build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
   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="${libDir}">
 122                                 <include name="*.jar" />
 123                                 <include name="**/*.jar" />
 124                         </fileset>
 125                         <fileset dir="appletlib">
 126                                 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 127                                 -->
 128                                 <include name="${jmolJar}" />
 129                         </fileset>
 130
 131                 </path>
 132                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 133                 <!-- The Location of the java 1.1.8 jdk -->
 134                 <property name="java118.home" value="C:\Sun\jdk1.1.8" />
 135                 <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 136                 <!-- jre for 1.4 version
 137                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 138                 -->
 139                 <!-- the classpath for building the 1.1 applet -->
 140                 <path id="jalviewlite.deps">
 141                         <fileset dir="${java118.home}">
 142                                 <include name="lib/classes.zip" />
 143                         </fileset>
 144                         <pathelement location="appletlib/${jmolJar}" />
 145                 </path>
 146         </target>
 147
 148
 149         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 150         <target name="buildPropertiesFile" depends="init">
 151                 <tstamp prefix="build">
 152                         <format property="date" pattern="dd MMMM yyyy" />
 153                 </tstamp>
 154                 <properties file="${outputDir}/.build_properties">
 155                         <header>
 156           ---Jalview Build Details---
 157         </header>
 158                         <property name="VERSION" value="${JALVIEW_VERSION}" />
 159                         <property name="BUILD_DATE" value="${build.date}" />
 160                 </properties>
 161         </target>
 162
 163
 164         <target name="clean" depends="init">
 165                 <!-- not efficient yet. -->
 166                 <delete dir="${outputDir}" />
 167         </target>
 168
 169         <target name="distclean" depends="init, clean">
 170
 171                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 172                 <delete>
 173                         <fileset dir=".">
 174                                 <include name="${outputJar}" />
 175                                 <include name="#*#" />
 176                                 <include name="#*.*#" />
 177                                 <include name="**/#*#" />
 178                                 <include name="**/#*.*#" />
 179                                 <include name="*~" />
 180                                 <include name="*.*~" />
 181                                 <include name="**/*~" />
 182                                 <include name="**/*.*~" />
 183                         </fileset>
 184                 </delete>
 185         </target>
 186
 187         <target name="prepare" depends="init">
 188                 <mkdir dir="${outputDir}" />
 189                 <copy todir="${outputDir}">
 190                         <fileset dir=".">
 191                                 <include name="${docDir}/**/*.*" />
 192                                 <include name="${helpDir}/**/*.*" />
 193                                 <include name="${libDir}/*.jar" />
 194                         </fileset>
 195                         <fileset dir="${resourceDir}">
 196                                 <include name="**/*.*" />
 197                         </fileset>
 198                 </copy>
 199         </target>
 200
 201         <target name="build" depends="prepare">
 202                 <!-- not efficient yet. -->
 203                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 204                         <exclude name="jalview/*applet*" />
 205                         <exclude name="jalview/appletgui/**" />
 206                         <exclude name="com/stevesoft/**" />
 207                 </javac>
 208         </target>
 209         <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 210                 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 211                         <arg line="html" />
 212                 </java>
 213         </target>
 214
 215         <target name="makefulldist" depends="makedist">
 216                 <!-- the default keystore details might need to be edited here -->
 217                 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 218
 219                         <fileset dir="${packageDir}">
 220                                 <include name="*.jar" />
 221                         </fileset>
 222                 </signjar>
 223                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 224
 225                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 226                 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 227                 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 228                         <information>
 229                                 <title>Jalview</title>
 230                                 <vendor>The Barton Group</vendor>
 231                                 <homepage href="http://www.jalview.org" />
 232                                 <description>Jalview Multiple Alignment Editor</description>
 233                                 <description kind="short">Jalview</description>
 234                                 <icon href="logo_big.gif" />
 235                                 <offline_allowed />
 236                                 <!--
 237         <association mime-type="application-x/ext-file" extensions="fa"/>
 238         <association mime-type="application-x/ext-file" extensions="fasta"/>
