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