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                 <!-- Webstart Image - looked for in resources/images -->
  92                 <property name="WebStartImage" value="JalviewLogo_big.png"/>
  93                 <!-- J2SE version needed for webstart launch -->
  94 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  95                 <property name="j2sev" value="1.7+"/>
  96                 <!-- build directory configuration -->
  97                 <property name="libDir" value="lib" />
  98                 <property name="resourceDir" value="resources" />
  99                 <property name="helpDir" value="help" />
 100                 <property name="docDir" value="doc" />
 101                 <property name="sourceDir" value="src" />
 102                 <property name="schemaDir" value="schemas" />
 103                 <property name="outputDir" value="classes" />
 104                 <property name="packageDir" value="dist" />
 105                 <property name="outputJar" value="jalview.jar" />
 106                 <!-- Jalview Applet JMol Jar Dependency -->
 107                 <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 108                 <property name="varnaJar" value="VARNAv3-9-dev.jar" />
 109                 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 110                 <!-- switch to indicate if we should obfuscate jalviewLite -->
 111                 <!--<property name="donotobfuscate" value="true"/> -->
 112
 113                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 114                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 115                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 116                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 117                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 118                 <property name="WSInterf" value="MsaWS" />
 119                 <property name="wsdl.Namespace" value="vamsas" />
 120                 <property name="wsdl.ClientNS" value="ext.vamsas" />
 121                 <!-- the class path for building the application -->
 122                 <path id="build.classpath">
 123                         <fileset dir="utils">
 124                                 <include name="*.jar" />
 125                                 <include name="**/*.jar" />
 126                         </fileset>
 127                         <fileset dir="${libDir}">
 128                                 <include name="*.jar" />
 129                                 <include name="**/*.jar" />
 130                         </fileset>
 131                         <fileset dir="${java.home}/lib">
 132                                 <include name="plugin.jar"/>
 133                         </fileset>
 134                         <fileset dir="appletlib">
 135                                 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 136                                 -->
 137                                 <include name="${jmolJar}" />
 138                                 <include name="${varnaJar}" />
 139                         </fileset>
 140
 141                 </path>
 142                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 143                 <!-- The Location of the java 1.1.8 jdk -->
 144                 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 145                 -->
 146                 <property name="java118.home" value="${java.home}" />
 147                     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 148                 --><!-- jre for 1.4 version -->
 149                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 150
 151                 <!-- the classpath for building the 1.1 applet -->
 152                 <path id="jalviewlite.deps">
 153                         <fileset dir="${java118.home}">
 154                                 <include name="lib/classes.zip" />
 155                         </fileset>
 156                         <fileset dir="${java.home}/lib">
 157                                 <include name="plugin.jar"/>
 158                         </fileset>
 159                         <pathelement location="appletlib/${jmolJar}" />
 160                 </path>
 161     <!-- default location for outputting javadoc -->
 162     <property name="javadocDir" value="${packageDir}/javadoc"/>
 163         </target>
 164
 165
 166         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 167         <target name="buildPropertiesFile" depends="init">
 168                 <tstamp prefix="build">
 169                         <format property="date" pattern="dd MMMM yyyy" />
 170                 </tstamp>
 171                 <properties file="${outputDir}/.build_properties">
 172                         <header>
 173           ---Jalview Build Details---
 174         </header>
 175                         <property name="VERSION" value="${JALVIEW_VERSION}" />
 176                         <property name="BUILD_DATE" value="${build.date}" />
 177                 </properties>
 178         </target>
 179
 180
 181         <target name="clean" depends="init">
 182                 <!-- not efficient yet. -->
 183                 <delete dir="${outputDir}" includes="*,**/*"/>
 184         </target>
 185
 186         <target name="distclean" depends="init, clean">
 187
 188                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 189                 <delete>
 190                         <fileset dir=".">
 191                                 <include name="${outputJar}" />
 192                                 <include name="#*#" />
 193                                 <include name="#*.*#" />
 194                                 <include name="**/#*#" />
 195                                 <include name="**/#*.*#" />
 196                                 <include name="*~" />
 197                                 <include name="*.*~" />
 198                                 <include name="**/*~" />
 199                                 <include name="**/*.*~" />
 200                         </fileset>
 201                 </delete>
 202         </target>
 203
 204         <target name="prepare" depends="init">
 205                 <mkdir dir="${outputDir}" />
 206                 <copy todir="${outputDir}">
 207                         <fileset dir=".">
 208                                 <include name="${docDir}/**/*.*" />
 209                                 <include name="${helpDir}/**/*.*" />
 210                                 <include name="${libDir}/*.jar" />
 211                         </fileset>
 212                         <fileset dir="${resourceDir}">
 213                                 <include name="**/*.*" />
 214                         </fileset>
