build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
   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
  90
  91     <!-- Don't change anything below here unless you know what you are doing! -->
  92     <!-- Url path for WebStart in JNLP file -->
  93     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  94     <!-- Webstart Image - looked for in resources/images -->
  95     <property name="WebStartImage" value="JalviewLogo_big.png"/>
  96     <!-- J2SE version needed for webstart launch -->
  97     <property name="j2sev" value="1.6+"/>
  98
  99     <!-- Permissions for running Java applets and applications. -->
 100     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 101     <property name="application.codebase" value="*.jalview.org" />
 102     <!-- and allowing the applet to be deployed from any URL -->
 103     <!-- 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 -->
 104     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 105     <property name="applet.caller-codebase" value="${applet.codebase}" />
 106
 107     <!-- build directory configuration -->
 108     <property name="libDir" value="lib" />
 109     <property name="resourceDir" value="resources" />
 110     <property name="helpDir" value="help" />
 111     <property name="docDir" value="doc" />
 112     <property name="sourceDir" value="src" />
 113     <property name="schemaDir" value="schemas" />
 114     <property name="outputDir" value="classes" />
 115     <property name="packageDir" value="dist" />
 116     <property name="outputJar" value="jalview.jar" />
 117     <!-- Jalview Applet JMol Jar Dependency -->
 118     <property name="jmolJar" value="JmolApplet-12.2.4.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       </fileset>
 151
 152     </path>
 153     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 154     <!-- The Location of the java 1.1.8 jdk -->
 155     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 156                 -->
 157     <property name="java118.home" value="${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/${jmolJar}" />
 172     </path>
 173     <!-- default location for outputting javadoc -->
 174     <property name="javadocDir" value="${packageDir}/javadoc"/>
 175   </target>
 176
 177
 178   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 179   <target name="buildPropertiesFile" depends="init">
 180     <tstamp prefix="build">
 181       <format property="date" pattern="dd MMMM yyyy" />
 182     </tstamp>
 183     <properties file="${outputDir}/.build_properties">
 184       <header>
 185           ---Jalview Build Details---
 186         </header>
 187       <property name="VERSION" value="${JALVIEW_VERSION}" />
 188       <property name="BUILD_DATE" value="${build.date}" />
 189     </properties>
 190   </target>
 191
 192
 193   <target name="clean" depends="init">
 194     <!-- not efficient yet. -->
 195     <delete dir="${outputDir}" includes="*,**/*"/>
 196   </target>
 197
 198   <target name="distclean" depends="init, clean">
 199
 200     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 201     <delete>
 202       <fileset dir=".">
 203         <include name="${outputJar}" />
 204         <include name="#*#" />
 205         <include name="#*.*#" />
 206         <include name="**/#*#" />
 207         <include name="**/#*.*#" />
 208         <include name="*~" />
 209         <include name="*.*~" />
 210         <include name="**/*~" />
 211         <include name="**/*.*~" />
 212       </fileset>
 213     </delete>
 214   </target>
 215
 216   <target name="prepare" depends="init">
 217     <mkdir dir="${outputDir}" />
 218     <copy todir="${outputDir}">
 219       <fileset dir=".">
 220         <include name="${docDir}/**/*.*" />
 221         <include name="${helpDir}/**/*.*" />
 222         <include name="${libDir}/*.jar" />
 223       </fileset>
 224       <fileset dir="${resourceDir}">
 225         <include name="**/*.*" />
 226       </fileset>
 227     </copy>
 228   </target>
 229
 230   <target name="build" depends="prepare">
 231     <!-- not efficient yet. -->
 232     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 233       <exclude name="jalview/*applet*" />
 234       <exclude name="jalview/appletgui/**" />
 235       <exclude name="com/stevesoft/**" />
 236     </javac>
 237   </target>
 238   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 239     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 240       <arg line="html" />
 241     </java>
 242   </target>
 243
 244   <target name="makefulldist" depends="makedist">
 245     <copy todir="${packageDir}">
 246       <fileset dir="${resourceDir}/images">
 247         <include name="${WebStartImage}"/>
 248       </fileset>
 249     </copy>
 250
 251     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 252
 253     <!-- create a dummy jar which will eventually contain the jnlp template -->
 254     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 255       <fileset dir="${packageDir}">
 256         <include name="jalview.jar" />
 257       </fileset>
 258     </jar>
 259
 260     <mkdir dir="${packageDir}/JNLP-INF"/>
 261     <antcall target="writejnlpf">
