build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
   4  * Copyright (C) 2014 The Jalview Authors
   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  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <project name="jalviewX" default="usage" basedir=".">
  21   <!-- we use jalopy to format our sources -->
  22   <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
  23     <classpath>
  24       <fileset dir="utils/jalopy/lib">
  25         <include name="*.jar" />
  26       </fileset>
  27     </classpath>
  28   </taskdef>
  29
  30   <target name="help" depends="usage" />
  31   <target name="usage">
  32     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  33     <echo message="Targets include:" />
  34     <echo message="usage - default target, displays this message" />
  35     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  36     <echo message="build - compiles all necessary files for Application" />
  37     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  38     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  39     <echo message="              this needs a keystore and key. See docs/building.html for more information." />
  40     <echo message="compileApplet - compiles all necessary files for Applet" />
  41     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  42     <echo message="See docs/building.html and the comments in build file for other targets." />
  43     <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  44     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  45   </target>
  46
  47
  48   <!-- utils is a class path to additional utilities needed for
  49     building docs, jars and webstart stuff -->
  50   <!--
  51         Userdefined build property defaults
  52
  53         wsdl.server list (plus namespace mapping info ???)  - also want
  54                 ... to make this a dynamically generatable property
  55         WebStart Location
  56         Build location - provide a temporary root for speed
  57         jarsigner keystore and info
  58         Jakarta and axis classpath ?
  59         Default argument for starting Jalview (if it exists).
  60
  61 -->
  62
  63   <target name="init">
  64     <path id="axis.classpath">
  65       <!-->
  66       <fileset dir="/usr/local/axis/lib">
  67         <include name="**/*.jar" />
  68       </fileset>
  69       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  70         <include name="**/*.jar"/>
  71         <include name="*.jar"/>
  72       </fileset> -->
  73       </path>
  74     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  75     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  76     <!-- 2.4 (VAMSAS)" -->
  77     <!-- Include debugging information in javac true or false -->
  78     <property name="javac.debug" value="true" />
  79
  80     <!-- JarSigner Key Store for Webstart Distribution -->
  81     <property name="jalview.keystore" value="./keys/.keystore" />
  82     <!-- Keystore Password -->
  83     <property name="jalview.keystore.pass" value="alignmentisfun" />
  84     <!-- Key Name -->
  85     <property name="jalview.key" value="jalview" />
  86     <!-- Key Password -->
  87     <property name="jalview.key.pass" value="alignmentisfun" />
  88
  89
  90
  91     <!-- Don't change anything below here unless you know what you are doing! -->
  92     <!-- Url path for WebStart in JNLP file -->
  93     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  94     <!-- Webstart Image - looked for in resources/images -->
  95     <property name="WebStartImage" value="JalviewLogo_big.png"/>
  96     <!-- J2SE version needed for webstart launch -->
  97     <property name="j2sev" value="1.6+"/>
  98
  99     <!-- Permissions for running Java applets and applications. -->
 100     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 101     <property name="application.codebase" value="*.jalview.org" />
 102     <!-- and allowing the applet to be deployed from any URL -->
 103     <property name="applet.codebase" value="*" />
 104     <property name="applet.caller-codebase" value="${applet.codebase}" />
 105
 106     <!-- build directory configuration -->
 107     <property name="libDir" value="lib" />
 108     <property name="resourceDir" value="resources" />
 109     <property name="helpDir" value="help" />
 110     <property name="docDir" value="doc" />
 111     <property name="sourceDir" value="src" />
 112     <property name="schemaDir" value="schemas" />
 113     <property name="outputDir" value="classes" />
 114     <property name="packageDir" value="dist" />
 115     <property name="outputJar" value="jalview.jar" />
 116     <!-- Jalview Applet JMol Jar Dependency -->
 117     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 118     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 119     <!-- switch to indicate if we should obfuscate jalviewLite -->
 120     <!--<property name="donotobfuscate" value="true"/> -->
 121
