build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   4  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18 -->
  19 <project name="jalviewX" default="usage" basedir=".">
  20         <!-- we use jalopy to format our sources -->
  21         <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
  22                 <classpath>
  23                         <fileset dir="utils/jalopy/lib">
  24                                 <include name="*.jar" />
  25                         </fileset>
  26                 </classpath>
  27         </taskdef>
  28
  29         <target name="help" depends="usage" />
  30         <target name="usage">
  31                 <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  32                 <echo message="Targets include:" />
  33                 <echo message="usage - default target, displays this message" />
  34                 <echo message="buildindices - generates JavaHelpSearch from the help files" />
  35                 <echo message="build - compiles all necessary files for Application" />
  36                 <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  37                 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  38                 <echo message="              this needs a keystore and key. See docs/building.html for more information." />
  39                 <echo message="compileApplet - compiles all necessary files for Applet" />
  40                 <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  41                 <echo message="See docs/building.html and the comments in build file for other targets." />
  42                 <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  43                 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  44         </target>
  45
  46
  47         <!-- utils is a class path to additional utilities needed for
  48     building docs, jars and webstart stuff -->
  49         <!--
  50         Userdefined build property defaults
  51
  52         wsdl.server list (plus namespace mapping info ???)  - also want
  53                 ... to make this a dynamically generatable property
  54         WebStart Location
  55         Build location - provide a temporary root for speed
  56         jarsigner keystore and info
  57         Jakarta and axis classpath ?
  58         Default argument for starting Jalview (if it exists).
  59
  60 -->
  61
  62         <target name="init">
  63                 <path id="axis.classpath">
  64                         <!-->
  65                         <fileset dir="/usr/local/axis/lib">
  66                                 <include name="**/*.jar" />
  67                         </fileset>
  68                         <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  69                                 <include name="**/*.jar"/>
  70                                 <include name="*.jar"/>
  71                         </fileset> -->
  72       </path>
  73                 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  74                 <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  75                 <!-- 2.4 (VAMSAS)" -->
  76                 <!-- Include debugging information in javac true or false -->
  77                 <property name="javac.debug" value="true" />
  78
  79                 <!-- JarSigner Key Store for Webstart Distribution -->
  80                 <property name="jalview.keystore" value="./keys/.keystore" />
  81                 <!-- Keystore Password -->
  82                 <property name="jalview.keystore.pass" value="alignmentisfun" />
  83                 <!-- Key Name -->
  84                 <property name="jalview.key" value="jalview" />
  85                 <!-- Key Password -->
  86                 <property name="jalview.key.pass" value="alignmentisfun" />
  87
  88                 <!-- 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                 <!-- J2SE version needed for webstart launch -->
  92 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  93                 <property name="j2sev" value="1.7+"/>
  94                 <!-- build directory configuration -->
  95                 <property name="libDir" value="lib" />
  96                 <property name="resourceDir" value="resources" />
  97                 <property name="helpDir" value="help" />
  98                 <property name="docDir" value="doc" />
  99                 <property name="sourceDir" value="src" />
 100                 <property name="schemaDir" value="schemas" />
 101                 <property name="outputDir" value="classes" />
 102                 <property name="packageDir" value="dist" />
 103                 <property name="outputJar" value="jalview.jar" />
 104                 <!-- Jalview Applet JMol Jar Dependency -->
 105                 <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 106                 <property name="varnaJar" value="VARNAv3-9-dev.jar" />
 107                 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 108                 <!-- switch to indicate if we should obfuscate jalviewLite -->
 109                 <!--<property name="donotobfuscate" value="true"/> -->
 110
 111                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 112                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 113                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 114                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 115                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 116                 <property name="WSInterf" value="MsaWS" />
 117                 <property name="wsdl.Namespace" value="vamsas" />
 118                 <property name="wsdl.ClientNS" value="ext.vamsas" />
 119                 <!-- the class path for building the application -->
 120                 <path id="build.classpath">
 121                         <fileset dir="utils">
 122                                 <include name="*.jar" />
 123                                 <include name="**/*.jar" />
 124                         </fileset>
 125                         <fileset dir="${libDir}">
 126                                 <include name="*.jar" />
 127                                 <include name="**/*.jar" />
 128                         </fileset>
 129                         <fileset dir="${java.home}/lib">
 130                                 <include name="plugin.jar"/>
 131                         </fileset>
