build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3    * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
   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"
  22          classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
  23                 <classpath>
  24                         <fileset dir="utils/jalopy/lib">
  25                                 <include name="*.jar" />
  26                         </fileset>
  27                 </classpath>
  28         </taskdef>
  29
  30         <target name="help" depends="usage"/>
  31         <target name="usage">
  32                 <echo message="~~~Jalview Ant build.xml Usage~~~~"/>
  33                 <echo message="Targets include:"/>
  34                 <echo message="usage - default target, displays this message"/>
  35                 <echo message="buildindices - generates JavaHelpSearch from the help files"/>
  36                 <echo message="build - compiles all necessary files for Application"/>
  37                 <echo message="makedist - compiles and places all necessary jar files into directory dist"/>
  38                 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution"/>
  39                 <echo message="              this needs a keystore and key. See docs/building.html for more information."/>
  40                 <echo message="compileApplet - compiles all necessary files for Applet"/>
  41                 <echo message="makeApplet - compiles, then packages and obfuscates the Applet"/>
  42                 <echo message="See docs/building.html and the comments in build file for other targets."/>
  43                 <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk."/>
  44                 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation"/>
  45         </target>
  46
  47
  48         <!-- utils is a class path to additional utilities needed for
  49     building docs, jars and webstart stuff -->
  50         <!--
  51         Userdefined build property defaults
  52
  53         wsdl.server list (plus namespace mapping info ???)  - also want
  54                 ... to make this a dynamically generatable property
  55         WebStart Location
  56         Build location - provide a temporary root for speed
  57         jarsigner keystore and info
  58         Jakarta and axis classpath ?
  59         Default argument for starting Jalview (if it exists).
  60
  61 -->
  62
  63         <target name="init">
  64                 <path id="axis.classpath">
  65                         <!-->
  66                         <fileset dir="/usr/local/axis/lib">
  67                                 <include name="**/*.jar" />
  68                         </fileset>
  69                         <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  70                                 <include name="**/*.jar"/>
  71                                 <include name="*.jar"/>
  72                         </fileset> -->
  73       </path>
  74                 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  75                 <property name="JALVIEW_VERSION" value="DEVELOPMENT"/>
  76                 <!-- 2.4 (VAMSAS)" -->
  77                 <!-- Include debugging information in javac true or false -->
  78                 <property name="javac.debug" value="true"/>
  79
  80                 <!-- JarSigner Key Store for Webstart Distribution -->
  81                 <property name="jalview.keystore" value="./keys/.keystore"/>
  82                 <!-- Keystore Password -->
  83                 <property name="jalview.keystore.pass" value="alignmentisfun"/>
  84                 <!-- Key Name -->
  85                 <property name="jalview.key" value="jalview"/>
  86                 <!-- Key Password -->
  87                 <property name="jalview.key.pass" value="alignmentisfun"/>
  88
  89                 <!-- Don't change anything below here unless you know what you are doing! -->
  90                 <!-- Url path for WebStart in JNLP file -->
  91                 <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
  92                 <!-- build directory configuration -->
  93                 <property name="libDir" value="lib"/>
  94                 <property name="resourceDir" value="resources"/>
  95                 <property name="helpDir" value="help"/>
  96                 <property name="docDir" value="doc"/>
  97                 <property name="sourceDir" value="src" />
  98                 <property name="schemaDir" value="schemas" />
  99                 <property name="outputDir" value="classes" />
 100                 <property name="packageDir" value="dist" />
 101                 <property name="outputJar" value="jalview.jar" />
 102                 <!-- Jalview Applet JMol Jar Dependency -->
 103                 <property name="jmolJar" value="JmolApplet-12.0.6.jar" />
 104                 <property name="jalviewLiteJar" value="jalviewApplet.jar"/>
 105                 <!-- switch to indicate if we should obfuscate jalviewLite -->
 106                 <!--<property name="donotobfuscate" value="true"/> -->
 107
 108                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 109                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 110                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 111                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 112                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 113                 <property name="WSInterf" value="MsaWS" />