 262       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 263       <param name="inih" value="*" />
 264       <param name="maxh" value="*"/>
 265     </antcall>
 266
 267     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 268       <fileset dir="${packageDir}">
 269         <include name="JNLP-INF"/>
 270       </fileset>
 271     </jar>
 272
 273     <antcall target="writejnlpf">
 274       <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 275       <param name="inih" value="10M" />
 276       <param name="maxh" value="256M"/>
 277     </antcall>
 278
 279     <antcall target="writejnlpf">
 280       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 281       <param name="inih" value="128M" />
 282       <param name="maxh" value="512M"/>
 283     </antcall>
 284
 285     <antcall target="writejnlpf">
 286       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 287       <param name="inih" value="256M" />
 288       <param name="maxh" value="1024M"/>
 289     </antcall>
 290
 291     <!-- finally, need to postprocess to add in associations at end of 'information' element
 292
 293                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 294
 295                 </xslt>
 296
 297
 298                         -->
 299     <!--
 300                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 301         <association mime-type="application-x/ext-file" extensions="fasta"/>
 302         <association mime-type="application-x/ext-file" extensions="mfa"/>
 303         <association mime-type="application-x/ext-file" extensions="fastq"/>
 304         <association mime-type="application-x/ext-file" extensions="blc"/>
 305         <association mime-type="application-x/ext-file" extensions="msf"/>
 306         <association mime-type="application-x/ext-file" extensions="pfam"/>
 307         <association mime-type="application-x/ext-file" extensions="aln"/>
 308         <association mime-type="application-x/ext-file" extensions="pir"/>
 309         <association mime-type="application-x/ext-file" extensions="amsa"/>
 310         <association mime-type="application-x/ext-file" extensions="stk"/>
 311         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 312     <!-- and sign the jars -->
 313     <!-- the default keystore details might need to be edited here -->
 314     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 315       <fileset dir="${packageDir}">
 316         <include name="*.jar" />
 317       </fileset>
 318     </signjar>
 319   </target>
 320
 321   <target name="runenv" depends="init">
 322     <path id="run.classpath">
 323       <pathelement location="${outputDir}" />
 324       <fileset dir="${outputDir}">
 325         <include name="${libDir}/*.jar" />
 326       </fileset>
 327     </path>
 328     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 329
 330     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 331       </echo>
 332   </target>
 333
 334   <target name="-generatejnlpf">
 335     <presetdef name="jnlpf">
 336       <jnlp codebase="${WebStartLocation}">
 337         <information>
 338           <title>Jalview</title>
 339           <vendor>The Barton Group</vendor>
 340           <homepage href="http://www.jalview.org" />
 341           <description>Jalview Multiple Alignment Editor</description>
 342           <description kind="short">Jalview</description>
 343           <icon href="${WebStartImage}" />
 344           <offline_allowed />
 345         </information>
 346         <resources>
 347           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 348           <fileset dir="${packageDir}">
 349             <include name="jalview.jar" />
 350           </fileset>
 351           <fileset dir="${packageDir}">
 352             <include name="*.jar" />
 353             <include name="*_*.jar" />
 354             <exclude name="jalview.jar" />
 355           </fileset>
 356           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 357         </resources>
 358         <application_desc main_class="jalview.bin.Jalview">
 359         </application_desc>
 360         <security>
 361           <all_permissions />
 362         </security>
 363       </jnlp>
 364     </presetdef>
 365
 366     <jnlpf toFile="${jnlpFile}"/>
 367
 368   </target>
 369
 370   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 371     <echo message="Not adding JNLP File Associations"/>
 372   </target>
 373
 374   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 375     <replace file="${jnlpFile}">
 376       <replacetoken>
 377         <![CDATA[</information>]]></replacetoken>
 378       <replacevalue>
 379         <![CDATA[
 380           <association mime-type="application-x/ext-file" extensions="fa" />
 381         <association mime-type="application-x/ext-file" extensions="fasta" />
 382         <association mime-type="application-x/ext-file" extensions="mfa" />
 383         <association mime-type="application-x/ext-file" extensions="fastq" />
 384         <association mime-type="application-x/ext-file" extensions="blc" />
 385         <association mime-type="application-x/ext-file" extensions="msf" />
 386         <association mime-type="application-x/ext-file" extensions="pfam" />