 122     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 123     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 124     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 125     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 126     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 127     <property name="WSInterf" value="MsaWS" />
 128     <property name="wsdl.Namespace" value="vamsas" />
 129     <property name="wsdl.ClientNS" value="ext.vamsas" />
 130     <!-- the class path for building the application -->
 131     <path id="build.classpath">
 132       <fileset dir="utils">
 133         <include name="*.jar" />
 134         <include name="**/*.jar" />
 135       </fileset>
 136       <fileset dir="${libDir}">
 137         <include name="*.jar" />
 138         <include name="**/*.jar" />
 139       </fileset>
 140       <fileset dir="${java.home}/lib">
 141         <include name="plugin.jar"/>
 142       </fileset>
 143       <fileset dir="appletlib">
 144         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 145                                 -->
 146         <include name="${jmolJar}" />
 147       </fileset>
 148
 149     </path>
 150     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 151     <!-- The Location of the java 1.1.8 jdk -->
 152     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 153                 -->
 154     <property name="java118.home" value="${java.home}" />
 155     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 156                 -->
 157     <!-- jre for 1.4 version -->
 158     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 159
 160     <!-- the classpath for building the 1.1 applet -->
 161     <path id="jalviewlite.deps">
 162       <fileset dir="${java118.home}">
 163         <include name="lib/classes.zip" />
 164       </fileset>
 165       <fileset dir="${java.home}/lib">
 166         <include name="plugin.jar"/>
 167       </fileset>
 168       <pathelement location="appletlib/${jmolJar}" />
 169     </path>
 170     <!-- default location for outputting javadoc -->
 171     <property name="javadocDir" value="${packageDir}/javadoc"/>
 172   </target>
 173
 174
 175   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 176   <target name="buildPropertiesFile" depends="init">
 177     <tstamp prefix="build">
 178       <format property="date" pattern="dd MMMM yyyy" />
 179     </tstamp>
 180     <properties file="${outputDir}/.build_properties">
 181       <header>
 182           ---Jalview Build Details---
 183         </header>
 184       <property name="VERSION" value="${JALVIEW_VERSION}" />
 185       <property name="BUILD_DATE" value="${build.date}" />
 186     </properties>
 187   </target>
 188
 189
 190   <target name="clean" depends="init">
 191     <!-- not efficient yet. -->
 192     <delete dir="${outputDir}" includes="*,**/*"/>
 193   </target>
 194
 195   <target name="distclean" depends="init, clean">
 196
 197     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 198     <delete>
 199       <fileset dir=".">
 200         <include name="${outputJar}" />
 201         <include name="#*#" />
 202         <include name="#*.*#" />
 203         <include name="**/#*#" />
 204         <include name="**/#*.*#" />
 205         <include name="*~" />
 206         <include name="*.*~" />
 207         <include name="**/*~" />
 208         <include name="**/*.*~" />
 209       </fileset>
 210     </delete>
 211   </target>
 212
 213   <target name="prepare" depends="init">
 214     <mkdir dir="${outputDir}" />
 215     <copy todir="${outputDir}">
 216       <fileset dir=".">
 217         <include name="${docDir}/**/*.*" />
 218         <include name="${helpDir}/**/*.*" />
 219         <include name="${libDir}/*.jar" />
 220       </fileset>
 221       <fileset dir="${resourceDir}">
 222         <include name="**/*.*" />
 223       </fileset>
 224     </copy>
 225   </target>
 226
 227   <target name="build" depends="prepare">
 228     <!-- not efficient yet. -->
 229     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 230       <exclude name="jalview/*applet*" />
 231       <exclude name="jalview/appletgui/**" />
 232       <exclude name="com/stevesoft/**" />
 233     </javac>
 234   </target>
 235   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 236     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 237       <arg line="html" />
 238     </java>
 239   </target>
 240
 241   <target name="makefulldist" depends="makedist">
 242     <copy todir="${packageDir}">
 243       <fileset dir="${resourceDir}/images">
 244         <include name="${WebStartImage}"/>
 245       </fileset>
 246     </copy>
 247
 248     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 249
 250     <!-- create a dummy jar which will eventually contain the jnlp template -->
 251     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 252       <fileset dir="${packageDir}">
 253         <include name="jalview.jar" />
 254       </fileset>
 255     </jar>
 256
 257     <mkdir dir="${packageDir}/JNLP-INF"/>
 258     <antcall target="writejnlpf">
