build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ 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
  66     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  67     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  68
  69     <property name="INSTALLATION" value="Source" />
  70
  71     <!-- 2.4 (VAMSAS)" -->
  72     <!-- Include debugging information in javac true or false -->
  73     <property name="javac.debug" value="true" />
  74
  75     <!-- JarSigner Key Store for Webstart Distribution -->
  76     <property name="jalview.keystore" value="./keys/.keystore" />
  77     <!-- Keystore Password -->
  78     <property name="jalview.keystore.pass" value="alignmentisfun" />
  79     <!-- Key Name -->
  80     <property name="jalview.key" value="jalview" />
  81     <!-- Key Password -->
  82     <property name="jalview.key.pass" value="alignmentisfun" />
  83
  84     <!-- Don't change anything below here unless you know what you are doing! -->
  85     <!-- Url path for WebStart in JNLP file -->
  86     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  87     <!-- Webstart Image - looked for in resources/images -->
  88     <property name="WebStartImage" value="JalviewLogo_big.png"/>
  89     <!-- J2SE version needed for webstart launch -->
  90     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  91     <property name="j2sev" value="1.7+"/>
  92         <!-- Java Compilation settings - source and target javac version -->
  93         <property name="javac.source" value="1.7"/>
  94         <property name="javac.target" value="1.7"/>
  95
  96     <!-- Permissions for running Java applets and applications. -->
  97     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
  98     <property name="application.codebase" value="*.jalview.org" />
  99     <!-- and allowing the applet to be deployed from any URL -->
 100     <!-- 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 -->
 101     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 102     <property name="applet.caller-codebase" value="${applet.codebase}" />
 103
 104     <!-- build directory configuration -->
 105     <property name="libDir" value="lib" />
 106     <property name="resourceDir" value="resources" />
 107     <property name="helpDir" value="help" />
 108     <property name="docDir" value="doc" />
 109     <property name="sourceDir" value="src" />
 110     <property name="schemaDir" value="schemas" />
 111     <property name="outputDir" value="classes" />
 112     <property name="packageDir" value="dist" />
 113     <property name="outputJar" value="jalview.jar" />
 114     <!-- Jalview Applet JMol Jar Dependency -->
 115     <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.01.jar" />
 116     <property name="varnaJar" value="VARNAv3-93.jar" />
 117     <property name="jsoup" value="jsoup-1.8.1.jar" />
 118     <property name="jsonSimple" value="json_simple-1.1.jar" />
 119     <property name="javaJson" value="java-json.jar" />
 120     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 121         <property name="reportDir" value="test-reports" />
 122         <property name="testDir" value="test" />
 123         <property name="testOutputDir" value="tests" />
 124     <!-- switch to indicate if we should obfuscate jalviewLite -->
 125     <!-- <property name="donotobfuscate" value="true"/> -->
 126     <!-- switch to exclude associations from generated jnlp files -->
 127     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 128
 129     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 130     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 131     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 132     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 133     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 134     <property name="WSInterf" value="MsaWS" />
 135     <property name="wsdl.Namespace" value="vamsas" />
 136     <property name="wsdl.ClientNS" value="ext.vamsas" />
 137     <!-- the class path for building the application -->
 138     <path id="build.classpath">
 139       <fileset dir="utils">
 140         <include name="*.jar" />
 141         <include name="**/*.jar" />
 142       </fileset>
 143       <fileset dir="${libDir}">
 144         <include name="*.jar" />
 145         <include name="**/*.jar" />
 146       </fileset>
 147       <fileset dir="${java.home}/lib">
 148         <include name="plugin.jar"/>
 149       </fileset>
 150       <fileset dir="appletlib">
 151         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 152                                 -->
 153         <include name="${jmolJar}" />
 154         <include name="${varnaJar}" />
 155       </fileset>
 156
 157     </path>
 158     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 159     <!-- The Location of the java 1.1.8 jdk -->
 160     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
 161     <property name="java118.home" value="${java.home}" />
 162     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 163                 -->
 164     <!-- jre for 1.4 version -->
 165     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 166
 167     <!-- the classpath for building the 1.1 applet -->
 168     <path id="jalviewlite.deps">
 169       <fileset dir="${java118.home}">
