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   <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           </fileset>
 353           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 354         </resources>
 355         <application_desc main_class="jalview.bin.Jalview">
 356         </application_desc>
 357         <security>
 358           <all_permissions />
 359         </security>
 360       </jnlp>
 361     </presetdef>
 362
 363     <jnlpf toFile="${jnlpFile}"/>
 364
 365   </target>
 366
 367   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 368     <echo message="Not adding JNLP File Associations"/>
 369   </target>
 370
 371   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 372     <replace file="${jnlpFile}">
 373       <replacetoken>
 374         <![CDATA[</information>]]></replacetoken>
 375       <replacevalue>
 376         <![CDATA[
 377           <association mime-type="application-x/ext-file" extensions="fa" />
 378         <association mime-type="application-x/ext-file" extensions="fasta" />
 379         <association mime-type="application-x/ext-file" extensions="mfa" />
 380         <association mime-type="application-x/ext-file" extensions="fastq" />
 381         <association mime-type="application-x/ext-file" extensions="blc" />
 382         <association mime-type="application-x/ext-file" extensions="msf" />
 383         <association mime-type="application-x/ext-file" extensions="pfam" />
 384         <association mime-type="application-x/ext-file" extensions="aln"/>
 385         <association mime-type="application-x/ext-file" extensions="pir"/>
 386         <association mime-type="application-x/ext-file" extensions="amsa"/>
 387         <association mime-type="application-x/ext-file" extensions="stk"/>
 388         <association mime-type="application-x/ext-file" extensions="jvp"/>
 389       </information>]]></replacevalue>
 390   </replace>
 391   <echo message="Added file associations to JNLP file"/>
 392 </target>
 393 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 394 </target>
 395
 396 <target name="buildextclients" depends="init">
 397   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 398   <condition property="dontextbuild">
 399     <equals arg1="n" arg2="${doextbuild.response}" />
 400   </condition>
 401   <condition property="dontextbuild">
 402     <equals arg1="N" arg2="${doextbuild.response}" />
 403   </condition>
 404   <fail if="dontextbuild">
 405         Build External Client Code process aborted by user. Jalview source is unchanged.
 406       </fail>
 407   <!-- Currently, this doesn't happen automatically.
 408      1. Run WSDL2Java as below, which generates an ext.vamsas +
 409      vamsas.<datapackages> fileset.
 410      2. refactor ext.vamsas.SpecificserviceWS* to
 411      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 412      3. Update the jalview.ws.*WServices classes to reflect the
 413      interface type, and all locations of this wsdl type that Jalview
 414      might be using.
 415
 416 -->
 417   <path id="axisbuild">
 418     <path refid="build.classpath" />
 419   </path>
 420   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 421   <move todir="./bak">
 422     <fileset dir="${sourceDir}" id="client">
 423       <include name="${wsdl.ClientNS}/*.*" />
 424     </fileset>
 425   </move>
 426
 427   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 428     <mappingSet>
 429       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 430       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 431     </mappingSet>
 432   </axis-wsdl2java>
 433 </target>
 434
 435 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 436   <!-- make the package jar if not already existing -->
 437   <mkdir dir="${packageDir}" />
 438   <!-- clean dir if it already existed -->
 439   <delete>
 440     <fileset dir="${packageDir}">
 441       <include name="*.jar"/>
 442     </fileset>
 443   </delete>
 444   <jar destfile="${packageDir}/${outputJar}" index="true">
 445     <manifest>
 446       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 447       <attribute name="Permissions" value="all-permissions" />
 448       <attribute name="Application-Name" value="Jalview Desktop" />
 449       <attribute name="Codebase" value="${application.codebase}" />
 450     </manifest>
 451     <fileset dir="${outputDir}/">
 452       <exclude name="cache*/**" />
 453       <exclude name="*.jar" />
 454       <exclude name="*.jar.*" />
 455       <exclude name="**/*.jar" />
 456       <exclude name="**/*.jar.*" />
 457     </fileset>
 458   </jar>
 459
 460   <copy toDir="${packageDir}" flatten="true">
 461     <fileset dir="${outputDir}">
 462       <include name="*.jar" />
 463       <include name="**/*.jar" />
 464     </fileset>
 465   </copy>
 466 </target>
 467
 468
 469 <!-- jalopy code reformatter -->
 470 <target name="sourcescrub" depends="init,build">
 471   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 472     <fileset dir="${sourceDir}">
 473       <include name="*.java" />
 474       <include name="**/*.java" />
 475       <include name="**/**/*.java" />
 476     </fileset>
 477   </jalopy>
 478 </target>
 479
 480
 481
 482 <!-- Compile, package and obfuscate Jalview Applet -->
 483 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 484
 485 <target name="compileApplet" depends="init,clean">
 486   <mkdir dir="${outputDir}" />
 487   <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 488                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 489                         excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 490 </target>
 491
