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   <target name="help" depends="usage" />
  22   <target name="usage">
  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="See docs/building.html and the comments in build file for other targets." />
  34     <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  35     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  36   </target>
  37
  38
  39   <!-- utils is a class path to additional utilities needed for
  40     building docs, jars and webstart stuff -->
  41   <!--
  42         Userdefined build property defaults
  43
  44         wsdl.server list (plus namespace mapping info ???)  - also want
  45                 ... to make this a dynamically generatable property
  46         WebStart Location
  47         Build location - provide a temporary root for speed
  48         jarsigner keystore and info
  49         Jakarta and axis classpath ?
  50         Default argument for starting Jalview (if it exists).
  51
  52 -->
  53
  54   <target name="init">
  55     <path id="axis.classpath">
  56       <!-->
  57       <fileset dir="/usr/local/axis/lib">
  58         <include name="**/*.jar" />
  59       </fileset>
  60       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  61         <include name="**/*.jar"/>
  62         <include name="*.jar"/>
  63       </fileset> -->
  64       </path>
  65
  66     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  67     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  68
  69     <property name="INSTALLATION" value="Source" />
  70
  71     <!-- 2.4 (VAMSAS)" -->
  72     <!-- Include debugging information in javac true or false -->
  73     <property name="javac.debug" value="true" />
  74
  75     <!-- JarSigner Key Store for Webstart Distribution -->
  76     <property name="jalview.keystore" value="./keys/.keystore" />
  77     <!-- Keystore Password -->
  78     <property name="jalview.keystore.pass" value="alignmentisfun" />
  79     <!-- Key Name -->
  80     <property name="jalview.key" value="jalview" />
  81     <!-- Key Password -->
  82     <property name="jalview.key.pass" value="alignmentisfun" />
  83
  84     <!-- Don't change anything below here unless you know what you are doing! -->
  85     <!-- Url path for WebStart in JNLP file -->
  86     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  87     <!-- Webstart Image - looked for in resources/images -->
  88     <property name="WebStartImage" value="JalviewLogo_big.png"/>
  89     <!-- J2SE version needed for webstart launch -->
  90     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  91     <property name="j2sev" value="1.7+"/>
  92
  93     <!-- Permissions for running Java applets and applications. -->
  94     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
  95     <property name="application.codebase" value="*.jalview.org" />
  96     <!-- and allowing the applet to be deployed from any URL -->
  97     <!-- 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 -->
  98     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
  99     <property name="applet.caller-codebase" value="${applet.codebase}" />
 100
 101     <!-- build directory configuration -->
 102     <property name="libDir" value="lib" />
 103     <property name="resourceDir" value="resources" />
 104     <property name="helpDir" value="help" />
 105     <property name="docDir" value="doc" />
 106     <property name="sourceDir" value="src" />
 107     <property name="schemaDir" value="schemas" />
 108     <property name="outputDir" value="classes" />
 109     <property name="packageDir" value="dist" />
 110     <property name="outputJar" value="jalview.jar" />
 111     <!-- Jalview Applet JMol Jar Dependency -->
 112     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 113     <property name="varnaJar" value="VARNAv3-91.jar" />
 114     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 115     <!-- switch to indicate if we should obfuscate jalviewLite -->
 116     <!-- <property name="donotobfuscate" value="true"/> -->
 117     <!-- switch to exclude associations from generated jnlp files -->
 118     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 119
 120     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 121     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 122     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 123     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 124     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 125     <property name="WSInterf" value="MsaWS" />
 126     <property name="wsdl.Namespace" value="vamsas" />
 127     <property name="wsdl.ClientNS" value="ext.vamsas" />
 128     <!-- the class path for building the application -->
 129     <path id="build.classpath">
 130       <fileset dir="utils">
 131         <include name="*.jar" />
 132         <include name="**/*.jar" />
