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
  93     <!-- Permissions for running Java applets and applications. -->
  94     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
  95     <property name="application.codebase" value="*.jalview.org" />
  96     <!-- and allowing the applet to be deployed from any URL -->
  97     <!-- 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 -->
  98     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
  99     <property name="applet.caller-codebase" value="${applet.codebase}" />
 100
 101     <!-- build directory configuration -->
 102     <property name="libDir" value="lib" />
 103     <property name="resourceDir" value="resources" />
 104     <property name="helpDir" value="help" />
 105     <property name="docDir" value="doc" />
 106     <property name="sourceDir" value="src" />
 107     <property name="schemaDir" value="schemas" />
 108     <property name="outputDir" value="classes" />
 109     <property name="packageDir" value="dist" />
 110     <property name="outputJar" value="jalview.jar" />
 111     <!-- Jalview Applet JMol Jar Dependency -->
 112     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 113     <property name="varnaJar" value="VARNAv3-91.jar" />
 114     <property name="jsoup" value="jsoup-1.8.1.jar" />
 115     <property name="jsonSimple" value="json_simple-1.1.jar" />
 116     <property name="javaJson" value="java-json.jar" />
 117     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 118         <property name="reportDir" value="test-reports" />
 119         <property name="testDir" value="test" />
 120         <property name="testOutputDir" value="tests" />
 121     <!-- switch to indicate if we should obfuscate jalviewLite -->
 122     <!-- <property name="donotobfuscate" value="true"/> -->
 123     <!-- switch to exclude associations from generated jnlp files -->
 124     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 125
 126     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 127     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 128     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 129     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 130     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 131     <property name="WSInterf" value="MsaWS" />
 132     <property name="wsdl.Namespace" value="vamsas" />
 133     <property name="wsdl.ClientNS" value="ext.vamsas" />
 134     <!-- the class path for building the application -->
 135     <path id="build.classpath">
 136       <fileset dir="utils">
 137         <include name="*.jar" />
 138         <include name="**/*.jar" />
 139       </fileset>
 140       <fileset dir="${libDir}">
 141         <include name="*.jar" />
 142         <include name="**/*.jar" />
 143       </fileset>
 144       <fileset dir="${java.home}/lib">
 145         <include name="plugin.jar"/>
 146       </fileset>
 147       <fileset dir="appletlib">
 148         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 149                                 -->
 150         <include name="${jmolJar}" />
 151         <include name="${varnaJar}" />
 152       </fileset>
 153
 154     </path>
 155     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 156     <!-- The Location of the java 1.1.8 jdk -->
 157     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
 158     <property name="java118.home" value="${java.home}" />
 159     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 160                 -->
 161     <!-- jre for 1.4 version -->
 162     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 163
 164     <!-- the classpath for building the 1.1 applet -->
 165     <path id="jalviewlite.deps">
 166       <fileset dir="${java118.home}">
 167         <include name="lib/classes.zip" />
 168       </fileset>
 169       <fileset dir="${java.home}/lib">
 170         <include name="plugin.jar"/>
 171       </fileset>
 172       <pathelement location="appletlib/${jmolJar}" />
 173       <pathelement location="lib/${varnaJar}" />
 174       <pathelement location="lib/${jsoup}" />
 175       <pathelement location="lib/${jsonSimple}" />
 176       <pathelement location="lib/${javaJson}" />
 177
 178     </path>
 179     <!-- default location for outputting javadoc -->
 180     <property name="javadocDir" value="${packageDir}/javadoc"/>
 181   </target>
 182
 183
 184   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 185   <target name="buildPropertiesFile" depends="init">
 186     <tstamp prefix="build">
 187       <format property="date" pattern="dd MMMM yyyy" />
 188     </tstamp>
 189     <properties file="${outputDir}/.build_properties">
 190       <header>
 191           ---Jalview Build Details---
 192         </header>
 193       <property name="VERSION" value="${JALVIEW_VERSION}" />
