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                 <property name="j2sev" value="1.6+"/>
  93                 <!-- build directory configuration -->
  94                 <property name="libDir" value="lib" />
  95                 <property name="resourceDir" value="resources" />
  96                 <property name="helpDir" value="help" />
  97                 <property name="docDir" value="doc" />
  98                 <property name="sourceDir" value="src" />
  99                 <property name="schemaDir" value="schemas" />
 100                 <property name="outputDir" value="classes" />
 101                 <property name="packageDir" value="dist" />
 102                 <property name="outputJar" value="jalview.jar" />
 103                 <!-- Jalview Applet JMol Jar Dependency -->
 104                 <property name="jmolJar" value="JmolApplet-12.1.13.jar" />
 105                 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 106                 <!-- switch to indicate if we should obfuscate jalviewLite -->
 107                 <!--<property name="donotobfuscate" value="true"/> -->
 108
 109                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 110                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 111                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 112                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 113                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 114                 <property name="WSInterf" value="MsaWS" />
 115                 <property name="wsdl.Namespace" value="vamsas" />
 116                 <property name="wsdl.ClientNS" value="ext.vamsas" />
 117                 <!-- the class path for building the application -->
 118                 <path id="build.classpath">
 119                         <fileset dir="utils">
 120                                 <include name="*.jar" />
 121                                 <include name="**/*.jar" />
 122                         </fileset>
 123                         <fileset dir="${libDir}">
 124                                 <include name="*.jar" />
 125                                 <include name="**/*.jar" />
 126                         </fileset>
 127                         <fileset dir="${java.home}/lib">
 128                                 <include name="plugin.jar"/>
 129                         </fileset>
 130                         <fileset dir="appletlib">
 131                                 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 132                                 -->
 133                                 <include name="${jmolJar}" />
 134                         </fileset>
 135
 136                 </path>
 137                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 138                 <!-- The Location of the java 1.1.8 jdk -->
 139                 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 140                 -->
 141                 <property name="java118.home" value="${java.home}" />
 142                     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 143                 --><!-- jre for 1.4 version -->
 144                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 145
 146                 <!-- the classpath for building the 1.1 applet -->
 147                 <path id="jalviewlite.deps">
 148                         <fileset dir="${java118.home}">
 149                                 <include name="lib/classes.zip" />
 150                         </fileset>
 151                         <fileset dir="${java.home}/lib">
 152                                 <include name="plugin.jar"/>
 153                         </fileset>
 154                         <pathelement location="appletlib/${jmolJar}" />
 155                 </path>
 156     <!-- default location for outputting javadoc -->
 157     <property name="javadocDir" value="${packageDir}/javadoc"/>
 158         </target>
 159
 160
 161         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 162         <target name="buildPropertiesFile" depends="init">
 163                 <tstamp prefix="build">
 164                         <format property="date" pattern="dd MMMM yyyy" />
 165                 </tstamp>
 166                 <properties file="${outputDir}/.build_properties">
 167                         <header>
 168           ---Jalview Build Details---
 169         </header>
 170                         <property name="VERSION" value="${JALVIEW_VERSION}" />
 171                         <property name="BUILD_DATE" value="${build.date}" />
 172                 </properties>
 173         </target>
 174
 175
 176         <target name="clean" depends="init">
 177                 <!-- not efficient yet. -->
 178                 <delete dir="${outputDir}" includes="*,**/*"/>
 179         </target>
 180
 181         <target name="distclean" depends="init, clean">
 182
 183                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 184                 <delete>
 185                         <fileset dir=".">
 186                                 <include name="${outputJar}" />
 187                                 <include name="#*#" />
 188                                 <include name="#*.*#" />
 189                                 <include name="**/#*#" />
 190                                 <include name="**/#*.*#" />
 191                                 <include name="*~" />
 192                                 <include name="*.*~" />
 193                                 <include name="**/*~" />
 194                                 <include name="**/*.*~" />
 195                         </fileset>
 196                 </delete>
 197         </target>
 198
 199         <target name="prepare" depends="init">
 200                 <mkdir dir="${outputDir}" />
 201                 <copy todir="${outputDir}">
 202                         <fileset dir=".">
 203                                 <include name="${docDir}/**/*.*" />
 204                                 <include name="${helpDir}/**/*.*" />
 205                                 <include name="${libDir}/*.jar" />
 206                         </fileset>
 207                         <fileset dir="${resourceDir}">
 208                                 <include name="**/*.*" />
 209                         </fileset>
 210                 </copy>
 211         </target>
 212
 213         <target name="build" depends="prepare">
 214                 <!-- not efficient yet. -->
 215                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 216                         <exclude name="jalview/*applet*" />
 217                         <exclude name="jalview/appletgui/**" />
 218                         <exclude name="com/stevesoft/**" />
 219                 </javac>
 220         </target>
 221         <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 222                 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 223                         <arg line="html" />
 224                 </java>
 225         </target>
 226
 227         <target name="makefulldist" depends="makedist">