 132                         <fileset dir="appletlib">
 133                                 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 134                                 -->
 135                                 <include name="${jmolJar}" />
 136                                 <include name="${varnaJar}" />
 137                         </fileset>
 138
 139                 </path>
 140                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 141                 <!-- The Location of the java 1.1.8 jdk -->
 142                 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 143                 -->
 144                 <property name="java118.home" value="${java.home}" />
 145                     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 146                 --><!-- jre for 1.4 version -->
 147                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 148
 149                 <!-- the classpath for building the 1.1 applet -->
 150                 <path id="jalviewlite.deps">
 151                         <fileset dir="${java118.home}">
 152                                 <include name="lib/classes.zip" />
 153                         </fileset>
 154                         <fileset dir="${java.home}/lib">
 155                                 <include name="plugin.jar"/>
 156                         </fileset>
 157                         <pathelement location="appletlib/${jmolJar}" />
 158                 </path>
 159     <!-- default location for outputting javadoc -->
 160     <property name="javadocDir" value="${packageDir}/javadoc"/>
 161         </target>
 162
 163
 164         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 165         <target name="buildPropertiesFile" depends="init">
 166                 <tstamp prefix="build">
 167                         <format property="date" pattern="dd MMMM yyyy" />
 168                 </tstamp>
 169                 <properties file="${outputDir}/.build_properties">
 170                         <header>
 171           ---Jalview Build Details---
 172         </header>
 173                         <property name="VERSION" value="${JALVIEW_VERSION}" />
 174                         <property name="BUILD_DATE" value="${build.date}" />
 175                 </properties>
 176         </target>
 177
 178
 179         <target name="clean" depends="init">
 180                 <!-- not efficient yet. -->
 181                 <delete dir="${outputDir}" includes="*,**/*"/>
 182         </target>
 183
 184         <target name="distclean" depends="init, clean">
 185
 186                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 187                 <delete>
 188                         <fileset dir=".">
 189                                 <include name="${outputJar}" />
 190                                 <include name="#*#" />
 191                                 <include name="#*.*#" />
 192                                 <include name="**/#*#" />
 193                                 <include name="**/#*.*#" />
 194                                 <include name="*~" />
 195                                 <include name="*.*~" />
 196                                 <include name="**/*~" />
 197                                 <include name="**/*.*~" />
 198                         </fileset>
 199                 </delete>
 200         </target>
 201
 202         <target name="prepare" depends="init">
 203                 <mkdir dir="${outputDir}" />
 204                 <copy todir="${outputDir}">
 205                         <fileset dir=".">
 206                                 <include name="${docDir}/**/*.*" />
 207                                 <include name="${helpDir}/**/*.*" />
 208                                 <include name="${libDir}/*.jar" />
 209                         </fileset>
 210                         <fileset dir="${resourceDir}">
 211                                 <include name="**/*.*" />
 212                         </fileset>
 213                 </copy>
 214         </target>
 215
 216         <target name="build" depends="prepare">
 217                 <!-- not efficient yet. -->
 218                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 219                         <exclude name="jalview/*applet*" />
 220                         <exclude name="jalview/appletgui/**" />
 221                         <exclude name="com/stevesoft/**" />
 222                 </javac>
 223         </target>
 224         <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 225                 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 226                         <arg line="html" />
 227                 </java>
 228         </target>
 229
 230         <target name="makefulldist" depends="makedist">
 231                 <!-- the default keystore details might need to be edited here -->
 232                 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 233
 234                         <fileset dir="${packageDir}">
 235                                 <include name="*.jar" />
 236                         </fileset>
 237                 </signjar>
 238                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 239
 240                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 241                 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 242                 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 243                         <information>
 244                                 <title>Jalview</title>
 245                                 <vendor>The Barton Group</vendor>
 246                                 <homepage href="http://www.jalview.org" />
 247                                 <description>Jalview Multiple Alignment Editor</description>
 248                                 <description kind="short">Jalview</description>
 249                                 <icon href="logo_big.gif" />
 250                                 <offline_allowed />
 251                         </information>
 252                         <resources>
 253                                 <j2se version="${j2sev}" initial_heap_size="10M"  />
 254                                 <fileset dir="${packageDir}">
 255                                         <include name="jalview.jar" />
 256                                 </fileset>
 257                                 <fileset dir="${packageDir}">
 258                                         <include name="*.jar" />
