build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
   4  * Copyright (C) 2010 J Procter, AM Waterhouse, 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                 <!-- Don't change anything below here unless you know what you are doing! -->
  89                 <!-- Url path for WebStart in JNLP file -->
  90                 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  91                 <!-- build directory configuration -->
  92                 <property name="libDir" value="lib" />
  93                 <property name="resourceDir" value="resources" />
  94                 <property name="helpDir" value="help" />
  95                 <property name="docDir" value="doc" />
  96                 <property name="sourceDir" value="src" />
  97                 <property name="schemaDir" value="schemas" />
  98                 <property name="outputDir" value="classes" />
  99                 <property name="packageDir" value="dist" />
 100                 <property name="outputJar" value="jalview.jar" />
 101                 <!-- Jalview Applet JMol Jar Dependency -->
 102                 <property name="jmolJar" value="JmolApplet-12.1.13.jar" />
 103                 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 104                 <!-- switch to indicate if we should obfuscate jalviewLite -->
 105                 <!--<property name="donotobfuscate" value="true"/> -->
 106
 107                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 108                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 109                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 110                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 111                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 112                 <property name="WSInterf" value="MsaWS" />
 113                 <property name="wsdl.Namespace" value="vamsas" />
 114                 <property name="wsdl.ClientNS" value="ext.vamsas" />
 115                 <!-- the class path for building the application -->
 116                 <path id="build.classpath">
 117                         <fileset dir="utils">
 118                                 <include name="*.jar" />
 119                                 <include name="**/*.jar" />
 120                         </fileset>
 121                         <fileset dir="${libDir}">
 122                                 <include name="*.jar" />
 123                                 <include name="**/*.jar" />
 124                         </fileset>
 125                         <fileset dir="${java.home}/lib">
 126                                 <include name="plugin.jar"/>
 127                         </fileset>
 128                         <fileset dir="appletlib">
 129                                 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 130                                 -->
 131                                 <include name="${jmolJar}" />
 132                         </fileset>
 133
 134                 </path>
 135                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 136                 <!-- The Location of the java 1.1.8 jdk -->
 137                 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 138                 -->
 139                 <property name="java118.home" value="${java.home}" />
 140                     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 141                 --><!-- jre for 1.4 version -->
 142                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 143
 144                 <!-- the classpath for building the 1.1 applet -->
 145                 <path id="jalviewlite.deps">
 146                         <fileset dir="${java118.home}">
 147                                 <include name="lib/classes.zip" />
 148                         </fileset>
 149                         <fileset dir="${java.home}/lib">
 150                                 <include name="plugin.jar"/>
 151                         </fileset>
 152                         <pathelement location="appletlib/${jmolJar}" />
 153                 </path>
 154     <!-- default location for outputting javadoc -->
 155     <property name="javadocDir" value="${packageDir}/javadoc"/>
 156         </target>
 157
 158
 159         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 160         <target name="buildPropertiesFile" depends="init">
 161                 <tstamp prefix="build">
 162                         <format property="date" pattern="dd MMMM yyyy" />
 163                 </tstamp>
 164                 <properties file="${outputDir}/.build_properties">
 165                         <header>
 166           ---Jalview Build Details---
 167         </header>
 168                         <property name="VERSION" value="${JALVIEW_VERSION}" />
 169                         <property name="BUILD_DATE" value="${build.date}" />
 170                 </properties>
 171         </target>
 172
 173
 174         <target name="clean" depends="init">
 175                 <!-- not efficient yet. -->
 176                 <delete dir="${outputDir}" includes="*,**/*"/>
 177         </target>
 178
 179         <target name="distclean" depends="init, clean">
 180
 181                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 182                 <delete>
 183                         <fileset dir=".">
 184                                 <include name="${outputJar}" />
 185                                 <include name="#*#" />
 186                                 <include name="#*.*#" />
 187                                 <include name="**/#*#" />
 188                                 <include name="**/#*.*#" />
 189                                 <include name="*~" />
 190                                 <include name="*.*~" />
 191                                 <include name="**/*~" />
 192                                 <include name="**/*.*~" />
 193                         </fileset>
 194                 </delete>
 195         </target>
 196
 197         <target name="prepare" depends="init">
 198                 <mkdir dir="${outputDir}" />
 199                 <copy todir="${outputDir}">
 200                         <fileset dir=".">
 201                                 <include name="${docDir}/**/*.*" />
 202                                 <include name="${helpDir}/**/*.*" />
 203                                 <include name="${libDir}/*.jar" />
 204                         </fileset>
 205                         <fileset dir="${resourceDir}">
 206                                 <include name="**/*.*" />
 207                         </fileset>
 208                 </copy>
 209         </target>
 210
 211         <target name="build" depends="prepare">
 212                 <!-- not efficient yet. -->
 213                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 214                         <exclude name="jalview/*applet*" />
 215                         <exclude name="jalview/appletgui/**" />
 216                         <exclude name="com/stevesoft/**" />
