build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   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   <target name="help" depends="usage" />
  22   <target name="usage">
  23     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  24     <echo message="Targets include:" />
  25     <echo message="usage - default target, displays this message" />
  26     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  27     <echo message="build - compiles all necessary files for Application" />
  28     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  29     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  30     <echo message="              this needs a keystore and key. See docs/building.html for more information." />
  31     <echo message="compileApplet - compiles all necessary files for Applet" />
  32     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  33     <echo message="See docs/building.html and the comments in build file for other targets." />
  34     <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  35     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  36   </target>
  37
  38
  39   <!-- utils is a class path to additional utilities needed for
  40     building docs, jars and webstart stuff -->
  41   <!--
  42         Userdefined build property defaults
  43
  44         wsdl.server list (plus namespace mapping info ???)  - also want
  45                 ... to make this a dynamically generatable property
  46         WebStart Location
  47         Build location - provide a temporary root for speed
  48         jarsigner keystore and info
  49         Jakarta and axis classpath ?
  50         Default argument for starting Jalview (if it exists).
  51
  52 -->
  53
  54   <target name="init">
  55     <path id="axis.classpath">
  56       <!-->
  57       <fileset dir="/usr/local/axis/lib">
  58         <include name="**/*.jar" />
  59       </fileset>
  60       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  61         <include name="**/*.jar"/>
  62         <include name="*.jar"/>
  63       </fileset> -->
  64       </path>
  65     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  66     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  67     <!-- 2.4 (VAMSAS)" -->
  68     <!-- Include debugging information in javac true or false -->
  69     <property name="javac.debug" value="true" />
  70
  71     <!-- JarSigner Key Store for Webstart Distribution -->
  72     <property name="jalview.keystore" value="./keys/.keystore" />
  73     <!-- Keystore Password -->
  74     <property name="jalview.keystore.pass" value="alignmentisfun" />
  75     <!-- Key Name -->
  76     <property name="jalview.key" value="jalview" />
  77     <!-- Key Password -->
  78     <property name="jalview.key.pass" value="alignmentisfun" />
  79
  80     <!-- Don't change anything below here unless you know what you are doing! -->
  81     <!-- Url path for WebStart in JNLP file -->
  82     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  83     <!-- Webstart Image - looked for in resources/images -->
  84     <property name="WebStartImage" value="JalviewLogo_big.png"/>
  85     <!-- J2SE version needed for webstart launch -->
  86     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  87     <property name="j2sev" value="1.7+"/>
  88
  89     <!-- Permissions for running Java applets and applications. -->
  90     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
  91     <property name="application.codebase" value="*.jalview.org" />
  92     <!-- and allowing the applet to be deployed from any URL -->
  93     <!-- 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 -->
  94     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
  95     <property name="applet.caller-codebase" value="${applet.codebase}" />
  96
  97     <!-- build directory configuration -->
  98     <property name="libDir" value="lib" />
  99     <property name="resourceDir" value="resources" />
 100     <property name="helpDir" value="help" />
 101     <property name="docDir" value="doc" />
 102     <property name="sourceDir" value="src" />
 103     <property name="schemaDir" value="schemas" />
 104     <property name="outputDir" value="classes" />
 105     <property name="packageDir" value="dist" />
 106     <property name="outputJar" value="jalview.jar" />
 107     <!-- Jalview Applet JMol Jar Dependency -->
 108     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 109     <property name="varnaJar" value="VARNAv3-9.jar" />
 110     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 111     <!-- switch to indicate if we should obfuscate jalviewLite -->
 112     <!-- <property name="donotobfuscate" value="true"/> -->
 113     <!-- switch to exclude associations from generated jnlp files -->
 114     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 115
 116     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 117     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 118     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 119     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 120     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 121     <property name="WSInterf" value="MsaWS" />
 122     <property name="wsdl.Namespace" value="vamsas" />
 123     <property name="wsdl.ClientNS" value="ext.vamsas" />