 215                 </copy>
 216         </target>
 217
 218         <target name="build" depends="prepare">
 219                 <!-- not efficient yet. -->
 220                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 221                         <exclude name="jalview/*applet*" />
 222                         <exclude name="jalview/appletgui/**" />
 223                         <exclude name="com/stevesoft/**" />
 224                 </javac>
 225         </target>
 226         <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 227                 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 228                         <arg line="html" />
 229                 </java>
 230         </target>
 231
 232         <target name="makefulldist" depends="makedist">
 233                 <!-- the default keystore details might need to be edited here -->
 234                 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 235
 236                         <fileset dir="${packageDir}">
 237                                 <include name="*.jar" />
 238                         </fileset>
 239                 </signjar>
 240                 <copy todir="${packageDir}">
 241                         <fileset dir="${resourceDir}/images">
 242                                 <include name="${WebStartImage}"/>
 243                         </fileset>
 244                                         </copy>
 245
 246                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 247
 248                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 249                 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 250                 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 251                         <information>
 252                                 <title>Jalview</title>
 253                                 <vendor>The Barton Group</vendor>
 254                                 <homepage href="http://www.jalview.org" />
 255                                 <description>Jalview Multiple Alignment Editor</description>
 256                                 <description kind="short">Jalview</description>
 257                                 <icon href="${WebStartImage}" />
 258                                 <offline_allowed/>
 259                         </information>
 260                         <resources>
 261                                 <j2se version="${j2sev}" initial_heap_size="10M"  />
 262                                 <fileset dir="${packageDir}">
 263                                         <include name="jalview.jar" />
 264                                 </fileset>
 265                                 <fileset dir="${packageDir}">
 266                                         <include name="*.jar" />
 267                                         <include name="*_*.jar" />
 268                                         <exclude name="jalview.jar" />
 269                                 </fileset>
 270                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 271                         </resources>
 272                         <application_desc main_class="jalview.bin.Jalview">
 273                         </application_desc>
 274                         <security>
 275                                 <all_permissions />
 276                         </security>
 277                 </jnlp>
 278                 <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 279                         <information>
 280                                 <title>Jalview</title>
 281                                 <vendor>The Barton Group</vendor>
 282                                 <homepage href="http://www.jalview.org" />
 283                                 <description>Jalview Multiple Alignment Editor</description>
 284                                 <description kind="short">Jalview</description>
 285                                 <icon href="${WebStartImage}" />
 286                                 <offline_allowed />
 287                         </information>
 288                         <resources>
 289                                 <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
 290                                 <fileset dir="${packageDir}">
 291                                         <include name="jalview.jar" />
 292                                 </fileset>
 293                                 <fileset dir="${packageDir}">
 294                                         <include name="*.jar" />
 295                                         <include name="*_*.jar" />
 296                                         <exclude name="jalview.jar" />
 297                                 </fileset>
 298                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 299                         </resources>
 300                         <application_desc main_class="jalview.bin.Jalview">
 301                         </application_desc>
 302                         <security>
 303                                 <all_permissions />
 304                         </security>
 305                 </jnlp>
 306                 <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
 307                         <information>
 308                                 <title>Jalview</title>
 309                                 <vendor>The Barton Group</vendor>
 310                                 <homepage href="http://www.jalview.org" />
 311                                 <description>Jalview Multiple Alignment Editor</description>
 312                                 <description kind="short">Jalview</description>
 313                                 <icon href="${WebStartImage}" />
 314                                 <offline_allowed />
 315                         </information>
 316                         <resources>
 317                                 <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
 318                                 <fileset dir="${packageDir}">
 319                                         <include name="jalview.jar" />
 320                                 </fileset>
 321                                 <fileset dir="${packageDir}">
 322                                         <include name="*.jar" />
 323                                         <include name="*_*.jar" />
 324                                         <exclude name="jalview.jar" />
 325                                 </fileset>
 326                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 327                         </resources>
 328                         <application_desc main_class="jalview.bin.Jalview">
 329                         </application_desc>
 330                         <security>
 331                                 <all_permissions />
