build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <project name="jalviewX" default="usage" basedir=".">
  21   <target name="help" depends="usage" />
  22   <target name="usage">
  23     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  24     <echo message="Targets include:" />
  25     <echo message="usage - default target, displays this message" />
  26     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  27     <echo message="build - compiles all necessary files for Application" />
  28     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  29     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  30     <echo message="              this needs a keystore and key. See docs/building.html for more information." />
  31     <echo message="compileApplet - compiles all necessary files for Applet" />
  32     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  33     <echo message="See docs/building.html and the comments in build file for other targets." />
  34     <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  35     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  36   </target>
  37
  38
  39   <!-- utils is a class path to additional utilities needed for
  40     building docs, jars and webstart stuff -->
  41   <!--
  42         Userdefined build property defaults
  43
  44         wsdl.server list (plus namespace mapping info ???)  - also want
  45                 ... to make this a dynamically generatable property
  46         WebStart Location
  47         Build location - provide a temporary root for speed
  48         jarsigner keystore and info
  49         Jakarta and axis classpath ?
  50         Default argument for starting Jalview (if it exists).
  51
  52 -->
  53
  54   <target name="init">
  55     <path id="axis.classpath">
  56       <!-->
  57       <fileset dir="/usr/local/axis/lib">
  58         <include name="**/*.jar" />
  59       </fileset>
  60       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  61         <include name="**/*.jar"/>
  62         <include name="*.jar"/>
  63       </fileset> -->
  64       </path>
  65
  66     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  67     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  68
  69     <property name="INSTALLATION" value="Source" />
  70
  71     <!-- 2.4 (VAMSAS)" -->
  72     <!-- Include debugging information in javac true or false -->
  73     <property name="javac.debug" value="true" />
  74
  75     <!-- JarSigner Key Store for Webstart Distribution -->
  76     <property name="jalview.keystore" value="./keys/.keystore" />
  77     <!-- Keystore Password -->
  78     <property name="jalview.keystore.pass" value="alignmentisfun" />
  79     <!-- Key Name -->
  80     <property name="jalview.key" value="jalview" />
  81     <!-- Key Password -->
  82     <property name="jalview.key.pass" value="alignmentisfun" />
  83
  84     <!-- Don't change anything below here unless you know what you are doing! -->
  85     <!-- Url path for WebStart in JNLP file -->
  86     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  87     <!-- Webstart Image - looked for in resources/images -->
  88     <property name="WebStartImage" value="JalviewLogo_big.png"/>
  89     <!-- J2SE version needed for webstart launch -->
  90     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  91     <property name="j2sev" value="1.7+"/>
  92
  93     <!-- Permissions for running Java applets and applications. -->
  94     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
  95     <property name="application.codebase" value="*.jalview.org" />
  96     <!-- and allowing the applet to be deployed from any URL -->
  97     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
  98     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
  99     <property name="applet.caller-codebase" value="${applet.codebase}" />
 100
 101     <!-- build directory configuration -->
 102     <property name="libDir" value="lib" />
 103     <property name="resourceDir" value="resources" />
 104     <property name="helpDir" value="help" />
 105     <property name="docDir" value="doc" />
 106     <property name="sourceDir" value="src" />
 107     <property name="schemaDir" value="schemas" />
 108     <property name="outputDir" value="classes" />
 109     <property name="packageDir" value="dist" />
 110     <property name="outputJar" value="jalview.jar" />
 111     <!-- Jalview Applet JMol Jar Dependency -->
 112     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 113     <property name="varnaJar" value="VARNAv3-91.jar" />
 114     <property name="jsoup" value="jsoup-1.8.1.jar" />
 115     <property name="jsonSimple" value="json_simple-1.1.jar" />
 116     <property name="javaJson" value="java-json.jar" />
 117     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 118     <!-- switch to indicate if we should obfuscate jalviewLite -->
 119     <!-- <property name="donotobfuscate" value="true"/> -->
 120     <!-- switch to exclude associations from generated jnlp files -->
 121     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 122