 124     <!-- the class path for building the application -->
 125     <path id="build.classpath">
 126       <fileset dir="utils">
 127         <include name="*.jar" />
 128         <include name="**/*.jar" />
 129       </fileset>
 130       <fileset dir="${libDir}">
 131         <include name="*.jar" />
 132         <include name="**/*.jar" />
 133       </fileset>
 134       <fileset dir="${java.home}/lib">
 135         <include name="plugin.jar"/>
 136       </fileset>
 137       <fileset dir="appletlib">
 138         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 139                                 -->
 140         <include name="${jmolJar}" />
 141         <include name="${varnaJar}" />
 142       </fileset>
 143
 144     </path>
 145     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 146     <!-- The Location of the java 1.1.8 jdk -->
 147     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
 148     <property name="java118.home" value="${java.home}" />
 149     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 150                 -->
 151     <!-- jre for 1.4 version -->
 152     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 153
 154     <!-- the classpath for building the 1.1 applet -->
 155     <path id="jalviewlite.deps">
 156       <fileset dir="${java118.home}">
 157         <include name="lib/classes.zip" />
 158       </fileset>
 159       <fileset dir="${java.home}/lib">
 160         <include name="plugin.jar"/>
 161       </fileset>
 162       <pathelement location="appletlib/${jmolJar}" />
 163       <pathelement location="lib/${varnaJar}" />
 164     </path>
 165     <!-- default location for outputting javadoc -->
 166     <property name="javadocDir" value="${packageDir}/javadoc"/>
 167   </target>
 168
 169
 170   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 171   <target name="buildPropertiesFile" depends="init">
 172     <tstamp prefix="build">
 173       <format property="date" pattern="dd MMMM yyyy" />
 174     </tstamp>
 175     <properties file="${outputDir}/.build_properties">
 176       <header>
 177           ---Jalview Build Details---
 178         </header>
 179       <property name="VERSION" value="${JALVIEW_VERSION}" />
 180       <property name="BUILD_DATE" value="${build.date}" />
 181     </properties>
 182   </target>
 183
 184
 185   <target name="clean" depends="init">
 186     <!-- not efficient yet. -->
 187     <delete dir="${outputDir}" includes="*,**/*"/>
 188   </target>
 189
 190   <target name="distclean" depends="init, clean">
 191
 192     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 193     <delete>
 194       <fileset dir=".">
 195         <include name="${outputJar}" />
 196         <include name="#*#" />
 197         <include name="#*.*#" />
 198         <include name="**/#*#" />
 199         <include name="**/#*.*#" />
 200         <include name="*~" />
 201         <include name="*.*~" />
 202         <include name="**/*~" />
 203         <include name="**/*.*~" />
 204       </fileset>
 205     </delete>
 206   </target>
 207
 208   <target name="prepare" depends="init">
 209     <mkdir dir="${outputDir}" />
 210     <copy todir="${outputDir}">
 211       <fileset dir=".">
 212         <include name="${docDir}/**/*.*" />
 213         <include name="${helpDir}/**/*.*" />
 214         <include name="${libDir}/*.jar" />
 215       </fileset>
 216       <fileset dir="${resourceDir}">
 217         <include name="**/*.*" />
 218       </fileset>
 219     </copy>
 220   </target>
 221
 222   <target name="build" depends="prepare">
 223     <!-- not efficient yet. -->
 224     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 225       <exclude name="jalview/*applet*" />
 226       <exclude name="jalview/appletgui/**" />
 227       <exclude name="com/stevesoft/**" />
 228     </javac>
 229   </target>
 230   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 231     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 232       <arg line="html" />
 233     </java>
 234   </target>
 235
 236   <target name="makefulldist" depends="makedist">
 237     <copy todir="${packageDir}">
 238       <fileset dir="${resourceDir}/images">
 239         <include name="${WebStartImage}"/>
 240       </fileset>
 241     </copy>
 242
 243     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 244
 245     <!-- create a dummy jar which will eventually contain the jnlp template -->
 246     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 247       <fileset dir="${packageDir}">
 248         <include name="jalview.jar" />
 249       </fileset>
 250     </jar>
 251
 252     <mkdir dir="${packageDir}/JNLP-INF"/>
 253     <antcall target="writejnlpf">
 254       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 255       <param name="inih" value="*" />
 256       <param name="maxh" value="*"/>
 257     </antcall>
 258
 259     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 260       <fileset dir="${packageDir}">
 261         <include name="JNLP-INF"/>
 262       </fileset>
 263     </jar>
 264
 265     <antcall target="writejnlpf">
 266       <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 267       <param name="inih" value="10M" />
 268       <param name="maxh" value="256M"/>
 269     </antcall>
 270
 271     <antcall target="writejnlpf">