 387         <association mime-type="application-x/ext-file" extensions="aln"/>
 388         <association mime-type="application-x/ext-file" extensions="pir"/>
 389         <association mime-type="application-x/ext-file" extensions="amsa"/>
 390         <association mime-type="application-x/ext-file" extensions="stk"/>
 391         <association mime-type="application-x/ext-file" extensions="jvp"/>
 392       </information>]]></replacevalue>
 393     </replace>
 394     <echo message="Added file associations to JNLP file"/>
 395     </target>
 396 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 397 </target>
 398
 399 <target name="buildextclients" depends="init">
 400   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 401   <condition property="dontextbuild">
 402     <equals arg1="n" arg2="${doextbuild.response}" />
 403   </condition>
 404   <condition property="dontextbuild">
 405     <equals arg1="N" arg2="${doextbuild.response}" />
 406   </condition>
 407   <fail if="dontextbuild">
 408         Build External Client Code process aborted by user. Jalview source is unchanged.
 409       </fail>
 410   <!-- Currently, this doesn't happen automatically.
 411      1. Run WSDL2Java as below, which generates an ext.vamsas +
 412      vamsas.<datapackages> fileset.
 413      2. refactor ext.vamsas.SpecificserviceWS* to
 414      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 415      3. Update the jalview.ws.*WServices classes to reflect the
 416      interface type, and all locations of this wsdl type that Jalview
 417      might be using.
 418
 419 -->
 420   <path id="axisbuild">
 421     <path refid="build.classpath" />
 422   </path>
 423   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 424   <move todir="./bak">
 425     <fileset dir="${sourceDir}" id="client">
 426       <include name="${wsdl.ClientNS}/*.*" />
 427     </fileset>
 428   </move>
 429
 430   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 431     <mappingSet>
 432       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 433       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 434     </mappingSet>
 435   </axis-wsdl2java>
 436 </target>
 437
 438 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 439   <!-- make the package jar if not already existing -->
 440   <mkdir dir="${packageDir}" />
 441   <!-- clean dir if it already existed -->
 442   <delete>
 443     <fileset dir="${packageDir}">
 444       <include name="*.jar"/>
 445     </fileset>
 446   </delete>
 447   <jar destfile="${packageDir}/${outputJar}" index="true">
 448     <manifest>
 449       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 450       <attribute name="Permissions" value="all-permissions" />
 451       <attribute name="Application-Name" value="Jalview Desktop" />
 452       <attribute name="Codebase" value="${application.codebase}" />
 453     </manifest>
 454     <fileset dir="${outputDir}/">
 455       <exclude name="cache*/**" />
 456       <exclude name="*.jar" />
 457       <exclude name="*.jar.*" />
 458       <exclude name="**/*.jar" />
 459       <exclude name="**/*.jar.*" />
 460     </fileset>
 461   </jar>
 462
 463   <copy toDir="${packageDir}" flatten="true">
 464     <fileset dir="${outputDir}">
 465       <include name="*.jar" />
 466       <include name="**/*.jar" />
 467     </fileset>
 468   </copy>
 469 </target>
 470
 471
 472 <!-- jalopy code reformatter -->
 473 <target name="sourcescrub" depends="init,build">
 474   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 475     <fileset dir="${sourceDir}">
 476       <include name="*.java" />
 477       <include name="**/*.java" />
 478       <include name="**/**/*.java" />
 479     </fileset>
 480   </jalopy>
 481 </target>
 482
 483
 484
 485 <!-- Compile, package and obfuscate Jalview Applet -->
 486 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 487
 488 <target name="compileApplet" depends="init,clean">
 489   <mkdir dir="${outputDir}" />
 490   <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 491                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 492                         excludes="ext/**,MCview/**,org/**,vamsas/**" />
 493 </target>
 494
 495 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 496   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 497   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 498   <copy todir="${outputDir}/lang">
 499     <fileset dir="${resourceDir}/lang">
 500       <include name="**.*"/>
 501     </fileset>
 502   </copy>
 503   <jar destfile="in.jar" index="true">
 504     <manifest>
 505       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 506       <attribute name="Application-Name" value="JalviewLite" />
 507       <attribute name="Codebase" value="${applet.codebase}" />
 508     </manifest>
 509     <fileset dir="${outputDir}">
 510       <include name="com/**" />
 511       <include name="MCview/**" />
 512       <include name="jalview/**" />
 513       <include name=".build_properties" />
 514       <include name="images/idwidth.gif" />
 515       <include name="images/link.gif" />
 516       <include name="lang/**" />
