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
  89
  90     <!-- Don't change anything below here unless you know what you are doing! -->
  91     <!-- Url path for WebStart in JNLP file -->
  92     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  93     <!-- Webstart Image - looked for in resources/images -->
  94     <property name="WebStartImage" value="JalviewLogo_big.png" />
  95     <!-- J2SE version needed for webstart launch -->
  96     <property name="j2sev" value="1.6+" />
  97
  98     <!-- Permissions for running Java applets and applications. -->
  99     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 100     <property name="application.codebase" value="*.jalview.org" />
 101     <!-- and allowing the applet to be deployed from any URL -->
 102     <property name="applet.codebase" value="*" />
 103     <property name="applet.caller-codebase" value="${applet.codebase}" />
 104
 105     <!-- build directory configuration -->
 106     <property name="libDir" value="lib" />
 107     <property name="resourceDir" value="resources" />
 108     <property name="helpDir" value="help" />
 109     <property name="docDir" value="doc" />
 110     <property name="sourceDir" value="src" />
 111     <property name="schemaDir" value="schemas" />
 112     <property name="outputDir" value="classes" />
 113     <property name="packageDir" value="dist" />
 114     <property name="outputJar" value="jalview.jar" />
 115     <!-- Jalview Applet JMol Jar Dependency -->
 116     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 117     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 118     <!-- switch to indicate if we should obfuscate jalviewLite -->
 119     <!--<property name="donotobfuscate" value="true"/> -->
 120
 121     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 122     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 123     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 124     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 125     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 126     <property name="WSInterf" value="MsaWS" />
 127     <property name="wsdl.Namespace" value="vamsas" />
 128     <property name="wsdl.ClientNS" value="ext.vamsas" />
 129     <!-- the class path for building the application -->
 130     <path id="build.classpath">
 131       <fileset dir="utils">
 132         <include name="*.jar" />
 133         <include name="**/*.jar" />
 134       </fileset>
 135       <fileset dir="${libDir}">
 136         <include name="*.jar" />
 137         <include name="**/*.jar" />
 138       </fileset>
 139       <fileset dir="${java.home}/lib">
 140         <include name="plugin.jar" />
 141       </fileset>
 142       <fileset dir="appletlib">
 143         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 144                                 -->
 145         <include name="${jmolJar}" />
 146       </fileset>
 147
 148     </path>
 149     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 150     <!-- The Location of the java 1.1.8 jdk -->
 151     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 152                 -->
 153     <property name="java118.home" value="${java.home}" />
 154     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 155                 -->
 156     <!-- jre for 1.4 version -->
 157     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
 158
 159     <!-- the classpath for building the 1.1 applet -->
 160     <path id="jalviewlite.deps">
 161       <fileset dir="${java118.home}">
 162         <include name="lib/classes.zip" />
 163       </fileset>
 164       <fileset dir="${java.home}/lib">
 165         <include name="plugin.jar" />
 166       </fileset>
 167       <pathelement location="appletlib/${jmolJar}" />
 168     </path>
 169     <!-- default location for outputting javadoc -->
 170     <property name="javadocDir" value="${packageDir}/javadoc" />
 171   </target>
 172
 173
 174   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 175   <target name="buildPropertiesFile" depends="init">
 176     <tstamp prefix="build">
 177       <format property="date" pattern="dd MMMM yyyy" />
 178     </tstamp>
 179     <properties file="${outputDir}/.build_properties">
 180       <header>
 181           ---Jalview Build Details---
 182         </header>
 183       <property name="VERSION" value="${JALVIEW_VERSION}" />
 184       <property name="BUILD_DATE" value="${build.date}" />
 185     </properties>
 186   </target>
 187
 188
 189   <target name="clean" depends="init">
 190     <!-- not efficient yet. -->
 191     <delete dir="${outputDir}" includes="*,**/*" />
 192   </target>
 193
 194   <target name="distclean" depends="init, clean">
 195
 196     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 197     <delete>
 198       <fileset dir=".">
 199         <include name="${outputJar}" />
 200         <include name="#*#" />
 201         <include name="#*.*#" />
 202         <include name="**/#*#" />
 203         <include name="**/#*.*#" />
 204         <include name="*~" />
 205         <include name="*.*~" />
 206         <include name="**/*~" />
 207         <include name="**/*.*~" />
 208       </fileset>
 209     </delete>
 210   </target>
 211
 212   <target name="prepare" depends="init">