 272       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 273       <param name="inih" value="128M" />
 274       <param name="maxh" value="512M"/>
 275     </antcall>
 276
 277     <antcall target="writejnlpf">
 278       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 279       <param name="inih" value="256M" />
 280       <param name="maxh" value="1024M"/>
 281     </antcall>
 282
 283     <!-- finally, need to postprocess to add in associations at end of 'information' element
 284
 285                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 286
 287                 </xslt>
 288
 289
 290                         -->
 291     <!--
 292                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 293         <association mime-type="application-x/ext-file" extensions="fasta"/>
 294         <association mime-type="application-x/ext-file" extensions="mfa"/>
 295         <association mime-type="application-x/ext-file" extensions="fastq"/>
 296         <association mime-type="application-x/ext-file" extensions="blc"/>
 297         <association mime-type="application-x/ext-file" extensions="msf"/>
 298         <association mime-type="application-x/ext-file" extensions="pfam"/>
 299         <association mime-type="application-x/ext-file" extensions="aln"/>
 300         <association mime-type="application-x/ext-file" extensions="pir"/>
 301         <association mime-type="application-x/ext-file" extensions="amsa"/>
 302         <association mime-type="application-x/ext-file" extensions="stk"/>
 303         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 304     <!-- and sign the jars -->
 305     <!-- the default keystore details might need to be edited here -->
 306     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 307       <fileset dir="${packageDir}">
 308         <include name="*.jar" />
 309       </fileset>
 310     </signjar>
 311   </target>
 312
 313   <target name="runenv" depends="init">
 314     <path id="run.classpath">
 315       <pathelement location="${outputDir}" />
 316       <fileset dir="${outputDir}">
 317         <include name="${libDir}/*.jar" />
 318       </fileset>
 319     </path>
 320     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 321
 322     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 323       </echo>
 324   </target>
 325
 326   <target name="-generatejnlpf">
 327     <presetdef name="jnlpf">
 328       <jnlp codebase="${WebStartLocation}">
 329         <information>
 330           <title>Jalview</title>
 331           <vendor>The Barton Group</vendor>
 332           <homepage href="http://www.jalview.org" />
 333           <description>Jalview Multiple Alignment Editor</description>
 334           <description kind="short">Jalview</description>
 335           <icon href="${WebStartImage}" />
 336           <offline_allowed />
 337         </information>
 338         <resources>
 339           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 340           <fileset dir="${packageDir}">
 341             <include name="jalview.jar" />
 342           </fileset>
 343           <fileset dir="${packageDir}">
 344             <include name="*.jar" />
 345             <include name="*_*.jar" />
 346             <exclude name="jalview.jar" />
 347           </fileset>
 348           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 349         </resources>
 350         <application_desc main_class="jalview.bin.Jalview">
 351         </application_desc>
 352         <security>
 353           <all_permissions />
 354         </security>
 355       </jnlp>
 356     </presetdef>
 357
 358     <jnlpf toFile="${jnlpFile}"/>
 359
 360   </target>
 361
 362   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 363     <echo message="Not adding JNLP File Associations"/>
 364   </target>
 365
 366   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 367     <replace file="${jnlpFile}">
 368       <replacetoken>
 369         <![CDATA[</information>]]></replacetoken>
 370       <replacevalue>
 371         <![CDATA[
 372           <association mime-type="application-x/ext-file" extensions="fa" />
 373         <association mime-type="application-x/ext-file" extensions="fasta" />
 374         <association mime-type="application-x/ext-file" extensions="mfa" />
 375         <association mime-type="application-x/ext-file" extensions="fastq" />
 376         <association mime-type="application-x/ext-file" extensions="blc" />
 377         <association mime-type="application-x/ext-file" extensions="msf" />
 378         <association mime-type="application-x/ext-file" extensions="pfam" />
 379         <association mime-type="application-x/ext-file" extensions="aln"/>
 380         <association mime-type="application-x/ext-file" extensions="pir"/>
 381         <association mime-type="application-x/ext-file" extensions="amsa"/>
 382         <association mime-type="application-x/ext-file" extensions="stk"/>
 383         <association mime-type="application-x/ext-file" extensions="jvp"/>
 384       </information>]]></replacevalue>
 385   </replace>
 386   <echo message="Added file associations to JNLP file"/>
 387 </target>
 388 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 389 </target>
 390
 391 <target name="buildextclients" depends="init">
 392   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 393   <condition property="dontextbuild">