 194       <property name="INSTALLATION" value="${INSTALLATION}" />
 195       <property name="BUILD_DATE" value="${build.date}" />
 196     </properties>
 197   </target>
 198
 199
 200   <target name="clean" depends="init">
 201     <!-- not efficient yet. -->
 202     <delete dir="${outputDir}" includes="*,**/*"/>
 203   </target>
 204
 205   <target name="distclean" depends="init, clean">
 206
 207     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 208     <delete>
 209       <fileset dir=".">
 210         <include name="${outputJar}" />
 211         <include name="#*#" />
 212         <include name="#*.*#" />
 213         <include name="**/#*#" />
 214         <include name="**/#*.*#" />
 215         <include name="*~" />
 216         <include name="*.*~" />
 217         <include name="**/*~" />
 218         <include name="**/*.*~" />
 219       </fileset>
 220     </delete>
 221   </target>
 222
 223   <target name="prepare" depends="init">
 224     <mkdir dir="${outputDir}" />
 225     <copy todir="${outputDir}">
 226       <fileset dir=".">
 227         <include name="${docDir}/**/*.*" />
 228         <include name="${helpDir}/**/*.*" />
 229         <include name="${libDir}/*.jar" />
 230       </fileset>
 231       <fileset dir="${resourceDir}">
 232         <include name="**/*.*" />
 233       </fileset>
 234     </copy>
 235   </target>
 236
 237   <target name="build" depends="prepare">
 238     <!-- not efficient yet. -->
 239     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 240       <exclude name="jalview/*applet*" />
 241       <exclude name="jalview/appletgui/**" />
 242       <exclude name="com/stevesoft/**" />
 243     </javac>
 244   </target>
 245
 246
 247   <target name="testclean" depends="init">
 248     <delete dir="${testOutputDir}" includes="*,**/*"/>
 249   </target>
 250
 251   <target name="prepareTests" depends="init">
 252         <mkdir dir="${testOutputDir}" />
 253         <copy todir="${testOutputDir}">
 254                 <fileset dir=".">
 255                         <include name="${docDir}/**/*.*" />
 256                         <include name="${helpDir}/**/*.*" />
 257                         <include name="${libDir}/*.jar" />
 258                 </fileset>
 259                 <fileset dir="${resourceDir}">
 260                         <include name="**/*.*" />
 261                 </fileset>
 262         </copy>
 263   </target>
 264
 265   <target name="buildTests" depends="prepareTests">
 266         <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${testOutputDir}"
 267                 debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
 268                 <exclude name="jalview/*applet*" />
 269                 <exclude name="jalview/appletgui/**" />
 270         </javac>
 271         <javac source="1.5" target="1.5" srcdir="${testDir}" destdir="${testOutputDir}"
 272                 debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
 273         </javac>
 274   </target>
 275
 276   <taskdef name="testng" classname="org.testng.TestNGAntTask" >
 277         <classpath location="utils/testnglibs/testng.jar" />
 278   </taskdef>
 279
 280   <target name="testng" depends="buildTests">
 281         <testng classpathref="build.classpath" outputDir="${reportDir}"
 282                 haltOnFailure="false">
 283                 <classpath location="${testOutputDir}" />
 284                 <xmlfileset dir="utils" includes="jalview_testng.xml" />
 285         </testng>
 286   </target>
 287
 288   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 289     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 290       <arg line="html" />
 291     </java>
 292   </target>
 293
 294   <target name="makefulldist" depends="makedist">
 295     <copy todir="${packageDir}">
 296       <fileset dir="${resourceDir}/images">
 297         <include name="${WebStartImage}"/>
 298       </fileset>
 299     </copy>
 300
 301     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 302
 303     <!-- create a dummy jar which will eventually contain the jnlp template -->
 304     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 305       <fileset dir="${packageDir}">
 306         <include name="jalview.jar" />
 307       </fileset>
 308     </jar>
 309
 310     <mkdir dir="${packageDir}/JNLP-INF"/>
 311     <antcall target="writejnlpf">
 312       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 313       <param name="inih" value="*" />
 314       <param name="maxh" value="*"/>
 315     </antcall>
 316
 317     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 318       <fileset dir="${packageDir}">
 319         <include name="JNLP-INF"/>
 320       </fileset>
 321     </jar>
 322
 323     <antcall target="writejnlpf">
