build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   4  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
   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 -->
  19 <project name="jalviewX" default="usage" basedir=".">
  20   <!-- we use jalopy to format our sources -->
  21   <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
  22     <classpath>
  23       <fileset dir="utils/jalopy/lib">
  24         <include name="*.jar" />
  25       </fileset>
  26     </classpath>
  27   </taskdef>
  28
  29   <target name="help" depends="usage" />
  30   <target name="usage">
  31     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  32     <echo message="Targets include:" />
  33     <echo message="usage - default target, displays this message" />
  34     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  35     <echo message="build - compiles all necessary files for Application" />
  36     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  37     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  38     <echo message="              this needs a keystore and key. See docs/building.html for more information." />
  39     <echo message="compileApplet - compiles all necessary files for Applet" />
  40     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  41     <echo message="See docs/building.html and the comments in build file for other targets." />
  42     <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  43     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  44   </target>
  45
  46
  47   <!-- utils is a class path to additional utilities needed for
  48     building docs, jars and webstart stuff -->
  49   <!--
  50         Userdefined build property defaults
  51
  52         wsdl.server list (plus namespace mapping info ???)  - also want
  53                 ... to make this a dynamically generatable property
  54         WebStart Location
  55         Build location - provide a temporary root for speed
  56         jarsigner keystore and info
  57         Jakarta and axis classpath ?
  58         Default argument for starting Jalview (if it exists).
  59
  60 -->
  61
  62   <target name="init">
  63     <path id="axis.classpath">
  64       <!-->
  65       <fileset dir="/usr/local/axis/lib">
  66         <include name="**/*.jar" />
  67       </fileset>
  68       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  69         <include name="**/*.jar"/>
  70         <include name="*.jar"/>
  71       </fileset> -->
  72       </path>
  73     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  74     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  75     <!-- 2.4 (VAMSAS)" -->
  76     <!-- Include debugging information in javac true or false -->
  77     <property name="javac.debug" value="true" />
  78
  79     <!-- JarSigner Key Store for Webstart Distribution -->
  80     <property name="jalview.keystore" value="./keys/.keystore" />
  81     <!-- Keystore Password -->
  82     <property name="jalview.keystore.pass" value="alignmentisfun" />
  83     <!-- Key Name -->
  84     <property name="jalview.key" value="jalview" />
  85     <!-- Key Password -->
  86     <property name="jalview.key.pass" value="alignmentisfun" />
  87
  88
  89
  90     <!-- Don't change anything below here unless you know what you are doing! -->
  91     <!-- Url path for WebStart in JNLP file -->
  92     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  93     <!-- Webstart Image - looked for in resources/images -->
  94     <property name="WebStartImage" value="JalviewLogo_big.png" />
  95     <!-- J2SE version needed for webstart launch -->
  96     <property name="j2sev" value="1.6+" />
  97
  98     <!-- Permissions for running Java applets and applications. -->
  99     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 100     <property name="application.codebase" value="*.jalview.org" />
 101     <!-- and allowing the applet to be deployed from any URL -->
 102     <property name="applet.codebase" value="*" />
 103     <property name="applet.caller-codebase" value="${applet.codebase}" />
 104
 105     <!-- build directory configuration -->
 106     <property name="libDir" value="lib" />
 107     <property name="resourceDir" value="resources" />
 108     <property name="helpDir" value="help" />
 109     <property name="docDir" value="doc" />
 110     <property name="sourceDir" value="src" />
 111     <property name="schemaDir" value="schemas" />
 112     <property name="outputDir" value="classes" />
 113     <property name="packageDir" value="dist" />
 114     <property name="outputJar" value="jalview.jar" />
 115     <!-- Jalview Applet JMol Jar Dependency -->
 116     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 117     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 118     <!-- switch to indicate if we should obfuscate jalviewLite -->
 119     <!--<property name="donotobfuscate" value="true"/> -->
 120
 121     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 122     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 123     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 124     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 125     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 126     <property name="WSInterf" value="MsaWS" />
