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     <replace file="${jnlpFile}">
 364       <replacetoken><![CDATA[</information>]]></replacetoken>
 365       <replacevalue><![CDATA[
 366         <association mime-type="application-x/ext-file" extensions="fa" />
 367         <association mime-type="application-x/ext-file" extensions="fasta" />
 368         <association mime-type="application-x/ext-file" extensions="mfa" />
 369         <association mime-type="application-x/ext-file" extensions="fastq" />
 370         <association mime-type="application-x/ext-file" extensions="blc" />
 371         <association mime-type="application-x/ext-file" extensions="msf" />
 372         <association mime-type="application-x/ext-file" extensions="pfam" />
 373         <association mime-type="application-x/ext-file" extensions="aln"/>
 374         <association mime-type="application-x/ext-file" extensions="pir"/>
 375         <association mime-type="application-x/ext-file" extensions="amsa"/>
 376         <association mime-type="application-x/ext-file" extensions="stk"/>
 377         <association mime-type="application-x/ext-file" extensions="jvp"/>
 378       </information>]]></replacevalue>
 379     </replace>
 380   </target>
 381   <target name="buildextclients" depends="init">
 382     <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 383     <condition property="dontextbuild">
 384       <equals arg1="n" arg2="${doextbuild.response}" />
 385     </condition>
 386     <condition property="dontextbuild">
 387       <equals arg1="N" arg2="${doextbuild.response}" />
 388     </condition>
 389     <fail if="dontextbuild">
 390         Build External Client Code process aborted by user. Jalview source is unchanged.
 391       </fail>
 392     <!-- Currently, this doesn't happen automatically.
 393      1. Run WSDL2Java as below, which generates an ext.vamsas +
 394      vamsas.<datapackages> fileset.
 395      2. refactor ext.vamsas.SpecificserviceWS* to
 396      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 397      3. Update the jalview.ws.*WServices classes to reflect the
 398      interface type, and all locations of this wsdl type that Jalview
 399      might be using.
 400
 401 -->
 402     <path id="axisbuild">
 403       <path refid="build.classpath" />
 404     </path>
 405     <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 406     <move todir="./bak">
 407       <fileset dir="${sourceDir}" id="client">
 408         <include name="${wsdl.ClientNS}/*.*" />
 409       </fileset>
 410     </move>
 411
 412     <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 413       <mappingSet>
 414         <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 415         <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 416       </mappingSet>
 417     </axis-wsdl2java>
 418   </target>
 419
 420   <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 421     <!-- make the package jar if not already existing -->
 422     <mkdir dir="${packageDir}" />
 423     <!-- clean dir if it already existed -->
 424     <delete>
 425       <fileset dir="${packageDir}">
 426         <include name="*.jar"/>
 427       </fileset>
 428     </delete>
 429     <jar destfile="${packageDir}/${outputJar}" index="true">
 430       <manifest>
 431         <attribute name="Main-Class" value="jalview.bin.Jalview" />
 432         <attribute name="Permissions" value="all-permissions" />
 433         <attribute name="Application-Name" value="Jalview Desktop" />
 434         <attribute name="Codebase" value="${application.codebase}" />
 435       </manifest>
 436       <fileset dir="${outputDir}/">
 437         <exclude name="cache*/**" />
 438         <exclude name="*.jar" />
 439         <exclude name="*.jar.*" />
 440         <exclude name="**/*.jar" />
 441         <exclude name="**/*.jar.*" />
 442       </fileset>
 443     </jar>
 444
 445     <copy toDir="${packageDir}" flatten="true">
 446       <fileset dir="${outputDir}">
 447         <include name="*.jar" />
 448         <include name="**/*.jar" />
 449       </fileset>
 450     </copy>
 451   </target>
 452
 453
 454   <!-- jalopy code reformatter -->
 455   <target name="sourcescrub" depends="init,build">
 456     <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 457       <fileset dir="${sourceDir}">
 458         <include name="*.java" />
 459         <include name="**/*.java" />
 460         <include name="**/**/*.java" />
 461       </fileset>
 462     </jalopy>
 463   </target>
 464
 465
 466
 467   <!-- Compile, package and obfuscate Jalview Applet -->
 468   <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 469
 470   <target name="compileApplet" depends="init,clean">
 471     <mkdir dir="${outputDir}" />
 472     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 473                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 474                         excludes="ext/**,MCview/**,org/**,vamsas/**" />
 475   </target>
 476
 477   <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 478     <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 479     <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 480     <copy todir="${outputDir}/lang">
 481       <fileset dir="${resourceDir}/lang">
 482         <include name="**.*"/>
 483       </fileset>
 484     </copy>
 485     <jar destfile="in.jar" index="true">
 486       <manifest>
 487         <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 488         <attribute name="Application-Name" value="JalviewLite" />
 489         <attribute name="Codebase" value="${applet.codebase}" />
 490       </manifest>