 228                 <!-- the default keystore details might need to be edited here -->
 229                 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 230
 231                         <fileset dir="${packageDir}">
 232                                 <include name="*.jar" />
 233                         </fileset>
 234                 </signjar>
 235                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 236
 237                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 238                 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 239                 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 240                         <information>
 241                                 <title>Jalview</title>
 242                                 <vendor>The Barton Group</vendor>
 243                                 <homepage href="http://www.jalview.org" />
 244                                 <description>Jalview Multiple Alignment Editor</description>
 245                                 <description kind="short">Jalview</description>
 246                                 <icon href="logo_big.gif" />
 247                                 <offline_allowed />
 248                         </information>
 249                         <resources>
 250                                 <j2se version="${j2sev}" initial_heap_size="10M"  />
 251                                 <fileset dir="${packageDir}">
 252                                         <include name="jalview.jar" />
 253                                 </fileset>
 254                                 <fileset dir="${packageDir}">
 255                                         <include name="*.jar" />
 256                                         <include name="*_*.jar" />
 257                                         <exclude name="jalview.jar" />
 258                                 </fileset>
 259                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 260                         </resources>
 261                         <application_desc main_class="jalview.bin.Jalview">
 262                         </application_desc>
 263                         <security>
 264                                 <all_permissions />
 265                         </security>
 266                 </jnlp>
 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                         </information>
 277                         <resources>
 278                                 <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
 279                                 <fileset dir="${packageDir}">
 280                                         <include name="jalview.jar" />
 281                                 </fileset>
 282                                 <fileset dir="${packageDir}">
 283                                         <include name="*.jar" />
 284                                         <include name="*_*.jar" />
 285                                         <exclude name="jalview.jar" />
 286                                 </fileset>
 287                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 288                         </resources>
 289                         <application_desc main_class="jalview.bin.Jalview">
 290                         </application_desc>
 291                         <security>
 292                                 <all_permissions />
 293                         </security>
 294                 </jnlp>
 295                 <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
 296                         <information>
 297                                 <title>Jalview</title>
 298                                 <vendor>The Barton Group</vendor>
 299                                 <homepage href="http://www.jalview.org" />
 300                                 <description>Jalview Multiple Alignment Editor</description>
 301                                 <description kind="short">Jalview</description>
 302                                 <icon href="logo_big.gif" />
 303                                 <offline_allowed />
 304                         </information>
 305                         <resources>
 306                                 <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
 307                                 <fileset dir="${packageDir}">
 308                                         <include name="jalview.jar" />
 309                                 </fileset>
 310                                 <fileset dir="${packageDir}">
 311                                         <include name="*.jar" />
 312                                         <include name="*_*.jar" />
 313                                         <exclude name="jalview.jar" />
 314                                 </fileset>
 315                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 316                         </resources>
 317                         <application_desc main_class="jalview.bin.Jalview">
 318                         </application_desc>
 319                         <security>
 320                                 <all_permissions />
 321                         </security>
 322                 </jnlp>
 323                         <!-- finally, need to postprocess to add in associations at end of 'information' element
 324
 325                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 326
 327                 </xslt>
 328
 329
 330                         -->
 331                                         <!--
 332                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 333         <association mime-type="application-x/ext-file" extensions="fasta"/>
 334         <association mime-type="application-x/ext-file" extensions="fastq"/>
 335         <association mime-type="application-x/ext-file" extensions="blc"/>
 336         <association mime-type="application-x/ext-file" extensions="msf"/>
 337         <association mime-type="application-x/ext-file" extensions="pfam"/>
 338         <association mime-type="application-x/ext-file" extensions="aln"/>
 339         <association mime-type="application-x/ext-file" extensions="pir"/>
 340         <association mime-type="application-x/ext-file" extensions="amsa"/>
 341         <association mime-type="application-x/ext-file" extensions="stk"/>-->
 342
 343         </target>
 344
 345         <target name="runenv" depends="init">
 346                 <path id="run.classpath">
 347                         <pathelement location="${outputDir}" />
 348                         <fileset dir="${outputDir}">
 349                                 <include name="${libDir}/*.jar" />
 350                         </fileset>
 351                 </path>
 352                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 353
 354                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 355       </echo>
 356         </target>
 357
 358         <target name="buildextclients" depends="init">
 359                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 360                 <condition property="dontextbuild">