 517     </fileset>
 518   </jar>
 519 </target>
 520 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 521 </target>
 522 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 523   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 524   <delete file="in.jar" />
 525 </target>
 526 <target name="-obfuscatereally" unless="donotobfuscate">
 527
 528   <path id="obfuscateDeps.path">
 529     <pathelement location="${applet.jre.tools}" />
 530     <pathelement location="appletlib/${jmolJar}" />
 531   </path>
 532   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 533
 534   <proguard>
 535     <injar file="in.jar" />
 536     <outjar file="${jalviewLiteJar}" />
 537     <libraryjar refid="obfuscateDeps.path" />
 538     <dontwarn/>
 539     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 540       <field access="public" />
 541       <method access="public" />
 542       <constructor access="public" />
 543     </keep>
 544     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 545       <field access="public" />
 546       <method access="public" />
 547       <constructor access="public" />
 548     </keep>
 549     <!--      -libraryjars "${obfuscateDeps}"
 550       -injars      in.jar
 551       -outjars     jalviewApplet.jar
 552       -keep public class jalview.bin.JalviewLite
 553        { public * ; } -->
 554   </proguard>
 555   <delete file="in.jar" />
 556 </target>
 557
 558 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 559   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 560   <delete>
 561     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 562       <include name="*.java" />
 563       <include name="descriptors/*.java" />
 564     </fileset>
 565   </delete>
 566   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 567   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 568   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 569   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 570   <!--
 571                 now build the jalview.binding package with the old schema set
 572                 -->
 573   <delete>
 574     <fileset dir="${sourceDir}/jalview/binding/">
 575       <include name="**" />
 576     </fileset>
 577   </delete>
 578   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 579   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 580   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 581 </target>
 582 <target name="sourcedist" description="create jalview source distribution" depends="init">
 583   <delete file="${source.dist.name}" />
 584   <tar destfile="${source.dist.name}" compression="gzip">
 585     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 586       <include name="LICENSE" />
 587       <include name="README" />
 588       <include name="build.xml" />
 589       <include name="jalview-jalopy.xml" />
 590       <include name="JalviewApplet.jpx" />
 591       <include name="JalviewX.jpx" />
 592       <include name="nbbuild.xml"/>
 593       <include name="nbproject/genfiles.properties"/>
 594       <include name="nbproject/project.properties"/>
 595       <include name="nbproject/project.xml"/>
 596       <include name="${sourceDir}/*.java" />
 597       <include name="${sourceDir}/**/*.java" />
 598       <include name="${sourceDir}/**/*.cdr" />
 599       <include name="${libDir}/**/*" />
 600       <include name="${resourceDir}/**/*" />
 601       <include name="${helpDir}/**/*" />
 602       <include name="appletlib/${jmolJar}" />
 603       <exclude name="**/*locales" />
 604       <exclude name="*locales/**" />
 605       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 606       <exclude name="utils/InstallAnywhere/**Build*/**" />
 607       <exclude name="utils/InstallAnywhere/**Build*/**" />
 608       <exclude name="utils/InstallAnywhere/**locale*" />
 609       <exclude name="utils/InstallAnywhere/**locale*/**" />
 610       <include name="${schemaDir}/**/*" />
 611       <include name="utils/**/*" />
 612       <include name="${docDir}/**/*" />
 613       <include name="examples/**/*" />
 614     </tarfileset>
 615   </tar>
 616 </target>
 617 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 618   <copy todir="${packageDir}/examples">
 619     <fileset dir="examples">
 620       <include name="**/*"/>
 621       <include name="javascript/*"/>
 622       <include name="jmol/*"/>
 623     </fileset>
 624     <fileset dir=".">
 625       <include name="${jalviewLiteJar}" />
 626     </fileset>
 627     <fileset dir="appletlib">
 628       <include name="**/*"/>
 629     </fileset>
 630   </copy>
 631   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 632   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 633     <manifest>
 634       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 635       <!--          <attribute name="Permissions" value="sandbox" /> -->
 636       <!--<attribute name="Trusted-Lib" value="true" /> -->
 637       <attribute name="Codebase" value="${applet.codebase}"/>
 638       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 639     </manifest>
 640   </jar>
 641   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 642     <fileset dir="${packageDir}/examples">