 170         <include name="lib/classes.zip" />
 171       </fileset>
 172       <fileset dir="${java.home}/lib">
 173         <include name="plugin.jar"/>
 174       </fileset>
 175       <pathelement location="appletlib/${jmolJar}" />
 176       <pathelement location="lib/${varnaJar}" />
 177       <pathelement location="lib/${jsoup}" />
 178       <pathelement location="lib/${jsonSimple}" />
 179       <pathelement location="lib/${javaJson}" />
 180
 181     </path>
 182     <!-- default location for outputting javadoc -->
 183     <property name="javadocDir" value="${packageDir}/javadoc"/>
 184   </target>
 185
 186
 187   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 188   <target name="buildPropertiesFile" depends="init">
 189     <tstamp prefix="build">
 190       <format property="date" pattern="dd MMMM yyyy" />
 191     </tstamp>
 192     <properties file="${outputDir}/.build_properties">
 193       <header>
 194           ---Jalview Build Details---
 195         </header>
 196       <property name="VERSION" value="${JALVIEW_VERSION}" />
 197       <property name="INSTALLATION" value="${INSTALLATION}" />
 198       <property name="BUILD_DATE" value="${build.date}" />
 199     </properties>
 200   </target>
 201
 202
 203   <target name="clean" depends="init">
 204     <!-- not efficient yet. -->
 205     <delete dir="${outputDir}" includes="*,**/*"/>
 206   </target>
 207
 208   <target name="distclean" depends="init, clean">
 209
 210     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 211     <delete>
 212       <fileset dir=".">
 213         <include name="${outputJar}" />
 214         <include name="#*#" />
 215         <include name="#*.*#" />
 216         <include name="**/#*#" />
 217         <include name="**/#*.*#" />
 218         <include name="*~" />
 219         <include name="*.*~" />
 220         <include name="**/*~" />
 221         <include name="**/*.*~" />
 222       </fileset>
 223     </delete>
 224   </target>
 225
 226   <target name="prepare" depends="init">
 227     <mkdir dir="${outputDir}" />
 228     <copy todir="${outputDir}">
 229       <fileset dir=".">
 230         <include name="${docDir}/**/*.*" />
 231         <include name="${helpDir}/**/*.*" />
 232         <include name="${libDir}/*.jar" />
 233       </fileset>
 234       <fileset dir="${resourceDir}">
 235         <include name="**/*.*" />
 236       </fileset>
 237     </copy>
 238   </target>
 239
 240   <target name="build" depends="prepare">
 241     <!-- not efficient yet. -->
 242     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 243       <exclude name="jalview/*applet*" />
 244       <exclude name="jalview/appletgui/**" />
 245       <exclude name="com/stevesoft/**" />
 246     </javac>
 247   </target>
 248
 249
 250   <target name="testclean" depends="init">
 251     <delete dir="${testOutputDir}" includes="*,**/*"/>
 252   </target>
 253
 254   <target name="prepareTests" depends="init">
 255         <mkdir dir="${testOutputDir}" />
 256         <copy todir="${testOutputDir}">
 257                 <fileset dir=".">
 258                         <include name="${docDir}/**/*.*" />
 259                         <include name="${helpDir}/**/*.*" />
 260                         <include name="${libDir}/*.jar" />
 261                 </fileset>
 262                 <fileset dir="${resourceDir}">
 263                         <include name="**/*.*" />
 264                 </fileset>
 265         </copy>
 266   </target>
 267
 268   <target name="buildTests" depends="prepareTests">
 269         <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${testOutputDir}"
 270                 debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
 271         </javac>
 272         <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}"
 273                 debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
 274         </javac>
 275   </target>
 276
 277   <taskdef name="testng" classname="org.testng.TestNGAntTask" >
 278         <classpath location="utils/testnglibs/testng.jar" />
 279   </taskdef>
 280
 281   <target name="testng" depends="buildTests">
 282         <testng classpathref="build.classpath" outputDir="${reportDir}"
 283                 haltOnFailure="false">
 284                 <classpath location="${testOutputDir}" />
 285                 <xmlfileset dir="utils" includes="jalview_testng.xml" />
 286         </testng>
 287   </target>
 288
 289   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 290     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 291       <arg line="html" />
 292     </java>
 293   </target>
 294
 295   <target name="makefulldist" depends="makedist">
 296     <copy todir="${packageDir}">
 297       <fileset dir="${resourceDir}/images">
 298         <include name="${WebStartImage}"/>
 299       </fileset>
 300     </copy>
 301
 302     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 303
 304     <!-- create a dummy jar which will eventually contain the jnlp template -->
 305     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 306       <fileset dir="${packageDir}">
 307         <include name="jalview.jar" />
 308       </fileset>
 309     </jar>
 310
 311     <mkdir dir="${packageDir}/JNLP-INF"/>
