 1.1.8 jdk -->
 169     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
 170     <property name="java118.home" value="${java.home}" />
 171     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 172                 -->
 173     <!-- jre for 1.4 version -->
 174     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
 175
 176     <!-- the classpath for building the 1.1 applet -->
 177     <path id="jalviewlite.deps">
 178       <fileset dir="${java118.home}">
 179         <include name="lib/classes.zip" />
 180       </fileset>
 181       <fileset dir="${java.home}/lib">
 182         <include name="plugin.jar" />
 183       </fileset>
 184       <pathelement location="appletlib/${jmolJar}" />
 185       <pathelement location="lib/${varnaJar}" />
 186       <pathelement location="lib/${jsoup}" />
 187       <pathelement location="lib/${jsonSimple}" />
 188       <pathelement location="lib/${javaJson}" />
 189
 190     </path>
 191     <!-- default location for outputting javadoc -->
 192     <property name="javadocDir" value="${packageDir}/javadoc" />
 193   </target>
 194
 195
 196   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 197   <target name="buildPropertiesFile" depends="init">
 198     <tstamp prefix="build">
 199       <format property="date" pattern="dd MMMM yyyy" />
 200     </tstamp>
 201     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 202       <arg value="rev-parse" />
 203       <arg value="--short" />
 204       <arg value="HEAD" />
 205     </exec>
 206     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 207       <arg value="rev-parse" />
 208       <arg value="--abbrev-ref" />
 209       <arg value="HEAD" />
 210     </exec>
 211     <properties file="${outputDir}/.build_properties">
 212       <header>
 213           ---Jalview Build Details---
 214         </header>
 215       <property name="VERSION" value="${JALVIEW_VERSION}" />
 216       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 217       <property name="BUILD_DATE" value="${build.date}" />
 218     </properties>
 219   </target>
 220
 221
 222   <target name="clean" depends="init">
 223     <!-- not efficient yet. -->
 224     <delete dir="${outputDir}" includes="*,**/*" />
 225   </target>
 226
 227   <target name="distclean" depends="init, clean">
 228
 229     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 230     <delete>
 231       <fileset dir=".">
 232         <include name="${outputJar}" />
 233         <include name="#*#" />
 234         <include name="#*.*#" />
 235         <include name="**/#*#" />
 236         <include name="**/#*.*#" />
 237         <include name="*~" />
 238         <include name="*.*~" />
 239         <include name="**/*~" />
 240         <include name="**/*.*~" />
 241       </fileset>
 242     </delete>
 243   </target>
 244
 245   <target name="prepare" depends="init">
 246     <mkdir dir="${outputDir}" />
 247     <copy todir="${outputDir}">
 248       <fileset dir=".">
 249         <include name="${docDir}/**/*.*" />
 250         <include name="${helpDir}/**/*.*" />
 251         <include name="${libDir}/*.jar" />
 252       </fileset>
 253       <fileset dir="${resourceDir}">
 254         <include name="**/*.*" />
 255       </fileset>
 256     </copy>
 257   </target>
 258
 259   <target name="build" depends="prepare">
 260     <!-- not efficient yet. -->
 261     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 262       <exclude name="jalview/*applet*" />
 263       <exclude name="jalview/appletgui/**" />
 264       <exclude name="com/stevesoft/**" />
 265     </javac>
 266   </target>
 267
 268
 269   <target name="testclean" depends="init">
 270     <delete dir="${testOutputDir}" includes="*,**/*" />
 271   </target>
 272
 273   <target name="prepareTests" depends="init,testclean">
 274     <mkdir dir="${testOutputDir}" />
 275   </target>
 276
 277   <target name="buildTests" depends="build,buildindices,prepareTests">
 278     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 279     </javac>
 280   </target>
 281
 282   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 283
 284   <target name="testng" depends="buildTests">
 285     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 286       verbose="2">
 287       <classpath>
 288         <pathelement location="${testOutputDir}" />
 289         <path refid="test.classpath" />
 290       </classpath>
 291       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 292     </testng>
 293   </target>
 294
 295   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 296     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 297       <arg line="html" />
 298     </java>
 299   </target>
 300
 301   <target name="makefulldist" depends="makedist">
 302     <copy todir="${packageDir}">
 303       <fileset dir="${resourceDir}/images">
 304         <include name="${WebStartImage}" />
 305       </fileset>
 306     </copy>
 307
 308     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 309
 310     <!-- create a dummy jar which will eventually contain the jnlp template -->
 311     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 312       <fileset dir="${packageDir}">
 313         <include name="jalview.jar" />
 314       </fileset>
 315     </jar>
 316
 317     <mkdir dir="${packageDir}/JNLP-INF" />
 318     <antcall target="writejnlpf">