 643       <include name="*.jar" />
 644     </fileset>
 645   </signjar>
 646   <presetdef name="ap_applet.jar">
 647     <!-- build a signed applet with 'all-permissions' -
 648                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 649                           JalviewLite+JmolApplet linked sequence/structure fails
 650                           Mixed code warnings are raised
 651                           -->
 652     <jar update="true" index="true">
 653       <manifest>
 654         <attribute name="Application-Name" value="JalviewLite" />
 655         <attribute name="Permissions" value="all-permissions" />
 656         <attribute name="Codebase" value="${applet.codebase}" />
 657         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 658         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 659       </manifest>
 660     </jar>
 661   </presetdef>
 662   <presetdef name="applet.jar">
 663     <!-- build signed applet with sandbox permissions -
 664                           Needs 'param name="permissions' value="sandbox"' in applet tag
 665                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 666                         -->
 667
 668     <jar update="true" index="true">
 669       <manifest>
 670         <attribute name="Application-Name" value="JalviewLite" />
 671         <attribute name="Permissions" value="sandbox" />
 672         <attribute name="Codebase" value="${applet.codebase}" />
 673         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 674         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 675       </manifest>
 676     </jar>
 677   </presetdef>
 678   <presetdef name="tl_applet.jar">
 679     <!-- build signed applet with trusted library/trusted permissions -
 680                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 681                                j1.7_45:
 682                                No mixed code warnings raised
 683                                Jmol/JalviewLite sequence/structure example doesn't link structures
 684                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 685
 686                               -->
 687
 688     <jar update="true" index="true">
 689       <manifest>
 690         <attribute name="Application-Name" value="JalviewLite" />
 691         <attribute name="Permissions" value="all-permissions" />
 692         <attribute name="Codebase" value="${applet.codebase}" />
 693         <attribute name="Trusted-Only" value="true" />
 694         <attribute name="Trusted-Library" value="true" />
 695       </manifest>
 696     </jar>
 697   </presetdef>
 698   <presetdef name="to_applet.jar">
 699     <!-- not fully test variant (yet) -->
 700     <jar update="true" index="true">
 701       <manifest>
 702         <attribute name="Application-Name" value="JalviewLite" />
 703         <attribute name="Permissions" value="all-permissions" />
 704         <attribute name="Codebase" value="${applet.codebase}" />
 705         <attribute name="Trusted-Only" value="true" />
 706       </manifest>
 707     </jar>
 708   </presetdef>
 709   <!-- create differently privileged artefacts -->
 710   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 711   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 712   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 713   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 714   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 715   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 716   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 717   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 718   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 719   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 720   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 721   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 722   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 723   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 724   <!-- finally, create manifest for original jars -->
 725   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 726   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 727
 728   <!-- todo - write examples/downloads for alternate versions of the applet -->
 729   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 730
 731     <fileset dir="${packageDir}/examples">
 732       <exclude name="u_*.jar"/>
 733       <include name="${jalviewLiteJar}" />
 734       <include name="${jmolJar}" />
 735       <include name="to_${jalviewLiteJar}" />
 736       <include name="to_${jmolJar}" />
 737       <include name="tl_${jalviewLiteJar}" />
 738       <include name="tl_${jmolJar}" />
 739       <include name="ap_${jalviewLiteJar}" />
 740       <include name="ap_${jmolJar}" />
 741     </fileset>
 742   </signjar>
 743   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 744   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 745 </target>
 746 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 747   <javadoc destdir="${javadocDir}">
 748     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 749     </packageset>
 750   </javadoc>
 751 </target>
 752 </project>