 361                         <equals arg1="n" arg2="${doextbuild.response}" />
 362                 </condition>
 363                 <condition property="dontextbuild">
 364                         <equals arg1="N" arg2="${doextbuild.response}" />
 365                 </condition>
 366                 <fail if="dontextbuild">
 367         Build External Client Code process aborted by user. Jalview source is unchanged.
 368       </fail>
 369                 <!-- Currently, this doesn't happen automatically.
 370      1. Run WSDL2Java as below, which generates an ext.vamsas +
 371      vamsas.<datapackages> fileset.
 372      2. refactor ext.vamsas.SpecificserviceWS* to
 373      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 374      3. Update the jalview.ws.*WServices classes to reflect the
 375      interface type, and all locations of this wsdl type that Jalview
 376      might be using.
 377
 378 -->
 379                 <path id="axisbuild">
 380                         <path refid="build.classpath" />
 381                 </path>
 382                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 383                 <move todir="./bak">
 384                         <fileset dir="${sourceDir}" id="client">
 385                                 <include name="${wsdl.ClientNS}/*.*" />
 386                         </fileset>
 387                 </move>
 388
 389                 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 390                         <mappingSet>
 391                                 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 392                                 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 393                         </mappingSet>
 394                 </axis-wsdl2java>
 395         </target>
 396
 397         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 398                 <!-- make the package jar if not already existing -->
 399                 <mkdir dir="${packageDir}" />
 400                 <!-- clean dir if it already existed -->
 401                 <delete>
 402                         <fileset dir="${packageDir}">
 403                                 <include name="*.jar"/>
 404                         </fileset>
 405                 </delete>
 406                 <jar destfile="${packageDir}/${outputJar}">
 407                         <manifest>
 408                                 <attribute name="Main-Class" value="jalview.bin.Jalview" />
 409                         </manifest>
 410                         <fileset dir="${outputDir}/">
 411                                 <exclude name="cache*/**" />
 412                                 <exclude name="*.jar" />
 413                                 <exclude name="*.jar.*" />
 414                                 <exclude name="**/*.jar" />
 415                                 <exclude name="**/*.jar.*" />
 416                         </fileset>
 417                 </jar>
 418
 419                 <copy toDir="${packageDir}" flatten="true">
 420                         <fileset dir="${outputDir}">
 421                                 <include name="*.jar" />
 422                                 <include name="**/*.jar" />
 423                         </fileset>
 424                 </copy>
 425         </target>
 426
 427
 428         <!-- jalopy code reformatter -->
 429         <target name="sourcescrub" depends="init,build">
 430                 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 431                         <fileset dir="${sourceDir}">
 432                                 <include name="*.java" />
 433                                 <include name="**/*.java" />
 434                                 <include name="**/**/*.java" />
 435                         </fileset>
 436                 </jalopy>
 437         </target>
 438
 439
 440
 441         <!-- Compile, package and obfuscate Jalview Applet -->
 442         <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 443
 444         <target name="compileApplet" depends="init,clean">
 445                 <mkdir dir="${outputDir}" />
 446                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 447                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 448                         excludes="ext/**,MCview/**,org/**,vamsas/**" />
 449         </target>
 450
 451         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 452                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 453                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 454                 <jar destfile="in.jar">
 455                         <manifest>
 456                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 457                         </manifest>
 458                         <fileset dir="${outputDir}">
 459                                 <include name="com/**" />
 460                                 <include name="MCview/**" />
 461                                 <include name="jalview/**" />
 462                                 <include name=".build_properties" />
 463                                 <include name="images/idwidth.gif" />
 464                                 <include name="images/link.gif" />
 465                         </fileset>
 466                 </jar>
 467         </target>
 468         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 469         </target>
 470         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 471                 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 472                 <delete file="in.jar" />
 473         </target>
 474         <target name="-obfuscatereally" unless="donotobfuscate">
 475
 476                 <path id="obfuscateDeps.path">
 477                         <pathelement location="${applet.jre.tools}" />