 319       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 320       <param name="inih" value="*" />
 321       <param name="maxh" value="*" />
 322     </antcall>
 323
 324     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 325       <fileset dir="${packageDir}">
 326         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 327       </fileset>
 328     </jar>
 329
 330     <antcall target="writejnlpf">
 331       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 332       <param name="inih" value="10M" />
 333       <param name="maxh" value="256M" />
 334     </antcall>
 335
 336     <antcall target="writejnlpf">
 337       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 338       <param name="inih" value="128M" />
 339       <param name="maxh" value="512M" />
 340     </antcall>
 341
 342     <antcall target="writejnlpf">
 343       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 344       <param name="inih" value="256M" />
 345       <param name="maxh" value="1024M" />
 346     </antcall>
 347
 348     <!-- finally, need to postprocess to add in associations at end of 'information' element
 349
 350                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 351
 352                 </xslt>
 353
 354
 355                         -->
 356     <!--
 357                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 358         <association mime-type="application-x/ext-file" extensions="fasta"/>
 359         <association mime-type="application-x/ext-file" extensions="mfa"/>
 360         <association mime-type="application-x/ext-file" extensions="fastq"/>
 361         <association mime-type="application-x/ext-file" extensions="blc"/>
 362         <association mime-type="application-x/ext-file" extensions="msf"/>
 363         <association mime-type="application-x/ext-file" extensions="pfam"/>
 364         <association mime-type="application-x/ext-file" extensions="aln"/>
 365         <association mime-type="application-x/ext-file" extensions="pir"/>
 366         <association mime-type="application-x/ext-file" extensions="amsa"/>
 367         <association mime-type="application-x/ext-file" extensions="stk"/>
 368         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 369     <!-- and sign the jars -->
 370     <!-- the default keystore details might need to be edited here -->
 371     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA"
 372       tsaurl="${jalview.tsaurl}">
 373       <fileset dir="${packageDir}">
 374         <include name="*.jar" />
 375       </fileset>
 376
 377     </signjar>
 378   </target>
 379
 380   <target name="runenv" depends="init">
 381     <path id="run.classpath">
 382       <pathelement location="${outputDir}" />
 383       <fileset dir="${outputDir}">
 384         <include name="${libDir}/*.jar" />
 385       </fileset>
 386     </path>
 387     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 388
 389     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 390       </echo>
 391   </target>
 392
 393   <target name="-generatejnlpf">
 394     <presetdef name="jnlpf">
 395       <jnlp codebase="${WebStartLocation}">
 396         <information>
 397           <title>Jalview</title>
 398           <vendor>The Barton Group</vendor>
 399           <homepage href="http://www.jalview.org" />
 400           <description>Jalview Multiple Alignment Editor</description>
 401           <description kind="short">Jalview</description>
 402           <icon href="${WebStartImage}" />
 403           <offline_allowed />
 404         </information>
 405         <resources>
 406           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 407           <fileset dir="${packageDir}">
 408             <include name="jalview.jar" />
 409           </fileset>
 410           <fileset dir="${packageDir}">
 411             <include name="*.jar" />
 412             <include name="*_*.jar" />
 413             <exclude name="jalview.jar" />
 414             <exclude name="*jnilib.jar" />
 415           </fileset>
 416         </resources>
 417         <resources os="Mac OS X">
 418           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 419           <fileset dir="${packageDir}">
 420             <include name="*quaqua*.jnilib.jar" />
 421           </fileset>
 422         </resources>
 423
 424         <application_desc main_class="jalview.bin.Jalview">
 425         </application_desc>
 426         <security>
 427           <all_permissions />
 428         </security>
 429       </jnlp>
 430     </presetdef>
 431
 432     <jnlpf toFile="${jnlpFile}" />
 433
 434   </target>
 435
 436   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 437     <echo message="Not adding JNLP File Associations" />
 438   </target>
 439
 440   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 441     <replace file="${jnlpFile}">
 442       <replacetoken>
 443         <![CDATA[</information>]]></replacetoken>
 444       <replacevalue>
 445         <![CDATA[
 446           <association mime-type="application-x/ext-file" extensions="fa" />
 447         <association mime-type="application-x/ext-file" extensions="fasta" />
 448         <association mime-type="application-x/ext-file" extensions="mfa" />
 449         <association mime-type="application-x/ext-file" extensions="fastq" />