 492 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 493   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 494   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 495   <copy todir="${outputDir}/lang">
 496     <fileset dir="${resourceDir}/lang">
 497       <include name="**.*"/>
 498     </fileset>
 499   </copy>
 500   <jar destfile="in.jar" index="true">
 501     <manifest>
 502       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 503       <attribute name="Application-Name" value="JalviewLite" />
 504       <attribute name="Codebase" value="${applet.codebase}" />
 505     </manifest>
 506     <fileset dir="${outputDir}">
 507       <include name="com/**" />
 508       <include name="MCview/**" />
 509       <include name="jalview/**" />
 510       <include name=".build_properties" />
 511       <include name="images/idwidth.gif" />
 512       <include name="images/link.gif" />
 513       <include name="lang/**" />
 514     </fileset>
 515   </jar>
 516 </target>
 517 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 518 </target>
 519 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 520   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 521   <delete file="in.jar" />
 522 </target>
 523 <target name="-obfuscatereally" unless="donotobfuscate">
 524
 525   <path id="obfuscateDeps.path">
 526     <pathelement location="${applet.jre.tools}" />
 527     <pathelement location="appletlib/${jmolJar}" />
 528   </path>
 529   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 530
 531   <proguard>
 532     <injar file="in.jar" />
 533     <outjar file="${jalviewLiteJar}" />
 534     <libraryjar refid="obfuscateDeps.path" />
 535     <dontwarn/>
 536     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 537       <field access="public" />
 538       <method access="public" />
 539       <constructor access="public" />
 540     </keep>
 541     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 542       <field access="public" />
 543       <method access="public" />
 544       <constructor access="public" />
 545     </keep>
 546     <!--      -libraryjars "${obfuscateDeps}"
 547       -injars      in.jar
 548       -outjars     jalviewApplet.jar
 549       -keep public class jalview.bin.JalviewLite
 550        { public * ; } -->
 551   </proguard>
 552   <delete file="in.jar" />
 553 </target>
 554
 555 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 556   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 557   <delete>
 558     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 559       <include name="*.java" />
 560       <include name="descriptors/*.java" />
 561     </fileset>
 562   </delete>
 563   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 564   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 565   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 566   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 567   <!--
 568                 now build the jalview.binding package with the old schema set
 569                 -->
 570   <delete>
 571     <fileset dir="${sourceDir}/jalview/binding/">
 572       <include name="**" />
 573     </fileset>
 574   </delete>
 575   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 576   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 577   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 578 </target>
 579 <target name="sourcedist" description="create jalview source distribution" depends="init">
 580   <delete file="${source.dist.name}" />
 581   <tar destfile="${source.dist.name}" compression="gzip">
 582     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 583       <include name="LICENSE" />
 584       <include name="README" />
 585       <include name="build.xml" />
 586       <include name="jalview-jalopy.xml" />
 587       <include name="JalviewApplet.jpx" />
 588       <include name="JalviewX.jpx" />
 589       <include name="nbbuild.xml"/>
 590       <include name="nbproject/genfiles.properties"/>
 591       <include name="nbproject/project.properties"/>
 592       <include name="nbproject/project.xml"/>
 593       <include name="${sourceDir}/*.java" />
 594       <include name="${sourceDir}/**/*.java" />
 595       <include name="${sourceDir}/**/*.cdr" />
 596       <include name="${libDir}/**/*" />
 597       <include name="${resourceDir}/**/*" />
 598       <include name="${helpDir}/**/*" />
 599       <include name="appletlib/${jmolJar}" />
 600       <exclude name="**/*locales" />
 601       <exclude name="*locales/**" />
 602       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 603       <exclude name="utils/InstallAnywhere/**Build*/**" />
 604       <exclude name="utils/InstallAnywhere/**Build*/**" />
 605       <exclude name="utils/InstallAnywhere/**locale*" />
 606       <exclude name="utils/InstallAnywhere/**locale*/**" />
 607       <include name="${schemaDir}/**/*" />
 608       <include name="utils/**/*" />
 609       <include name="${docDir}/**/*" />
 610       <include name="examples/**/*" />
 611     </tarfileset>
 612   </tar>
 613 </target>
 614 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 615   <copy todir="${packageDir}/examples">
 616     <fileset dir="examples">
 617       <include name="**/*"/>
 618       <include name="javascript/*"/>
 619       <include name="jmol/*"/>
 620     </fileset>
 621     <fileset dir=".">
 622       <include name="${jalviewLiteJar}" />
 623     </fileset>
 624     <fileset dir="appletlib">
 625       <include name="**/*"/>
 626     </fileset>
 627   </copy>
 628   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 629   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 630     <manifest>