 312     <antcall target="writejnlpf">
 313       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 314       <param name="inih" value="*" />
 315       <param name="maxh" value="*"/>
 316     </antcall>
 317
 318     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 319       <fileset dir="${packageDir}">
 320         <include name="JNLP-INF"/>
 321       </fileset>
 322     </jar>
 323
 324     <antcall target="writejnlpf">
 325       <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 326       <param name="inih" value="10M" />
 327       <param name="maxh" value="256M"/>
 328     </antcall>
 329
 330     <antcall target="writejnlpf">
 331       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 332       <param name="inih" value="128M" />
 333       <param name="maxh" value="512M"/>
 334     </antcall>
 335
 336     <antcall target="writejnlpf">
 337       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 338       <param name="inih" value="256M" />
 339       <param name="maxh" value="1024M"/>
 340     </antcall>
 341
 342     <!-- finally, need to postprocess to add in associations at end of 'information' element
 343
 344                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 345
 346                 </xslt>
 347
 348
 349                         -->
 350     <!--
 351                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 352         <association mime-type="application-x/ext-file" extensions="fasta"/>
 353         <association mime-type="application-x/ext-file" extensions="mfa"/>
 354         <association mime-type="application-x/ext-file" extensions="fastq"/>
 355         <association mime-type="application-x/ext-file" extensions="blc"/>
 356         <association mime-type="application-x/ext-file" extensions="msf"/>
 357         <association mime-type="application-x/ext-file" extensions="pfam"/>
 358         <association mime-type="application-x/ext-file" extensions="aln"/>
 359         <association mime-type="application-x/ext-file" extensions="pir"/>
 360         <association mime-type="application-x/ext-file" extensions="amsa"/>
 361         <association mime-type="application-x/ext-file" extensions="stk"/>
 362         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 363     <!-- and sign the jars -->
 364     <!-- the default keystore details might need to be edited here -->
 365     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 366       <fileset dir="${packageDir}">
 367         <include name="*.jar" />
 368       </fileset>
 369     </signjar>
 370   </target>
 371
 372   <target name="runenv" depends="init">
 373     <path id="run.classpath">
 374       <pathelement location="${outputDir}" />
 375       <fileset dir="${outputDir}">
 376         <include name="${libDir}/*.jar" />
 377       </fileset>
 378     </path>
 379     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 380
 381     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 382       </echo>
 383   </target>
 384
 385   <target name="-generatejnlpf">
 386     <presetdef name="jnlpf">
 387       <jnlp codebase="${WebStartLocation}">
 388         <information>
 389           <title>Jalview</title>
 390           <vendor>The Barton Group</vendor>
 391           <homepage href="http://www.jalview.org" />
 392           <description>Jalview Multiple Alignment Editor</description>
 393           <description kind="short">Jalview</description>
 394           <icon href="${WebStartImage}" />
 395           <offline_allowed />
 396         </information>
 397         <resources>
 398           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 399           <fileset dir="${packageDir}">
 400             <include name="jalview.jar" />
 401           </fileset>
 402           <fileset dir="${packageDir}">
 403             <include name="*.jar" />
 404             <include name="*_*.jar" />
 405             <exclude name="jalview.jar" />
 406                 <exclude name="*jnilib.jar"/>
 407           </fileset>
 408         </resources>
 409         <resources os="Mac OS X">
 410           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 411                 <fileset dir="${packageDir}">
 412                         <include name="*quaqua*.jnilib.jar"/>
 413                 </fileset>
 414         </resources>
 415
 416         <application_desc main_class="jalview.bin.Jalview">
 417         </application_desc>
 418         <security>
 419           <all_permissions />
 420         </security>
 421       </jnlp>
 422     </presetdef>
 423
 424     <jnlpf toFile="${jnlpFile}"/>
 425
 426   </target>
 427
 428   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 429     <echo message="Not adding JNLP File Associations"/>
 430   </target>
 431
 432   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 433     <replace file="${jnlpFile}">
 434       <replacetoken>
 435         <![CDATA[</information>]]></replacetoken>
 436       <replacevalue>
 437         <![CDATA[
 438           <association mime-type="application-x/ext-file" extensions="fa" />
 439         <association mime-type="application-x/ext-file" extensions="fasta" />
 440         <association mime-type="application-x/ext-file" extensions="mfa" />
 441         <association mime-type="application-x/ext-file" extensions="fastq" />