 259                                         <include name="*_*.jar" />
 260                                         <exclude name="jalview.jar" />
 261                                 </fileset>
 262                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 263                         </resources>
 264                         <application_desc main_class="jalview.bin.Jalview">
 265                         </application_desc>
 266                         <security>
 267                                 <all_permissions />
 268                         </security>
 269                 </jnlp>
 270                 <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 271                         <information>
 272                                 <title>Jalview</title>
 273                                 <vendor>The Barton Group</vendor>
 274                                 <homepage href="http://www.jalview.org" />
 275                                 <description>Jalview Multiple Alignment Editor</description>
 276                                 <description kind="short">Jalview</description>
 277                                 <icon href="logo_big.gif" />
 278                                 <offline_allowed />
 279                         </information>
 280                         <resources>
 281                                 <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
 282                                 <fileset dir="${packageDir}">
 283                                         <include name="jalview.jar" />
 284                                 </fileset>
 285                                 <fileset dir="${packageDir}">
 286                                         <include name="*.jar" />
 287                                         <include name="*_*.jar" />
 288                                         <exclude name="jalview.jar" />
 289                                 </fileset>
 290                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 291                         </resources>
 292                         <application_desc main_class="jalview.bin.Jalview">
 293                         </application_desc>
 294                         <security>
 295                                 <all_permissions />
 296                         </security>
 297                 </jnlp>
 298                 <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
 299                         <information>
 300                                 <title>Jalview</title>
 301                                 <vendor>The Barton Group</vendor>
 302                                 <homepage href="http://www.jalview.org" />
 303                                 <description>Jalview Multiple Alignment Editor</description>
 304                                 <description kind="short">Jalview</description>
 305                                 <icon href="logo_big.gif" />
 306                                 <offline_allowed />
 307                         </information>
 308                         <resources>
 309                                 <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
 310                                 <fileset dir="${packageDir}">
 311                                         <include name="jalview.jar" />
 312                                 </fileset>
 313                                 <fileset dir="${packageDir}">
 314                                         <include name="*.jar" />
 315                                         <include name="*_*.jar" />
 316                                         <exclude name="jalview.jar" />
 317                                 </fileset>
 318                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 319                         </resources>
 320                         <application_desc main_class="jalview.bin.Jalview">
 321                         </application_desc>
 322                         <security>
 323                                 <all_permissions />
 324                         </security>
 325                 </jnlp>
 326                         <!-- finally, need to postprocess to add in associations at end of 'information' element
 327
 328                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 329
 330                 </xslt>
 331
 332
 333                         -->
 334                                         <!--
 335                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 336         <association mime-type="application-x/ext-file" extensions="fasta"/>
 337         <association mime-type="application-x/ext-file" extensions="fastq"/>
 338         <association mime-type="application-x/ext-file" extensions="blc"/>
 339         <association mime-type="application-x/ext-file" extensions="msf"/>
 340         <association mime-type="application-x/ext-file" extensions="pfam"/>
 341         <association mime-type="application-x/ext-file" extensions="aln"/>
 342         <association mime-type="application-x/ext-file" extensions="pir"/>
 343         <association mime-type="application-x/ext-file" extensions="amsa"/>
 344         <association mime-type="application-x/ext-file" extensions="stk"/>-->
 345
 346         </target>
 347
 348         <target name="runenv" depends="init">
 349                 <path id="run.classpath">
 350                         <pathelement location="${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" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 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}"
 450                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 451                         excludes="ext/**,MCview/**,org/**,vamsas/**" />
 452         </target>
 453
 454         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 455                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 456                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 457                 <jar destfile="in.jar">
 458                         <manifest>
 459                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 460                         </manifest>
 461                         <fileset dir="${outputDir}">
 462                                 <include name="com/**" />
 463                                 <include name="MCview/**" />
 464                                 <include name="jalview/**" />
 465                                 <include name=".build_properties" />