 631       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 632       <!--          <attribute name="Permissions" value="sandbox" /> -->
 633       <!--<attribute name="Trusted-Lib" value="true" /> -->
 634       <attribute name="Codebase" value="${applet.codebase}"/>
 635       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 636     </manifest>
 637   </jar>
 638   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 639     <fileset dir="${packageDir}/examples">
 640       <include name="*.jar" />
 641     </fileset>
 642   </signjar>
 643   <presetdef name="ap_applet.jar">
 644     <!-- build a signed applet with 'all-permissions' -
 645                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 646                           JalviewLite+JmolApplet linked sequence/structure fails
 647                           Mixed code warnings are raised
 648                           -->
 649     <jar update="true" index="true">
 650       <manifest>
 651         <attribute name="Application-Name" value="JalviewLite" />
 652         <attribute name="Permissions" value="all-permissions" />
 653         <attribute name="Codebase" value="${applet.codebase}" />
 654         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 655         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 656       </manifest>
 657     </jar>
 658   </presetdef>
 659   <presetdef name="applet.jar">
 660     <!-- build signed applet with sandbox permissions -
 661                           Needs 'param name="permissions' value="sandbox"' in applet tag
 662                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 663                         -->
 664
 665     <jar update="true" index="true">
 666       <manifest>
 667         <attribute name="Application-Name" value="JalviewLite" />
 668         <attribute name="Permissions" value="sandbox" />
 669         <attribute name="Codebase" value="${applet.codebase}" />
 670         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 671         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 672       </manifest>
 673     </jar>
 674   </presetdef>
 675   <presetdef name="tl_applet.jar">
 676     <!-- build signed applet with trusted library/trusted permissions -
 677                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 678                                j1.7_45:
 679                                No mixed code warnings raised
 680                                Jmol/JalviewLite sequence/structure example doesn't link structures
 681                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 682
 683                               -->
 684
 685     <jar update="true" index="true">
 686       <manifest>
 687         <attribute name="Application-Name" value="JalviewLite" />
 688         <attribute name="Permissions" value="all-permissions" />
 689         <attribute name="Codebase" value="${applet.codebase}" />
 690         <attribute name="Trusted-Only" value="true" />
 691         <attribute name="Trusted-Library" value="true" />
 692       </manifest>
 693     </jar>
 694   </presetdef>
 695   <presetdef name="to_applet.jar">
 696     <!-- not fully test variant (yet) -->
 697     <jar update="true" index="true">
 698       <manifest>
 699         <attribute name="Application-Name" value="JalviewLite" />
 700         <attribute name="Permissions" value="all-permissions" />
 701         <attribute name="Codebase" value="${applet.codebase}" />
 702         <attribute name="Trusted-Only" value="true" />
 703       </manifest>
 704     </jar>
 705   </presetdef>
 706   <!-- create differently privileged artefacts -->
 707   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 708   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 709   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 710   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 711   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 712   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 713   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 714   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 715   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 716   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 717   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 718   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 719   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 720   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 721   <!-- finally, create manifest for original jars -->
 722   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 723   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 724
 725   <!-- todo - write examples/downloads for alternate versions of the applet -->
 726   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 727
 728     <fileset dir="${packageDir}/examples">
 729       <exclude name="u_*.jar"/>
 730       <include name="${jalviewLiteJar}" />
 731       <include name="${jmolJar}" />
 732       <include name="to_${jalviewLiteJar}" />
 733       <include name="to_${jmolJar}" />
 734       <include name="tl_${jalviewLiteJar}" />
 735       <include name="tl_${jmolJar}" />
 736       <include name="ap_${jalviewLiteJar}" />
 737       <include name="ap_${jmolJar}" />
 738     </fileset>
 739   </signjar>
 740   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 741   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 742 </target>
 743 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 744   <javadoc destdir="${javadocDir}">
 745     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 746     </packageset>
 747   </javadoc>
 748 </target>
 749 </project>