 442         <association mime-type="application-x/ext-file" extensions="blc" />
 443         <association mime-type="application-x/ext-file" extensions="msf" />
 444         <association mime-type="application-x/ext-file" extensions="pfam" />
 445         <association mime-type="application-x/ext-file" extensions="aln"/>
 446         <association mime-type="application-x/ext-file" extensions="pir"/>
 447         <association mime-type="application-x/ext-file" extensions="amsa"/>
 448         <association mime-type="application-x/ext-file" extensions="stk"/>
 449         <association mime-type="application-x/ext-file" extensions="jvp"/>
 450       </information>]]></replacevalue>
 451   </replace>
 452   <echo message="Added file associations to JNLP file"/>
 453 </target>
 454 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 455 </target>
 456
 457 <target name="buildextclients" depends="init">
 458   <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" />
 459   <condition property="dontextbuild">
 460     <equals arg1="n" arg2="${doextbuild.response}" />
 461   </condition>
 462   <condition property="dontextbuild">
 463     <equals arg1="N" arg2="${doextbuild.response}" />
 464   </condition>
 465   <fail if="dontextbuild">
 466         Build External Client Code process aborted by user. Jalview source is unchanged.
 467       </fail>
 468   <!-- Currently, this doesn't happen automatically.
 469      1. Run WSDL2Java as below, which generates an ext.vamsas +
 470      vamsas.<datapackages> fileset.
 471      2. refactor ext.vamsas.SpecificserviceWS* to
 472      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 473      3. Update the jalview.ws.*WServices classes to reflect the
 474      interface type, and all locations of this wsdl type that Jalview
 475      might be using.
 476
 477 -->
 478   <path id="axisbuild">
 479     <path refid="build.classpath" />
 480   </path>
 481   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 482   <move todir="./bak">
 483     <fileset dir="${sourceDir}" id="client">
 484       <include name="${wsdl.ClientNS}/*.*" />
 485     </fileset>
 486   </move>
 487
 488   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 489     <mappingSet>
 490       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 491       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 492     </mappingSet>
 493   </axis-wsdl2java>
 494 </target>
 495
 496 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 497   <!-- make the package jar if not already existing -->
 498   <mkdir dir="${packageDir}" />
 499   <!-- clean dir if it already existed -->
 500   <delete>
 501     <fileset dir="${packageDir}">
 502       <include name="*.jar"/>
 503     </fileset>
 504   </delete>
 505   <jar destfile="${packageDir}/${outputJar}" index="true">
 506     <manifest>
 507       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 508       <attribute name="Permissions" value="all-permissions" />
 509       <attribute name="Application-Name" value="Jalview Desktop" />
 510       <attribute name="Codebase" value="${application.codebase}" />
 511     </manifest>
 512     <fileset dir="${outputDir}/">
 513       <exclude name="cache*/**" />
 514       <exclude name="*.jar" />
 515       <exclude name="*.jar.*" />
 516       <exclude name="**/*.jar" />
 517       <exclude name="**/*.jar.*" />
 518     </fileset>
 519   </jar>
 520
 521   <copy toDir="${packageDir}" flatten="true">
 522     <fileset dir="${outputDir}">
 523       <include name="*.jar" />
 524       <include name="**/*.jar" />
 525     </fileset>
 526   </copy>
 527 </target>
 528
 529
 530 <!-- jalopy code reformatter -->
 531 <target name="sourcescrub" depends="init,build">
 532   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 533     <fileset dir="${sourceDir}">
 534       <include name="*.java" />
 535       <include name="**/*.java" />
 536       <include name="**/**/*.java" />
 537     </fileset>
 538   </jalopy>
 539 </target>
 540
 541
 542
 543 <!-- Compile, package and obfuscate Jalview Applet -->
 544 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 545
 546 <target name="compileApplet" depends="init,clean">
 547   <mkdir dir="${outputDir}" />
 548   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 549                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 550                         excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 551 </target>
 552
 553 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 554   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 555   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 556   <copy todir="${outputDir}/lang">
 557     <fileset dir="${resourceDir}/lang">
 558       <include name="**.*"/>
 559     </fileset>
 560   </copy>
 561   <jar destfile="in.jar" index="true">
 562     <manifest>
 563       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 564       <attribute name="Application-Name" value="JalviewLite" />
 565       <attribute name="Codebase" value="${applet.codebase}" />
 566     </manifest>
 567     <fileset dir="${outputDir}">
 568       <include name="com/**" />
 569       <include name="MCview/**" />
 570       <include name="jalview/**" />
 571       <include name=".build_properties" />
 572       <include name="images/idwidth.gif" />
 573       <include name="images/link.gif" />
 574       <include name="lang/**" />
 575     </fileset>
 576   </jar>
 577 </target>
 578 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 579 </target>
 580 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 581   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 582   <delete file="in.jar" />
 583 </target>
 584 <target name="-obfuscatereally" unless="donotobfuscate">
 585
 586   <path id="obfuscateDeps.path">
 587     <pathelement location="${applet.jre.tools}" />
 588     <pathelement location="appletlib/${jmolJar}" />
 589     <pathelement location="appletlib/${jsonSimple}" />
 590     <pathelement location="appletlib/${javaJson}" />
 591   </path>