 239         <association mime-type="application-x/ext-file" extensions="fastq"/>
 240         <association mime-type="application-x/ext-file" extensions="blc"/>
 241         <association mime-type="application-x/ext-file" extensions="msf"/>
 242         <association mime-type="application-x/ext-file" extensions="pfam"/>
 243         <association mime-type="application-x/ext-file" extensions="aln"/>
 244         <association mime-type="application-x/ext-file" extensions="pir"/>
 245         <association mime-type="application-x/ext-file" extensions="amsa"/>
 246         -->
 247                         </information>
 248                         <resources>
 249                                 <j2se version="1.5+" initial_heap_size="10M" />
 250                                 <fileset dir="${packageDir}">
 251                                         <include name="jalview.jar" />
 252                                 </fileset>
 253                                 <fileset dir="${packageDir}">
 254                                         <include name="*.jar" />
 255                                         <include name="*_*.jar" />
 256                                         <exclude name="jalview.jar" />
 257                                 </fileset>
 258                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 259                         </resources>
 260                         <application_desc main_class="jalview.bin.Jalview">
 261                         </application_desc>
 262                         <security>
 263                                 <all_permissions />
 264                         </security>
 265                 </jnlp>
 266                 <!-- the rest of these jnlp tasks are copy and pastes of the above but with different Vm args -->
 267                 <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 268                         <information>
 269                                 <title>Jalview</title>
 270                                 <vendor>The Barton Group</vendor>
 271                                 <homepage href="http://www.jalview.org" />
 272                                 <description>Jalview Multiple Alignment Editor</description>
 273                                 <description kind="short">Jalview</description>
 274                                 <icon href="logo_big.gif" />
 275                                 <offline_allowed />
 276                                 <!--
 277                 <association mime-type="application-x/ext-file" extensions="fa"/>
 278                 <association mime-type="application-x/ext-file" extensions="fasta"/>
 279                 <association mime-type="application-x/ext-file" extensions="fastq"/>
 280                 <association mime-type="application-x/ext-file" extensions="blc"/>
 281                 <association mime-type="application-x/ext-file" extensions="msf"/>
 282                 <association mime-type="application-x/ext-file" extensions="pfam"/>
 283                 <association mime-type="application-x/ext-file" extensions="aln"/>
 284                 <association mime-type="application-x/ext-file" extensions="pir"/>
 285                 <association mime-type="application-x/ext-file" extensions="amsa"/>
 286                 -->
 287                         </information>
 288                         <resources>
 289                                 <j2se version="1.5+" initial_heap_size="64M" max_heap_size="512M" />
 290                                 <fileset dir="${packageDir}">
 291                                         <include name="jalview.jar" />
 292                                 </fileset>
 293                                 <fileset dir="${packageDir}">
 294                                         <include name="*.jar" />
 295                                         <include name="*_*.jar" />
 296                                         <exclude name="jalview.jar" />
 297                                 </fileset>
 298                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 299                         </resources>
 300                         <application_desc main_class="jalview.bin.Jalview">
 301                         </application_desc>
 302                         <security>
 303                                 <all_permissions />
 304                         </security>
 305                 </jnlp>
 306                 <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
 307                         <information>
 308                                 <title>Jalview</title>
 309                                 <vendor>The Barton Group</vendor>
 310                                 <homepage href="http://www.jalview.org" />
 311                                 <description>Jalview Multiple Alignment Editor</description>
 312                                 <description kind="short">Jalview</description>
 313                                 <icon href="logo_big.gif" />
 314                                 <offline_allowed />
 315                                 <!--
 316                         <association mime-type="application-x/ext-file" extensions="fa"/>
 317                         <association mime-type="application-x/ext-file" extensions="fasta"/>
 318                         <association mime-type="application-x/ext-file" extensions="fastq"/>
 319                         <association mime-type="application-x/ext-file" extensions="blc"/>
 320                         <association mime-type="application-x/ext-file" extensions="msf"/>
 321                         <association mime-type="application-x/ext-file" extensions="pfam"/>
 322                         <association mime-type="application-x/ext-file" extensions="aln"/>
 323                         <association mime-type="application-x/ext-file" extensions="pir"/>
 324                         <association mime-type="application-x/ext-file" extensions="amsa"/>
 325                         -->
 326                         </information>
 327                         <resources>