 133       </fileset>
 134       <fileset dir="${libDir}">
 135         <include name="*.jar" />
 136         <include name="**/*.jar" />
 137       </fileset>
 138       <fileset dir="${java.home}/lib">
 139         <include name="plugin.jar"/>
 140       </fileset>
 141       <fileset dir="appletlib">
 142         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 143                                 -->
 144         <include name="${jmolJar}" />
 145         <include name="${varnaJar}" />
 146       </fileset>
 147
 148     </path>
 149     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 150     <!-- The Location of the java 1.1.8 jdk -->
 151     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
 152     <property name="java118.home" value="${java.home}" />
 153     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 154                 -->
 155     <!-- jre for 1.4 version -->
 156     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 157
 158     <!-- the classpath for building the 1.1 applet -->
 159     <path id="jalviewlite.deps">
 160       <fileset dir="${java118.home}">
 161         <include name="lib/classes.zip" />
 162       </fileset>
 163       <fileset dir="${java.home}/lib">
 164         <include name="plugin.jar"/>
 165       </fileset>
 166       <pathelement location="appletlib/${jmolJar}" />
 167       <pathelement location="lib/${varnaJar}" />
 168     </path>
 169     <!-- default location for outputting javadoc -->
 170     <property name="javadocDir" value="${packageDir}/javadoc"/>
 171   </target>
 172
 173
 174   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 175   <target name="buildPropertiesFile" depends="init">
 176     <tstamp prefix="build">
 177       <format property="date" pattern="dd MMMM yyyy" />
 178     </tstamp>
 179     <properties file="${outputDir}/.build_properties">
 180       <header>
 181           ---Jalview Build Details---
 182         </header>
 183       <property name="VERSION" value="${JALVIEW_VERSION}" />
 184       <property name="INSTALLATION" value="${INSTALLATION}" />
 185       <property name="BUILD_DATE" value="${build.date}" />
 186     </properties>
 187   </target>
 188
 189
 190   <target name="clean" depends="init">
 191     <!-- not efficient yet. -->
 192     <delete dir="${outputDir}" includes="*,**/*"/>
 193   </target>
 194
 195   <target name="distclean" depends="init, clean">
 196
 197     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 198     <delete>
 199       <fileset dir=".">
 200         <include name="${outputJar}" />
 201         <include name="#*#" />
 202         <include name="#*.*#" />
 203         <include name="**/#*#" />
 204         <include name="**/#*.*#" />
 205         <include name="*~" />
 206         <include name="*.*~" />
 207         <include name="**/*~" />
 208         <include name="**/*.*~" />
 209       </fileset>
 210     </delete>
 211   </target>
 212
 213   <target name="prepare" depends="init">
 214     <mkdir dir="${outputDir}" />
 215     <copy todir="${outputDir}">
 216       <fileset dir=".">
 217         <include name="${docDir}/**/*.*" />
 218         <include name="${helpDir}/**/*.*" />
 219         <include name="${libDir}/*.jar" />
 220       </fileset>
 221       <fileset dir="${resourceDir}">
 222         <include name="**/*.*" />
 223       </fileset>
 224     </copy>
 225   </target>
 226
 227   <target name="build" depends="prepare">
 228     <!-- not efficient yet. -->
 229     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 230       <exclude name="jalview/*applet*" />
 231       <exclude name="jalview/appletgui/**" />
 232       <exclude name="com/stevesoft/**" />
 233     </javac>
 234   </target>
 235   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 236     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 237       <arg line="html" />
 238     </java>
 239   </target>
 240
 241   <target name="makefulldist" depends="makedist">
 242     <copy todir="${packageDir}">
 243       <fileset dir="${resourceDir}/images">
 244         <include name="${WebStartImage}"/>
 245       </fileset>
 246     </copy>
 247
 248     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 249
 250     <!-- create a dummy jar which will eventually contain the jnlp template -->
 251     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 252       <fileset dir="${packageDir}">
 253         <include name="jalview.jar" />
 254       </fileset>
 255     </jar>
 256
 257     <mkdir dir="${packageDir}/JNLP-INF"/>
 258     <antcall target="writejnlpf">
 259       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 260       <param name="inih" value="*" />
 261       <param name="maxh" value="*"/>
 262     </antcall>
 263
 264     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 265       <fileset dir="${packageDir}">
 266         <include name="JNLP-INF"/>
 267       </fileset>
 268     </jar>
 269