 213     <mkdir dir="${outputDir}" />
 214     <copy todir="${outputDir}">
 215       <fileset dir=".">
 216         <include name="${docDir}/**/*.*" />
 217         <include name="${helpDir}/**/*.*" />
 218         <include name="${libDir}/*.jar" />
 219       </fileset>
 220       <fileset dir="${resourceDir}">
 221         <include name="**/*.*" />
 222       </fileset>
 223     </copy>
 224   </target>
 225
 226   <target name="build" depends="prepare">
 227     <!-- not efficient yet. -->
 228     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 229       <exclude name="jalview/*applet*" />
 230       <exclude name="jalview/appletgui/**" />
 231       <exclude name="com/stevesoft/**" />
 232     </javac>
 233   </target>
 234   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 235     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 236       <arg line="html" />
 237     </java>
 238   </target>
 239
 240   <target name="makefulldist" depends="makedist">
 241     <!-- the default keystore details might need to be edited here -->
 242     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 243
 244       <fileset dir="${packageDir}">
 245         <include name="*.jar" />
 246       </fileset>
 247     </signjar>
 248     <copy todir="${packageDir}">
 249       <fileset dir="${resourceDir}/images">
 250         <include name="${WebStartImage}" />
 251       </fileset>
 252     </copy>
 253
 254     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 255
 256     <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 257     <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 258     <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 259       <information>
 260         <title>Jalview</title>
 261         <vendor>The Barton Group</vendor>
 262         <homepage href="http://www.jalview.org" />
 263         <description>Jalview Multiple Alignment Editor</description>
 264         <description kind="short">Jalview</description>
 265         <icon href="${WebStartImage}" />
 266         <offline_allowed />
 267       </information>
 268       <resources>
 269         <j2se version="${j2sev}" initial_heap_size="10M" />
 270         <fileset dir="${packageDir}">
 271           <include name="jalview.jar" />
 272         </fileset>
 273         <fileset dir="${packageDir}">
 274           <include name="*.jar" />
 275           <include name="*_*.jar" />
 276           <exclude name="jalview.jar" />
 277         </fileset>
 278         <property name="jalview.version" value="${JALVIEW_VERSION}" />
 279       </resources>
 280       <application_desc main_class="jalview.bin.Jalview">
 281       </application_desc>
 282       <security>
 283         <all_permissions />
 284       </security>
 285     </jnlp>
 286     <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 287       <information>
 288         <title>Jalview</title>
 289         <vendor>The Barton Group</vendor>
 290         <homepage href="http://www.jalview.org" />
 291         <description>Jalview Multiple Alignment Editor</description>
 292         <description kind="short">Jalview</description>
 293         <icon href="${WebStartImage}" />
 294         <offline_allowed />
 295       </information>
 296       <resources>
 297         <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
 298         <fileset dir="${packageDir}">
 299           <include name="jalview.jar" />
 300         </fileset>
 301         <fileset dir="${packageDir}">
 302           <include name="*.jar" />
 303           <include name="*_*.jar" />
 304           <exclude name="jalview.jar" />
 305         </fileset>
 306         <property name="jalview.version" value="${JALVIEW_VERSION}" />
 307       </resources>
 308       <application_desc main_class="jalview.bin.Jalview">
 309       </application_desc>
 310       <security>
 311         <all_permissions />
 312       </security>
 313     </jnlp>
 314     <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
 315       <information>
 316         <title>Jalview</title>
 317         <vendor>The Barton Group</vendor>
 318         <homepage href="http://www.jalview.org" />
 319         <description>Jalview Multiple Alignment Editor</description>
 320         <description kind="short">Jalview</description>
 321         <icon href="${WebStartImage}" />
 322         <offline_allowed />
 323       </information>
 324       <resources>
 325         <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
 326         <fileset dir="${packageDir}">
 327           <include name="jalview.jar" />
 328         </fileset>
 329         <fileset dir="${packageDir}">
 330           <include name="*.jar" />
 331           <include name="*_*.jar" />
 332           <exclude name="jalview.jar" />
 333         </fileset>
 334         <property name="jalview.version" value="${JALVIEW_VERSION}" />
 335       </resources>
 336       <application_desc main_class="jalview.bin.Jalview">
 337       </application_desc>
 338       <security>
 339         <all_permissions />
 340       </security>
 341     </jnlp>
 342     <!-- finally, need to postprocess to add in associations at end of 'information' element
 343
 344                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 345
 346                 </xslt>
 347
 348