 114                 <property name="wsdl.Namespace" value="vamsas" />
 115                 <property name="wsdl.ClientNS" value="ext.vamsas" />
 116                 <!-- the class path for building the application -->
 117                 <path id="build.classpath">
 118                         <fileset dir="utils">
 119                                 <include name="*.jar"/>
 120                                 <include name="**/*.jar"/>
 121                         </fileset>
 122                         <fileset dir="${libDir}">
 123                                 <include name="*.jar"/>
 124                                 <include name="**/*.jar"/>
 125                         </fileset>
 126
 127                 </path>
 128                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz"/>
 129                 <!-- The Location of the java 1.1.8 jdk -->
 130                 <property name="java118.home" value="C:\Sun\jdk1.1.8" />
 131                 <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip"/>
 132                 <!-- jre for 1.4 version
 133                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 134                 -->
 135                 <!-- the classpath for building the 1.1 applet -->
 136                 <path id="jalviewlite.deps">
 137                         <fileset dir="${java118.home}">
 138                                 <include name="lib/classes.zip"/>
 139                         </fileset>
 140                         <pathelement location="appletlib/${jmolJar}"/>
 141                 </path>
 142         </target>
 143
 144
 145         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
 146         <target name="buildPropertiesFile" depends="init">
 147                 <tstamp prefix="build">
 148                         <format property="date" pattern="dd MMMM yyyy"/>
 149                 </tstamp>
 150                 <properties file="${outputDir}/.build_properties">
 151                         <header>
 152           ---Jalview Build Details---
 153         </header>
 154                         <property name="VERSION" value="${JALVIEW_VERSION}"/>
 155                         <property name="BUILD_DATE" value="${build.date}"/>
 156                 </properties>
 157         </target>
 158
 159
 160         <target name="clean" depends="init">
 161                 <!-- not efficient yet. -->
 162                 <delete dir="${outputDir}"/>
 163         </target>
 164
 165         <target name="distclean" depends="init, clean">
 166
 167                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
 168                 <delete>
 169                         <fileset dir=".">
 170                                 <include name="${outputJar}"/>
 171                                 <include name="#*#"/>
 172                                 <include name="#*.*#"/>
 173                                 <include name="**/#*#"/>
 174                                 <include name="**/#*.*#"/>
 175                                 <include name="*~"/>
 176                                 <include name="*.*~"/>
 177                                 <include name="**/*~"/>
 178                                 <include name="**/*.*~"/>
 179                         </fileset>
 180                 </delete>
 181         </target>
 182
 183         <target name="prepare" depends="init">
 184                 <mkdir dir="${outputDir}"/>
 185                 <copy todir="${outputDir}">
 186                         <fileset dir=".">
 187                                 <include name="${docDir}/**/*.*"/>
 188                                 <include name="${helpDir}/**/*.*"/>
 189                                 <include name="${libDir}/*.jar"/>
 190                         </fileset>
 191                         <fileset dir="${resourceDir}">
 192                                 <include name="**/*.*"/>
 193                         </fileset>
 194                 </copy>
 195         </target>
 196
 197         <target name="build" depends="prepare">
 198                 <!-- not efficient yet. -->
 199                 <javac source="1.5" target="1.5"
 200         srcdir ="${sourceDir}"
 201         destdir="${outputDir}"
 202                                 debug="${javac.debug}"
 203       classpathref="build.classpath">
 204                         <exclude name="jalview/*applet*"/>
 205                         <exclude name="com/stevesoft/**"/>
 206                 </javac>
 207         </target>
 208         <target name="buildindices" depends="init, prepare"
 209     unless="help.uptodate">
 210                 <java
 211       classname="com.sun.java.help.search.Indexer"
 212       classpathref="build.classpath"
 213       fork="true"
 214       dir="${outputDir}/${helpDir}"
 215       >
 216                         <arg line="html"/>
 217                 </java>
 218         </target>
 219
 220         <target name="makefulldist" depends="makedist">
 221                 <!-- the default keystore details might need to be edited here -->
 222                 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 223
 224                         <fileset dir="${packageDir}">
 225                                 <include name="*.jar" />
 226                         </fileset>
 227                 </signjar>
 228                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 229