 270     <antcall target="writejnlpf">
 271       <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 272       <param name="inih" value="10M" />
 273       <param name="maxh" value="256M"/>
 274     </antcall>
 275
 276     <antcall target="writejnlpf">
 277       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 278       <param name="inih" value="128M" />
 279       <param name="maxh" value="512M"/>
 280     </antcall>
 281
 282     <antcall target="writejnlpf">
 283       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 284       <param name="inih" value="256M" />
 285       <param name="maxh" value="1024M"/>
 286     </antcall>
 287
 288     <!-- finally, need to postprocess to add in associations at end of 'information' element
 289
 290                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 291
 292                 </xslt>
 293
 294
 295                         -->
 296     <!--
 297                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 298         <association mime-type="application-x/ext-file" extensions="fasta"/>
 299         <association mime-type="application-x/ext-file" extensions="mfa"/>
 300         <association mime-type="application-x/ext-file" extensions="fastq"/>
 301         <association mime-type="application-x/ext-file" extensions="blc"/>
 302         <association mime-type="application-x/ext-file" extensions="msf"/>
 303         <association mime-type="application-x/ext-file" extensions="pfam"/>
 304         <association mime-type="application-x/ext-file" extensions="aln"/>
 305         <association mime-type="application-x/ext-file" extensions="pir"/>
 306         <association mime-type="application-x/ext-file" extensions="amsa"/>
 307         <association mime-type="application-x/ext-file" extensions="stk"/>
 308         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 309     <!-- and sign the jars -->
 310     <!-- the default keystore details might need to be edited here -->
 311     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 312       <fileset dir="${packageDir}">
 313         <include name="*.jar" />
 314       </fileset>
 315     </signjar>
 316   </target>
 317
 318   <target name="runenv" depends="init">
 319     <path id="run.classpath">
 320       <pathelement location="${outputDir}" />
 321       <fileset dir="${outputDir}">
 322         <include name="${libDir}/*.jar" />
 323       </fileset>
 324     </path>
 325     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 326
 327     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 328       </echo>
 329   </target>
 330
 331   <target name="-generatejnlpf">
 332     <presetdef name="jnlpf">
 333       <jnlp codebase="${WebStartLocation}">
 334         <information>
 335           <title>Jalview</title>
 336           <vendor>The Barton Group</vendor>
 337           <homepage href="http://www.jalview.org" />
 338           <description>Jalview Multiple Alignment Editor</description>
 339           <description kind="short">Jalview</description>
 340           <icon href="${WebStartImage}" />
 341           <offline_allowed />
 342         </information>
 343         <resources>
 344           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 345           <fileset dir="${packageDir}">
 346             <include name="jalview.jar" />
 347           </fileset>
 348           <fileset dir="${packageDir}">
 349             <include name="*.jar" />
 350             <include name="*_*.jar" />
 351             <exclude name="jalview.jar" />
 352                 <exclude name="*jnilib.jar"/>
 353           </fileset>
 354         </resources>
 355         <resources os="Mac OS X">
 356           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 357                 <fileset dir="${packageDir}">
 358                         <include name="*quaqua*.jnilib.jar"/>
 359                 </fileset>
 360         </resources>
 361
 362         <application_desc main_class="jalview.bin.Jalview">
 363         </application_desc>
 364         <security>
 365           <all_permissions />
 366         </security>
 367       </jnlp>
 368     </presetdef>
 369
 370     <jnlpf toFile="${jnlpFile}"/>
 371
 372   </target>
 373
 374   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 375     <echo message="Not adding JNLP File Associations"/>
 376   </target>
 377
 378   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 379     <replace file="${jnlpFile}">
 380       <replacetoken>
 381         <![CDATA[</information>]]></replacetoken>
 382       <replacevalue>
 383         <![CDATA[
 384           <association mime-type="application-x/ext-file" extensions="fa" />
 385         <association mime-type="application-x/ext-file" extensions="fasta" />
 386         <association mime-type="application-x/ext-file" extensions="mfa" />
 387         <association mime-type="application-x/ext-file" extensions="fastq" />