 328                                 <j2se version="1.5+" initial_heap_size="256M" max_heap_size="1024M" />
 329                                 <fileset dir="${packageDir}">
 330                                         <include name="jalview.jar" />
 331                                 </fileset>
 332                                 <fileset dir="${packageDir}">
 333                                         <include name="*.jar" />
 334                                         <include name="*_*.jar" />
 335                                         <exclude name="jalview.jar" />
 336                                 </fileset>
 337                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 338                         </resources>
 339                         <application_desc main_class="jalview.bin.Jalview">
 340                         </application_desc>
 341                         <security>
 342                                 <all_permissions />
 343                         </security>
 344                 </jnlp>
 345
 346         </target>
 347
 348         <target name="runenv" depends="init">
 349                 <path id="run.classpath">
 350                         <pathelement location="${outputDir}" />
 351                         <fileset dir="${outputDir}">
 352                                 <include name="${libDir}/*.jar" />
 353                         </fileset>
 354                 </path>
 355                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 356
 357                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 358       </echo>
 359         </target>
 360
 361         <target name="buildextclients" depends="init">
 362                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 363                 <condition property="dontextbuild">
 364                         <equals arg1="n" arg2="${doextbuild.response}" />
 365                 </condition>
 366                 <condition property="dontextbuild">
 367                         <equals arg1="N" arg2="${doextbuild.response}" />
 368                 </condition>
 369                 <fail if="dontextbuild">
 370         Build External Client Code process aborted by user. Jalview source is unchanged.
 371       </fail>
 372                 <!-- Currently, this doesn't happen automatically.
 373      1. Run WSDL2Java as below, which generates an ext.vamsas +
 374      vamsas.<datapackages> fileset.
 375      2. refactor ext.vamsas.SpecificserviceWS* to
 376      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 377      3. Update the jalview.ws.*WServices classes to reflect the
 378      interface type, and all locations of this wsdl type that Jalview
 379      might be using.
 380
 381 -->
 382                 <path id="axisbuild">
 383                         <path refid="build.classpath" />
 384                 </path>
 385                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 386                 <move todir="./bak">
 387                         <fileset dir="${sourceDir}" id="client">
 388                                 <include name="${wsdl.ClientNS}/*.*" />
 389                         </fileset>
 390                 </move>
 391
 392                 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 393                         <mappingSet>
 394                                 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 395                                 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 396                         </mappingSet>
 397                 </axis-wsdl2java>
 398         </target>
 399
 400         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 401                 <!-- make the package jar if not already existing -->
 402                 <mkdir dir="${packageDir}" />
 403                 <!-- clean dir if it already existed -->
 404                 <delete>
 405                         <fileset dir="${packageDir}">
 406                                 <include name="*.jar"/>
 407                         </fileset>
 408                 </delete>
 409                 <jar destfile="${packageDir}/${outputJar}">
 410                         <manifest>
 411                                 <attribute name="Main-Class" value="jalview.bin.Jalview" />
 412                         </manifest>
 413                         <fileset dir="${outputDir}/">
 414                                 <exclude name="cache*/**" />
 415                                 <exclude name="*.jar" />
 416                                 <exclude name="*.jar.*" />
 417                                 <exclude name="**/*.jar" />
 418                                 <exclude name="**/*.jar.*" />
 419                         </fileset>
 420                 </jar>
 421
 422                 <copy toDir="${packageDir}" flatten="true">
 423                         <fileset dir="${outputDir}">
 424                                 <include name="*.jar" />
 425                                 <include name="**/*.jar" />
 426                         </fileset>
 427                 </copy>
 428         </target>
 429
 430
 431         <!-- jalopy code reformatter -->
 432         <target name="sourcescrub" depends="init,build">
 433                 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 434                         <fileset dir="${sourceDir}">
 435                                 <include name="*.java" />
 436                                 <include name="**/*.java" />
 437                                 <include name="**/**/*.java" />
 438                         </fileset>
 439                 </jalopy>
 440         </target>
 441
 442
 443
 444         <!-- Compile, package and obfuscate Jalview Applet -->
 445         <target name="makeApplet" depends="obfuscate" />
 446
 447         <target name="compileApplet" depends="init,clean">
 448                 <mkdir dir="${outputDir}" />
 449                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpath="appletlib/${jmolJar}" includes="jalview/appletgui/**" excludes="ext/**,MCview/**,org/**,vamsas/**" />