 217                 </javac>
 218         </target>
 219         <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 220                 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 221                         <arg line="html" />
 222                 </java>
 223         </target>
 224
 225         <target name="makefulldist" depends="makedist">
 226                 <!-- the default keystore details might need to be edited here -->
 227                 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 228
 229                         <fileset dir="${packageDir}">
 230                                 <include name="*.jar" />
 231                         </fileset>
 232                 </signjar>
 233                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 234
 235                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 236                 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 237                 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 238                         <information>
 239                                 <title>Jalview</title>
 240                                 <vendor>The Barton Group</vendor>
 241                                 <homepage href="http://www.jalview.org" />
 242                                 <description>Jalview Multiple Alignment Editor</description>
 243                                 <description kind="short">Jalview</description>
 244                                 <icon href="logo_big.gif" />
 245                                 <offline_allowed />
 246                                 <!--
 247         <association mime-type="application-x/ext-file" extensions="fa"/>
 248         <association mime-type="application-x/ext-file" extensions="fasta"/>
 249         <association mime-type="application-x/ext-file" extensions="fastq"/>
 250         <association mime-type="application-x/ext-file" extensions="blc"/>
 251         <association mime-type="application-x/ext-file" extensions="msf"/>
 252         <association mime-type="application-x/ext-file" extensions="pfam"/>
 253         <association mime-type="application-x/ext-file" extensions="aln"/>
 254         <association mime-type="application-x/ext-file" extensions="pir"/>
 255         <association mime-type="application-x/ext-file" extensions="amsa"/>
 256         -->
 257                         </information>
 258                         <resources>
 259                                 <j2se version="1.5+" initial_heap_size="10M" />
 260                                 <fileset dir="${packageDir}">
 261                                         <include name="jalview.jar" />
 262                                 </fileset>
 263                                 <fileset dir="${packageDir}">
 264                                         <include name="*.jar" />
 265                                         <include name="*_*.jar" />
 266                                         <exclude name="jalview.jar" />
 267                                 </fileset>
 268                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 269                         </resources>
 270                         <application_desc main_class="jalview.bin.Jalview">
 271                         </application_desc>
 272                         <security>
 273                                 <all_permissions />
 274                         </security>
 275                 </jnlp>
 276                 <!-- the rest of these jnlp tasks are copy and pastes of the above but with different Vm args -->
 277                 <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 278                         <information>
 279                                 <title>Jalview</title>
 280                                 <vendor>The Barton Group</vendor>
 281                                 <homepage href="http://www.jalview.org" />
 282                                 <description>Jalview Multiple Alignment Editor</description>
 283                                 <description kind="short">Jalview</description>
 284                                 <icon href="logo_big.gif" />
 285                                 <offline_allowed />
 286                                 <!--
 287                 <association mime-type="application-x/ext-file" extensions="fa"/>
 288                 <association mime-type="application-x/ext-file" extensions="fasta"/>
 289                 <association mime-type="application-x/ext-file" extensions="fastq"/>
 290                 <association mime-type="application-x/ext-file" extensions="blc"/>
 291                 <association mime-type="application-x/ext-file" extensions="msf"/>
 292                 <association mime-type="application-x/ext-file" extensions="pfam"/>
 293                 <association mime-type="application-x/ext-file" extensions="aln"/>
 294                 <association mime-type="application-x/ext-file" extensions="pir"/>
 295                 <association mime-type="application-x/ext-file" extensions="amsa"/>
 296                 -->
 297                         </information>
 298                         <resources>
 299                                 <j2se version="1.5+" initial_heap_size="64M" max_heap_size="512M" />
 300                                 <fileset dir="${packageDir}">
 301                                         <include name="jalview.jar" />
 302                                 </fileset>
 303                                 <fileset dir="${packageDir}">
 304                                         <include name="*.jar" />
 305                                         <include name="*_*.jar" />
 306                                         <exclude name="jalview.jar" />
 307                                 </fileset>
 308                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 309                         </resources>
 310                         <application_desc main_class="jalview.bin.Jalview">
 311                         </application_desc>
 312                         <security>
 313                                 <all_permissions />
 314                         </security>
 315                 </jnlp>
 316                 <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
 317                         <information>
 318                                 <title>Jalview</title>
 319                                 <vendor>The Barton Group</vendor>
 320                                 <homepage href="http://www.jalview.org" />
 321                                 <description>Jalview Multiple Alignment Editor</description>
 322                                 <description kind="short">Jalview</description>
 323                                 <icon href="logo_big.gif" />
 324                                 <offline_allowed />
 325                                 <!--
 326                         <association mime-type="application-x/ext-file" extensions="fa"/>
 327                         <association mime-type="application-x/ext-file" extensions="fasta"/>