 388         <association mime-type="application-x/ext-file" extensions="blc" />
 389         <association mime-type="application-x/ext-file" extensions="msf" />
 390         <association mime-type="application-x/ext-file" extensions="pfam" />
 391         <association mime-type="application-x/ext-file" extensions="aln"/>
 392         <association mime-type="application-x/ext-file" extensions="pir"/>
 393         <association mime-type="application-x/ext-file" extensions="amsa"/>
 394         <association mime-type="application-x/ext-file" extensions="stk"/>
 395         <association mime-type="application-x/ext-file" extensions="jvp"/>
 396       </information>]]></replacevalue>
 397   </replace>
 398   <echo message="Added file associations to JNLP file"/>
 399 </target>
 400 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 401 </target>
 402
 403 <target name="buildextclients" depends="init">
 404   <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" />
 405   <condition property="dontextbuild">
 406     <equals arg1="n" arg2="${doextbuild.response}" />
 407   </condition>
 408   <condition property="dontextbuild">
 409     <equals arg1="N" arg2="${doextbuild.response}" />
 410   </condition>
 411   <fail if="dontextbuild">
 412         Build External Client Code process aborted by user. Jalview source is unchanged.
 413       </fail>
 414   <!-- Currently, this doesn't happen automatically.
 415      1. Run WSDL2Java as below, which generates an ext.vamsas +
 416      vamsas.<datapackages> fileset.
 417      2. refactor ext.vamsas.SpecificserviceWS* to
 418      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 419      3. Update the jalview.ws.*WServices classes to reflect the
 420      interface type, and all locations of this wsdl type that Jalview
 421      might be using.
 422
 423 -->
 424   <path id="axisbuild">
 425     <path refid="build.classpath" />
 426   </path>
 427   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 428   <move todir="./bak">
 429     <fileset dir="${sourceDir}" id="client">
 430       <include name="${wsdl.ClientNS}/*.*" />
 431     </fileset>
 432   </move>
 433
 434   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 435     <mappingSet>
 436       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 437       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 438     </mappingSet>
 439   </axis-wsdl2java>
 440 </target>
 441
 442 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 443   <!-- make the package jar if not already existing -->
 444   <mkdir dir="${packageDir}" />
 445   <!-- clean dir if it already existed -->
 446   <delete>
 447     <fileset dir="${packageDir}">
 448       <include name="*.jar"/>
 449     </fileset>
 450   </delete>
 451   <jar destfile="${packageDir}/${outputJar}" index="true">
 452     <manifest>
 453       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 454       <attribute name="Permissions" value="all-permissions" />
 455       <attribute name="Application-Name" value="Jalview Desktop" />
 456       <attribute name="Codebase" value="${application.codebase}" />
 457     </manifest>
 458     <fileset dir="${outputDir}/">
 459       <exclude name="cache*/**" />
 460       <exclude name="*.jar" />
 461       <exclude name="*.jar.*" />
 462       <exclude name="**/*.jar" />
 463       <exclude name="**/*.jar.*" />
 464     </fileset>
 465   </jar>
 466
 467   <copy toDir="${packageDir}" flatten="true">
 468     <fileset dir="${outputDir}">
 469       <include name="*.jar" />
 470       <include name="**/*.jar" />
 471     </fileset>
 472   </copy>
 473 </target>
 474
 475
 476 <!-- jalopy code reformatter -->
 477 <target name="sourcescrub" depends="init,build">
 478   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 479     <fileset dir="${sourceDir}">
 480       <include name="*.java" />
 481       <include name="**/*.java" />
 482       <include name="**/**/*.java" />
 483     </fileset>
 484   </jalopy>
 485 </target>
 486
 487
 488
 489 <!-- Compile, package and obfuscate Jalview Applet -->
 490 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 491
 492 <target name="compileApplet" depends="init,clean">
 493   <mkdir dir="${outputDir}" />
 494   <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 495                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 496                         excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 497 </target>
 498
 499 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 500   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 501   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 502   <copy todir="${outputDir}/lang">
 503     <fileset dir="${resourceDir}/lang">
 504       <include name="**.*"/>
 505     </fileset>
 506   </copy>
 507   <jar destfile="in.jar" index="true">
 508     <manifest>
 509       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 510       <attribute name="Application-Name" value="JalviewLite" />
 511       <attribute name="Codebase" value="${applet.codebase}" />
 512     </manifest>
 513     <fileset dir="${outputDir}">
 514       <include name="com/**" />
 515       <include name="MCview/**" />
 516       <include name="jalview/**" />
 517       <include name=".build_properties" />
 518       <include name="images/idwidth.gif" />
 519       <include name="images/link.gif" />
 520       <include name="lang/**" />
 521     </fileset>
 522   </jar>
 523 </target>
 524 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 525 </target>