 394     <equals arg1="n" arg2="${doextbuild.response}" />
 395   </condition>
 396   <condition property="dontextbuild">
 397     <equals arg1="N" arg2="${doextbuild.response}" />
 398   </condition>
 399   <fail if="dontextbuild">
 400         Build External Client Code process aborted by user. Jalview source is unchanged.
 401       </fail>
 402   <!-- Currently, this doesn't happen automatically.
 403      1. Run WSDL2Java as below, which generates an ext.vamsas +
 404      vamsas.<datapackages> fileset.
 405      2. refactor ext.vamsas.SpecificserviceWS* to
 406      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 407      3. Update the jalview.ws.*WServices classes to reflect the
 408      interface type, and all locations of this wsdl type that Jalview
 409      might be using.
 410
 411 -->
 412   <path id="axisbuild">
 413     <path refid="build.classpath" />
 414   </path>
 415   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 416   <move todir="./bak">
 417     <fileset dir="${sourceDir}" id="client">
 418       <include name="${wsdl.ClientNS}/*.*" />
 419     </fileset>
 420   </move>
 421
 422   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 423     <mappingSet>
 424       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 425       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 426     </mappingSet>
 427   </axis-wsdl2java>
 428 </target>
 429
 430 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 431   <!-- make the package jar if not already existing -->
 432   <mkdir dir="${packageDir}" />
 433   <!-- clean dir if it already existed -->
 434   <delete>
 435     <fileset dir="${packageDir}">
 436       <include name="*.jar"/>
 437     </fileset>
 438   </delete>
 439   <jar destfile="${packageDir}/${outputJar}" index="true">
 440     <manifest>
 441       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 442       <attribute name="Permissions" value="all-permissions" />
 443       <attribute name="Application-Name" value="Jalview Desktop" />
 444       <attribute name="Codebase" value="${application.codebase}" />
 445     </manifest>
 446     <fileset dir="${outputDir}/">
 447       <exclude name="cache*/**" />
 448       <exclude name="*.jar" />
 449       <exclude name="*.jar.*" />
 450       <exclude name="**/*.jar" />
 451       <exclude name="**/*.jar.*" />
 452     </fileset>
 453   </jar>
 454
 455   <copy toDir="${packageDir}" flatten="true">
 456     <fileset dir="${outputDir}">
 457       <include name="*.jar" />
 458       <include name="**/*.jar" />
 459     </fileset>
 460   </copy>
 461 </target>
 462
 463
 464 <!-- jalopy code reformatter -->
 465 <target name="sourcescrub" depends="init,build">
 466   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 467     <fileset dir="${sourceDir}">
 468       <include name="*.java" />
 469       <include name="**/*.java" />
 470       <include name="**/**/*.java" />
 471     </fileset>
 472   </jalopy>
 473 </target>
 474
 475
 476
 477 <!-- Compile, package and obfuscate Jalview Applet -->
 478 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 479
 480 <target name="compileApplet" depends="init,clean">
 481   <mkdir dir="${outputDir}" />
 482   <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 483                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 484                         excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 485 </target>
 486
 487 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 488   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 489   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 490   <copy todir="${outputDir}/lang">
 491     <fileset dir="${resourceDir}/lang">
 492       <include name="**.*"/>
 493     </fileset>
 494   </copy>
 495   <jar destfile="in.jar" index="true">
 496     <manifest>
 497       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 498       <attribute name="Application-Name" value="JalviewLite" />
 499       <attribute name="Codebase" value="${applet.codebase}" />
 500     </manifest>
 501     <fileset dir="${outputDir}">
 502       <include name="com/**" />
 503       <include name="MCview/**" />
 504       <include name="jalview/**" />
 505       <include name=".build_properties" />
 506       <include name="images/idwidth.gif" />
 507       <include name="images/link.gif" />
 508       <include name="lang/**" />
 509     </fileset>
 510   </jar>
 511 </target>
 512 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 513 </target>
 514 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 515   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 516   <delete file="in.jar" />
 517 </target>
 518 <target name="-obfuscatereally" unless="donotobfuscate">
 519
 520   <path id="obfuscateDeps.path">
 521     <pathelement location="${applet.jre.tools}" />
 522     <pathelement location="appletlib/${jmolJar}" />
 523   </path>