 328                         <association mime-type="application-x/ext-file" extensions="fastq"/>
 329                         <association mime-type="application-x/ext-file" extensions="blc"/>
 330                         <association mime-type="application-x/ext-file" extensions="msf"/>
 331                         <association mime-type="application-x/ext-file" extensions="pfam"/>
 332                         <association mime-type="application-x/ext-file" extensions="aln"/>
 333                         <association mime-type="application-x/ext-file" extensions="pir"/>
 334                         <association mime-type="application-x/ext-file" extensions="amsa"/>
 335                         -->
 336                         </information>
 337                         <resources>
 338                                 <j2se version="1.5+" initial_heap_size="256M" max_heap_size="1024M" />
 339                                 <fileset dir="${packageDir}">
 340                                         <include name="jalview.jar" />
 341                                 </fileset>
 342                                 <fileset dir="${packageDir}">
 343                                         <include name="*.jar" />
 344                                         <include name="*_*.jar" />
 345                                         <exclude name="jalview.jar" />
 346                                 </fileset>
 347                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 348                         </resources>
 349                         <application_desc main_class="jalview.bin.Jalview">
 350                         </application_desc>
 351                         <security>
 352                                 <all_permissions />
 353                         </security>
 354                 </jnlp>
 355
 356         </target>
 357
 358         <target name="runenv" depends="init">
 359                 <path id="run.classpath">
 360                         <pathelement location="${outputDir}" />
 361                         <fileset dir="${outputDir}">
 362                                 <include name="${libDir}/*.jar" />
 363                         </fileset>
 364                 </path>
 365                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 366
 367                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 368       </echo>
 369         </target>
 370
 371         <target name="buildextclients" depends="init">
 372                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 373                 <condition property="dontextbuild">
 374                         <equals arg1="n" arg2="${doextbuild.response}" />
 375                 </condition>
 376                 <condition property="dontextbuild">
 377                         <equals arg1="N" arg2="${doextbuild.response}" />
 378                 </condition>
 379                 <fail if="dontextbuild">
 380         Build External Client Code process aborted by user. Jalview source is unchanged.
 381       </fail>
 382                 <!-- Currently, this doesn't happen automatically.
 383      1. Run WSDL2Java as below, which generates an ext.vamsas +
 384      vamsas.<datapackages> fileset.
 385      2. refactor ext.vamsas.SpecificserviceWS* to
 386      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 387      3. Update the jalview.ws.*WServices classes to reflect the
 388      interface type, and all locations of this wsdl type that Jalview
 389      might be using.
 390
 391 -->
 392                 <path id="axisbuild">
 393                         <path refid="build.classpath" />
 394                 </path>
 395                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 396                 <move todir="./bak">
 397                         <fileset dir="${sourceDir}" id="client">
 398                                 <include name="${wsdl.ClientNS}/*.*" />
 399                         </fileset>
 400                 </move>
 401
 402                 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 403                         <mappingSet>
 404                                 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 405                                 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 406                         </mappingSet>
 407                 </axis-wsdl2java>
 408         </target>
 409
 410         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 411                 <!-- make the package jar if not already existing -->
 412                 <mkdir dir="${packageDir}" />
 413                 <!-- clean dir if it already existed -->
 414                 <delete>
 415                         <fileset dir="${packageDir}">
 416                                 <include name="*.jar"/>
 417                         </fileset>
 418                 </delete>
 419                 <jar destfile="${packageDir}/${outputJar}">
 420                         <manifest>
 421                                 <attribute name="Main-Class" value="jalview.bin.Jalview" />
 422                         </manifest>
 423                         <fileset dir="${outputDir}/">
 424                                 <exclude name="cache*/**" />
 425                                 <exclude name="*.jar" />
 426                                 <exclude name="*.jar.*" />
 427                                 <exclude name="**/*.jar" />
 428                                 <exclude name="**/*.jar.*" />
 429                         </fileset>
 430                 </jar>
 431
 432                 <copy toDir="${packageDir}" flatten="true">
 433                         <fileset dir="${outputDir}">
 434                                 <include name="*.jar" />
 435                                 <include name="**/*.jar" />
 436                         </fileset>
 437                 </copy>
 438         </target>
 439
 440
 441         <!-- jalopy code reformatter -->
 442         <target name="sourcescrub" depends="init,build">
 443                 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 444                         <fileset dir="${sourceDir}">
 445                                 <include name="*.java" />
 446                                 <include name="**/*.java" />
 447                                 <include name="**/**/*.java" />
 448                         </fileset>
 449                 </jalopy>
 450         </target>
 451
 452
 453
 454         <!-- Compile, package and obfuscate Jalview Applet -->
 455         <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 456
 457         <target name="compileApplet" depends="init,clean">
 458                 <mkdir dir="${outputDir}" />
 459                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 460                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 461                         excludes="ext/**,MCview/**,org/**,vamsas/**" />
 462         </target>
 463
 464         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 465                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 466                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 467                 <jar destfile="in.jar">