 332                         </security>
 333                 </jnlp>
 334                         <!-- finally, need to postprocess to add in associations at end of 'information' element
 335
 336                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 337
 338                 </xslt>
 339
 340
 341                         -->
 342                                         <!--
 343                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 344         <association mime-type="application-x/ext-file" extensions="fasta"/>
 345         <association mime-type="application-x/ext-file" extensions="fastq"/>
 346         <association mime-type="application-x/ext-file" extensions="blc"/>
 347         <association mime-type="application-x/ext-file" extensions="msf"/>
 348         <association mime-type="application-x/ext-file" extensions="pfam"/>
 349         <association mime-type="application-x/ext-file" extensions="aln"/>
 350         <association mime-type="application-x/ext-file" extensions="pir"/>
 351         <association mime-type="application-x/ext-file" extensions="amsa"/>
 352         <association mime-type="application-x/ext-file" extensions="stk"/>
 353         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 354
 355         </target>
 356
 357         <target name="runenv" depends="init">
 358                 <path id="run.classpath">
 359                         <pathelement location="${outputDir}" />
 360                         <fileset dir="${outputDir}">
 361                                 <include name="${libDir}/*.jar" />
 362                         </fileset>
 363                 </path>
 364                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 365
 366                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 367       </echo>
 368         </target>
 369
 370         <target name="buildextclients" depends="init">
 371                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 372                 <condition property="dontextbuild">
 373                         <equals arg1="n" arg2="${doextbuild.response}" />
 374                 </condition>
 375                 <condition property="dontextbuild">
 376                         <equals arg1="N" arg2="${doextbuild.response}" />
 377                 </condition>
 378                 <fail if="dontextbuild">
 379         Build External Client Code process aborted by user. Jalview source is unchanged.
 380       </fail>
 381                 <!-- Currently, this doesn't happen automatically.
 382      1. Run WSDL2Java as below, which generates an ext.vamsas +
 383      vamsas.<datapackages> fileset.
 384      2. refactor ext.vamsas.SpecificserviceWS* to
 385      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 386      3. Update the jalview.ws.*WServices classes to reflect the
 387      interface type, and all locations of this wsdl type that Jalview
 388      might be using.
 389
 390 -->
 391                 <path id="axisbuild">
 392                         <path refid="build.classpath" />
 393                 </path>
 394                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 395                 <move todir="./bak">
 396                         <fileset dir="${sourceDir}" id="client">
 397                                 <include name="${wsdl.ClientNS}/*.*" />
 398                         </fileset>
 399                 </move>
 400
 401                 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 402                         <mappingSet>
 403                                 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 404                                 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 405                         </mappingSet>
 406                 </axis-wsdl2java>
 407         </target>
 408
 409         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 410                 <!-- make the package jar if not already existing -->
 411                 <mkdir dir="${packageDir}" />
 412                 <!-- clean dir if it already existed -->
 413                 <delete>
 414                         <fileset dir="${packageDir}">
 415                                 <include name="*.jar"/>
 416                         </fileset>
 417                 </delete>
 418                 <jar destfile="${packageDir}/${outputJar}">
 419                         <manifest>
 420                                 <attribute name="Main-Class" value="jalview.bin.Jalview" />
 421                         </manifest>
 422                         <fileset dir="${outputDir}/">
 423                                 <exclude name="cache*/**" />
 424                                 <exclude name="*.jar" />
 425                                 <exclude name="*.jar.*" />
 426                                 <exclude name="**/*.jar" />
 427                                 <exclude name="**/*.jar.*" />
 428                         </fileset>
 429                 </jar>
 430
 431                 <copy toDir="${packageDir}" flatten="true">
 432                         <fileset dir="${outputDir}">
 433                                 <include name="*.jar" />
 434                                 <include name="**/*.jar" />
 435                         </fileset>
 436                 </copy>
 437         </target>
 438
 439
 440         <!-- jalopy code reformatter -->
 441         <target name="sourcescrub" depends="init,build">
 442                 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 443                         <fileset dir="${sourceDir}">
 444                                 <include name="*.java" />
 445                                 <include name="**/*.java" />
 446                                 <include name="**/**/*.java" />
 447                         </fileset>
 448                 </jalopy>
 449         </target>
 450
 451
 452
 453         <!-- Compile, package and obfuscate Jalview Applet -->
 454         <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 455
 456         <target name="compileApplet" depends="init,clean">
 457                 <mkdir dir="${outputDir}" />
 458                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 459                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 460                         excludes="ext/**,MCview/**,org/**,vamsas/**" />
 461         </target>
 462
 463         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 464                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 465                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 466                 <jar destfile="in.jar">
 467                         <manifest>
 468                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 469                         </manifest>