 450         <association mime-type="application-x/ext-file" extensions="blc" />
 451         <association mime-type="application-x/ext-file" extensions="msf" />
 452         <association mime-type="application-x/ext-file" extensions="pfam" />
 453         <association mime-type="application-x/ext-file" extensions="aln"/>
 454         <association mime-type="application-x/ext-file" extensions="pir"/>
 455         <association mime-type="application-x/ext-file" extensions="amsa"/>
 456         <association mime-type="application-x/ext-file" extensions="stk"/>
 457         <association mime-type="application-x/ext-file" extensions="jvp"/>
 458       </information>]]></replacevalue>
 459   </replace>
 460   <echo message="Added file associations to JNLP file" />
 461 </target>
 462 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 463 </target>
 464
 465 <target name="buildextclients" depends="init">
 466   <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" />
 467   <condition property="dontextbuild">
 468     <equals arg1="n" arg2="${doextbuild.response}" />
 469   </condition>
 470   <condition property="dontextbuild">
 471     <equals arg1="N" arg2="${doextbuild.response}" />
 472   </condition>
 473   <fail if="dontextbuild">
 474         Build External Client Code process aborted by user. Jalview source is unchanged.
 475       </fail>
 476   <!-- Currently, this doesn't happen automatically.
 477      1. Run WSDL2Java as below, which generates an ext.vamsas +
 478      vamsas.<datapackages> fileset.
 479      2. refactor ext.vamsas.SpecificserviceWS* to
 480      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 481      3. Update the jalview.ws.*WServices classes to reflect the
 482      interface type, and all locations of this wsdl type that Jalview
 483      might be using.
 484
 485 -->
 486   <path id="axisbuild">
 487     <path refid="build.classpath" />
 488   </path>
 489   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 490   <move todir="./bak">
 491     <fileset dir="${sourceDir}" id="client">
 492       <include name="${wsdl.ClientNS}/*.*" />
 493     </fileset>
 494   </move>
 495
 496   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 497     <mappingSet>
 498       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 499       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 500     </mappingSet>
 501   </axis-wsdl2java>
 502 </target>
 503
 504 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 505   <!-- make the package jar if not already existing -->
 506   <mkdir dir="${packageDir}" />
 507   <!-- clean dir if it already existed -->
 508   <delete>
 509     <fileset dir="${packageDir}">
 510       <include name="*.jar" />
 511     </fileset>
 512   </delete>
 513   <jar destfile="${packageDir}/${outputJar}" index="true">
 514     <manifest>
 515       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 516       <attribute name="Permissions" value="all-permissions" />
 517       <attribute name="Application-Name" value="Jalview Desktop" />
 518       <attribute name="Codebase" value="${application.codebase}" />
 519     </manifest>
 520     <fileset dir="${outputDir}/">
 521       <exclude name="cache*/**" />
 522       <exclude name="*.jar" />
 523       <exclude name="*.jar.*" />
 524       <exclude name="**/*.jar" />
 525       <exclude name="**/*.jar.*" />
 526     </fileset>
 527   </jar>
 528
 529   <copy toDir="${packageDir}" flatten="true">
 530     <fileset dir="${outputDir}">
 531       <include name="*.jar" />
 532       <include name="**/*.jar" />
 533     </fileset>
 534   </copy>
 535 </target>
 536
 537
 538 <!-- jalopy code reformatter -->
 539 <target name="sourcescrub" depends="init,build">
 540   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 541     <fileset dir="${sourceDir}">
 542       <include name="*.java" />
 543       <include name="**/*.java" />
 544       <include name="**/**/*.java" />
 545     </fileset>
 546   </jalopy>
 547 </target>
 548
 549
 550
 551 <!-- Compile, package and obfuscate Jalview Applet -->
 552 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 553
 554 <target name="compileApplet" depends="init,clean">
 555   <mkdir dir="${outputDir}" />
 556   <javac source="${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/**" />
 557 </target>
 558
 559 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 560   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 561   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 562   <copy todir="${outputDir}/lang">
 563     <fileset dir="${resourceDir}/lang">
 564       <include name="**.*" />
 565     </fileset>
 566   </copy>
 567   <jar destfile="in.jar" index="true">
 568     <manifest>
 569       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 570       <attribute name="Application-Name" value="JalviewLite" />
 571       <attribute name="Codebase" value="${applet.codebase}" />
 572     </manifest>
 573     <fileset dir="${outputDir}">
 574       <include name="com/**" />
 575       <include name="MCview/**" />
 576       <include name="jalview/**" />
 577       <include name=".build_properties" />
 578       <include name="images/idwidth.gif" />
 579       <include name="images/link.gif" />
 580       <include name="lang/**" />
 581     </fileset>
 582   </jar>
 583 </target>
 584 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 585 </target>
 586 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 587   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 588   <delete file="in.jar" />
 589 </target>
 590 <target name="-obfuscatereally" unless="donotobfuscate">
 591
 592   <path id="obfuscateDeps.path">
 593     <pathelement location="${applet.jre.tools}" />
 594     <pathelement location="appletlib/${jmolJar}" />
 595     <pathelement location="appletlib/${jsonSimple}" />
 596     <pathelement location="appletlib/${javaJson}" />
 597   </path>
 598   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 599