 526 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 527   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 528   <delete file="in.jar" />
 529 </target>
 530 <target name="-obfuscatereally" unless="donotobfuscate">
 531
 532   <path id="obfuscateDeps.path">
 533     <pathelement location="${applet.jre.tools}" />
 534     <pathelement location="appletlib/${jmolJar}" />
 535   </path>
 536   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 537
 538   <proguard>
 539     <injar file="in.jar" />
 540     <outjar file="${jalviewLiteJar}" />
 541     <libraryjar refid="obfuscateDeps.path" />
 542     <dontwarn/>
 543     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 544       <field access="public" />
 545       <method access="public" />
 546       <constructor access="public" />
 547     </keep>
 548     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 549       <field access="public" />
 550       <method access="public" />
 551       <constructor access="public" />
 552     </keep>
 553     <!--      -libraryjars "${obfuscateDeps}"
 554       -injars      in.jar
 555       -outjars     jalviewApplet.jar
 556       -keep public class jalview.bin.JalviewLite
 557        { public * ; } -->
 558   </proguard>
 559   <delete file="in.jar" />
 560 </target>
 561
 562 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 563   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 564   <delete>
 565     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 566       <include name="*.java" />
 567       <include name="descriptors/*.java" />
 568     </fileset>
 569   </delete>
 570   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 571   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 572   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 573   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 574   <!--
 575                 now build the jalview.binding package with the old schema set
 576                 -->
 577   <delete>
 578     <fileset dir="${sourceDir}/jalview/binding/">
 579       <include name="**" />
 580     </fileset>
 581   </delete>
 582   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 583   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 584   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 585 </target>
 586 <target name="sourcedist" description="create jalview source distribution" depends="init">
 587   <delete file="${source.dist.name}" />
 588   <tar destfile="${source.dist.name}" compression="gzip">
 589     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 590       <include name="LICENSE" />
 591       <include name="README" />
 592       <include name="build.xml" />
 593       <include name="jalview-jalopy.xml" />
 594       <include name="JalviewApplet.jpx" />
 595       <include name="JalviewX.jpx" />
 596       <include name="nbbuild.xml"/>
 597       <include name="nbproject/genfiles.properties"/>
 598       <include name="nbproject/project.properties"/>
 599       <include name="nbproject/project.xml"/>
 600       <include name="${sourceDir}/*.java" />
 601       <include name="${sourceDir}/**/*.java" />
 602       <include name="${sourceDir}/**/*.cdr" />
 603       <include name="${libDir}/**/*" />
 604       <include name="${resourceDir}/**/*" />
 605       <include name="${helpDir}/**/*" />
 606       <include name="appletlib/${jmolJar}" />
 607       <exclude name="**/*locales" />
 608       <exclude name="*locales/**" />
 609       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 610       <exclude name="utils/InstallAnywhere/**Build*/**" />
 611       <exclude name="utils/InstallAnywhere/**Build*/**" />
 612       <exclude name="utils/InstallAnywhere/**locale*" />
 613       <exclude name="utils/InstallAnywhere/**locale*/**" />
 614       <include name="${schemaDir}/**/*" />
 615       <include name="utils/**/*" />
 616       <include name="${docDir}/**/*" />
 617       <include name="examples/**/*" />
 618     </tarfileset>
 619   </tar>
 620 </target>
 621 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 622   <copy todir="${packageDir}/examples">
 623     <fileset dir="examples">
 624       <include name="**/*"/>
 625       <include name="javascript/*"/>
 626       <include name="jmol/*"/>
 627     </fileset>
 628     <fileset dir=".">
 629       <include name="${jalviewLiteJar}" />
 630     </fileset>
 631     <fileset dir="appletlib">
 632       <include name="**/*"/>
 633     </fileset>
 634   </copy>
 635   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 636   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 637     <manifest>
 638       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 639       <!--          <attribute name="Permissions" value="sandbox" /> -->
 640       <!--<attribute name="Trusted-Lib" value="true" /> -->
 641       <attribute name="Codebase" value="${applet.codebase}"/>
 642       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 643     </manifest>
 644   </jar>
 645   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 646     <fileset dir="${packageDir}/examples">
 647       <include name="*.jar" />
 648     </fileset>
 649   </signjar>
 650   <presetdef name="ap_applet.jar">
 651     <!-- build a signed applet with 'all-permissions' -
 652                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 653                           JalviewLite+JmolApplet linked sequence/structure fails
 654                           Mixed code warnings are raised
