build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   4  * Copyright (C) 2014 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   <!-- we use jalopy to format our sources -->
  22   <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
  23     <classpath>
  24       <fileset dir="utils/jalopy/lib">
  25         <include name="*.jar" />
  26       </fileset>
  27     </classpath>
  28   </taskdef>
  29
  30   <target name="help" depends="usage" />
  31   <target name="usage">
  32     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  33     <echo message="Targets include:" />
  34     <echo message="usage - default target, displays this message" />
  35     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  36     <echo message="build - compiles all necessary files for Application" />
  37     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  38     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  39     <echo message="              this needs a keystore and key. See docs/building.html for more information." />
  40     <echo message="compileApplet - compiles all necessary files for Applet" />
  41     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  42     <echo message="See docs/building.html and the comments in build file for other targets." />
  43     <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  44     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  45   </target>
  46
  47
  48   <!-- utils is a class path to additional utilities needed for
  49     building docs, jars and webstart stuff -->
  50   <!--
  51         Userdefined build property defaults
  52
  53         wsdl.server list (plus namespace mapping info ???)  - also want
  54                 ... to make this a dynamically generatable property
  55         WebStart Location
  56         Build location - provide a temporary root for speed
  57         jarsigner keystore and info
  58         Jakarta and axis classpath ?
  59         Default argument for starting Jalview (if it exists).
  60
  61 -->
  62
  63   <target name="init">
  64     <path id="axis.classpath">
  65       <!-->
  66       <fileset dir="/usr/local/axis/lib">
  67         <include name="**/*.jar" />
  68       </fileset>
  69       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  70         <include name="**/*.jar"/>
  71         <include name="*.jar"/>
  72       </fileset> -->
  73       </path>
  74     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  75     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  76     <!-- 2.4 (VAMSAS)" -->
  77     <!-- Include debugging information in javac true or false -->
  78     <property name="javac.debug" value="true" />
  79
  80     <!-- JarSigner Key Store for Webstart Distribution -->
  81     <property name="jalview.keystore" value="./keys/.keystore" />
  82     <!-- Keystore Password -->
  83     <property name="jalview.keystore.pass" value="alignmentisfun" />
  84     <!-- Key Name -->
  85     <property name="jalview.key" value="jalview" />
  86     <!-- Key Password -->
  87     <property name="jalview.key.pass" value="alignmentisfun" />
  88
  89     <!-- Don't change anything below here unless you know what you are doing! -->
  90     <!-- Url path for WebStart in JNLP file -->
  91     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  92     <!-- Webstart Image - looked for in resources/images -->
  93     <property name="WebStartImage" value="JalviewLogo_big.png"/>
  94     <!-- J2SE version needed for webstart launch -->
  95 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  96     <property name="j2sev" value="1.7+"/>
  97
  98     <!-- Permissions for running Java applets and applications. -->
  99     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 100     <property name="application.codebase" value="*.jalview.org" />
 101     <!-- and allowing the applet to be deployed from any URL -->
 102     <!-- 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 -->
 103     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 104     <property name="applet.caller-codebase" value="${applet.codebase}" />
 105
 106     <!-- build directory configuration -->
 107     <property name="libDir" value="lib" />
 108     <property name="resourceDir" value="resources" />
 109     <property name="helpDir" value="help" />
 110     <property name="docDir" value="doc" />
 111     <property name="sourceDir" value="src" />
 112     <property name="schemaDir" value="schemas" />
 113     <property name="outputDir" value="classes" />
 114     <property name="packageDir" value="dist" />
 115     <property name="outputJar" value="jalview.jar" />
 116     <!-- Jalview Applet JMol Jar Dependency -->
 117     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 118     <property name="varnaJar" value="VARNAv3-9.jar" />
 119     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 120     <!-- switch to indicate if we should obfuscate jalviewLite -->
 121     <!-- <property name="donotobfuscate" value="true"/> -->
 122     <!-- switch to exclude associations from generated jnlp files -->
 123     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 124
 125     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 126     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 127     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 128     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 129     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 130     <property name="WSInterf" value="MsaWS" />