 600   <proguard>
 601     <injar file="in.jar" />
 602     <outjar file="${jalviewLiteJar}" />
 603     <libraryjar refid="obfuscateDeps.path" />
 604     <dontwarn />
 605     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 606       <field access="public" />
 607       <method access="public" />
 608       <constructor access="public" />
 609     </keep>
 610     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 611       <field access="public" />
 612       <method access="public" />
 613       <constructor access="public" />
 614     </keep>
 615     <!--      -libraryjars "${obfuscateDeps}"
 616       -injars      in.jar
 617       -outjars     jalviewApplet.jar
 618       -keep public class jalview.bin.JalviewLite
 619        { public * ; } -->
 620   </proguard>
 621   <delete file="in.jar" />
 622 </target>
 623
 624 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 625   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 626   <delete>
 627     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 628       <include name="*.java" />
 629       <include name="descriptors/*.java" />
 630     </fileset>
 631   </delete>
 632   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 633   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 634   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 635   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 636   <!--
 637                 now build the jalview.binding package with the old schema set
 638                 -->
 639   <delete>
 640     <fileset dir="${sourceDir}/jalview/binding/">
 641       <include name="**" />
 642     </fileset>
 643   </delete>
 644   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 645   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 646   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 647 </target>
 648 <target name="sourcedist" description="create jalview source distribution" depends="init">
 649   <delete file="${source.dist.name}" />
 650   <tar destfile="${source.dist.name}" compression="gzip">
 651     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 652       <include name="LICENSE" />
 653       <include name="README" />
 654       <include name="build.xml" />
 655       <include name="jalview-jalopy.xml" />
 656       <include name="JalviewApplet.jpx" />
 657       <include name="JalviewX.jpx" />
 658       <include name="nbbuild.xml" />
 659       <include name="nbproject/genfiles.properties" />
 660       <include name="nbproject/project.properties" />
 661       <include name="nbproject/project.xml" />
 662       <include name="${sourceDir}/*.java" />
 663       <include name="${sourceDir}/**/*.java" />
 664       <include name="${sourceDir}/**/*.cdr" />
 665       <include name="${libDir}/**/*" />
 666       <include name="${resourceDir}/**/*" />
 667       <include name="${helpDir}/**/*" />
 668       <include name="appletlib/${jmolJar}" />
 669       <exclude name="**/*locales" />
 670       <exclude name="*locales/**" />
 671       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 672       <exclude name="utils/InstallAnywhere/**Build*/**" />
 673       <exclude name="utils/InstallAnywhere/**Build*/**" />
 674       <exclude name="utils/InstallAnywhere/**locale*" />
 675       <exclude name="utils/InstallAnywhere/**locale*/**" />
 676       <include name="${schemaDir}/**/*" />
 677       <include name="utils/**/*" />
 678       <include name="${docDir}/**/*" />
 679       <include name="examples/**/*" />
 680     </tarfileset>
 681   </tar>
 682 </target>
 683 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 684   <copy todir="${packageDir}/examples">
 685     <fileset dir="examples">
 686       <include name="**/*" />
 687       <include name="javascript/*" />
 688       <include name="jmol/*" />
 689     </fileset>
 690     <fileset dir=".">
 691       <include name="${jalviewLiteJar}" />
 692     </fileset>
 693     <fileset dir="appletlib">
 694       <include name="**/*" />
 695     </fileset>
 696   </copy>
 697   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 698   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 699   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 700   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 701     <manifest>
 702       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 703       <!--          <attribute name="Permissions" value="sandbox" /> -->
 704       <!--<attribute name="Trusted-Lib" value="true" /> -->
 705       <attribute name="Codebase" value="${applet.codebase}" />
 706       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 707     </manifest>
 708   </jar>
 709   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 710     <fileset dir="${packageDir}/examples">
 711       <include name="*.jar" />
 712     </fileset>
 713   </signjar>
 714   <presetdef name="ap_applet.jar">
 715     <!-- build a signed applet with 'all-permissions' -
 716                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 717                           JalviewLite+JmolApplet linked sequence/structure fails
 718                           Mixed code warnings are raised
 719                           -->
 720     <jar update="true" index="true">
 721       <manifest>
 722         <attribute name="Application-Name" value="JalviewLite" />
 723         <attribute name="Permissions" value="all-permissions" />
 724         <attribute name="Codebase" value="${applet.codebase}" />
 725         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 726         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 727       </manifest>
 728     </jar>
 729   </presetdef>
 730   <presetdef name="applet.jar">
 731     <!-- build signed applet with sandbox permissions -
 732                           Needs 'param name="permissions' value="sandbox"' in applet tag
 733                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 734                         -->
 735
 736     <jar update="true" index="true">