 259       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 260       <param name="inih" value="*" />
 261       <param name="maxh" value="*"/>
 262     </antcall>
 263
 264     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 265       <fileset dir="${packageDir}">
 266         <include name="JNLP-INF"/>
 267       </fileset>
 268     </jar>
 269
 270     <antcall target="writejnlpf">
 271       <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 272       <param name="inih" value="10M" />
 273       <param name="maxh" value="256M"/>
 274     </antcall>
 275
 276     <antcall target="writejnlpf">
 277       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 278       <param name="inih" value="128M" />
 279       <param name="maxh" value="512M"/>
 280     </antcall>
 281
 282     <antcall target="writejnlpf">
 283       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 284       <param name="inih" value="256M" />
 285       <param name="maxh" value="1024M"/>
 286     </antcall>
 287
 288     <!-- finally, need to postprocess to add in associations at end of 'information' element
 289
 290                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 291
 292                 </xslt>
 293
 294
 295                         -->
 296                                         <!--
 297                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 298         <association mime-type="application-x/ext-file" extensions="fasta"/>
 299         <association mime-type="application-x/ext-file" extensions="mfa"/>
 300         <association mime-type="application-x/ext-file" extensions="fastq"/>
 301         <association mime-type="application-x/ext-file" extensions="blc"/>
 302         <association mime-type="application-x/ext-file" extensions="msf"/>
 303         <association mime-type="application-x/ext-file" extensions="pfam"/>
 304         <association mime-type="application-x/ext-file" extensions="aln"/>
 305         <association mime-type="application-x/ext-file" extensions="pir"/>
 306         <association mime-type="application-x/ext-file" extensions="amsa"/>
 307         <association mime-type="application-x/ext-file" extensions="stk"/>
 308         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 309     <!-- and sign the jars -->
 310     <!-- the default keystore details might need to be edited here -->
 311     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 312       <fileset dir="${packageDir}">
 313         <include name="*.jar" />
 314       </fileset>
 315     </signjar>
 316   </target>
 317
 318   <target name="runenv" depends="init">
 319     <path id="run.classpath">
 320       <pathelement location="${outputDir}" />
 321       <fileset dir="${outputDir}">
 322         <include name="${libDir}/*.jar" />
 323       </fileset>
 324     </path>
 325     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 326
 327     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 328       </echo>
 329   </target>
 330   <target name="writejnlpf">
 331         <presetdef name="jnlpf">
 332             <jnlp codebase="${WebStartLocation}">
 333               <information>
 334                 <title>Jalview</title>
 335                 <vendor>The Barton Group</vendor>
 336                 <homepage href="http://www.jalview.org" />
 337                 <description>Jalview Multiple Alignment Editor</description>
 338                 <description kind="short">Jalview</description>
 339                 <icon href="${WebStartImage}" />
 340                 <offline_allowed />
 341               </information>
 342               <resources>
 343                 <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 344                 <fileset dir="${packageDir}">
 345                   <include name="jalview.jar" />
 346                 </fileset>
 347                 <fileset dir="${packageDir}">
 348                   <include name="*.jar" />
 349                   <include name="*_*.jar" />
 350                   <exclude name="jalview.jar" />
 351                 </fileset>
 352                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 353               </resources>
 354               <application_desc main_class="jalview.bin.Jalview">
 355               </application_desc>
 356               <security>
 357                 <all_permissions />
 358               </security>
 359             </jnlp>
 360             </presetdef>
 361
 362             <jnlpf toFile="${jnlpFile}"/>
 363   </target>
 364   <target name="buildextclients" depends="init">
 365     <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" />
 366     <condition property="dontextbuild">
 367       <equals arg1="n" arg2="${doextbuild.response}" />
 368     </condition>
 369     <condition property="dontextbuild">
 370       <equals arg1="N" arg2="${doextbuild.response}" />
 371     </condition>
 372     <fail if="dontextbuild">
 373         Build External Client Code process aborted by user. Jalview source is unchanged.
 374       </fail>
 375     <!-- Currently, this doesn't happen automatically.