 131     <property name="wsdl.Namespace" value="vamsas" />
 132     <property name="wsdl.ClientNS" value="ext.vamsas" />
 133     <!-- the class path for building the application -->
 134     <path id="build.classpath">
 135       <fileset dir="utils">
 136         <include name="*.jar" />
 137         <include name="**/*.jar" />
 138       </fileset>
 139       <fileset dir="${libDir}">
 140         <include name="*.jar" />
 141         <include name="**/*.jar" />
 142       </fileset>
 143       <fileset dir="${java.home}/lib">
 144         <include name="plugin.jar"/>
 145       </fileset>
 146       <fileset dir="appletlib">
 147         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 148                                 -->
 149         <include name="${jmolJar}" />
 150         <include name="${varnaJar}" />
 151       </fileset>
 152
 153     </path>
 154     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 155     <!-- The Location of the java 1.1.8 jdk -->
 156     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
 157     <property name="java118.home" value="${java.home}" />
 158     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 159                 -->
 160     <!-- jre for 1.4 version -->
 161     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 162
 163     <!-- the classpath for building the 1.1 applet -->
 164     <path id="jalviewlite.deps">
 165       <fileset dir="${java118.home}">
 166         <include name="lib/classes.zip" />
 167       </fileset>
 168       <fileset dir="${java.home}/lib">
 169         <include name="plugin.jar"/>
 170       </fileset>
 171       <pathelement location="appletlib/${jmolJar}" />
 172       <pathelement location="lib/${varnaJar}" />
 173     </path>
 174     <!-- default location for outputting javadoc -->
 175     <property name="javadocDir" value="${packageDir}/javadoc"/>
 176   </target>
 177
 178
 179   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 180   <target name="buildPropertiesFile" depends="init">
 181     <tstamp prefix="build">
 182       <format property="date" pattern="dd MMMM yyyy" />
 183     </tstamp>
 184     <properties file="${outputDir}/.build_properties">
 185       <header>
 186           ---Jalview Build Details---
 187         </header>
 188       <property name="VERSION" value="${JALVIEW_VERSION}" />
 189       <property name="BUILD_DATE" value="${build.date}" />
 190     </properties>
 191   </target>
 192
 193
 194   <target name="clean" depends="init">
 195     <!-- not efficient yet. -->
 196     <delete dir="${outputDir}" includes="*,**/*"/>
 197   </target>
 198
 199   <target name="distclean" depends="init, clean">
 200
 201     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 202     <delete>
 203       <fileset dir=".">
 204         <include name="${outputJar}" />
 205         <include name="#*#" />
 206         <include name="#*.*#" />
 207         <include name="**/#*#" />
 208         <include name="**/#*.*#" />
 209         <include name="*~" />
 210         <include name="*.*~" />
 211         <include name="**/*~" />
 212         <include name="**/*.*~" />
 213       </fileset>
 214     </delete>
 215   </target>
 216
 217   <target name="prepare" depends="init">
 218     <mkdir dir="${outputDir}" />
 219     <copy todir="${outputDir}">
 220       <fileset dir=".">
 221         <include name="${docDir}/**/*.*" />
 222         <include name="${helpDir}/**/*.*" />
 223         <include name="${libDir}/*.jar" />
 224       </fileset>
 225       <fileset dir="${resourceDir}">
 226         <include name="**/*.*" />
 227       </fileset>
 228     </copy>
 229   </target>
 230
 231   <target name="build" depends="prepare">
 232     <!-- not efficient yet. -->
 233     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 234       <exclude name="jalview/*applet*" />
 235       <exclude name="jalview/appletgui/**" />
 236       <exclude name="com/stevesoft/**" />
 237     </javac>
 238   </target>
 239   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 240     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 241       <arg line="html" />
 242     </java>
 243   </target>
 244
 245   <target name="makefulldist" depends="makedist">
 246     <copy todir="${packageDir}">
 247       <fileset dir="${resourceDir}/images">
 248         <include name="${WebStartImage}"/>
 249       </fileset>
 250     </copy>
 251
 252     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 253
 254     <!-- create a dummy jar which will eventually contain the jnlp template -->
 255     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 256       <fileset dir="${packageDir}">
 257         <include name="jalview.jar" />
 258       </fileset>
 259     </jar>
 260
 261     <mkdir dir="${packageDir}/JNLP-INF"/>
 262     <antcall target="writejnlpf">
 263       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 264       <param name="inih" value="*" />
 265       <param name="maxh" value="*"/>
 266     </antcall>
 267
 268     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 269       <fileset dir="${packageDir}">
 270         <include name="JNLP-INF"/>
 271       </fileset>
 272     </jar>
 273
 274     <antcall target="writejnlpf">
 275       <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 276       <param name="inih" value="10M" />
 277       <param name="maxh" value="256M"/>