 655                           -->
 656     <jar update="true" index="true">
 657       <manifest>
 658         <attribute name="Application-Name" value="JalviewLite" />
 659         <attribute name="Permissions" value="all-permissions" />
 660         <attribute name="Codebase" value="${applet.codebase}" />
 661         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 662         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 663       </manifest>
 664     </jar>
 665   </presetdef>
 666   <presetdef name="applet.jar">
 667     <!-- build signed applet with sandbox permissions -
 668                           Needs 'param name="permissions' value="sandbox"' in applet tag
 669                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 670                         -->
 671
 672     <jar update="true" index="true">
 673       <manifest>
 674         <attribute name="Application-Name" value="JalviewLite" />
 675         <attribute name="Permissions" value="sandbox" />
 676         <attribute name="Codebase" value="${applet.codebase}" />
 677         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 678         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 679       </manifest>
 680     </jar>
 681   </presetdef>
 682   <presetdef name="tl_applet.jar">
 683     <!-- build signed applet with trusted library/trusted permissions -
 684                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 685                                j1.7_45:
 686                                No mixed code warnings raised
 687                                Jmol/JalviewLite sequence/structure example doesn't link structures
 688                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 689
 690                               -->
 691
 692     <jar update="true" index="true">
 693       <manifest>
 694         <attribute name="Application-Name" value="JalviewLite" />
 695         <attribute name="Permissions" value="all-permissions" />
 696         <attribute name="Codebase" value="${applet.codebase}" />
 697         <attribute name="Trusted-Only" value="true" />
 698         <attribute name="Trusted-Library" value="true" />
 699       </manifest>
 700     </jar>
 701   </presetdef>
 702   <presetdef name="to_applet.jar">
 703     <!-- not fully test variant (yet) -->
 704     <jar update="true" index="true">
 705       <manifest>
 706         <attribute name="Application-Name" value="JalviewLite" />
 707         <attribute name="Permissions" value="all-permissions" />
 708         <attribute name="Codebase" value="${applet.codebase}" />
 709         <attribute name="Trusted-Only" value="true" />
 710       </manifest>
 711     </jar>
 712   </presetdef>
 713   <!-- create differently privileged artefacts -->
 714   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 715   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 716   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 717   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 718   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 719   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 720   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 721   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 722   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 723   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 724   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 725   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 726   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 727   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 728   <!-- finally, create manifest for original jars -->
 729   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 730   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 731
 732   <!-- todo - write examples/downloads for alternate versions of the applet -->
 733   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 734
 735     <fileset dir="${packageDir}/examples">
 736       <exclude name="u_*.jar"/>
 737       <include name="${jalviewLiteJar}" />
 738       <include name="${jmolJar}" />
 739       <include name="to_${jalviewLiteJar}" />
 740       <include name="to_${jmolJar}" />
 741       <include name="tl_${jalviewLiteJar}" />
 742       <include name="tl_${jmolJar}" />
 743       <include name="ap_${jalviewLiteJar}" />
 744       <include name="ap_${jmolJar}" />
 745     </fileset>
 746   </signjar>
 747   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 748   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 749         <!-- finally, replace any launchApp servlet tags with a version specification -->
 750         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 751                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
 752                 <fileset dir="${packageDir}/examples">
 753                         <include name="**/*.html"/>
 754                 </fileset>
 755         </replace>
 756         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 757                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
 758                 <fileset dir="${packageDir}/examples">
 759                         <include name="**/*.html"/>
 760                 </fileset>
 761         </replace>
 762
 763 </target>
 764 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 765   <javadoc destdir="${javadocDir}">
 766     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 767     </packageset>
 768   </javadoc>
 769 </target>
 770 </project>