 324       <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 325       <param name="inih" value="10M" />
 326       <param name="maxh" value="256M"/>
 327     </antcall>
 328
 329     <antcall target="writejnlpf">
 330       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 331       <param name="inih" value="128M" />
 332       <param name="maxh" value="512M"/>
 333     </antcall>
 334
 335     <antcall target="writejnlpf">
 336       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 337       <param name="inih" value="256M" />
 338       <param name="maxh" value="1024M"/>
 339     </antcall>
 340
 341     <!-- finally, need to postprocess to add in associations at end of 'information' element
 342
 343                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 344
 345                 </xslt>
 346
 347
 348                         -->
 349     <!--
 350                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 351         <association mime-type="application-x/ext-file" extensions="fasta"/>
 352         <association mime-type="application-x/ext-file" extensions="mfa"/>
 353         <association mime-type="application-x/ext-file" extensions="fastq"/>
 354         <association mime-type="application-x/ext-file" extensions="blc"/>
 355         <association mime-type="application-x/ext-file" extensions="msf"/>
 356         <association mime-type="application-x/ext-file" extensions="pfam"/>
 357         <association mime-type="application-x/ext-file" extensions="aln"/>
 358         <association mime-type="application-x/ext-file" extensions="pir"/>
 359         <association mime-type="application-x/ext-file" extensions="amsa"/>
 360         <association mime-type="application-x/ext-file" extensions="stk"/>
 361         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 362     <!-- and sign the jars -->
 363     <!-- the default keystore details might need to be edited here -->
 364     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 365       <fileset dir="${packageDir}">
 366         <include name="*.jar" />
 367       </fileset>
 368     </signjar>
 369   </target>
 370
 371   <target name="runenv" depends="init">
 372     <path id="run.classpath">
 373       <pathelement location="${outputDir}" />
 374       <fileset dir="${outputDir}">
 375         <include name="${libDir}/*.jar" />
 376       </fileset>
 377     </path>
 378     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 379
 380     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 381       </echo>
 382   </target>
 383
 384   <target name="-generatejnlpf">
 385     <presetdef name="jnlpf">
 386       <jnlp codebase="${WebStartLocation}">
 387         <information>
 388           <title>Jalview</title>
 389           <vendor>The Barton Group</vendor>
 390           <homepage href="http://www.jalview.org" />
 391           <description>Jalview Multiple Alignment Editor</description>
 392           <description kind="short">Jalview</description>
 393           <icon href="${WebStartImage}" />
 394           <offline_allowed />
 395         </information>
 396         <resources>
 397           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 398           <fileset dir="${packageDir}">
 399             <include name="jalview.jar" />
 400           </fileset>
 401           <fileset dir="${packageDir}">
 402             <include name="*.jar" />
 403             <include name="*_*.jar" />
 404             <exclude name="jalview.jar" />
 405                 <exclude name="*jnilib.jar"/>
 406           </fileset>
 407         </resources>
 408         <resources os="Mac OS X">
 409           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 410                 <fileset dir="${packageDir}">
 411                         <include name="*quaqua*.jnilib.jar"/>
 412                 </fileset>
 413         </resources>
 414
 415         <application_desc main_class="jalview.bin.Jalview">
 416         </application_desc>
 417         <security>
 418           <all_permissions />
 419         </security>
 420       </jnlp>
 421     </presetdef>
 422
 423     <jnlpf toFile="${jnlpFile}"/>
 424
 425   </target>
 426
 427   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 428     <echo message="Not adding JNLP File Associations"/>
 429   </target>
 430
 431   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 432     <replace file="${jnlpFile}">
 433       <replacetoken>
 434         <![CDATA[</information>]]></replacetoken>
 435       <replacevalue>
 436         <![CDATA[
 437           <association mime-type="application-x/ext-file" extensions="fa" />
 438         <association mime-type="application-x/ext-file" extensions="fasta" />
 439         <association mime-type="application-x/ext-file" extensions="mfa" />
 440         <association mime-type="application-x/ext-file" extensions="fastq" />