 592   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 593
 594   <proguard>
 595     <injar file="in.jar" />
 596     <outjar file="${jalviewLiteJar}" />
 597     <libraryjar refid="obfuscateDeps.path" />
 598     <dontwarn/>
 599     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 600       <field access="public" />
 601       <method access="public" />
 602       <constructor access="public" />
 603     </keep>
 604     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 605       <field access="public" />
 606       <method access="public" />
 607       <constructor access="public" />
 608     </keep>
 609     <!--      -libraryjars "${obfuscateDeps}"
 610       -injars      in.jar
 611       -outjars     jalviewApplet.jar
 612       -keep public class jalview.bin.JalviewLite
 613        { public * ; } -->
 614   </proguard>
 615   <delete file="in.jar" />
 616 </target>
 617
 618 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 619   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 620   <delete>
 621     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 622       <include name="*.java" />
 623       <include name="descriptors/*.java" />
 624     </fileset>
 625   </delete>
 626   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 627   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 628   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 629   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 630   <!--
 631                 now build the jalview.binding package with the old schema set
 632                 -->
 633   <delete>
 634     <fileset dir="${sourceDir}/jalview/binding/">
 635       <include name="**" />
 636     </fileset>
 637   </delete>
 638   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 639   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 640   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 641 </target>
 642 <target name="sourcedist" description="create jalview source distribution" depends="init">
 643   <delete file="${source.dist.name}" />
 644   <tar destfile="${source.dist.name}" compression="gzip">
 645     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 646       <include name="LICENSE" />
 647       <include name="README" />
 648       <include name="build.xml" />
 649       <include name="jalview-jalopy.xml" />
 650       <include name="JalviewApplet.jpx" />
 651       <include name="JalviewX.jpx" />
 652       <include name="nbbuild.xml"/>
 653       <include name="nbproject/genfiles.properties"/>
 654       <include name="nbproject/project.properties"/>
 655       <include name="nbproject/project.xml"/>
 656       <include name="${sourceDir}/*.java" />
 657       <include name="${sourceDir}/**/*.java" />
 658       <include name="${sourceDir}/**/*.cdr" />
 659       <include name="${libDir}/**/*" />
 660       <include name="${resourceDir}/**/*" />
 661       <include name="${helpDir}/**/*" />
 662       <include name="appletlib/${jmolJar}" />
 663       <exclude name="**/*locales" />
 664       <exclude name="*locales/**" />
 665       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 666       <exclude name="utils/InstallAnywhere/**Build*/**" />
 667       <exclude name="utils/InstallAnywhere/**Build*/**" />
 668       <exclude name="utils/InstallAnywhere/**locale*" />
 669       <exclude name="utils/InstallAnywhere/**locale*/**" />
 670       <include name="${schemaDir}/**/*" />
 671       <include name="utils/**/*" />
 672       <include name="${docDir}/**/*" />
 673       <include name="examples/**/*" />
 674     </tarfileset>
 675   </tar>
 676 </target>
 677 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 678   <copy todir="${packageDir}/examples">
 679     <fileset dir="examples">
 680       <include name="**/*"/>
 681       <include name="javascript/*"/>
 682       <include name="jmol/*"/>
 683     </fileset>
 684     <fileset dir=".">
 685       <include name="${jalviewLiteJar}" />
 686     </fileset>
 687     <fileset dir="appletlib">
 688       <include name="**/*"/>
 689     </fileset>
 690   </copy>
 691   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 692   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
 693   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
 694   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 695     <manifest>
 696       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 697       <!--          <attribute name="Permissions" value="sandbox" /> -->
 698       <!--<attribute name="Trusted-Lib" value="true" /> -->
 699       <attribute name="Codebase" value="${applet.codebase}"/>
 700       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 701     </manifest>
 702   </jar>
 703   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 704     <fileset dir="${packageDir}/examples">
 705       <include name="*.jar" />
 706     </fileset>
 707   </signjar>
 708   <presetdef name="ap_applet.jar">
 709     <!-- build a signed applet with 'all-permissions' -
 710                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 711                           JalviewLite+JmolApplet linked sequence/structure fails
 712                           Mixed code warnings are raised
 713                           -->
 714     <jar update="true" index="true">
 715       <manifest>
 716         <attribute name="Application-Name" value="JalviewLite" />
 717         <attribute name="Permissions" value="all-permissions" />
 718         <attribute name="Codebase" value="${applet.codebase}" />
 719         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 720         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 721       </manifest>
 722     </jar>
 723   </presetdef>
 724   <presetdef name="applet.jar">
 725     <!-- build signed applet with sandbox permissions -
 726                           Needs 'param name="permissions' value="sandbox"' in applet tag
 727                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 728                         -->
 729