 123     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 124     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 125     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 126     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 127     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 128     <property name="WSInterf" value="MsaWS" />
 129     <property name="wsdl.Namespace" value="vamsas" />
 130     <property name="wsdl.ClientNS" value="ext.vamsas" />
 131     <!-- the class path for building the application -->
 132     <path id="build.classpath">
 133       <fileset dir="utils">
 134         <include name="*.jar" />
 135         <include name="**/*.jar" />
 136       </fileset>
 137       <fileset dir="${libDir}">
 138         <include name="*.jar" />
 139         <include name="**/*.jar" />
 140       </fileset>
 141       <fileset dir="${java.home}/lib">
 142         <include name="plugin.jar"/>
 143       </fileset>
 144       <fileset dir="appletlib">
 145         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 146                                 -->
 147         <include name="${jmolJar}" />
 148         <include name="${varnaJar}" />
 149       </fileset>
 150
 151     </path>
 152     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 153     <!-- The Location of the java 1.1.8 jdk -->
 154     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
 155     <property name="java118.home" value="${java.home}" />
 156     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 157                 -->
 158     <!-- jre for 1.4 version -->
 159     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 160
 161     <!-- the classpath for building the 1.1 applet -->
 162     <path id="jalviewlite.deps">
 163       <fileset dir="${java118.home}">
 164         <include name="lib/classes.zip" />
 165       </fileset>
 166       <fileset dir="${java.home}/lib">
 167         <include name="plugin.jar"/>
 168       </fileset>
 169       <pathelement location="appletlib/${jmolJar}" />
 170       <pathelement location="lib/${varnaJar}" />
 171       <pathelement location="lib/${jsoup}" />
 172       <pathelement location="lib/${jsonSimple}" />
 173       <pathelement location="lib/${javaJson}" />
 174
 175     </path>
 176     <!-- default location for outputting javadoc -->
 177     <property name="javadocDir" value="${packageDir}/javadoc"/>
 178   </target>
 179
 180
 181   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 182   <target name="buildPropertiesFile" depends="init">
 183     <tstamp prefix="build">
 184       <format property="date" pattern="dd MMMM yyyy" />
 185     </tstamp>
 186     <properties file="${outputDir}/.build_properties">
 187       <header>
 188           ---Jalview Build Details---
 189         </header>
 190       <property name="VERSION" value="${JALVIEW_VERSION}" />
 191       <property name="INSTALLATION" value="${INSTALLATION}" />
 192       <property name="BUILD_DATE" value="${build.date}" />
 193     </properties>
 194   </target>
 195
 196
 197   <target name="clean" depends="init">
 198     <!-- not efficient yet. -->
 199     <delete dir="${outputDir}" includes="*,**/*"/>
 200   </target>
 201
 202   <target name="distclean" depends="init, clean">
 203
 204     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 205     <delete>
 206       <fileset dir=".">
 207         <include name="${outputJar}" />
 208         <include name="#*#" />
 209         <include name="#*.*#" />
 210         <include name="**/#*#" />
 211         <include name="**/#*.*#" />
 212         <include name="*~" />
 213         <include name="*.*~" />
 214         <include name="**/*~" />
 215         <include name="**/*.*~" />
 216       </fileset>
 217     </delete>
 218   </target>
 219
 220   <target name="prepare" depends="init">
 221     <mkdir dir="${outputDir}" />
 222     <copy todir="${outputDir}">
 223       <fileset dir=".">
 224         <include name="${docDir}/**/*.*" />
 225         <include name="${helpDir}/**/*.*" />
 226         <include name="${libDir}/*.jar" />
 227       </fileset>
 228       <fileset dir="${resourceDir}">
 229         <include name="**/*.*" />
 230       </fileset>
 231     </copy>
 232   </target>
 233
 234   <target name="build" depends="prepare">
 235     <!-- not efficient yet. -->
 236     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 237       <exclude name="jalview/*applet*" />
 238       <exclude name="jalview/appletgui/**" />
 239       <exclude name="com/stevesoft/**" />
 240     </javac>
 241   </target>
 242   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 243     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 244       <arg line="html" />
 245     </java>
 246   </target>
 247
 248   <target name="makefulldist" depends="makedist">
 249     <copy todir="${packageDir}">
 250       <fileset dir="${resourceDir}/images">
 251         <include name="${WebStartImage}"/>
 252       </fileset>
 253     </copy>
 254
 255     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 256
 257     <!-- create a dummy jar which will eventually contain the jnlp template -->
 258     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 259       <fileset dir="${packageDir}">
 260         <include name="jalview.jar" />
 261       </fileset>
 262     </jar>
 263
 264     <mkdir dir="${packageDir}/JNLP-INF"/>
 265     <antcall target="writejnlpf">