 441         <association mime-type="application-x/ext-file" extensions="blc" />
 442         <association mime-type="application-x/ext-file" extensions="msf" />
 443         <association mime-type="application-x/ext-file" extensions="pfam" />
 444         <association mime-type="application-x/ext-file" extensions="aln"/>
 445         <association mime-type="application-x/ext-file" extensions="pir"/>
 446         <association mime-type="application-x/ext-file" extensions="amsa"/>
 447         <association mime-type="application-x/ext-file" extensions="stk"/>
 448         <association mime-type="application-x/ext-file" extensions="jvp"/>
 449       </information>]]></replacevalue>
 450   </replace>
 451   <echo message="Added file associations to JNLP file"/>
 452 </target>
 453 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 454 </target>
 455
 456 <target name="buildextclients" depends="init">
 457   <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" />
 458   <condition property="dontextbuild">
 459     <equals arg1="n" arg2="${doextbuild.response}" />
 460   </condition>
 461   <condition property="dontextbuild">
 462     <equals arg1="N" arg2="${doextbuild.response}" />
 463   </condition>
 464   <fail if="dontextbuild">
 465         Build External Client Code process aborted by user. Jalview source is unchanged.
 466       </fail>
 467   <!-- Currently, this doesn't happen automatically.
 468      1. Run WSDL2Java as below, which generates an ext.vamsas +
 469      vamsas.<datapackages> fileset.
 470      2. refactor ext.vamsas.SpecificserviceWS* to
 471      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 472      3. Update the jalview.ws.*WServices classes to reflect the
 473      interface type, and all locations of this wsdl type that Jalview
 474      might be using.
 475
 476 -->
 477   <path id="axisbuild">
 478     <path refid="build.classpath" />
 479   </path>
 480   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 481   <move todir="./bak">
 482     <fileset dir="${sourceDir}" id="client">
 483       <include name="${wsdl.ClientNS}/*.*" />
 484     </fileset>
 485   </move>
 486
 487   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 488     <mappingSet>
 489       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 490       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 491     </mappingSet>
 492   </axis-wsdl2java>
 493 </target>
 494
 495 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 496   <!-- make the package jar if not already existing -->
 497   <mkdir dir="${packageDir}" />
 498   <!-- clean dir if it already existed -->
 499   <delete>
 500     <fileset dir="${packageDir}">
 501       <include name="*.jar"/>
 502     </fileset>
 503   </delete>
 504   <jar destfile="${packageDir}/${outputJar}" index="true">
 505     <manifest>
 506       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 507       <attribute name="Permissions" value="all-permissions" />
 508       <attribute name="Application-Name" value="Jalview Desktop" />
 509       <attribute name="Codebase" value="${application.codebase}" />
 510     </manifest>
 511     <fileset dir="${outputDir}/">
 512       <exclude name="cache*/**" />
 513       <exclude name="*.jar" />
 514       <exclude name="*.jar.*" />
 515       <exclude name="**/*.jar" />
 516       <exclude name="**/*.jar.*" />
 517     </fileset>
 518   </jar>
 519
 520   <copy toDir="${packageDir}" flatten="true">
 521     <fileset dir="${outputDir}">
 522       <include name="*.jar" />
 523       <include name="**/*.jar" />
 524     </fileset>
 525   </copy>
 526 </target>
 527
 528
 529 <!-- jalopy code reformatter -->
 530 <target name="sourcescrub" depends="init,build">
 531   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 532     <fileset dir="${sourceDir}">
 533       <include name="*.java" />
 534       <include name="**/*.java" />
 535       <include name="**/**/*.java" />
 536     </fileset>
 537   </jalopy>
 538 </target>
 539
 540
 541
 542 <!-- Compile, package and obfuscate Jalview Applet -->
 543 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 544
 545 <target name="compileApplet" depends="init,clean">
 546   <mkdir dir="${outputDir}" />
 547   <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 548                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 549                         excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 550 </target>
 551
 552 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 553   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 554   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 555   <copy todir="${outputDir}/lang">
 556     <fileset dir="${resourceDir}/lang">
 557       <include name="**.*"/>
 558     </fileset>
 559   </copy>
 560   <jar destfile="in.jar" index="true">
 561     <manifest>
 562       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 563       <attribute name="Application-Name" value="JalviewLite" />
 564       <attribute name="Codebase" value="${applet.codebase}" />
 565     </manifest>
 566     <fileset dir="${outputDir}">
 567       <include name="com/**" />
 568       <include name="MCview/**" />
 569       <include name="jalview/**" />
 570       <include name=".build_properties" />
 571       <include name="images/idwidth.gif" />
 572       <include name="images/link.gif" />
 573       <include name="lang/**" />
 574     </fileset>
 575   </jar>
 576 </target>
 577 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 578 </target>