 730     <jar update="true" index="true">
 731       <manifest>
 732         <attribute name="Application-Name" value="JalviewLite" />
 733         <attribute name="Permissions" value="sandbox" />
 734         <attribute name="Codebase" value="${applet.codebase}" />
 735         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 736         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 737       </manifest>
 738     </jar>
 739   </presetdef>
 740   <presetdef name="tl_applet.jar">
 741     <!-- build signed applet with trusted library/trusted permissions -
 742                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 743                                j1.7_45:
 744                                No mixed code warnings raised
 745                                Jmol/JalviewLite sequence/structure example doesn't link structures
 746                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 747
 748                               -->
 749
 750     <jar update="true" index="true">
 751       <manifest>
 752         <attribute name="Application-Name" value="JalviewLite" />
 753         <attribute name="Permissions" value="all-permissions" />
 754         <attribute name="Codebase" value="${applet.codebase}" />
 755         <attribute name="Trusted-Only" value="true" />
 756         <attribute name="Trusted-Library" value="true" />
 757       </manifest>
 758     </jar>
 759   </presetdef>
 760   <presetdef name="to_applet.jar">
 761     <!-- not fully test variant (yet) -->
 762     <jar update="true" index="true">
 763       <manifest>
 764         <attribute name="Application-Name" value="JalviewLite" />
 765         <attribute name="Permissions" value="all-permissions" />
 766         <attribute name="Codebase" value="${applet.codebase}" />
 767         <attribute name="Trusted-Only" value="true" />
 768       </manifest>
 769     </jar>
 770   </presetdef>
 771   <!-- create differently privileged artefacts -->
 772   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 773   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 774   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
 775   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
 776   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 777   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 778   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
 779   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
 780   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 781   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 782   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 783   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 784   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 785   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 786   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 787   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 788   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 789   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 790   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 791   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 792   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 793   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 794   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 795   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 796   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 797   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 798   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 799   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 800   <!-- finally, create manifest for original jars -->
 801   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 802   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 803   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 804   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 805
 806   <!-- todo - write examples/downloads for alternate versions of the applet -->
 807   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 808
 809     <fileset dir="${packageDir}/examples">
 810       <exclude name="u_*.jar"/>
 811       <include name="${jalviewLiteJar}" />
 812       <include name="${jmolJar}" />
 813       <include name="${javaJson}" />
 814       <include name="${jsonSimple}" />
 815       <include name="to_${jalviewLiteJar}" />
 816       <include name="to_${jmolJar}" />
 817       <include name="to_${javaJson}" />
 818       <include name="to_${jsonSimple}" />
 819       <include name="tl_${jalviewLiteJar}" />
 820       <include name="tl_${jmolJar}" />
 821       <include name="tl_${javaJson}" />
 822       <include name="tl_${jsonSimple}" />
 823       <include name="ap_${jalviewLiteJar}" />
 824       <include name="ap_${jmolJar}" />
 825       <include name="ap_${javaJson}" />
 826       <include name="ap_${jsonSimple}" />
 827     </fileset>
 828   </signjar>
 829   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 830   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 831         <!-- finally, replace any launchApp servlet tags with a version specification -->
 832         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 833                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
 834                 <fileset dir="${packageDir}/examples">
 835                         <include name="**/*.html"/>
 836                 </fileset>
 837         </replace>
 838         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 839                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
 840                 <fileset dir="${packageDir}/examples">
 841                         <include name="**/*.html"/>
 842                 </fileset>
 843         </replace>
 844
 845 </target>
 846 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 847   <javadoc destdir="${javadocDir}">
 848     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 849     </packageset>
 850   </javadoc>
 851 </target>
 852 </project>