 466                                 <include name="images/idwidth.gif" />
 467                                 <include name="images/link.gif" />
 468                         </fileset>
 469                 </jar>
 470         </target>
 471         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 472         </target>
 473         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 474                 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 475                 <delete file="in.jar" />
 476         </target>
 477         <target name="-obfuscatereally" unless="donotobfuscate">
 478
 479                 <path id="obfuscateDeps.path">
 480                         <pathelement location="${applet.jre.tools}" />
 481                         <pathelement location="appletlib/${jmolJar}" />
 482                 </path>
 483                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 484
 485                 <proguard>
 486                         <injar file="in.jar" />
 487                         <outjar file="${jalviewLiteJar}" />
 488                         <libraryjar refid="obfuscateDeps.path" />
 489                         <keep access="public" type="class" name="jalview.bin.JalviewLite">
 490                                 <field access="public" />
 491                                 <method access="public" />
 492                                 <constructor access="public" />
 493                         </keep>
 494                         <!--      -libraryjars "${obfuscateDeps}"
 495       -injars      in.jar
 496       -outjars     jalviewApplet.jar
 497       -keep public class jalview.bin.JalviewLite
 498        { public * ; } -->
 499                 </proguard>
 500                 <delete file="in.jar" />
 501         </target>
 502
 503         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 504                 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 505                 <delete>
 506                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 507                                 <include name="*.java" />
 508                                 <include name="descriptors/*.java" />
 509                         </fileset>
 510                 </delete>
 511                 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 512                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 513                 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 514                 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 515                 <!--
 516                 now build the jalview.binding package with the old schema set
 517                 -->
 518                 <delete>
 519                         <fileset dir="${sourceDir}/jalview/binding/">
 520                                 <include name="**" />
 521                         </fileset>
 522                 </delete>
 523                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 524                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 525                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 526         </target>
 527         <target name="sourcedist" description="create jalview source distribution" depends="init">
 528                 <delete file="${source.dist.name}" />
 529                 <tar destfile="${source.dist.name}" compression="gzip">
 530                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 531                                 <include name="LICENSE" />
 532                                 <include name="README" />
 533                                 <include name="build.xml" />
 534                                 <include name="jalview-jalopy.xml" />
 535                                 <include name="JalviewApplet.jpx" />
 536                                 <include name="JalviewX.jpx" />
 537                                 <include name="nbbuild.xml"/>
 538                                 <include name="nbproject/genfiles.properties"/>
 539         <include name="nbproject/project.properties"/>
 540         <include name="nbproject/project.xml"/>
 541                                 <include name="${sourceDir}/*.java" />
 542                                 <include name="${sourceDir}/**/*.java" />
 543                                 <include name="${sourceDir}/**/*.cdr" />
 544                                 <include name="${libDir}/**/*" />
 545                                 <include name="${resourceDir}/**/*" />
 546                                 <include name="${helpDir}/**/*" />
 547                                 <include name="appletlib/${jmolJar}" />
 548                                 <exclude name="**/*locales" />
 549                                 <exclude name="*locales/**" />
 550                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 551                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 552                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 553                                 <exclude name="utils/InstallAnywhere/**locale*" />
 554                                 <exclude name="utils/InstallAnywhere/**locale*/**" />
 555                                 <include name="${schemaDir}/**/*" />
 556                                 <include name="utils/**/*" />
 557                                 <include name="${docDir}/**/*" />
 558                                 <include name="examples/**/*" />
 559                         </tarfileset>
 560                 </tar>
 561         </target>
 562         <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 563           <copy todir="${packageDir}/examples">
 564           <fileset dir="examples">
 565                 <include name="**/*"/>
 566                 <include name="javascript/*"/>
 567       <include name="jmol/*"/>
 568           </fileset>
 569                 <fileset dir=".">
 570                 <include name="jalviewApplet.jar"/>
 571                         </fileset>
 572                 <fileset dir="appletlib">
 573                       <include name="**/*"/>
 574                         </fileset>
 575           </copy>
 576
 577         </target>
 578         <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 579          <javadoc destdir="${javadocDir}">
 580                 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 581                 </packageset>
 582                 </javadoc>
 583         </target>
 584
 585 </project>