 579 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 580   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 581   <delete file="in.jar" />
 582 </target>
 583 <target name="-obfuscatereally" unless="donotobfuscate">
 584
 585   <path id="obfuscateDeps.path">
 586     <pathelement location="${applet.jre.tools}" />
 587     <pathelement location="appletlib/${jmolJar}" />
 588     <pathelement location="appletlib/${jsonSimple}" />
 589     <pathelement location="appletlib/${javaJson}" />
 590   </path>
 591   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 592
 593   <proguard>
 594     <injar file="in.jar" />
 595     <outjar file="${jalviewLiteJar}" />
 596     <libraryjar refid="obfuscateDeps.path" />
 597     <dontwarn/>
 598     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 599       <field access="public" />
 600       <method access="public" />
 601       <constructor access="public" />
 602     </keep>
 603     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 604       <field access="public" />
 605       <method access="public" />
 606       <constructor access="public" />
 607     </keep>
 608     <!--      -libraryjars "${obfuscateDeps}"
 609       -injars      in.jar
 610       -outjars     jalviewApplet.jar
 611       -keep public class jalview.bin.JalviewLite
 612        { public * ; } -->
 613   </proguard>
 614   <delete file="in.jar" />
 615 </target>
 616
 617 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 618   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 619   <delete>
 620     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 621       <include name="*.java" />
 622       <include name="descriptors/*.java" />
 623     </fileset>
 624   </delete>
 625   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 626   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 627   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 628   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 629   <!--
 630                 now build the jalview.binding package with the old schema set
 631                 -->
 632   <delete>
 633     <fileset dir="${sourceDir}/jalview/binding/">
 634       <include name="**" />
 635     </fileset>
 636   </delete>
 637   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 638   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 639   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 640 </target>
 641 <target name="sourcedist" description="create jalview source distribution" depends="init">
 642   <delete file="${source.dist.name}" />
 643   <tar destfile="${source.dist.name}" compression="gzip">
 644     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 645       <include name="LICENSE" />
 646       <include name="README" />
 647       <include name="build.xml" />
 648       <include name="jalview-jalopy.xml" />
 649       <include name="JalviewApplet.jpx" />
 650       <include name="JalviewX.jpx" />
 651       <include name="nbbuild.xml"/>
 652       <include name="nbproject/genfiles.properties"/>
 653       <include name="nbproject/project.properties"/>
 654       <include name="nbproject/project.xml"/>
 655       <include name="${sourceDir}/*.java" />
 656       <include name="${sourceDir}/**/*.java" />
 657       <include name="${sourceDir}/**/*.cdr" />
 658       <include name="${libDir}/**/*" />
 659       <include name="${resourceDir}/**/*" />
 660       <include name="${helpDir}/**/*" />
 661       <include name="appletlib/${jmolJar}" />
 662       <exclude name="**/*locales" />
 663       <exclude name="*locales/**" />
 664       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 665       <exclude name="utils/InstallAnywhere/**Build*/**" />
 666       <exclude name="utils/InstallAnywhere/**Build*/**" />
 667       <exclude name="utils/InstallAnywhere/**locale*" />
 668       <exclude name="utils/InstallAnywhere/**locale*/**" />
 669       <include name="${schemaDir}/**/*" />
 670       <include name="utils/**/*" />
 671       <include name="${docDir}/**/*" />
 672       <include name="examples/**/*" />
 673     </tarfileset>
 674   </tar>
 675 </target>
 676 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 677   <copy todir="${packageDir}/examples">
 678     <fileset dir="examples">
 679       <include name="**/*"/>
 680       <include name="javascript/*"/>
 681       <include name="jmol/*"/>
 682     </fileset>
 683     <fileset dir=".">
 684       <include name="${jalviewLiteJar}" />
 685     </fileset>
 686     <fileset dir="appletlib">
 687       <include name="**/*"/>
 688     </fileset>
 689   </copy>
 690   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 691   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
 692   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
 693   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 694     <manifest>
 695       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 696       <!--          <attribute name="Permissions" value="sandbox" /> -->
 697       <!--<attribute name="Trusted-Lib" value="true" /> -->
 698       <attribute name="Codebase" value="${applet.codebase}"/>
 699       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 700     </manifest>
 701   </jar>
 702   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 703     <fileset dir="${packageDir}/examples">
 704       <include name="*.jar" />
 705     </fileset>
 706   </signjar>
 707   <presetdef name="ap_applet.jar">
 708     <!-- build a signed applet with 'all-permissions' -