 230                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 231                 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 232                 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 233                         <information>
 234                                 <title>Jalview</title>
 235                                 <vendor>The Barton Group</vendor>
 236                                 <homepage href="http://www.jalview.org" />
 237                                 <description>Jalview Multiple Alignment Editor</description>
 238                                 <description kind="short">Jalview</description>
 239                                 <icon href="logo_big.gif" />
 240                                 <offline_allowed />
 241                                 <!--
 242         <association mime-type="application-x/ext-file" extensions="fa"/>
 243         <association mime-type="application-x/ext-file" extensions="fasta"/>
 244         <association mime-type="application-x/ext-file" extensions="fastq"/>
 245         <association mime-type="application-x/ext-file" extensions="blc"/>
 246         <association mime-type="application-x/ext-file" extensions="msf"/>
 247         <association mime-type="application-x/ext-file" extensions="pfam"/>
 248         <association mime-type="application-x/ext-file" extensions="aln"/>
 249         <association mime-type="application-x/ext-file" extensions="pir"/>
 250         <association mime-type="application-x/ext-file" extensions="amsa"/>
 251         -->
 252                         </information>
 253                         <resources>
 254                                 <j2se version="1.5+" initial_heap_size="10M"/>
 255                                 <fileset dir="${packageDir}">
 256                                         <include name="jalview.jar" />
 257                                 </fileset>
 258                                 <fileset dir="${packageDir}">
 259                                         <include name="*.jar" />
 260                                         <include name="*_*.jar" />
 261                                         <exclude name="jalview.jar" />
 262                                 </fileset>
 263                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 264                         </resources>
 265                         <application_desc main_class="jalview.bin.Jalview">
 266                         </application_desc>
 267                         <security>
 268                                 <all_permissions />
 269                         </security>
 270                 </jnlp>
 271                 <!-- the rest of these jnlp tasks are copy and pastes of the above but with different Vm args -->
 272                                         <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 273                                 <information>
 274                                         <title>Jalview</title>
 275                                         <vendor>The Barton Group</vendor>
 276                                         <homepage href="http://www.jalview.org" />
 277                                         <description>Jalview Multiple Alignment Editor</description>
 278                                         <description kind="short">Jalview</description>
 279                                         <icon href="logo_big.gif" />
 280                                         <offline_allowed />
 281                                         <!--
 282                 <association mime-type="application-x/ext-file" extensions="fa"/>
 283                 <association mime-type="application-x/ext-file" extensions="fasta"/>
 284                 <association mime-type="application-x/ext-file" extensions="fastq"/>
 285                 <association mime-type="application-x/ext-file" extensions="blc"/>
 286                 <association mime-type="application-x/ext-file" extensions="msf"/>
 287                 <association mime-type="application-x/ext-file" extensions="pfam"/>
 288                 <association mime-type="application-x/ext-file" extensions="aln"/>
 289                 <association mime-type="application-x/ext-file" extensions="pir"/>
 290                 <association mime-type="application-x/ext-file" extensions="amsa"/>
 291                 -->
 292                                 </information>
 293                                 <resources>
 294                                         <j2se version="1.5+" initial_heap_size="64M" max_heap_size="512M"/>
 295                                         <fileset dir="${packageDir}">
 296                                                 <include name="jalview.jar" />
 297                                         </fileset>
 298                                         <fileset dir="${packageDir}">
 299                                                 <include name="*.jar" />
 300                                                 <include name="*_*.jar" />
 301                                                 <exclude name="jalview.jar" />
 302                                         </fileset>
 303                                         <property name="jalview.version" value="${JALVIEW_VERSION}" />
 304                                 </resources>
 305                                 <application_desc main_class="jalview.bin.Jalview">
 306                                 </application_desc>