 737       <manifest>
 738         <attribute name="Application-Name" value="JalviewLite" />
 739         <attribute name="Permissions" value="sandbox" />
 740         <attribute name="Codebase" value="${applet.codebase}" />
 741         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 742         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 743       </manifest>
 744     </jar>
 745   </presetdef>
 746   <presetdef name="tl_applet.jar">
 747     <!-- build signed applet with trusted library/trusted permissions -
 748                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 749                                j1.7_45:
 750                                No mixed code warnings raised
 751                                Jmol/JalviewLite sequence/structure example doesn't link structures
 752                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 753
 754                               -->
 755
 756     <jar update="true" index="true">
 757       <manifest>
 758         <attribute name="Application-Name" value="JalviewLite" />
 759         <attribute name="Permissions" value="all-permissions" />
 760         <attribute name="Codebase" value="${applet.codebase}" />
 761         <attribute name="Trusted-Only" value="true" />
 762         <attribute name="Trusted-Library" value="true" />
 763       </manifest>
 764     </jar>
 765   </presetdef>
 766   <presetdef name="to_applet.jar">
 767     <!-- not fully test variant (yet) -->
 768     <jar update="true" index="true">
 769       <manifest>
 770         <attribute name="Application-Name" value="JalviewLite" />
 771         <attribute name="Permissions" value="all-permissions" />
 772         <attribute name="Codebase" value="${applet.codebase}" />
 773         <attribute name="Trusted-Only" value="true" />
 774       </manifest>
 775     </jar>
 776   </presetdef>
 777   <!-- create differently privileged artefacts -->
 778   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 779   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 780   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 781   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 782   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 783   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 784   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 785   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 786   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 787   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 788   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 789   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 790   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 791   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 792   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 793   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 794   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 795   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 796   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 797   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 798   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 799   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 800   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 801   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 802   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 803   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 804   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 805   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 806   <!-- finally, create manifest for original jars -->
 807   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 808   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 809   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 810   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 811
 812   <!-- todo - write examples/downloads for alternate versions of the applet -->
 813   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 814
 815     <fileset dir="${packageDir}/examples">
 816       <exclude name="u_*.jar" />
 817       <include name="${jalviewLiteJar}" />
 818       <include name="${jmolJar}" />
 819       <include name="${javaJson}" />
 820       <include name="${jsonSimple}" />
 821       <include name="to_${jalviewLiteJar}" />
 822       <include name="to_${jmolJar}" />
 823       <include name="to_${javaJson}" />
 824       <include name="to_${jsonSimple}" />
 825       <include name="tl_${jalviewLiteJar}" />
 826       <include name="tl_${jmolJar}" />
 827       <include name="tl_${javaJson}" />
 828       <include name="tl_${jsonSimple}" />
 829       <include name="ap_${jalviewLiteJar}" />
 830       <include name="ap_${jmolJar}" />
 831       <include name="ap_${javaJson}" />
 832       <include name="ap_${jsonSimple}" />
 833     </fileset>
 834   </signjar>
 835   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 836   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 837   <!-- finally, replace any launchApp servlet tags with a version specification -->
 838   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 839     <replacetoken>
 840       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 841     </replacetoken>
 842     <fileset dir="${packageDir}/examples">
 843       <include name="**/*.html" />
 844     </fileset>
 845   </replace>
 846   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 847     <replacetoken>
 848       <![CDATA[http://www.jalview.org/services/launchApp']]>
 849     </replacetoken>
 850     <fileset dir="${packageDir}/examples">
 851       <include name="**/*.html" />
 852     </fileset>
 853   </replace>
 854
 855 </target>
 856 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 857   <javadoc destdir="${javadocDir}">
 858     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 859     </packageset>
 860   </javadoc>
 861 </target>
 862 </project>