 376      1. Run WSDL2Java as below, which generates an ext.vamsas +
 377      vamsas.<datapackages> fileset.
 378      2. refactor ext.vamsas.SpecificserviceWS* to
 379      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 380      3. Update the jalview.ws.*WServices classes to reflect the
 381      interface type, and all locations of this wsdl type that Jalview
 382      might be using.
 383
 384 -->
 385     <path id="axisbuild">
 386       <path refid="build.classpath" />
 387     </path>
 388     <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 389     <move todir="./bak">
 390       <fileset dir="${sourceDir}" id="client">
 391         <include name="${wsdl.ClientNS}/*.*" />
 392       </fileset>
 393     </move>
 394
 395     <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 396       <mappingSet>
 397         <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 398         <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 399       </mappingSet>
 400     </axis-wsdl2java>
 401   </target>
 402
 403   <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 404     <!-- make the package jar if not already existing -->
 405     <mkdir dir="${packageDir}" />
 406     <!-- clean dir if it already existed -->
 407     <delete>
 408       <fileset dir="${packageDir}">
 409         <include name="*.jar"/>
 410       </fileset>
 411     </delete>
 412     <jar destfile="${packageDir}/${outputJar}" index="true">
 413       <manifest>
 414         <attribute name="Main-Class" value="jalview.bin.Jalview" />
 415         <attribute name="Permissions" value="all-permissions" />
 416         <attribute name="Application-Name" value="Jalview Desktop" />
 417         <attribute name="Codebase" value="${application.codebase}" />
 418       </manifest>
 419       <fileset dir="${outputDir}/">
 420         <exclude name="cache*/**" />
 421         <exclude name="*.jar" />
 422         <exclude name="*.jar.*" />
 423         <exclude name="**/*.jar" />
 424         <exclude name="**/*.jar.*" />
 425       </fileset>
 426     </jar>
 427
 428     <copy toDir="${packageDir}" flatten="true">
 429       <fileset dir="${outputDir}">
 430         <include name="*.jar" />
 431         <include name="**/*.jar" />
 432       </fileset>
 433     </copy>
 434   </target>
 435
 436
 437   <!-- jalopy code reformatter -->
 438   <target name="sourcescrub" depends="init,build">
 439     <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 440       <fileset dir="${sourceDir}">
 441         <include name="*.java" />
 442         <include name="**/*.java" />
 443         <include name="**/**/*.java" />
 444       </fileset>
 445     </jalopy>
 446   </target>
 447
 448
 449
 450   <!-- Compile, package and obfuscate Jalview Applet -->
 451   <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 452
 453   <target name="compileApplet" depends="init,clean">
 454     <mkdir dir="${outputDir}" />
 455     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 456                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 457                         excludes="ext/**,MCview/**,org/**,vamsas/**" />
 458   </target>
 459
 460   <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 461     <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 462     <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 463     <copy todir="${outputDir}/lang">
 464       <fileset dir="${resourceDir}/lang">
 465         <include name="**.*"/>
 466       </fileset>
 467     </copy>
 468     <jar destfile="in.jar" index="true">
 469       <manifest>
 470         <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 471         <attribute name="Application-Name" value="JalviewLite" />
 472         <attribute name="Codebase" value="${applet.codebase}" />
 473       </manifest>
 474       <fileset dir="${outputDir}">
 475         <include name="com/**" />
 476         <include name="MCview/**" />
 477         <include name="jalview/**" />
 478         <include name=".build_properties" />
 479         <include name="images/idwidth.gif" />
 480         <include name="images/link.gif" />
 481         <include name="lang/**" />
 482       </fileset>
 483     </jar>
 484   </target>
 485   <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 486   </target>
 487   <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 488     <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 489     <delete file="in.jar" />
 490   </target>
 491   <target name="-obfuscatereally" unless="donotobfuscate">
 492
 493     <path id="obfuscateDeps.path">
 494       <pathelement location="${applet.jre.tools}" />
 495       <pathelement location="appletlib/${jmolJar}" />
 496     </path>
 497     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 498
 499     <proguard>
 500       <injar file="in.jar" />
 501       <outjar file="${jalviewLiteJar}" />
 502       <libraryjar refid="obfuscateDeps.path" />
 503       <dontwarn/>
 504       <keep access="public" type="class" name="jalview.bin.JalviewLite">