 266       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 267       <param name="inih" value="*" />
 268       <param name="maxh" value="*"/>
 269     </antcall>
 270
 271     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 272       <fileset dir="${packageDir}">
 273         <include name="JNLP-INF"/>
 274       </fileset>
 275     </jar>
 276
 277     <antcall target="writejnlpf">
 278       <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 279       <param name="inih" value="10M" />
 280       <param name="maxh" value="256M"/>
 281     </antcall>
 282
 283     <antcall target="writejnlpf">
 284       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 285       <param name="inih" value="128M" />
 286       <param name="maxh" value="512M"/>
 287     </antcall>
 288
 289     <antcall target="writejnlpf">
 290       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 291       <param name="inih" value="256M" />
 292       <param name="maxh" value="1024M"/>
 293     </antcall>
 294
 295     <!-- finally, need to postprocess to add in associations at end of 'information' element
 296
 297                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 298
 299                 </xslt>
 300
 301
 302                         -->
 303     <!--
 304                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 305         <association mime-type="application-x/ext-file" extensions="fasta"/>
 306         <association mime-type="application-x/ext-file" extensions="mfa"/>
 307         <association mime-type="application-x/ext-file" extensions="fastq"/>
 308         <association mime-type="application-x/ext-file" extensions="blc"/>
 309         <association mime-type="application-x/ext-file" extensions="msf"/>
 310         <association mime-type="application-x/ext-file" extensions="pfam"/>
 311         <association mime-type="application-x/ext-file" extensions="aln"/>
 312         <association mime-type="application-x/ext-file" extensions="pir"/>
 313         <association mime-type="application-x/ext-file" extensions="amsa"/>
 314         <association mime-type="application-x/ext-file" extensions="stk"/>
 315         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 316     <!-- and sign the jars -->
 317     <!-- the default keystore details might need to be edited here -->
 318     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 319       <fileset dir="${packageDir}">
 320         <include name="*.jar" />
 321       </fileset>
 322     </signjar>
 323   </target>
 324
 325   <target name="runenv" depends="init">
 326     <path id="run.classpath">
 327       <pathelement location="${outputDir}" />
 328       <fileset dir="${outputDir}">
 329         <include name="${libDir}/*.jar" />
 330       </fileset>
 331     </path>
 332     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 333
 334     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 335       </echo>
 336   </target>
 337
 338   <target name="-generatejnlpf">
 339     <presetdef name="jnlpf">
 340       <jnlp codebase="${WebStartLocation}">
 341         <information>
 342           <title>Jalview</title>
 343           <vendor>The Barton Group</vendor>
 344           <homepage href="http://www.jalview.org" />
 345           <description>Jalview Multiple Alignment Editor</description>
 346           <description kind="short">Jalview</description>
 347           <icon href="${WebStartImage}" />
 348           <offline_allowed />
 349         </information>
 350         <resources>
 351           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 352           <fileset dir="${packageDir}">
 353             <include name="jalview.jar" />
 354           </fileset>
 355           <fileset dir="${packageDir}">
 356             <include name="*.jar" />
 357             <include name="*_*.jar" />
 358             <exclude name="jalview.jar" />
 359                 <exclude name="*jnilib.jar"/>
 360           </fileset>
 361         </resources>
 362         <resources os="Mac OS X">
 363           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 364                 <fileset dir="${packageDir}">
 365                         <include name="*quaqua*.jnilib.jar"/>
 366                 </fileset>
 367         </resources>
 368
 369         <application_desc main_class="jalview.bin.Jalview">
 370         </application_desc>
 371         <security>
 372           <all_permissions />
 373         </security>
 374       </jnlp>
 375     </presetdef>
 376
 377     <jnlpf toFile="${jnlpFile}"/>
 378
 379   </target>
 380
 381   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 382     <echo message="Not adding JNLP File Associations"/>
 383   </target>
 384
 385   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 386     <replace file="${jnlpFile}">
 387       <replacetoken>
 388         <![CDATA[</information>]]></replacetoken>
 389       <replacevalue>
 390         <![CDATA[
 391           <association mime-type="application-x/ext-file" extensions="fa" />
 392         <association mime-type="application-x/ext-file" extensions="fasta" />
 393         <association mime-type="application-x/ext-file" extensions="mfa" />
 394         <association mime-type="application-x/ext-file" extensions="fastq" />