 127     <property name="wsdl.Namespace" value="vamsas" />
 128     <property name="wsdl.ClientNS" value="ext.vamsas" />
 129     <!-- the class path for building the application -->
 130     <path id="build.classpath">
 131       <fileset dir="utils">
 132         <include name="*.jar" />
 133         <include name="**/*.jar" />
 134       </fileset>
 135       <fileset dir="${libDir}">
 136         <include name="*.jar" />
 137         <include name="**/*.jar" />
 138       </fileset>
 139       <fileset dir="${java.home}/lib">
 140         <include name="plugin.jar" />
 141       </fileset>
 142       <fileset dir="appletlib">
 143         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 144                                 -->
 145         <include name="${jmolJar}" />
 146       </fileset>
 147
 148     </path>
 149     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 150     <!-- The Location of the java 1.1.8 jdk -->
 151     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 152                 -->
 153     <property name="java118.home" value="${java.home}" />
 154     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 155                 -->
 156     <!-- jre for 1.4 version -->
 157     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
 158
 159     <!-- the classpath for building the 1.1 applet -->
 160     <path id="jalviewlite.deps">
 161       <fileset dir="${java118.home}">
 162         <include name="lib/classes.zip" />
 163       </fileset>
 164       <fileset dir="${java.home}/lib">
 165         <include name="plugin.jar" />
 166       </fileset>
 167       <pathelement location="appletlib/${jmolJar}" />
 168     </path>
 169     <!-- default location for outputting javadoc -->
 170     <property name="javadocDir" value="${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="BUILD_DATE" value="${build.date}" />
 185     </properties>
 186   </target>
 187
 188
 189   <target name="clean" depends="init">
 190     <!-- not efficient yet. -->
 191     <delete dir="${outputDir}" includes="*,**/*" />
 192   </target>
 193
 194   <target name="distclean" depends="init, clean">
 195
 196     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 197     <delete>
 198       <fileset dir=".">
 199         <include name="${outputJar}" />
 200         <include name="#*#" />
 201         <include name="#*.*#" />
 202         <include name="**/#*#" />
 203         <include name="**/#*.*#" />
 204         <include name="*~" />
 205         <include name="*.*~" />
 206         <include name="**/*~" />
 207         <include name="**/*.*~" />
 208       </fileset>
 209     </delete>
 210   </target>
 211
 212   <target name="prepare" depends="init">
 213     <mkdir dir="${outputDir}" />
 214     <copy todir="${outputDir}">
 215       <fileset dir=".">
 216         <include name="${docDir}/**/*.*" />
 217         <include name="${helpDir}/**/*.*" />
 218         <include name="${libDir}/*.jar" />
 219       </fileset>
 220       <fileset dir="${resourceDir}">
 221         <include name="**/*.*" />
 222       </fileset>
 223     </copy>
 224   </target>
 225
 226   <target name="build" depends="prepare">
 227     <!-- not efficient yet. -->
 228     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 229       <exclude name="jalview/*applet*" />
 230       <exclude name="jalview/appletgui/**" />
 231       <exclude name="com/stevesoft/**" />
 232     </javac>
 233   </target>
 234   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 235     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 236       <arg line="html" />
 237     </java>
 238   </target>
 239
 240   <target name="makefulldist" depends="makedist">
 241
 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 ${run.classpath} jalview.bin.Jalview
 328       </echo>
 329   </target>
 330   <target name="writejnlpf">
 331         <presetdef name="jnlpf">
 332             <jnlp codebase="${WebStartLocation}">
 333               <information>
 334                 <title>Jalview</title>
 335                 <vendor>The Barton Group</vendor>
 336                 <homepage href="http://www.jalview.org" />
 337                 <description>Jalview Multiple Alignment Editor</description>
 338                 <description kind="short">Jalview</description>
 339                 <icon href="${WebStartImage}" />
 340                 <offline_allowed />
 341               </information>
 342               <resources>
 343                 <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 344                 <fileset dir="${packageDir}">
 345                   <include name="jalview.jar" />
 346                 </fileset>
 347                 <fileset dir="${packageDir}">
 348                   <include name="*.jar" />
 349                   <include name="*_*.jar" />
 350                   <exclude name="jalview.jar" />
 351                 </fileset>
 352                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 353               </resources>