 524   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 525
 526   <proguard>
 527     <injar file="in.jar" />
 528     <outjar file="${jalviewLiteJar}" />
 529     <libraryjar refid="obfuscateDeps.path" />
 530     <dontwarn/>
 531     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 532       <field access="public" />
 533       <method access="public" />
 534       <constructor access="public" />
 535     </keep>
 536     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 537       <field access="public" />
 538       <method access="public" />
 539       <constructor access="public" />
 540     </keep>
 541     <!--      -libraryjars "${obfuscateDeps}"
 542       -injars      in.jar
 543       -outjars     jalviewApplet.jar
 544       -keep public class jalview.bin.JalviewLite
 545        { public * ; } -->
 546   </proguard>
 547   <delete file="in.jar" />
 548 </target>
 549
 550 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 551   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 552   <delete>
 553     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 554       <include name="*.java" />
 555       <include name="descriptors/*.java" />
 556     </fileset>
 557   </delete>
 558   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 559   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 560   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 561   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 562   <!--
 563                 now build the jalview.binding package with the old schema set
 564                 -->
 565   <delete>
 566     <fileset dir="${sourceDir}/jalview/binding/">
 567       <include name="**" />
 568     </fileset>
 569   </delete>
 570   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 571   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 572   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 573 </target>
 574 <target name="sourcedist" description="create jalview source distribution" depends="init">
 575   <delete file="${source.dist.name}" />
 576   <tar destfile="${source.dist.name}" compression="gzip">
 577     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 578       <include name="LICENSE" />
 579       <include name="README" />
 580       <include name="build.xml" />
 581       <include name="jalview-jalopy.xml" />
 582       <include name="JalviewApplet.jpx" />
 583       <include name="JalviewX.jpx" />
 584       <include name="nbbuild.xml"/>
 585       <include name="nbproject/genfiles.properties"/>
 586       <include name="nbproject/project.properties"/>
 587       <include name="nbproject/project.xml"/>
 588       <include name="${sourceDir}/*.java" />
 589       <include name="${sourceDir}/**/*.java" />
 590       <include name="${sourceDir}/**/*.cdr" />
 591       <include name="${libDir}/**/*" />
 592       <include name="${resourceDir}/**/*" />
 593       <include name="${helpDir}/**/*" />
 594       <include name="appletlib/${jmolJar}" />
 595       <exclude name="**/*locales" />
 596       <exclude name="*locales/**" />
 597       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 598       <exclude name="utils/InstallAnywhere/**Build*/**" />
 599       <exclude name="utils/InstallAnywhere/**Build*/**" />
 600       <exclude name="utils/InstallAnywhere/**locale*" />
 601       <exclude name="utils/InstallAnywhere/**locale*/**" />
 602       <include name="${schemaDir}/**/*" />
 603       <include name="utils/**/*" />
 604       <include name="${docDir}/**/*" />
 605       <include name="examples/**/*" />
 606     </tarfileset>
 607   </tar>
 608 </target>
 609 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 610   <copy todir="${packageDir}/examples">
 611     <fileset dir="examples">
 612       <include name="**/*"/>
 613       <include name="javascript/*"/>
 614       <include name="jmol/*"/>
 615     </fileset>
 616     <fileset dir=".">
 617       <include name="${jalviewLiteJar}" />
 618     </fileset>
 619     <fileset dir="appletlib">
 620       <include name="**/*"/>
 621     </fileset>
 622   </copy>
 623   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 624   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 625     <manifest>
 626       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 627       <!--          <attribute name="Permissions" value="sandbox" /> -->
 628       <!--<attribute name="Trusted-Lib" value="true" /> -->
 629       <attribute name="Codebase" value="${applet.codebase}"/>
 630       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 631     </manifest>
 632   </jar>
 633   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 634     <fileset dir="${packageDir}/examples">
 635       <include name="*.jar" />
 636     </fileset>
 637   </signjar>
 638   <presetdef name="ap_applet.jar">
 639     <!-- build a signed applet with 'all-permissions' -
 640                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 641                           JalviewLite+JmolApplet linked sequence/structure fails