 395         <association mime-type="application-x/ext-file" extensions="blc" />
 396         <association mime-type="application-x/ext-file" extensions="msf" />
 397         <association mime-type="application-x/ext-file" extensions="pfam" />
 398         <association mime-type="application-x/ext-file" extensions="aln"/>
 399         <association mime-type="application-x/ext-file" extensions="pir"/>
 400         <association mime-type="application-x/ext-file" extensions="amsa"/>
 401         <association mime-type="application-x/ext-file" extensions="stk"/>
 402         <association mime-type="application-x/ext-file" extensions="jvp"/>
 403       </information>]]></replacevalue>
 404   </replace>
 405   <echo message="Added file associations to JNLP file"/>
 406 </target>
 407 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 408 </target>
 409
 410 <target name="buildextclients" depends="init">
 411   <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" />
 412   <condition property="dontextbuild">
 413     <equals arg1="n" arg2="${doextbuild.response}" />
 414   </condition>
 415   <condition property="dontextbuild">
 416     <equals arg1="N" arg2="${doextbuild.response}" />
 417   </condition>
 418   <fail if="dontextbuild">
 419         Build External Client Code process aborted by user. Jalview source is unchanged.
 420       </fail>
 421   <!-- Currently, this doesn't happen automatically.
 422      1. Run WSDL2Java as below, which generates an ext.vamsas +
 423      vamsas.<datapackages> fileset.
 424      2. refactor ext.vamsas.SpecificserviceWS* to
 425      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 426      3. Update the jalview.ws.*WServices classes to reflect the
 427      interface type, and all locations of this wsdl type that Jalview
 428      might be using.
 429
 430 -->
 431   <path id="axisbuild">
 432     <path refid="build.classpath" />
 433   </path>
 434   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 435   <move todir="./bak">
 436     <fileset dir="${sourceDir}" id="client">
 437       <include name="${wsdl.ClientNS}/*.*" />
 438     </fileset>
 439   </move>
 440
 441   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 442     <mappingSet>
 443       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 444       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 445     </mappingSet>
 446   </axis-wsdl2java>
 447 </target>
 448
 449 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 450   <!-- make the package jar if not already existing -->
 451   <mkdir dir="${packageDir}" />
 452   <!-- clean dir if it already existed -->
 453   <delete>
 454     <fileset dir="${packageDir}">
 455       <include name="*.jar"/>
 456     </fileset>
 457   </delete>
 458   <jar destfile="${packageDir}/${outputJar}" index="true">
 459     <manifest>
 460       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 461       <attribute name="Permissions" value="all-permissions" />
 462       <attribute name="Application-Name" value="Jalview Desktop" />
 463       <attribute name="Codebase" value="${application.codebase}" />
 464     </manifest>
 465     <fileset dir="${outputDir}/">
 466       <exclude name="cache*/**" />
 467       <exclude name="*.jar" />
 468       <exclude name="*.jar.*" />
 469       <exclude name="**/*.jar" />
 470       <exclude name="**/*.jar.*" />
 471     </fileset>
 472   </jar>
 473
 474   <copy toDir="${packageDir}" flatten="true">
 475     <fileset dir="${outputDir}">
 476       <include name="*.jar" />
 477       <include name="**/*.jar" />
 478     </fileset>
 479   </copy>
 480 </target>
 481
 482
 483 <!-- jalopy code reformatter -->
 484 <target name="sourcescrub" depends="init,build">
 485   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 486     <fileset dir="${sourceDir}">
 487       <include name="*.java" />
 488       <include name="**/*.java" />
 489       <include name="**/**/*.java" />
 490     </fileset>
 491   </jalopy>
 492 </target>
 493
 494
 495
 496 <!-- Compile, package and obfuscate Jalview Applet -->
 497 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 498
 499 <target name="compileApplet" depends="init,clean">
 500   <mkdir dir="${outputDir}" />
 501   <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 502                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 503                         excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 504 </target>
 505
 506 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 507   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 508   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 509   <copy todir="${outputDir}/lang">
 510     <fileset dir="${resourceDir}/lang">
 511       <include name="**.*"/>
 512     </fileset>
 513   </copy>
 514   <jar destfile="in.jar" index="true">
 515     <manifest>
 516       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 517       <attribute name="Application-Name" value="JalviewLite" />
 518       <attribute name="Codebase" value="${applet.codebase}" />
 519     </manifest>
 520     <fileset dir="${outputDir}">
 521       <include name="com/**" />
 522       <include name="MCview/**" />
 523       <include name="jalview/**" />
 524       <include name=".build_properties" />
 525       <include name="images/idwidth.gif" />
 526       <include name="images/link.gif" />
 527       <include name="lang/**" />
 528     </fileset>
 529   </jar>
 530 </target>
 531 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 532 </target>
 533 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 534   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 535   <delete file="in.jar" />
 536 </target>
 537 <target name="-obfuscatereally" unless="donotobfuscate">
 538
 539   <path id="obfuscateDeps.path">
 540     <pathelement location="${applet.jre.tools}" />
 541     <pathelement location="appletlib/${jmolJar}" />
 542     <pathelement location="appletlib/${jsonSimple}" />
 543     <pathelement location="appletlib/${javaJson}" />
 544   </path>