 354               <application_desc main_class="jalview.bin.Jalview">
 355               </application_desc>
 356               <security>
 357                 <all_permissions />
 358               </security>
 359             </jnlp>
 360             </presetdef>
 361
 362             <jnlpf toFile="${jnlpFile}"/>
 363   </target>
 364   <target name="buildextclients" depends="init">
 365     <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" />
 366     <condition property="dontextbuild">
 367       <equals arg1="n" arg2="${doextbuild.response}" />
 368     </condition>
 369     <condition property="dontextbuild">
 370       <equals arg1="N" arg2="${doextbuild.response}" />
 371     </condition>
 372     <fail if="dontextbuild">
 373         Build External Client Code process aborted by user. Jalview source is unchanged.
 374       </fail>
 375     <!-- Currently, this doesn't happen automatically.
 376      1. Run WSDL2Java as below, which generates an ext.vamsas +
 377      vamsas.<datapackages> fileset.
 378      2. refactor ext.vamsas.SpecificserviceWS* to
 379      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 380      3. Update the jalview.ws.*WServices classes to reflect the
 381      interface type, and all locations of this wsdl type that Jalview
 382      might be using.
 383
 384 -->
 385     <path id="axisbuild">
 386       <path refid="build.classpath" />
 387     </path>
 388     <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 389     <move todir="./bak">
 390       <fileset dir="${sourceDir}" id="client">
 391         <include name="${wsdl.ClientNS}/*.*" />
 392       </fileset>
 393     </move>
 394
 395     <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 396       <mappingSet>
 397         <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 398         <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 399       </mappingSet>
 400     </axis-wsdl2java>
 401   </target>
 402
 403   <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 404     <!-- make the package jar if not already existing -->
 405     <mkdir dir="${packageDir}" />
 406     <!-- clean dir if it already existed -->
 407     <delete>
 408       <fileset dir="${packageDir}">
 409         <include name="*.jar" />
 410       </fileset>
 411     </delete>
 412     <jar destfile="${packageDir}/${outputJar}" index="true">
 413       <manifest>
 414         <attribute name="Main-Class" value="jalview.bin.Jalview" />
 415         <attribute name="Permissions" value="all-permissions" />
 416         <attribute name="Application-Name" value="Jalview Desktop" />
 417         <attribute name="Codebase" value="${application.codebase}" />
 418       </manifest>
 419       <fileset dir="${outputDir}/">
 420         <exclude name="cache*/**" />
 421         <exclude name="*.jar" />
 422         <exclude name="*.jar.*" />
 423         <exclude name="**/*.jar" />
 424         <exclude name="**/*.jar.*" />
 425       </fileset>
 426     </jar>
 427
 428     <copy toDir="${packageDir}" flatten="true">
 429       <fileset dir="${outputDir}">
 430         <include name="*.jar" />
 431         <include name="**/*.jar" />
 432       </fileset>
 433     </copy>
 434   </target>
 435
 436
 437   <!-- jalopy code reformatter -->
 438   <target name="sourcescrub" depends="init,build">
 439     <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 440       <fileset dir="${sourceDir}">
 441         <include name="*.java" />
 442         <include name="**/*.java" />
 443         <include name="**/**/*.java" />
 444       </fileset>
 445     </jalopy>
 446   </target>
 447
 448
 449
 450   <!-- Compile, package and obfuscate Jalview Applet -->
 451   <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 452
 453   <target name="compileApplet" depends="init,clean">
 454     <mkdir dir="${outputDir}" />
 455     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,MCview/**,org/**,vamsas/**" />
 456   </target>
 457
 458   <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 459     <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 460     <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 461     <jar destfile="in.jar" index="true">
 462       <manifest>
 463         <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 464         <attribute name="Application-Name" value="JalviewLite" />
 465         <attribute name="Codebase" value="${applet.codebase}" />
 466       </manifest>
 467       <fileset dir="${outputDir}">
 468         <include name="com/**" />
 469         <include name="MCview/**" />
 470         <include name="jalview/**" />
 471         <include name=".build_properties" />
 472         <include name="images/idwidth.gif" />
 473         <include name="images/link.gif" />
 474       </fileset>
 475     </jar>
 476   </target>
 477   <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 478   </target>