 505         <field access="public" />
 506         <method access="public" />
 507         <constructor access="public" />
 508       </keep>
 509       <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 510         <field access="public" />
 511         <method access="public" />
 512         <constructor access="public" />
 513       </keep>
 514       <!--      -libraryjars "${obfuscateDeps}"
 515       -injars      in.jar
 516       -outjars     jalviewApplet.jar
 517       -keep public class jalview.bin.JalviewLite
 518        { public * ; } -->
 519     </proguard>
 520     <delete file="in.jar" />
 521   </target>
 522
 523   <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 524     <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 525     <delete>
 526       <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 527         <include name="*.java" />
 528         <include name="descriptors/*.java" />
 529       </fileset>
 530     </delete>
 531     <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 532     <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 533     <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 534     <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 535     <!--
 536                 now build the jalview.binding package with the old schema set
 537                 -->
 538     <delete>
 539       <fileset dir="${sourceDir}/jalview/binding/">
 540         <include name="**" />
 541       </fileset>
 542     </delete>
 543     <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 544     <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 545     <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 546   </target>
 547   <target name="sourcedist" description="create jalview source distribution" depends="init">
 548     <delete file="${source.dist.name}" />
 549     <tar destfile="${source.dist.name}" compression="gzip">
 550       <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 551         <include name="LICENSE" />
 552         <include name="README" />
 553         <include name="build.xml" />
 554         <include name="jalview-jalopy.xml" />
 555         <include name="JalviewApplet.jpx" />
 556         <include name="JalviewX.jpx" />
 557         <include name="nbbuild.xml"/>
 558         <include name="nbproject/genfiles.properties"/>
 559         <include name="nbproject/project.properties"/>
 560         <include name="nbproject/project.xml"/>
 561         <include name="${sourceDir}/*.java" />
 562         <include name="${sourceDir}/**/*.java" />
 563         <include name="${sourceDir}/**/*.cdr" />
 564         <include name="${libDir}/**/*" />
 565         <include name="${resourceDir}/**/*" />
 566         <include name="${helpDir}/**/*" />
 567         <include name="appletlib/${jmolJar}" />
 568         <exclude name="**/*locales" />
 569         <exclude name="*locales/**" />
 570         <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 571         <exclude name="utils/InstallAnywhere/**Build*/**" />
 572         <exclude name="utils/InstallAnywhere/**Build*/**" />
 573         <exclude name="utils/InstallAnywhere/**locale*" />
 574         <exclude name="utils/InstallAnywhere/**locale*/**" />
 575         <include name="${schemaDir}/**/*" />
 576         <include name="utils/**/*" />
 577         <include name="${docDir}/**/*" />
 578         <include name="examples/**/*" />
 579       </tarfileset>
 580     </tar>
 581   </target>
 582   <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 583     <copy todir="${packageDir}/examples">
 584       <fileset dir="examples">
 585         <include name="**/*"/>
 586         <include name="javascript/*"/>
 587         <include name="jmol/*"/>
 588       </fileset>
 589       <fileset dir=".">
 590         <include name="${jalviewLiteJar}" />
 591       </fileset>
 592       <fileset dir="appletlib">
 593         <include name="**/*"/>
 594       </fileset>
 595     </copy>
 596     <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 597     <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 598       <manifest>
 599         <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 600         <!--          <attribute name="Permissions" value="sandbox" /> -->
 601         <!--<attribute name="Trusted-Lib" value="true" /> -->
 602         <attribute name="Codebase" value="${applet.codebase}"/>
 603         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 604       </manifest>
 605     </jar>
 606     <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 607       <fileset dir="${packageDir}/examples">
 608         <include name="*.jar" />
 609       </fileset>
 610     </signjar>
 611     <presetdef name="ap_applet.jar">
 612       <!-- build a signed applet with 'all-permissions' -
 613                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 614                           JalviewLite+JmolApplet linked sequence/structure fails