 545   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 546
 547   <proguard>
 548     <injar file="in.jar" />
 549     <outjar file="${jalviewLiteJar}" />
 550     <libraryjar refid="obfuscateDeps.path" />
 551     <dontwarn/>
 552     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 553       <field access="public" />
 554       <method access="public" />
 555       <constructor access="public" />
 556     </keep>
 557     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 558       <field access="public" />
 559       <method access="public" />
 560       <constructor access="public" />
 561     </keep>
 562     <!--      -libraryjars "${obfuscateDeps}"
 563       -injars      in.jar
 564       -outjars     jalviewApplet.jar
 565       -keep public class jalview.bin.JalviewLite
 566        { public * ; } -->
 567   </proguard>
 568   <delete file="in.jar" />
 569 </target>
 570
 571 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 572   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 573   <delete>
 574     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 575       <include name="*.java" />
 576       <include name="descriptors/*.java" />
 577     </fileset>
 578   </delete>
 579   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 580   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 581   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 582   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 583   <!--
 584                 now build the jalview.binding package with the old schema set
 585                 -->
 586   <delete>
 587     <fileset dir="${sourceDir}/jalview/binding/">
 588       <include name="**" />
 589     </fileset>
 590   </delete>
 591   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 592   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 593   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 594 </target>
 595 <target name="sourcedist" description="create jalview source distribution" depends="init">
 596   <delete file="${source.dist.name}" />
 597   <tar destfile="${source.dist.name}" compression="gzip">
 598     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 599       <include name="LICENSE" />
 600       <include name="README" />
 601       <include name="build.xml" />
 602       <include name="jalview-jalopy.xml" />
 603       <include name="JalviewApplet.jpx" />
 604       <include name="JalviewX.jpx" />
 605       <include name="nbbuild.xml"/>
 606       <include name="nbproject/genfiles.properties"/>
 607       <include name="nbproject/project.properties"/>
 608       <include name="nbproject/project.xml"/>
 609       <include name="${sourceDir}/*.java" />
 610       <include name="${sourceDir}/**/*.java" />
 611       <include name="${sourceDir}/**/*.cdr" />
 612       <include name="${libDir}/**/*" />
 613       <include name="${resourceDir}/**/*" />
 614       <include name="${helpDir}/**/*" />
 615       <include name="appletlib/${jmolJar}" />
 616       <exclude name="**/*locales" />
 617       <exclude name="*locales/**" />
 618       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 619       <exclude name="utils/InstallAnywhere/**Build*/**" />
 620       <exclude name="utils/InstallAnywhere/**Build*/**" />
 621       <exclude name="utils/InstallAnywhere/**locale*" />
 622       <exclude name="utils/InstallAnywhere/**locale*/**" />
 623       <include name="${schemaDir}/**/*" />
 624       <include name="utils/**/*" />
 625       <include name="${docDir}/**/*" />
 626       <include name="examples/**/*" />
 627     </tarfileset>
 628   </tar>
 629 </target>
 630 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 631   <copy todir="${packageDir}/examples">
 632     <fileset dir="examples">
 633       <include name="**/*"/>
 634       <include name="javascript/*"/>
 635       <include name="jmol/*"/>
 636     </fileset>
 637     <fileset dir=".">
 638       <include name="${jalviewLiteJar}" />
 639     </fileset>
 640     <fileset dir="appletlib">
 641       <include name="**/*"/>
 642     </fileset>
 643   </copy>
 644   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 645   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
 646   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
 647   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 648     <manifest>
 649       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 650       <!--          <attribute name="Permissions" value="sandbox" /> -->
 651       <!--<attribute name="Trusted-Lib" value="true" /> -->
 652       <attribute name="Codebase" value="${applet.codebase}"/>
 653       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 654     </manifest>
 655   </jar>
 656   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 657     <fileset dir="${packageDir}/examples">
 658       <include name="*.jar" />
 659     </fileset>
 660   </signjar>
 661   <presetdef name="ap_applet.jar">
 662     <!-- build a signed applet with 'all-permissions' -
 663                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 664                           JalviewLite+JmolApplet linked sequence/structure fails
 665                           Mixed code warnings are raised
 666                           -->
 667     <jar update="true" index="true">
 668       <manifest>
 669         <attribute name="Application-Name" value="JalviewLite" />
 670         <attribute name="Permissions" value="all-permissions" />
 671         <attribute name="Codebase" value="${applet.codebase}" />
 672         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 673         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 674       </manifest>
 675     </jar>
 676   </presetdef>
 677   <presetdef name="applet.jar">
 678     <!-- build signed applet with sandbox permissions -
 679                           Needs 'param name="permissions' value="sandbox"' in applet tag
 680                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 681                         -->
 682