 278     </antcall>
 279
 280     <antcall target="writejnlpf">
 281       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 282       <param name="inih" value="128M" />
 283       <param name="maxh" value="512M"/>
 284     </antcall>
 285
 286     <antcall target="writejnlpf">
 287       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 288       <param name="inih" value="256M" />
 289       <param name="maxh" value="1024M"/>
 290     </antcall>
 291
 292     <!-- finally, need to postprocess to add in associations at end of 'information' element
 293
 294                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 295
 296                 </xslt>
 297
 298
 299                         -->
 300     <!--
 301                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 302         <association mime-type="application-x/ext-file" extensions="fasta"/>
 303         <association mime-type="application-x/ext-file" extensions="mfa"/>
 304         <association mime-type="application-x/ext-file" extensions="fastq"/>
 305         <association mime-type="application-x/ext-file" extensions="blc"/>
 306         <association mime-type="application-x/ext-file" extensions="msf"/>
 307         <association mime-type="application-x/ext-file" extensions="pfam"/>
 308         <association mime-type="application-x/ext-file" extensions="aln"/>
 309         <association mime-type="application-x/ext-file" extensions="pir"/>
 310         <association mime-type="application-x/ext-file" extensions="amsa"/>
 311         <association mime-type="application-x/ext-file" extensions="stk"/>
 312         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 313     <!-- and sign the jars -->
 314     <!-- the default keystore details might need to be edited here -->
 315     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 316       <fileset dir="${packageDir}">
 317         <include name="*.jar" />
 318       </fileset>
 319     </signjar>
 320   </target>
 321
 322   <target name="runenv" depends="init">
 323     <path id="run.classpath">
 324       <pathelement location="${outputDir}" />
 325       <fileset dir="${outputDir}">
 326         <include name="${libDir}/*.jar" />
 327       </fileset>
 328     </path>
 329     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 330
 331     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 332       </echo>
 333   </target>
 334
 335   <target name="-generatejnlpf">
 336     <presetdef name="jnlpf">
 337       <jnlp codebase="${WebStartLocation}">
 338         <information>
 339           <title>Jalview</title>
 340           <vendor>The Barton Group</vendor>
 341           <homepage href="http://www.jalview.org" />
 342           <description>Jalview Multiple Alignment Editor</description>
 343           <description kind="short">Jalview</description>
 344           <icon href="${WebStartImage}" />
 345           <offline_allowed />
 346         </information>
 347         <resources>
 348           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 349           <fileset dir="${packageDir}">
 350             <include name="jalview.jar" />
 351           </fileset>
 352           <fileset dir="${packageDir}">
 353             <include name="*.jar" />
 354             <include name="*_*.jar" />
 355             <exclude name="jalview.jar" />
 356           </fileset>
 357           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 358         </resources>
 359         <application_desc main_class="jalview.bin.Jalview">
 360         </application_desc>
 361         <security>
 362           <all_permissions />
 363         </security>
 364       </jnlp>
 365     </presetdef>
 366
 367     <jnlpf toFile="${jnlpFile}"/>
 368
 369   </target>
 370
 371   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 372     <echo message="Not adding JNLP File Associations"/>
 373   </target>
 374
 375   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 376     <replace file="${jnlpFile}">
 377       <replacetoken>
 378         <![CDATA[</information>]]></replacetoken>
 379       <replacevalue>
 380         <![CDATA[
 381           <association mime-type="application-x/ext-file" extensions="fa" />
 382         <association mime-type="application-x/ext-file" extensions="fasta" />
 383         <association mime-type="application-x/ext-file" extensions="mfa" />
 384         <association mime-type="application-x/ext-file" extensions="fastq" />
 385         <association mime-type="application-x/ext-file" extensions="blc" />
 386         <association mime-type="application-x/ext-file" extensions="msf" />
 387         <association mime-type="application-x/ext-file" extensions="pfam" />
 388         <association mime-type="application-x/ext-file" extensions="aln"/>
 389         <association mime-type="application-x/ext-file" extensions="pir"/>
 390         <association mime-type="application-x/ext-file" extensions="amsa"/>
 391         <association mime-type="application-x/ext-file" extensions="stk"/>
 392         <association mime-type="application-x/ext-file" extensions="jvp"/>
 393       </information>]]></replacevalue>
 394     </replace>
 395     <echo message="Added file associations to JNLP file"/>
 396     </target>
 397 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 398 </target>
 399
 400 <target name="buildextclients" depends="init">
 401   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 402   <condition property="dontextbuild">