 307                                 <security>
 308                                         <all_permissions />
 309                                 </security>
 310                         </jnlp>
 311                         <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
 312                                         <information>
 313                                                 <title>Jalview</title>
 314                                                 <vendor>The Barton Group</vendor>
 315                                                 <homepage href="http://www.jalview.org" />
 316                                                 <description>Jalview Multiple Alignment Editor</description>
 317                                                 <description kind="short">Jalview</description>
 318                                                 <icon href="logo_big.gif" />
 319                                                 <offline_allowed />
 320                                                 <!--
 321                         <association mime-type="application-x/ext-file" extensions="fa"/>
 322                         <association mime-type="application-x/ext-file" extensions="fasta"/>
 323                         <association mime-type="application-x/ext-file" extensions="fastq"/>
 324                         <association mime-type="application-x/ext-file" extensions="blc"/>
 325                         <association mime-type="application-x/ext-file" extensions="msf"/>
 326                         <association mime-type="application-x/ext-file" extensions="pfam"/>
 327                         <association mime-type="application-x/ext-file" extensions="aln"/>
 328                         <association mime-type="application-x/ext-file" extensions="pir"/>
 329                         <association mime-type="application-x/ext-file" extensions="amsa"/>
 330                         -->
 331                                         </information>
 332                                         <resources>
 333                                                 <j2se version="1.5+" initial_heap_size="256M" max_heap_size="1024M"/>
 334                                                 <fileset dir="${packageDir}">
 335                                                         <include name="jalview.jar" />
 336                                                 </fileset>
 337                                                 <fileset dir="${packageDir}">
 338                                                         <include name="*.jar" />
 339                                                         <include name="*_*.jar" />
 340                                                         <exclude name="jalview.jar" />
 341                                                 </fileset>
 342                                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 343                                         </resources>
 344                                         <application_desc main_class="jalview.bin.Jalview">
 345                                         </application_desc>
 346                                         <security>
 347                                                 <all_permissions />
 348                                         </security>
 349                                 </jnlp>
 350
 351                         </target>
 352
 353                         <target name="runenv" depends="init">
 354                                 <path id="run.classpath">
 355                                         <pathelement location="${outputDir}"/>
 356                                         <fileset dir="${outputDir}">
 357                                                 <include name="${libDir}/*.jar"/>
 358                                         </fileset>
 359                                 </path>
 360                                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
 361
 362                                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 363       </echo>
 364                         </target>
 365
 366                         <target name="buildextclients" depends="init">
 367                                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
 368       validargs="Y,y,n,N" defaultvalue="N"
 369       addproperty="doextbuild.response"/>
 370                                 <condition property="dontextbuild">
 371                                         <equals arg1="n" arg2="${doextbuild.response}"/>
 372                                 </condition>
 373                                 <condition property="dontextbuild">
 374                                         <equals arg1="N" arg2="${doextbuild.response}"/>
 375                                 </condition>
 376                                 <fail if="dontextbuild">
 377         Build External Client Code process aborted by user. Jalview source is unchanged.
 378       </fail>
 379                                 <!-- Currently, this doesn't happen automatically.
 380      1. Run WSDL2Java as below, which generates an ext.vamsas +
 381      vamsas.<datapackages> fileset.
 382      2. refactor ext.vamsas.SpecificserviceWS* to
 383      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 384      3. Update the jalview.ws.*WServices classes to reflect the
 385      interface type, and all locations of this wsdl type that Jalview
 386      might be using.