 479   <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 480     <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 481     <delete file="in.jar" />
 482   </target>
 483   <target name="-obfuscatereally" unless="donotobfuscate">
 484
 485     <path id="obfuscateDeps.path">
 486       <pathelement location="${applet.jre.tools}" />
 487       <pathelement location="appletlib/${jmolJar}" />
 488     </path>
 489     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 490
 491     <proguard>
 492       <injar file="in.jar" />
 493       <outjar file="${jalviewLiteJar}" />
 494       <libraryjar refid="obfuscateDeps.path" />
 495       <dontwarn />
 496       <keep access="public" type="class" name="jalview.bin.JalviewLite">
 497         <field access="public" />
 498         <method access="public" />
 499         <constructor access="public" />
 500       </keep>
 501       <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 502         <field access="public" />
 503         <method access="public" />
 504         <constructor access="public" />
 505       </keep>
 506       <!--      -libraryjars "${obfuscateDeps}"
 507       -injars      in.jar
 508       -outjars     jalviewApplet.jar
 509       -keep public class jalview.bin.JalviewLite
 510        { public * ; } -->
 511     </proguard>
 512     <delete file="in.jar" />
 513   </target>
 514
 515   <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 516     <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 517     <delete>
 518       <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 519         <include name="*.java" />
 520         <include name="descriptors/*.java" />
 521       </fileset>
 522     </delete>
 523     <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 524     <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 525     <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 526     <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 527     <!--
 528                 now build the jalview.binding package with the old schema set
 529                 -->
 530     <delete>
 531       <fileset dir="${sourceDir}/jalview/binding/">
 532         <include name="**" />
 533       </fileset>
 534     </delete>
 535     <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 536     <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 537     <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 538   </target>
 539   <target name="sourcedist" description="create jalview source distribution" depends="init">
 540     <delete file="${source.dist.name}" />
 541     <tar destfile="${source.dist.name}" compression="gzip">
 542       <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 543         <include name="LICENSE" />
 544         <include name="README" />
 545         <include name="build.xml" />
 546         <include name="jalview-jalopy.xml" />
 547         <include name="JalviewApplet.jpx" />
 548         <include name="JalviewX.jpx" />
 549         <include name="nbbuild.xml" />
 550         <include name="nbproject/genfiles.properties" />
 551         <include name="nbproject/project.properties" />
 552         <include name="nbproject/project.xml" />
 553         <include name="${sourceDir}/*.java" />
 554         <include name="${sourceDir}/**/*.java" />
 555         <include name="${sourceDir}/**/*.cdr" />
 556         <include name="${libDir}/**/*" />
 557         <include name="${resourceDir}/**/*" />
 558         <include name="${helpDir}/**/*" />
 559         <include name="appletlib/${jmolJar}" />
 560         <exclude name="**/*locales" />
 561         <exclude name="*locales/**" />
 562         <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 563         <exclude name="utils/InstallAnywhere/**Build*/**" />
 564         <exclude name="utils/InstallAnywhere/**Build*/**" />
 565         <exclude name="utils/InstallAnywhere/**locale*" />
 566         <exclude name="utils/InstallAnywhere/**locale*/**" />
 567         <include name="${schemaDir}/**/*" />
 568         <include name="utils/**/*" />
 569         <include name="${docDir}/**/*" />
 570         <include name="examples/**/*" />
 571       </tarfileset>
 572     </tar>
 573   </target>
 574   <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 575     <copy todir="${packageDir}/examples">
 576       <fileset dir="examples">
 577         <include name="**/*" />
 578         <include name="javascript/*" />
 579         <include name="jmol/*" />
 580       </fileset>
 581       <fileset dir=".">
 582         <include name="${jalviewLiteJar}" />
 583       </fileset>
 584       <fileset dir="appletlib">
 585         <include name="**/*" />
 586       </fileset>
 587     </copy>
 588
 589     <presetdef name="ap_applet.jar">
 590       <!-- build a signed applet with 'all-permissions' -
 591                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 592                           JalviewLite+JmolApplet linked sequence/structure fails