 615                           Mixed code warnings are raised
 616                           -->
 617       <jar update="true" index="true">
 618         <manifest>
 619           <attribute name="Application-Name" value="JalviewLite" />
 620           <attribute name="Permissions" value="all-permissions" />
 621           <attribute name="Codebase" value="${applet.codebase}" />
 622           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 623           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 624         </manifest>
 625       </jar>
 626     </presetdef>
 627     <presetdef name="applet.jar">
 628       <!-- build signed applet with sandbox permissions -
 629                           Needs 'param name="permissions' value="sandbox"' in applet tag
 630                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 631                         -->
 632
 633       <jar update="true" index="true">
 634         <manifest>
 635           <attribute name="Application-Name" value="JalviewLite" />
 636           <attribute name="Permissions" value="sandbox" />
 637           <attribute name="Codebase" value="${applet.codebase}" />
 638           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 639           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 640         </manifest>
 641       </jar>
 642     </presetdef>
 643     <presetdef name="tl_applet.jar">
 644       <!-- build signed applet with trusted library/trusted permissions -
 645                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 646                                j1.7_45:
 647                                No mixed code warnings raised
 648                                Jmol/JalviewLite sequence/structure example doesn't link structures
 649                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 650
 651                               -->
 652
 653       <jar update="true" index="true">
 654         <manifest>
 655           <attribute name="Application-Name" value="JalviewLite" />
 656           <attribute name="Permissions" value="all-permissions" />
 657           <attribute name="Codebase" value="${applet.codebase}" />
 658           <attribute name="Trusted-Only" value="true" />
 659           <attribute name="Trusted-Library" value="true" />
 660         </manifest>
 661       </jar>
 662     </presetdef>
 663     <presetdef name="to_applet.jar">
 664       <!-- not fully test variant (yet) -->
 665       <jar update="true" index="true">
 666         <manifest>
 667           <attribute name="Application-Name" value="JalviewLite" />
 668           <attribute name="Permissions" value="all-permissions" />
 669           <attribute name="Codebase" value="${applet.codebase}" />
 670           <attribute name="Trusted-Only" value="true" />
 671         </manifest>
 672       </jar>
 673     </presetdef>
 674     <!-- create differently privileged artefacts -->
 675     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 676     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 677     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 678     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 679     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 680     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 681     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 682     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 683     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 684     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 685     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 686     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 687     <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 688     <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 689     <!-- finally, create manifest for original jars -->
 690     <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 691     <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 692
 693     <!-- todo - write examples/downloads for alternate versions of the applet -->
 694     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 695
 696       <fileset dir="${packageDir}/examples">
 697         <exclude name="u_*.jar"/>
 698         <include name="${jalviewLiteJar}" />
 699         <include name="${jmolJar}" />
 700         <include name="to_${jalviewLiteJar}" />
 701         <include name="to_${jmolJar}" />
 702         <include name="tl_${jalviewLiteJar}" />
 703         <include name="tl_${jmolJar}" />
 704         <include name="ap_${jalviewLiteJar}" />
 705         <include name="ap_${jmolJar}" />
 706       </fileset>
 707     </signjar>
 708     <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 709     <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 710   </target>
 711   <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 712     <javadoc destdir="${javadocDir}">
 713       <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 714       </packageset>
 715     </javadoc>
 716   </target>
 717 </project>