 387
 388 -->
 389                                 <path id="axisbuild">
 390                                         <path refid="build.classpath"/>
 391                                 </path>
 392                                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
 393                                 <move todir="./bak">
 394                                         <fileset dir="${sourceDir}" id="client">
 395                                                 <include name="${wsdl.ClientNS}/*.*"/>
 396                                         </fileset>
 397                                 </move>
 398
 399                                 <axis-wsdl2java
 400       output="${sourceDir}"
 401       verbose="true"
 402       url="${wsdl.MsaWS2}"
 403       serverside="false"
 404       deployscope="Request"
 405       debug="false"
 406       helpergen="true"
 407       all="true"
 408       >
 409                                         <mappingSet>
 410                                                 <mapping
 411         namespace="${wsdl.Namespace}"
 412         package="${wsdl.ClientNS}"
 413         />
 414                                                 <mapping namespace="http://dataTypes.vamsas"
 415         package="${wsdl.ClientNS}"/>
 416                                         </mappingSet>
 417                                 </axis-wsdl2java>
 418                         </target>
 419
 420                         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 421                                 <!-- make the package jar -->
 422                                 <mkdir dir="${packageDir}"/>
 423
 424                                 <jar destfile="${packageDir}/${outputJar}">
 425                                         <manifest>
 426                                                 <attribute name="Main-Class" value="jalview.bin.Jalview"/>
 427                                         </manifest>
 428                                         <fileset dir="${outputDir}/">
 429                                                 <exclude name="cache*/**"/>
 430                                                 <exclude name="*.jar" />
 431                                                 <exclude name="*.jar.*" />
 432                                                 <exclude name="**/*.jar" />
 433                                                 <exclude name="**/*.jar.*" />
 434                                         </fileset>
 435                                 </jar>
 436
 437                                 <copy toDir="${packageDir}" flatten="true">
 438                                         <fileset dir="${outputDir}">
 439                                                 <include name="*.jar"/>
 440                                                 <include name="**/*.jar"/>
 441                                         </fileset>
 442                                 </copy>
 443                         </target>
 444
 445
 446                         <!-- jalopy code reformatter -->
 447                         <target name="sourcescrub" depends="init,build">
 448                                 <jalopy destdir="jsrc" classpathref="run.classpath"
 449       convention="jalview-jalopy.xml">
 450                                         <fileset dir="${sourceDir}">
 451                                                 <include name="*.java"/>
 452                                                 <include name="**/*.java"/>
 453                                                 <include name="**/**/*.java"/>
 454                                         </fileset>
 455                                 </jalopy>
 456                         </target>
 457
 458
 459
 460                         <!-- Compile, package and obfuscate Jalview Applet -->
 461                         <target name="makeApplet" depends="obfuscate"/>
 462
 463                         <target name="compileApplet" depends="init,clean">
 464                                 <mkdir dir="${outputDir}"/>
 465                                 <javac source="1.2"
 466     target="1.1"
 467     srcdir="${sourceDir}"
 468     destdir="${outputDir}"
 469         debug="${javac.debug}"
 470     classpath="lib/${jmolJar}"
 471        includes="jalview/appletgui/**"
 472        excludes="ext/**,MCview/**,org/**,vamsas/**"
 473        />
 474                         </target>
 475
 476                         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 477                                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
 478                                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
 479                                 <jar destfile="in.jar">
 480                                         <manifest>
 481                                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
 482                                         </manifest>
 483                                         <fileset dir="${outputDir}">
 484                                                 <include name="com/**"/>
 485                                                 <include name="MCview/**"/>
 486                                                 <include name="jalview/**"/>
 487                                                 <include name=".build_properties"/>
 488                                                 <include name="images/idwidth.gif"/>
 489                                                 <include name="images/link.gif"/>
 490                                         </fileset>
 491                                 </jar>
 492                         </target>
 493                         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
 494                         </target>
 495                         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 496                                 <copy file="in.jar" tofile="${jalviewLiteJar}" />
 497                                 <delete file="in.jar"/>
 498                         </target>
 499                         <target name="-obfuscatereally" unless="donotobfuscate">
 500
 501                                 <path id="obfuscateDeps.path">
 502                                         <pathelement location="${applet.jre.tools}"/>
 503                                         <pathelement location="lib/${jmolJar}"/>
 504                                 </path>
 505                                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 506
 507                                 <proguard>
 508                                         <injar file="in.jar"/>
 509                                         <outjar file="${jalviewLiteJar}"/>
 510                                         <libraryjar refid="obfuscateDeps.path"/>
 511                                         <keep access="public" type="class"
 512       name="jalview.bin.JalviewLite">
 513                                                 <field access="public"/>
 514                                                 <method access="public"/>
 515                                                 <constructor access="public"/>
 516                                         </keep>