 349                         -->
 350     <!--
 351                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 352         <association mime-type="application-x/ext-file" extensions="fasta"/>
 353         <association mime-type="application-x/ext-file" extensions="mfa"/>
 354         <association mime-type="application-x/ext-file" extensions="fastq"/>
 355         <association mime-type="application-x/ext-file" extensions="blc"/>
 356         <association mime-type="application-x/ext-file" extensions="msf"/>
 357         <association mime-type="application-x/ext-file" extensions="pfam"/>
 358         <association mime-type="application-x/ext-file" extensions="aln"/>
 359         <association mime-type="application-x/ext-file" extensions="pir"/>
 360         <association mime-type="application-x/ext-file" extensions="amsa"/>
 361         <association mime-type="application-x/ext-file" extensions="stk"/>
 362         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 363
 364   </target>
 365
 366   <target name="runenv" depends="init">
 367     <path id="run.classpath">
 368       <pathelement location="${outputDir}" />
 369       <fileset dir="${outputDir}">
 370         <include name="${libDir}/*.jar" />
 371       </fileset>
 372     </path>
 373     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 374
 375     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 376       </echo>
 377   </target>
 378
 379   <target name="buildextclients" depends="init">
 380     <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 381     <condition property="dontextbuild">
 382       <equals arg1="n" arg2="${doextbuild.response}" />
 383     </condition>
 384     <condition property="dontextbuild">
 385       <equals arg1="N" arg2="${doextbuild.response}" />
 386     </condition>
 387     <fail if="dontextbuild">
 388         Build External Client Code process aborted by user. Jalview source is unchanged.
 389       </fail>
 390     <!-- Currently, this doesn't happen automatically.
 391      1. Run WSDL2Java as below, which generates an ext.vamsas +
 392      vamsas.<datapackages> fileset.
 393      2. refactor ext.vamsas.SpecificserviceWS* to
 394      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 395      3. Update the jalview.ws.*WServices classes to reflect the
 396      interface type, and all locations of this wsdl type that Jalview
 397      might be using.
 398
 399 -->
 400     <path id="axisbuild">
 401       <path refid="build.classpath" />
 402     </path>
 403     <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 404     <move todir="./bak">
 405       <fileset dir="${sourceDir}" id="client">
 406         <include name="${wsdl.ClientNS}/*.*" />
 407       </fileset>
 408     </move>
 409
 410     <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 411       <mappingSet>
 412         <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 413         <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 414       </mappingSet>
 415     </axis-wsdl2java>
 416   </target>
 417
 418   <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 419     <!-- make the package jar if not already existing -->
 420     <mkdir dir="${packageDir}" />
 421     <!-- clean dir if it already existed -->
 422     <delete>
 423       <fileset dir="${packageDir}">
 424         <include name="*.jar" />
 425       </fileset>
 426     </delete>
 427     <jar destfile="${packageDir}/${outputJar}" index="true">
 428       <manifest>
 429         <attribute name="Main-Class" value="jalview.bin.Jalview" />
 430         <attribute name="Permissions" value="all-permissions" />
 431         <attribute name="Application-Name" value="Jalview Desktop" />
 432         <attribute name="Codebase" value="${application.codebase}" />
 433       </manifest>
 434       <fileset dir="${outputDir}/">
 435         <exclude name="cache*/**" />
 436         <exclude name="*.jar" />
 437         <exclude name="*.jar.*" />
 438         <exclude name="**/*.jar" />
 439         <exclude name="**/*.jar.*" />
 440       </fileset>
 441     </jar>
 442
 443     <copy toDir="${packageDir}" flatten="true">
 444       <fileset dir="${outputDir}">
 445         <include name="*.jar" />
 446         <include name="**/*.jar" />
 447       </fileset>
 448     </copy>
 449   </target>
 450
 451
 452   <!-- jalopy code reformatter -->
 453   <target name="sourcescrub" depends="init,build">
 454     <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 455       <fileset dir="${sourceDir}">
 456         <include name="*.java" />
 457         <include name="**/*.java" />
 458         <include name="**/**/*.java" />
 459       </fileset>
 460     </jalopy>
 461   </target>
 462
 463
 464
 465   <!-- Compile, package and obfuscate Jalview Applet -->
 466   <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 467
 468   <target name="compileApplet" depends="init,clean">
 469     <mkdir dir="${outputDir}" />
 470     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,MCview/**,org/**,vamsas/**" />
 471   </target>
 472
 473   <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 474     <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 475     <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 476     <jar destfile="in.jar" index="true">