 403     <equals arg1="n" arg2="${doextbuild.response}" />
 404   </condition>
 405   <condition property="dontextbuild">
 406     <equals arg1="N" arg2="${doextbuild.response}" />
 407   </condition>
 408   <fail if="dontextbuild">
 409         Build External Client Code process aborted by user. Jalview source is unchanged.
 410       </fail>
 411   <!-- Currently, this doesn't happen automatically.
 412      1. Run WSDL2Java as below, which generates an ext.vamsas +
 413      vamsas.<datapackages> fileset.
 414      2. refactor ext.vamsas.SpecificserviceWS* to
 415      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 416      3. Update the jalview.ws.*WServices classes to reflect the
 417      interface type, and all locations of this wsdl type that Jalview
 418      might be using.
 419
 420 -->
 421   <path id="axisbuild">
 422     <path refid="build.classpath" />
 423   </path>
 424   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 425   <move todir="./bak">
 426     <fileset dir="${sourceDir}" id="client">
 427       <include name="${wsdl.ClientNS}/*.*" />
 428     </fileset>
 429   </move>
 430
 431   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 432     <mappingSet>
 433       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 434       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 435     </mappingSet>
 436   </axis-wsdl2java>
 437 </target>
 438
 439 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 440   <!-- make the package jar if not already existing -->
 441   <mkdir dir="${packageDir}" />
 442   <!-- clean dir if it already existed -->
 443   <delete>
 444     <fileset dir="${packageDir}">
 445       <include name="*.jar"/>
 446     </fileset>
 447   </delete>
 448   <jar destfile="${packageDir}/${outputJar}" index="true">
 449     <manifest>
 450       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 451       <attribute name="Permissions" value="all-permissions" />
 452       <attribute name="Application-Name" value="Jalview Desktop" />
 453       <attribute name="Codebase" value="${application.codebase}" />
 454     </manifest>
 455     <fileset dir="${outputDir}/">
 456       <exclude name="cache*/**" />
 457       <exclude name="*.jar" />
 458       <exclude name="*.jar.*" />
 459       <exclude name="**/*.jar" />
 460       <exclude name="**/*.jar.*" />
 461     </fileset>
 462   </jar>
 463
 464   <copy toDir="${packageDir}" flatten="true">
 465     <fileset dir="${outputDir}">
 466       <include name="*.jar" />
 467       <include name="**/*.jar" />
 468     </fileset>
 469   </copy>
 470 </target>
 471
 472
 473 <!-- jalopy code reformatter -->
 474 <target name="sourcescrub" depends="init,build">
 475   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 476     <fileset dir="${sourceDir}">
 477       <include name="*.java" />
 478       <include name="**/*.java" />
 479       <include name="**/**/*.java" />
 480     </fileset>
 481   </jalopy>
 482 </target>
 483
 484
 485
 486 <!-- Compile, package and obfuscate Jalview Applet -->
 487 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 488
 489 <target name="compileApplet" depends="init,clean">
 490   <mkdir dir="${outputDir}" />
 491   <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 492                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 493                         excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 494 </target>
 495
 496 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 497   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 498   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 499   <copy todir="${outputDir}/lang">
 500     <fileset dir="${resourceDir}/lang">
 501       <include name="**.*"/>
 502     </fileset>
 503   </copy>
 504   <jar destfile="in.jar" index="true">
 505     <manifest>
 506       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 507       <attribute name="Application-Name" value="JalviewLite" />
 508       <attribute name="Codebase" value="${applet.codebase}" />
 509     </manifest>
 510     <fileset dir="${outputDir}">
 511       <include name="com/**" />
 512       <include name="MCview/**" />
 513       <include name="jalview/**" />
 514       <include name=".build_properties" />
 515       <include name="images/idwidth.gif" />
 516       <include name="images/link.gif" />
 517       <include name="lang/**" />
 518     </fileset>
 519   </jar>
 520 </target>
 521 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 522 </target>
 523 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 524   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 525   <delete file="in.jar" />
 526 </target>
 527 <target name="-obfuscatereally" unless="donotobfuscate">
 528
 529   <path id="obfuscateDeps.path">
 530     <pathelement location="${applet.jre.tools}" />
 531     <pathelement location="appletlib/${jmolJar}" />
 532   </path>