 470                         <fileset dir="${outputDir}">
 471                                 <include name="com/**" />
 472                                 <include name="MCview/**" />
 473                                 <include name="jalview/**" />
 474                                 <include name=".build_properties" />
 475                                 <include name="images/idwidth.gif" />
 476                                 <include name="images/link.gif" />
 477                         </fileset>
 478                 </jar>
 479         </target>
 480         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 481         </target>
 482         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 483                 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 484                 <delete file="in.jar" />
 485         </target>
 486         <target name="-obfuscatereally" unless="donotobfuscate">
 487
 488                 <path id="obfuscateDeps.path">
 489                         <pathelement location="${applet.jre.tools}" />
 490                         <pathelement location="appletlib/${jmolJar}" />
 491                 </path>
 492                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 493
 494                 <proguard>
 495                         <injar file="in.jar" />
 496                         <outjar file="${jalviewLiteJar}" />
 497                         <libraryjar refid="obfuscateDeps.path" />
 498                         <keep access="public" type="class" name="jalview.bin.JalviewLite">
 499                                 <field access="public" />
 500                                 <method access="public" />
 501                                 <constructor access="public" />
 502                         </keep>
 503                         <!--      -libraryjars "${obfuscateDeps}"
 504       -injars      in.jar
 505       -outjars     jalviewApplet.jar
 506       -keep public class jalview.bin.JalviewLite
 507        { public * ; } -->
 508                 </proguard>
 509                 <delete file="in.jar" />
 510         </target>
 511
 512         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 513                 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 514                 <delete>
 515                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 516                                 <include name="*.java" />
 517                                 <include name="descriptors/*.java" />
 518                         </fileset>
 519                 </delete>
 520                 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 521                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 522                 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 523                 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 524                 <!--
 525                 now build the jalview.binding package with the old schema set
 526                 -->
 527                 <delete>
 528                         <fileset dir="${sourceDir}/jalview/binding/">
 529                                 <include name="**" />
 530                         </fileset>
 531                 </delete>
 532                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 533                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 534                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 535         </target>
 536         <target name="sourcedist" description="create jalview source distribution" depends="init">
 537                 <delete file="${source.dist.name}" />
 538                 <tar destfile="${source.dist.name}" compression="gzip">
 539                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 540                                 <include name="LICENSE" />
 541                                 <include name="README" />
 542                                 <include name="build.xml" />
 543                                 <include name="jalview-jalopy.xml" />
 544                                 <include name="JalviewApplet.jpx" />
 545                                 <include name="JalviewX.jpx" />
 546                                 <include name="nbbuild.xml"/>
 547                                 <include name="nbproject/genfiles.properties"/>
 548         <include name="nbproject/project.properties"/>
 549         <include name="nbproject/project.xml"/>
 550                                 <include name="${sourceDir}/*.java" />
 551                                 <include name="${sourceDir}/**/*.java" />
 552                                 <include name="${sourceDir}/**/*.cdr" />
 553                                 <include name="${libDir}/**/*" />
 554                                 <include name="${resourceDir}/**/*" />
 555                                 <include name="${helpDir}/**/*" />
 556                                 <include name="appletlib/${jmolJar}" />
 557                                 <exclude name="**/*locales" />
 558                                 <exclude name="*locales/**" />
 559                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 560                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 561                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 562                                 <exclude name="utils/InstallAnywhere/**locale*" />
 563                                 <exclude name="utils/InstallAnywhere/**locale*/**" />
 564                                 <include name="${schemaDir}/**/*" />
 565                                 <include name="utils/**/*" />
 566                                 <include name="${docDir}/**/*" />
 567                                 <include name="examples/**/*" />
 568                         </tarfileset>
 569                 </tar>
 570         </target>
 571         <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 572           <copy todir="${packageDir}/examples">
 573           <fileset dir="examples">
 574                 <include name="**/*"/>
 575                 <include name="javascript/*"/>
 576       <include name="jmol/*"/>
 577           </fileset>
 578                 <fileset dir=".">
 579                 <include name="jalviewApplet.jar"/>
 580                         </fileset>
 581                 <fileset dir="appletlib">
 582                       <include name="**/*"/>
 583                         </fileset>
 584           </copy>
 585
 586         </target>
 587         <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 588          <javadoc destdir="${javadocDir}">
 589                 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 590                 </packageset>
 591                 </javadoc>
 592         </target>
 593
 594 </project>