 477       <manifest>
 478         <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 479         <attribute name="Application-Name" value="JalviewLite" />
 480         <attribute name="Codebase" value="${applet.codebase}" />
 481       </manifest>
 482       <fileset dir="${outputDir}">
 483         <include name="com/**" />
 484         <include name="MCview/**" />
 485         <include name="jalview/**" />
 486         <include name=".build_properties" />
 487         <include name="images/idwidth.gif" />
 488         <include name="images/link.gif" />
 489       </fileset>
 490     </jar>
 491   </target>
 492   <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 493   </target>
 494   <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 495     <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 496     <delete file="in.jar" />
 497   </target>
 498   <target name="-obfuscatereally" unless="donotobfuscate">
 499
 500     <path id="obfuscateDeps.path">
 501       <pathelement location="${applet.jre.tools}" />
 502       <pathelement location="appletlib/${jmolJar}" />
 503     </path>
 504     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 505
 506     <proguard>
 507       <injar file="in.jar" />
 508       <outjar file="${jalviewLiteJar}" />
 509       <libraryjar refid="obfuscateDeps.path" />
 510       <dontwarn />
 511       <keep access="public" type="class" name="jalview.bin.JalviewLite">
 512         <field access="public" />
 513         <method access="public" />
 514         <constructor access="public" />
 515       </keep>
 516       <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 517         <field access="public" />
 518         <method access="public" />
 519         <constructor access="public" />
 520       </keep>
 521       <!--      -libraryjars "${obfuscateDeps}"
 522       -injars      in.jar
 523       -outjars     jalviewApplet.jar
 524       -keep public class jalview.bin.JalviewLite
 525        { public * ; } -->
 526     </proguard>
 527     <delete file="in.jar" />
 528   </target>
 529
 530   <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 531     <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 532     <delete>
 533       <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 534         <include name="*.java" />
 535         <include name="descriptors/*.java" />
 536       </fileset>
 537     </delete>
 538     <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 539     <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 540     <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 541     <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 542     <!--
 543                 now build the jalview.binding package with the old schema set
 544                 -->
 545     <delete>
 546       <fileset dir="${sourceDir}/jalview/binding/">
 547         <include name="**" />
 548       </fileset>
 549     </delete>
 550     <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 551     <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 552     <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 553   </target>
 554   <target name="sourcedist" description="create jalview source distribution" depends="init">
 555     <delete file="${source.dist.name}" />
 556     <tar destfile="${source.dist.name}" compression="gzip">
 557       <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 558         <include name="LICENSE" />
 559         <include name="README" />
 560         <include name="build.xml" />
 561         <include name="jalview-jalopy.xml" />
 562         <include name="JalviewApplet.jpx" />
 563         <include name="JalviewX.jpx" />
 564         <include name="nbbuild.xml" />
 565         <include name="nbproject/genfiles.properties" />
 566         <include name="nbproject/project.properties" />
 567         <include name="nbproject/project.xml" />
 568         <include name="${sourceDir}/*.java" />
 569         <include name="${sourceDir}/**/*.java" />
 570         <include name="${sourceDir}/**/*.cdr" />
 571         <include name="${libDir}/**/*" />
 572         <include name="${resourceDir}/**/*" />
 573         <include name="${helpDir}/**/*" />
 574         <include name="appletlib/${jmolJar}" />
 575         <exclude name="**/*locales" />
 576         <exclude name="*locales/**" />
 577         <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 578         <exclude name="utils/InstallAnywhere/**Build*/**" />
 579         <exclude name="utils/InstallAnywhere/**Build*/**" />
 580         <exclude name="utils/InstallAnywhere/**locale*" />
 581         <exclude name="utils/InstallAnywhere/**locale*/**" />
 582         <include name="${schemaDir}/**/*" />
 583         <include name="utils/**/*" />
 584         <include name="${docDir}/**/*" />
 585         <include name="examples/**/*" />
 586       </tarfileset>
 587     </tar>
 588   </target>
 589   <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 590     <copy todir="${packageDir}/examples">
 591       <fileset dir="examples">
 592         <include name="**/*" />
 593         <include name="javascript/*" />
 594         <include name="jmol/*" />
 595       </fileset>
 596       <fileset dir=".">
 597         <include name="${jalviewLiteJar}" />