 517                                         <!--      -libraryjars "${obfuscateDeps}"
 518       -injars      in.jar
 519       -outjars     jalviewApplet.jar
 520       -keep public class jalview.bin.JalviewLite
 521        { public * ; } -->
 522                                 </proguard>
 523                                 <delete file="in.jar"/>
 524                         </target>
 525
 526                         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 527                                 <taskdef name="castor-srcgen"
 528                           classname="org.castor.anttask.CastorCodeGenTask"
 529                       classpathref="build.classpath" />
 530                                 <delete>
 531                                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 532                                                 <include name="*.java"/>
 533                                                 <include name="descriptors/*.java"/>
 534                                         </fileset>
 535                                 </delete>
 536                                 <castor-srcgen file="${schemaDir}/vamsas.xsd"
 537                               todir="${sourceDir}"
 538                               package="jalview.schemabinding.version2"
 539                               warnings="false"
 540                                         nodesc="false"
 541                                                 verbose="true"
 542                                                 properties="${schemaDir}/jalview.properties"
 543                 />
 544                                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
 545                               todir="${sourceDir}"
 546                               package="jalview.schemabinding.version2"
 547                               warnings="false"
 548                                         nodesc="false"
 549                                                 verbose="true"
 550                                                 properties="${schemaDir}/jalview.properties"
 551                 />
 552                                 <castor-srcgen file="${schemaDir}/jalview.xsd"
 553                               todir="${sourceDir}"
 554                               package="jalview.schemabinding.version2"
 555                               warnings="false"
 556                                           nodesc="false"
 557                                                 verbose="true"
 558                                                 properties="${schemaDir}/jalview.properties"
 559
 560                 />
 561                                 <!--
 562                 now build the jalview.binding package with the old schema set
 563                 -->
 564                                 <delete>
 565                                         <fileset dir="${sourceDir}/jalview/binding/">
 566                                                 <include name="**"/>
 567                                         </fileset>
 568                                 </delete>
 569                                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd"
 570                               todir="${sourceDir}"
 571                               package="jalview.binding"
 572                               warnings="false"
 573                                         nodesc="true"
 574                                                 verbose="true"
 575                                                 properties="${schemaDir}/jalview.nodesc.properties"
 576                 />
 577                                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
 578                               todir="${sourceDir}"
 579                               package="jalview.binding"
 580                               warnings="false"
 581                                         nodesc="true"
 582                                                 verbose="true"
 583                                                 properties="${schemaDir}/jalview.nodesc.properties"
 584                 />
 585                                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
 586                               todir="${sourceDir}"
 587                               package="jalview.binding"
 588                               warnings="false"
 589                                           nodesc="true"
 590                                                 verbose="true"
 591                                                 properties="${schemaDir}/jalview.nodesc.properties"
 592         />
 593                         </target>
 594                         <target name="sourcedist" description="create jalview source distribution" depends="init">
 595                                 <delete file="${source.dist.name}"/>
 596                                 <tar destfile="${source.dist.name}" compression="gzip">
 597                                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 598                                                 <include name="LICENSE"/>
 599                                                 <include name="README"/>
 600                                                 <include name="build.xml"/>
 601                                                 <include name="jalview-jalopy.xml"/>
 602                                                 <include name="JalviewApplet.jpx"/>
 603                                                 <include name="JalviewX.jpx"/>
 604                                                 <include name="${sourceDir}/*.java"/>
 605                                                 <include name="${sourceDir}/**/*.java"/>
 606                                                 <include name="${sourceDir}/**/*.cdr"/>
 607                                                 <include name="${libDir}/**/*"/>
 608                                                 <include name="${resourceDir}/**/*"/>
 609                                                 <include name="${helpDir}/**/*"/>
 610                                                 <exclude name="**/*locales"/>
 611                                                 <exclude name="*locales/**"/>
 612                                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml"/>
 613                                                 <exclude name="utils/InstallAnywhere/**Build*/**"/>
 614                                                 <exclude name="utils/InstallAnywhere/**Build*/**"/>
 615                                                 <exclude name="utils/InstallAnywhere/**locale*"/>
 616                                                 <exclude name="utils/InstallAnywhere/**locale*/**"/>
 617                                                 <include name="${schemaDir}/**/*"/>
 618                                                 <include name="utils/**/*"/>
 619                                                 <include name="${docDir}/**/*"/>
 620                                         </tarfileset>
 621                                 </tar>
 622                         </target>
 623                 </project>