 683     <jar update="true" index="true">
 684       <manifest>
 685         <attribute name="Application-Name" value="JalviewLite" />
 686         <attribute name="Permissions" value="sandbox" />
 687         <attribute name="Codebase" value="${applet.codebase}" />
 688         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 689         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 690       </manifest>
 691     </jar>
 692   </presetdef>
 693   <presetdef name="tl_applet.jar">
 694     <!-- build signed applet with trusted library/trusted permissions -
 695                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 696                                j1.7_45:
 697                                No mixed code warnings raised
 698                                Jmol/JalviewLite sequence/structure example doesn't link structures
 699                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 700
 701                               -->
 702
 703     <jar update="true" index="true">
 704       <manifest>
 705         <attribute name="Application-Name" value="JalviewLite" />
 706         <attribute name="Permissions" value="all-permissions" />
 707         <attribute name="Codebase" value="${applet.codebase}" />
 708         <attribute name="Trusted-Only" value="true" />
 709         <attribute name="Trusted-Library" value="true" />
 710       </manifest>
 711     </jar>
 712   </presetdef>
 713   <presetdef name="to_applet.jar">
 714     <!-- not fully test variant (yet) -->
 715     <jar update="true" index="true">
 716       <manifest>
 717         <attribute name="Application-Name" value="JalviewLite" />
 718         <attribute name="Permissions" value="all-permissions" />
 719         <attribute name="Codebase" value="${applet.codebase}" />
 720         <attribute name="Trusted-Only" value="true" />
 721       </manifest>
 722     </jar>
 723   </presetdef>
 724   <!-- create differently privileged artefacts -->
 725   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 726   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 727   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
 728   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
 729   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 730   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 731   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
 732   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
 733   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 734   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 735   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 736   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 737   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 738   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 739   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 740   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 741   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 742   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 743   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 744   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 745   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 746   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 747   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 748   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 749   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 750   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 751   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 752   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 753   <!-- finally, create manifest for original jars -->
 754   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 755   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 756   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 757   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 758
 759   <!-- todo - write examples/downloads for alternate versions of the applet -->
 760   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 761
 762     <fileset dir="${packageDir}/examples">
 763       <exclude name="u_*.jar"/>
 764       <include name="${jalviewLiteJar}" />
 765       <include name="${jmolJar}" />
 766       <include name="${javaJson}" />
 767       <include name="${jsonSimple}" />
 768       <include name="to_${jalviewLiteJar}" />
 769       <include name="to_${jmolJar}" />
 770       <include name="to_${javaJson}" />
 771       <include name="to_${jsonSimple}" />
 772       <include name="tl_${jalviewLiteJar}" />
 773       <include name="tl_${jmolJar}" />
 774       <include name="tl_${javaJson}" />
 775       <include name="tl_${jsonSimple}" />
 776       <include name="ap_${jalviewLiteJar}" />
 777       <include name="ap_${jmolJar}" />
 778       <include name="ap_${javaJson}" />
 779       <include name="ap_${jsonSimple}" />
 780     </fileset>
 781   </signjar>
 782   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 783   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 784         <!-- finally, replace any launchApp servlet tags with a version specification -->
 785         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 786                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
 787                 <fileset dir="${packageDir}/examples">
 788                         <include name="**/*.html"/>
 789                 </fileset>
 790         </replace>
 791         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 792                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
 793                 <fileset dir="${packageDir}/examples">
 794                         <include name="**/*.html"/>
 795                 </fileset>
 796         </replace>
 797
 798 </target>
 799 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 800   <javadoc destdir="${javadocDir}">
 801     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 802     </packageset>
 803   </javadoc>
 804 </target>
 805 </project>