 598       </fileset>
 599       <fileset dir="appletlib">
 600         <include name="**/*" />
 601       </fileset>
 602     </copy>
 603
 604     <presetdef name="ap_applet.jar">
 605       <!-- build a signed applet with 'all-permissions' -
 606                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 607                           JalviewLite+JmolApplet linked sequence/structure fails
 608                           Mixed code warnings are raised
 609                           -->
 610       <jar update="true" index="true">
 611         <manifest>
 612           <attribute name="Application-Name" value="JalviewLite" />
 613           <attribute name="Permissions" value="all-permissions" />
 614           <attribute name="Codebase" value="${applet.codebase}" />
 615           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 616           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 617         </manifest>
 618       </jar>
 619     </presetdef>
 620     <presetdef name="applet.jar">
 621       <!-- build signed applet with sandbox permissions -
 622                           Needs 'param name="permissions' value="sandbox"' in applet tag
 623                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 624                         -->
 625
 626       <jar update="true" index="true">
 627         <manifest>
 628           <attribute name="Application-Name" value="JalviewLite" />
 629           <attribute name="Permissions" value="sandbox" />
 630           <attribute name="Codebase" value="${applet.codebase}" />
 631           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 632           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 633         </manifest>
 634       </jar>
 635     </presetdef>
 636     <presetdef name="tl_applet.jar">
 637       <!-- build signed applet with trusted library/trusted permissions -
 638                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 639                                j1.7_45:
 640                                No mixed code warnings raised
 641                                Jmol/JalviewLite sequence/structure example doesn't link structures
 642                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 643
 644                               -->
 645
 646       <jar update="true" index="true">
 647         <manifest>
 648           <attribute name="Application-Name" value="JalviewLite" />
 649           <attribute name="Permissions" value="all-permissions" />
 650           <attribute name="Codebase" value="${applet.codebase}" />
 651           <attribute name="Trusted-Only" value="true" />
 652           <attribute name="Trusted-Library" value="true" />
 653         </manifest>
 654       </jar>
 655     </presetdef>
 656     <presetdef name="to_applet.jar">
 657       <!-- not fully test variant (yet) -->
 658       <jar update="true" index="true">
 659         <manifest>
 660           <attribute name="Application-Name" value="JalviewLite" />
 661           <attribute name="Permissions" value="all-permissions" />
 662           <attribute name="Codebase" value="${applet.codebase}" />
 663           <attribute name="Trusted-Only" value="true" />
 664         </manifest>
 665       </jar>
 666     </presetdef>
 667     <!-- create differently privileged artefacts -->
 668     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 669     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}"/>
 670     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 671     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 672     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 673     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 674     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 675     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 676     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 677     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 678     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 679     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 680     <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 681     <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 682     <!-- finally, create manifest for original jars -->
 683     <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 684     <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 685
 686     <!-- todo - write examples/downloads for alternate versions of the applet -->
 687     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 688
 689       <fileset dir="${packageDir}/examples">
 690         <include name="${jalviewLiteJar}" />
 691         <include name="${jmolJar}" />
 692         <include name="to_${jalviewLiteJar}" />
 693         <include name="to_${jmolJar}" />
 694         <include name="tl_${jalviewLiteJar}" />
 695         <include name="tl_${jmolJar}" />
 696         <include name="ap_${jalviewLiteJar}" />
 697         <include name="ap_${jmolJar}" />
 698       </fileset>
 699     </signjar>
 700   </target>
 701   <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 702     <javadoc destdir="${javadocDir}">
 703       <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 704       </packageset>
 705     </javadoc>
 706   </target>
 707
 708 </project>