 478                         <pathelement location="appletlib/${jmolJar}" />
 479                 </path>
 480                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 481
 482                 <proguard>
 483                         <injar file="in.jar" />
 484                         <outjar file="${jalviewLiteJar}" />
 485                         <libraryjar refid="obfuscateDeps.path" />
 486                         <keep access="public" type="class" name="jalview.bin.JalviewLite">
 487                                 <field access="public" />
 488                                 <method access="public" />
 489                                 <constructor access="public" />
 490                         </keep>
 491                         <!--      -libraryjars "${obfuscateDeps}"
 492       -injars      in.jar
 493       -outjars     jalviewApplet.jar
 494       -keep public class jalview.bin.JalviewLite
 495        { public * ; } -->
 496                 </proguard>
 497                 <delete file="in.jar" />
 498         </target>
 499
 500         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 501                 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 502                 <delete>
 503                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 504                                 <include name="*.java" />
 505                                 <include name="descriptors/*.java" />
 506                         </fileset>
 507                 </delete>
 508                 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 509                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 510                 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 511                 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 512                 <!--
 513                 now build the jalview.binding package with the old schema set
 514                 -->
 515                 <delete>
 516                         <fileset dir="${sourceDir}/jalview/binding/">
 517                                 <include name="**" />
 518                         </fileset>
 519                 </delete>
 520                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 521                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 522                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 523         </target>
 524         <target name="sourcedist" description="create jalview source distribution" depends="init">
 525                 <delete file="${source.dist.name}" />
 526                 <tar destfile="${source.dist.name}" compression="gzip">
 527                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 528                                 <include name="LICENSE" />
 529                                 <include name="README" />
 530                                 <include name="build.xml" />
 531                                 <include name="jalview-jalopy.xml" />
 532                                 <include name="JalviewApplet.jpx" />
 533                                 <include name="JalviewX.jpx" />
 534                                 <include name="nbbuild.xml"/>
 535                                 <include name="nbproject/genfiles.properties"/>
 536         <include name="nbproject/project.properties"/>
 537         <include name="nbproject/project.xml"/>
 538                                 <include name="${sourceDir}/*.java" />
 539                                 <include name="${sourceDir}/**/*.java" />
 540                                 <include name="${sourceDir}/**/*.cdr" />
 541                                 <include name="${libDir}/**/*" />
 542                                 <include name="${resourceDir}/**/*" />
 543                                 <include name="${helpDir}/**/*" />
 544                                 <include name="appletlib/${jmolJar}" />
 545                                 <exclude name="**/*locales" />
 546                                 <exclude name="*locales/**" />
 547                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 548                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 549                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 550                                 <exclude name="utils/InstallAnywhere/**locale*" />
 551                                 <exclude name="utils/InstallAnywhere/**locale*/**" />
 552                                 <include name="${schemaDir}/**/*" />
 553                                 <include name="utils/**/*" />
 554                                 <include name="${docDir}/**/*" />
 555                                 <include name="examples/**/*" />
 556                         </tarfileset>
 557                 </tar>
 558         </target>
 559         <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 560           <copy todir="${packageDir}/examples">
 561           <fileset dir="examples">
 562                 <include name="**/*"/>
 563                 <include name="javascript/*"/>
 564       <include name="jmol/*"/>
 565           </fileset>
 566                 <fileset dir=".">
 567                 <include name="jalviewApplet.jar"/>
 568                         </fileset>
 569                 <fileset dir="appletlib">
 570                       <include name="**/*"/>
 571                         </fileset>
 572           </copy>
 573
 574         </target>
 575         <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 576          <javadoc destdir="${javadocDir}">
 577                 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 578                 </packageset>
 579                 </javadoc>
 580         </target>
 581
 582 </project>