 642                           Mixed code warnings are raised
 643                           -->
 644     <jar update="true" index="true">
 645       <manifest>
 646         <attribute name="Application-Name" value="JalviewLite" />
 647         <attribute name="Permissions" value="all-permissions" />
 648         <attribute name="Codebase" value="${applet.codebase}" />
 649         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 650         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 651       </manifest>
 652     </jar>
 653   </presetdef>
 654   <presetdef name="applet.jar">
 655     <!-- build signed applet with sandbox permissions -
 656                           Needs 'param name="permissions' value="sandbox"' in applet tag
 657                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 658                         -->
 659
 660     <jar update="true" index="true">
 661       <manifest>
 662         <attribute name="Application-Name" value="JalviewLite" />
 663         <attribute name="Permissions" value="sandbox" />
 664         <attribute name="Codebase" value="${applet.codebase}" />
 665         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 666         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 667       </manifest>
 668     </jar>
 669   </presetdef>
 670   <presetdef name="tl_applet.jar">
 671     <!-- build signed applet with trusted library/trusted permissions -
 672                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 673                                j1.7_45:
 674                                No mixed code warnings raised
 675                                Jmol/JalviewLite sequence/structure example doesn't link structures
 676                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 677
 678                               -->
 679
 680     <jar update="true" index="true">
 681       <manifest>
 682         <attribute name="Application-Name" value="JalviewLite" />
 683         <attribute name="Permissions" value="all-permissions" />
 684         <attribute name="Codebase" value="${applet.codebase}" />
 685         <attribute name="Trusted-Only" value="true" />
 686         <attribute name="Trusted-Library" value="true" />
 687       </manifest>
 688     </jar>
 689   </presetdef>
 690   <presetdef name="to_applet.jar">
 691     <!-- not fully test variant (yet) -->
 692     <jar update="true" index="true">
 693       <manifest>
 694         <attribute name="Application-Name" value="JalviewLite" />
 695         <attribute name="Permissions" value="all-permissions" />
 696         <attribute name="Codebase" value="${applet.codebase}" />
 697         <attribute name="Trusted-Only" value="true" />
 698       </manifest>
 699     </jar>
 700   </presetdef>
 701   <!-- create differently privileged artefacts -->
 702   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 703   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 704   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 705   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 706   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 707   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 708   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 709   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 710   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 711   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 712   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 713   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 714   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 715   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 716   <!-- finally, create manifest for original jars -->
 717   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 718   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 719
 720   <!-- todo - write examples/downloads for alternate versions of the applet -->
 721   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 722
 723     <fileset dir="${packageDir}/examples">
 724       <exclude name="u_*.jar"/>
 725       <include name="${jalviewLiteJar}" />
 726       <include name="${jmolJar}" />
 727       <include name="to_${jalviewLiteJar}" />
 728       <include name="to_${jmolJar}" />
 729       <include name="tl_${jalviewLiteJar}" />
 730       <include name="tl_${jmolJar}" />
 731       <include name="ap_${jalviewLiteJar}" />
 732       <include name="ap_${jmolJar}" />
 733     </fileset>
 734   </signjar>
 735   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 736   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 737 </target>
 738 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 739   <javadoc destdir="${javadocDir}">
 740     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 741     </packageset>
 742   </javadoc>
 743 </target>
 744 </project>