 450         </target>
 451
 452         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 453                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 454                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 455                 <jar destfile="in.jar">
 456                         <manifest>
 457                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 458                         </manifest>
 459                         <fileset dir="${outputDir}">
 460                                 <include name="com/**" />
 461                                 <include name="MCview/**" />
 462                                 <include name="jalview/**" />
 463                                 <include name=".build_properties" />
 464                                 <include name="images/idwidth.gif" />
 465                                 <include name="images/link.gif" />
 466                         </fileset>
 467                 </jar>
 468         </target>
 469         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
 470         </target>
 471         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 472                 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 473                 <delete file="in.jar" />
 474         </target>
 475         <target name="-obfuscatereally" unless="donotobfuscate">
 476
 477                 <path id="obfuscateDeps.path">
 478                         <pathelement location="${applet.jre.tools}" />
 479                         <pathelement location="appletlib/${jmolJar}" />
 480                 </path>
 481                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 482
 483                 <proguard>
 484                         <injar file="in.jar" />
 485                         <outjar file="${jalviewLiteJar}" />
 486                         <libraryjar refid="obfuscateDeps.path" />
 487                         <keep access="public" type="class" name="jalview.bin.JalviewLite">
 488                                 <field access="public" />
 489                                 <method access="public" />
 490                                 <constructor access="public" />
 491                         </keep>
 492                         <!--      -libraryjars "${obfuscateDeps}"
 493       -injars      in.jar
 494       -outjars     jalviewApplet.jar
 495       -keep public class jalview.bin.JalviewLite
 496        { public * ; } -->
 497                 </proguard>
 498                 <delete file="in.jar" />
 499         </target>
 500
 501         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 502                 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 503                 <delete>
 504                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 505                                 <include name="*.java" />
 506                                 <include name="descriptors/*.java" />
 507                         </fileset>
 508                 </delete>
 509                 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 510                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 511                 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 512                 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 513                 <!--
 514                 now build the jalview.binding package with the old schema set
 515                 -->
 516                 <delete>
 517                         <fileset dir="${sourceDir}/jalview/binding/">
 518                                 <include name="**" />
 519                         </fileset>
 520                 </delete>
 521                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 522                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 523                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 524         </target>
 525         <target name="sourcedist" description="create jalview source distribution" depends="init">
 526                 <delete file="${source.dist.name}" />
 527                 <tar destfile="${source.dist.name}" compression="gzip">
 528                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 529                                 <include name="LICENSE" />
 530                                 <include name="README" />
 531                                 <include name="build.xml" />
 532                                 <include name="jalview-jalopy.xml" />
 533                                 <include name="JalviewApplet.jpx" />
 534                                 <include name="JalviewX.jpx" />
 535                                 <include name="${sourceDir}/*.java" />
 536                                 <include name="${sourceDir}/**/*.java" />
 537                                 <include name="${sourceDir}/**/*.cdr" />
 538                                 <include name="${libDir}/**/*" />
 539                                 <include name="${resourceDir}/**/*" />
 540                                 <include name="${helpDir}/**/*" />
 541                                 <include name="appletlib/${jmolJar}" />
 542                                 <exclude name="**/*locales" />
 543                                 <exclude name="*locales/**" />
 544                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 545                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 546                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 547                                 <exclude name="utils/InstallAnywhere/**locale*" />
 548                                 <exclude name="utils/InstallAnywhere/**locale*/**" />
 549                                 <include name="${schemaDir}/**/*" />
 550                                 <include name="utils/**/*" />
 551                                 <include name="${docDir}/**/*" />
 552                         </tarfileset>
 553                 </tar>
 554         </target>
 555 </project>