 468                         <manifest>
 469                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 470                         </manifest>
 471                         <fileset dir="${outputDir}">
 472                                 <include name="com/**" />
 473                                 <include name="MCview/**" />
 474                                 <include name="jalview/**" />
 475                                 <include name=".build_properties" />
 476                                 <include name="images/idwidth.gif" />
 477                                 <include name="images/link.gif" />
 478                         </fileset>
 479                 </jar>
 480         </target>
 481         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 482         </target>
 483         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 484                 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 485                 <delete file="in.jar" />
 486         </target>
 487         <target name="-obfuscatereally" unless="donotobfuscate">
 488
 489                 <path id="obfuscateDeps.path">
 490                         <pathelement location="${applet.jre.tools}" />
 491                         <pathelement location="appletlib/${jmolJar}" />
 492                 </path>
 493                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 494
 495                 <proguard>
 496                         <injar file="in.jar" />
 497                         <outjar file="${jalviewLiteJar}" />
 498                         <libraryjar refid="obfuscateDeps.path" />
 499                         <keep access="public" type="class" name="jalview.bin.JalviewLite">
 500                                 <field access="public" />
 501                                 <method access="public" />
 502                                 <constructor access="public" />
 503                         </keep>
 504                         <!--      -libraryjars "${obfuscateDeps}"
 505       -injars      in.jar
 506       -outjars     jalviewApplet.jar
 507       -keep public class jalview.bin.JalviewLite
 508        { public * ; } -->
 509                 </proguard>
 510                 <delete file="in.jar" />
 511         </target>
 512
 513         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 514                 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 515                 <delete>
 516                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 517                                 <include name="*.java" />
 518                                 <include name="descriptors/*.java" />
 519                         </fileset>
 520                 </delete>
 521                 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 522                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 523                 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 524                 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 525                 <!--
 526                 now build the jalview.binding package with the old schema set
 527                 -->
 528                 <delete>
 529                         <fileset dir="${sourceDir}/jalview/binding/">
 530                                 <include name="**" />
 531                         </fileset>
 532                 </delete>
 533                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 534                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 535                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 536         </target>
 537         <target name="sourcedist" description="create jalview source distribution" depends="init">
 538                 <delete file="${source.dist.name}" />
 539                 <tar destfile="${source.dist.name}" compression="gzip">
 540                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 541                                 <include name="LICENSE" />
 542                                 <include name="README" />
 543                                 <include name="build.xml" />
 544                                 <include name="jalview-jalopy.xml" />
 545                                 <include name="JalviewApplet.jpx" />
 546                                 <include name="JalviewX.jpx" />
 547                                 <include name="nbbuild.xml"/>
 548                                 <include name="nbproject/genfiles.properties"/>
 549         <include name="nbproject/project.properties"/>
 550         <include name="nbproject/project.xml"/>
 551                                 <include name="${sourceDir}/*.java" />
 552                                 <include name="${sourceDir}/**/*.java" />
 553                                 <include name="${sourceDir}/**/*.cdr" />
 554                                 <include name="${libDir}/**/*" />
 555                                 <include name="${resourceDir}/**/*" />
 556                                 <include name="${helpDir}/**/*" />
 557                                 <include name="appletlib/${jmolJar}" />
 558                                 <exclude name="**/*locales" />
 559                                 <exclude name="*locales/**" />
 560                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 561                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 562                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 563                                 <exclude name="utils/InstallAnywhere/**locale*" />
 564                                 <exclude name="utils/InstallAnywhere/**locale*/**" />
 565                                 <include name="${schemaDir}/**/*" />
 566                                 <include name="utils/**/*" />
 567                                 <include name="${docDir}/**/*" />
 568                                 <include name="examples/**/*" />
 569                         </tarfileset>
 570                 </tar>
 571         </target>
 572         <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 573           <copy todir="${packageDir}/examples">
 574           <fileset dir="examples">
 575                 <include name="**/*"/>
 576                 <include name="javascript/*"/>
 577       <include name="jmol/*"/>
 578           </fileset>
 579                 <fileset dir=".">
 580                 <include name="jalviewApplet.jar"/>
 581                         </fileset>
 582                 <fileset dir="appletlib">
 583                       <include name="**/*"/>
 584                         </fileset>
 585           </copy>
 586
 587         </target>
 588         <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 589          <javadoc destdir="${javadocDir}">
 590                 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 591                 </packageset>
 592                 </javadoc>
 593         </target>
 594
 595 </project>