 593                           Mixed code warnings are raised
 594                           -->
 595       <jar update="true" index="true">
 596         <manifest>
 597           <attribute name="Application-Name" value="JalviewLite" />
 598           <attribute name="Permissions" value="all-permissions" />
 599           <attribute name="Codebase" value="${applet.codebase}" />
 600           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 601           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 602         </manifest>
 603       </jar>
 604     </presetdef>
 605     <presetdef name="applet.jar">
 606       <!-- build signed applet with sandbox permissions -
 607                           Needs 'param name="permissions' value="sandbox"' in applet tag
 608                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 609                         -->
 610
 611       <jar update="true" index="true">
 612         <manifest>
 613           <attribute name="Application-Name" value="JalviewLite" />
 614           <attribute name="Permissions" value="sandbox" />
 615           <attribute name="Codebase" value="${applet.codebase}" />
 616           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 617           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 618         </manifest>
 619       </jar>
 620     </presetdef>
 621     <presetdef name="tl_applet.jar">
 622       <!-- build signed applet with trusted library/trusted permissions -
 623                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 624                                j1.7_45:
 625                                No mixed code warnings raised
 626                                Jmol/JalviewLite sequence/structure example doesn't link structures
 627                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 628
 629                               -->
 630
 631       <jar update="true" index="true">
 632         <manifest>
 633           <attribute name="Application-Name" value="JalviewLite" />
 634           <attribute name="Permissions" value="all-permissions" />
 635           <attribute name="Codebase" value="${applet.codebase}" />
 636           <attribute name="Trusted-Only" value="true" />
 637           <attribute name="Trusted-Library" value="true" />
 638         </manifest>
 639       </jar>
 640     </presetdef>
 641     <presetdef name="to_applet.jar">
 642       <!-- not fully test variant (yet) -->
 643       <jar update="true" index="true">
 644         <manifest>
 645           <attribute name="Application-Name" value="JalviewLite" />
 646           <attribute name="Permissions" value="all-permissions" />
 647           <attribute name="Codebase" value="${applet.codebase}" />
 648           <attribute name="Trusted-Only" value="true" />
 649         </manifest>
 650       </jar>
 651     </presetdef>
 652     <!-- create differently privileged artefacts -->
 653     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 654     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}"/>
 655     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 656     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 657     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 658     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 659     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 660     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 661     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 662     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 663     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 664     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 665     <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 666     <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 667     <!-- finally, create manifest for original jars -->
 668     <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 669     <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 670
 671     <!-- todo - write examples/downloads for alternate versions of the applet -->
 672     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 673
 674       <fileset dir="${packageDir}/examples">
 675         <include name="${jalviewLiteJar}" />
 676         <include name="${jmolJar}" />
 677         <include name="to_${jalviewLiteJar}" />
 678         <include name="to_${jmolJar}" />
 679         <include name="tl_${jalviewLiteJar}" />
 680         <include name="tl_${jmolJar}" />
 681         <include name="ap_${jalviewLiteJar}" />
 682         <include name="ap_${jmolJar}" />
 683       </fileset>
 684     </signjar>
 685   </target>
 686   <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 687     <javadoc destdir="${javadocDir}">
 688       <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 689       </packageset>
 690     </javadoc>
 691   </target>
 692
 693 </project>