 491       <fileset dir="${outputDir}">
 492         <include name="com/**" />
 493         <include name="MCview/**" />
 494         <include name="jalview/**" />
 495         <include name=".build_properties" />
 496         <include name="images/idwidth.gif" />
 497         <include name="images/link.gif" />
 498         <include name="lang/**" />
 499       </fileset>
 500     </jar>
 501   </target>
 502   <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 503   </target>
 504   <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 505     <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 506     <delete file="in.jar" />
 507   </target>
 508   <target name="-obfuscatereally" unless="donotobfuscate">
 509
 510     <path id="obfuscateDeps.path">
 511       <pathelement location="${applet.jre.tools}" />
 512       <pathelement location="appletlib/${jmolJar}" />
 513     </path>
 514     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 515
 516     <proguard>
 517       <injar file="in.jar" />
 518       <outjar file="${jalviewLiteJar}" />
 519       <libraryjar refid="obfuscateDeps.path" />
 520       <dontwarn/>
 521       <keep access="public" type="class" name="jalview.bin.JalviewLite">
 522         <field access="public" />
 523         <method access="public" />
 524         <constructor access="public" />
 525       </keep>
 526       <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 527         <field access="public" />
 528         <method access="public" />
 529         <constructor access="public" />
 530       </keep>
 531       <!--      -libraryjars "${obfuscateDeps}"
 532       -injars      in.jar
 533       -outjars     jalviewApplet.jar
 534       -keep public class jalview.bin.JalviewLite
 535        { public * ; } -->
 536     </proguard>
 537     <delete file="in.jar" />
 538   </target>
 539
 540   <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 541     <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 542     <delete>
 543       <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 544         <include name="*.java" />
 545         <include name="descriptors/*.java" />
 546       </fileset>
 547     </delete>
 548     <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 549     <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 550     <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 551     <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 552     <!--
 553                 now build the jalview.binding package with the old schema set
 554                 -->
 555     <delete>
 556       <fileset dir="${sourceDir}/jalview/binding/">
 557         <include name="**" />
 558       </fileset>
 559     </delete>
 560     <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 561     <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 562     <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 563   </target>
 564   <target name="sourcedist" description="create jalview source distribution" depends="init">
 565     <delete file="${source.dist.name}" />
 566     <tar destfile="${source.dist.name}" compression="gzip">
 567       <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 568         <include name="LICENSE" />
 569         <include name="README" />
 570         <include name="build.xml" />
 571         <include name="jalview-jalopy.xml" />
 572         <include name="JalviewApplet.jpx" />
 573         <include name="JalviewX.jpx" />
 574         <include name="nbbuild.xml"/>
 575         <include name="nbproject/genfiles.properties"/>
 576         <include name="nbproject/project.properties"/>
 577         <include name="nbproject/project.xml"/>
 578         <include name="${sourceDir}/*.java" />
 579         <include name="${sourceDir}/**/*.java" />
 580         <include name="${sourceDir}/**/*.cdr" />
 581         <include name="${libDir}/**/*" />
 582         <include name="${resourceDir}/**/*" />
 583         <include name="${helpDir}/**/*" />
 584         <include name="appletlib/${jmolJar}" />
 585         <exclude name="**/*locales" />
 586         <exclude name="*locales/**" />
 587         <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 588         <exclude name="utils/InstallAnywhere/**Build*/**" />
 589         <exclude name="utils/InstallAnywhere/**Build*/**" />
 590         <exclude name="utils/InstallAnywhere/**locale*" />
 591         <exclude name="utils/InstallAnywhere/**locale*/**" />
 592         <include name="${schemaDir}/**/*" />
 593         <include name="utils/**/*" />
 594         <include name="${docDir}/**/*" />
 595         <include name="examples/**/*" />
 596       </tarfileset>
 597     </tar>
 598   </target>
 599   <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 600     <copy todir="${packageDir}/examples">
 601       <fileset dir="examples">
 602         <include name="**/*"/>
 603         <include name="javascript/*"/>
 604         <include name="jmol/*"/>
 605       </fileset>
 606       <fileset dir=".">
 607         <include name="${jalviewLiteJar}" />
 608       </fileset>
 609       <fileset dir="appletlib">
 610         <include name="**/*"/>
 611       </fileset>
 612     </copy>
 613     <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 614     <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 615       <manifest>
 616         <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 617         <!--          <attribute name="Permissions" value="sandbox" /> -->
 618         <!--<attribute name="Trusted-Lib" value="true" /> -->
 619         <attribute name="Codebase" value="${applet.codebase}"/>