 533   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 534
 535   <proguard>
 536     <injar file="in.jar" />
 537     <outjar file="${jalviewLiteJar}" />
 538     <libraryjar refid="obfuscateDeps.path" />
 539     <dontwarn/>
 540     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 541       <field access="public" />
 542       <method access="public" />
 543       <constructor access="public" />
 544     </keep>
 545     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 546       <field access="public" />
 547       <method access="public" />
 548       <constructor access="public" />
 549     </keep>
 550     <!--      -libraryjars "${obfuscateDeps}"
 551       -injars      in.jar
 552       -outjars     jalviewApplet.jar
 553       -keep public class jalview.bin.JalviewLite
 554        { public * ; } -->
 555   </proguard>
 556   <delete file="in.jar" />
 557 </target>
 558
 559 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 560   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 561   <delete>
 562     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 563       <include name="*.java" />
 564       <include name="descriptors/*.java" />
 565     </fileset>
 566   </delete>
 567   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 568   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 569   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 570   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 571   <!--
 572                 now build the jalview.binding package with the old schema set
 573                 -->
 574   <delete>
 575     <fileset dir="${sourceDir}/jalview/binding/">
 576       <include name="**" />
 577     </fileset>
 578   </delete>
 579   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 580   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 581   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 582 </target>
 583 <target name="sourcedist" description="create jalview source distribution" depends="init">
 584   <delete file="${source.dist.name}" />
 585   <tar destfile="${source.dist.name}" compression="gzip">
 586     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 587       <include name="LICENSE" />
 588       <include name="README" />
 589       <include name="build.xml" />
 590       <include name="jalview-jalopy.xml" />
 591       <include name="JalviewApplet.jpx" />
 592       <include name="JalviewX.jpx" />
 593       <include name="nbbuild.xml"/>
 594       <include name="nbproject/genfiles.properties"/>
 595       <include name="nbproject/project.properties"/>
 596       <include name="nbproject/project.xml"/>
 597       <include name="${sourceDir}/*.java" />
 598       <include name="${sourceDir}/**/*.java" />
 599       <include name="${sourceDir}/**/*.cdr" />
 600       <include name="${libDir}/**/*" />
 601       <include name="${resourceDir}/**/*" />
 602       <include name="${helpDir}/**/*" />
 603       <include name="appletlib/${jmolJar}" />
 604       <exclude name="**/*locales" />
 605       <exclude name="*locales/**" />
 606       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 607       <exclude name="utils/InstallAnywhere/**Build*/**" />
 608       <exclude name="utils/InstallAnywhere/**Build*/**" />
 609       <exclude name="utils/InstallAnywhere/**locale*" />
 610       <exclude name="utils/InstallAnywhere/**locale*/**" />
 611       <include name="${schemaDir}/**/*" />
 612       <include name="utils/**/*" />
 613       <include name="${docDir}/**/*" />
 614       <include name="examples/**/*" />
 615     </tarfileset>
 616   </tar>
 617 </target>
 618 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 619   <copy todir="${packageDir}/examples">
 620     <fileset dir="examples">
 621       <include name="**/*"/>
 622       <include name="javascript/*"/>
 623       <include name="jmol/*"/>
 624     </fileset>
 625     <fileset dir=".">
 626       <include name="${jalviewLiteJar}" />
 627     </fileset>
 628     <fileset dir="appletlib">
 629       <include name="**/*"/>
 630     </fileset>
 631   </copy>
 632   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 633   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 634     <manifest>
 635       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 636       <!--          <attribute name="Permissions" value="sandbox" /> -->
 637       <!--<attribute name="Trusted-Lib" value="true" /> -->
 638       <attribute name="Codebase" value="${applet.codebase}"/>
 639       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 640     </manifest>
 641   </jar>
 642   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 643     <fileset dir="${packageDir}/examples">
 644       <include name="*.jar" />
 645     </fileset>
 646   </signjar>
 647   <presetdef name="ap_applet.jar">
 648     <!-- build a signed applet with 'all-permissions' -
 649                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 650                           JalviewLite+JmolApplet linked sequence/structure fails