 620         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 621       </manifest>
 622     </jar>
 623     <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 624       <fileset dir="${packageDir}/examples">
 625         <include name="*.jar" />
 626       </fileset>
 627     </signjar>
 628     <presetdef name="ap_applet.jar">
 629       <!-- build a signed applet with 'all-permissions' -
 630                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 631                           JalviewLite+JmolApplet linked sequence/structure fails
 632                           Mixed code warnings are raised
 633                           -->
 634       <jar update="true" index="true">
 635         <manifest>
 636           <attribute name="Application-Name" value="JalviewLite" />
 637           <attribute name="Permissions" value="all-permissions" />
 638           <attribute name="Codebase" value="${applet.codebase}" />
 639           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 640           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 641         </manifest>
 642       </jar>
 643     </presetdef>
 644     <presetdef name="applet.jar">
 645       <!-- build signed applet with sandbox permissions -
 646                           Needs 'param name="permissions' value="sandbox"' in applet tag
 647                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 648                         -->
 649
 650       <jar update="true" index="true">
 651         <manifest>
 652           <attribute name="Application-Name" value="JalviewLite" />
 653           <attribute name="Permissions" value="sandbox" />
 654           <attribute name="Codebase" value="${applet.codebase}" />
 655           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 656           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 657         </manifest>
 658       </jar>
 659     </presetdef>
 660     <presetdef name="tl_applet.jar">
 661       <!-- build signed applet with trusted library/trusted permissions -
 662                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 663                                j1.7_45:
 664                                No mixed code warnings raised
 665                                Jmol/JalviewLite sequence/structure example doesn't link structures
 666                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 667
 668                               -->
 669
 670       <jar update="true" index="true">
 671         <manifest>
 672           <attribute name="Application-Name" value="JalviewLite" />
 673           <attribute name="Permissions" value="all-permissions" />
 674           <attribute name="Codebase" value="${applet.codebase}" />
 675           <attribute name="Trusted-Only" value="true" />
 676           <attribute name="Trusted-Library" value="true" />
 677         </manifest>
 678       </jar>
 679     </presetdef>
 680     <presetdef name="to_applet.jar">
 681       <!-- not fully test variant (yet) -->
 682       <jar update="true" index="true">
 683         <manifest>
 684           <attribute name="Application-Name" value="JalviewLite" />
 685           <attribute name="Permissions" value="all-permissions" />
 686           <attribute name="Codebase" value="${applet.codebase}" />
 687           <attribute name="Trusted-Only" value="true" />
 688         </manifest>
 689       </jar>
 690     </presetdef>
 691     <!-- create differently privileged artefacts -->
 692     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 693     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 694     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 695     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 696     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 697     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 698     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 699     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 700     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 701     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 702     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 703     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 704     <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 705     <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 706     <!-- finally, create manifest for original jars -->
 707     <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 708     <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 709
 710     <!-- todo - write examples/downloads for alternate versions of the applet -->
 711     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 712
 713       <fileset dir="${packageDir}/examples">
 714         <exclude name="u_*.jar"/>
 715         <include name="${jalviewLiteJar}" />
 716         <include name="${jmolJar}" />
 717         <include name="to_${jalviewLiteJar}" />
 718         <include name="to_${jmolJar}" />
 719         <include name="tl_${jalviewLiteJar}" />
 720         <include name="tl_${jmolJar}" />
 721         <include name="ap_${jalviewLiteJar}" />
 722         <include name="ap_${jmolJar}" />
 723       </fileset>
 724     </signjar>
 725     <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 726     <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 727   </target>
 728   <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 729     <javadoc destdir="${javadocDir}">
 730       <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 731       </packageset>
 732     </javadoc>
 733   </target>
 734 </project>