 651                           Mixed code warnings are raised
 652                           -->
 653     <jar update="true" index="true">
 654       <manifest>
 655         <attribute name="Application-Name" value="JalviewLite" />
 656         <attribute name="Permissions" value="all-permissions" />
 657         <attribute name="Codebase" value="${applet.codebase}" />
 658         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 659         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 660       </manifest>
 661     </jar>
 662   </presetdef>
 663   <presetdef name="applet.jar">
 664     <!-- build signed applet with sandbox permissions -
 665                           Needs 'param name="permissions' value="sandbox"' in applet tag
 666                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 667                         -->
 668
 669     <jar update="true" index="true">
 670       <manifest>
 671         <attribute name="Application-Name" value="JalviewLite" />
 672         <attribute name="Permissions" value="sandbox" />
 673         <attribute name="Codebase" value="${applet.codebase}" />
 674         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 675         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 676       </manifest>
 677     </jar>
 678   </presetdef>
 679   <presetdef name="tl_applet.jar">
 680     <!-- build signed applet with trusted library/trusted permissions -
 681                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 682                                j1.7_45:
 683                                No mixed code warnings raised
 684                                Jmol/JalviewLite sequence/structure example doesn't link structures
 685                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 686
 687                               -->
 688
 689     <jar update="true" index="true">
 690       <manifest>
 691         <attribute name="Application-Name" value="JalviewLite" />
 692         <attribute name="Permissions" value="all-permissions" />
 693         <attribute name="Codebase" value="${applet.codebase}" />
 694         <attribute name="Trusted-Only" value="true" />
 695         <attribute name="Trusted-Library" value="true" />
 696       </manifest>
 697     </jar>
 698   </presetdef>
 699   <presetdef name="to_applet.jar">
 700     <!-- not fully test variant (yet) -->
 701     <jar update="true" index="true">
 702       <manifest>
 703         <attribute name="Application-Name" value="JalviewLite" />
 704         <attribute name="Permissions" value="all-permissions" />
 705         <attribute name="Codebase" value="${applet.codebase}" />
 706         <attribute name="Trusted-Only" value="true" />
 707       </manifest>
 708     </jar>
 709   </presetdef>
 710   <!-- create differently privileged artefacts -->
 711   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 712   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 713   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 714   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 715   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 716   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 717   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 718   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 719   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 720   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 721   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 722   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 723   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 724   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 725   <!-- finally, create manifest for original jars -->
 726   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 727   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 728
 729   <!-- todo - write examples/downloads for alternate versions of the applet -->
 730   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 731
 732     <fileset dir="${packageDir}/examples">
 733       <exclude name="u_*.jar"/>
 734       <include name="${jalviewLiteJar}" />
 735       <include name="${jmolJar}" />
 736       <include name="to_${jalviewLiteJar}" />
 737       <include name="to_${jmolJar}" />
 738       <include name="tl_${jalviewLiteJar}" />
 739       <include name="tl_${jmolJar}" />
 740       <include name="ap_${jalviewLiteJar}" />
 741       <include name="ap_${jmolJar}" />
 742     </fileset>
 743   </signjar>
 744   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 745   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 746 </target>
 747 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 748   <javadoc destdir="${javadocDir}">
 749     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 750     </packageset>
 751   </javadoc>
 752 </target>
 753 </project>