 709                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 710                           JalviewLite+JmolApplet linked sequence/structure fails
 711                           Mixed code warnings are raised
 712                           -->
 713     <jar update="true" index="true">
 714       <manifest>
 715         <attribute name="Application-Name" value="JalviewLite" />
 716         <attribute name="Permissions" value="all-permissions" />
 717         <attribute name="Codebase" value="${applet.codebase}" />
 718         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 719         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 720       </manifest>
 721     </jar>
 722   </presetdef>
 723   <presetdef name="applet.jar">
 724     <!-- build signed applet with sandbox permissions -
 725                           Needs 'param name="permissions' value="sandbox"' in applet tag
 726                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 727                         -->
 728
 729     <jar update="true" index="true">
 730       <manifest>
 731         <attribute name="Application-Name" value="JalviewLite" />
 732         <attribute name="Permissions" value="sandbox" />
 733         <attribute name="Codebase" value="${applet.codebase}" />
 734         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 735         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 736       </manifest>
 737     </jar>
 738   </presetdef>
 739   <presetdef name="tl_applet.jar">
 740     <!-- build signed applet with trusted library/trusted permissions -
 741                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 742                                j1.7_45:
 743                                No mixed code warnings raised
 744                                Jmol/JalviewLite sequence/structure example doesn't link structures
 745                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 746
 747                               -->
 748
 749     <jar update="true" index="true">
 750       <manifest>
 751         <attribute name="Application-Name" value="JalviewLite" />
 752         <attribute name="Permissions" value="all-permissions" />
 753         <attribute name="Codebase" value="${applet.codebase}" />
 754         <attribute name="Trusted-Only" value="true" />
 755         <attribute name="Trusted-Library" value="true" />
 756       </manifest>
 757     </jar>
 758   </presetdef>
 759   <presetdef name="to_applet.jar">
 760     <!-- not fully test variant (yet) -->
 761     <jar update="true" index="true">
 762       <manifest>
 763         <attribute name="Application-Name" value="JalviewLite" />
 764         <attribute name="Permissions" value="all-permissions" />
 765         <attribute name="Codebase" value="${applet.codebase}" />
 766         <attribute name="Trusted-Only" value="true" />
 767       </manifest>
 768     </jar>
 769   </presetdef>
 770   <!-- create differently privileged artefacts -->
 771   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 772   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 773   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
 774   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
 775   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 776   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 777   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
 778   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
 779   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 780   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 781   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 782   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 783   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 784   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 785   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 786   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 787   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 788   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 789   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 790   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 791   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 792   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 793   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 794   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 795   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 796   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 797   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 798   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 799   <!-- finally, create manifest for original jars -->
 800   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 801   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 802   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 803   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 804
 805   <!-- todo - write examples/downloads for alternate versions of the applet -->
 806   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 807
 808     <fileset dir="${packageDir}/examples">
 809       <exclude name="u_*.jar"/>
 810       <include name="${jalviewLiteJar}" />
 811       <include name="${jmolJar}" />
 812       <include name="${javaJson}" />
 813       <include name="${jsonSimple}" />
 814       <include name="to_${jalviewLiteJar}" />
 815       <include name="to_${jmolJar}" />
 816       <include name="to_${javaJson}" />
 817       <include name="to_${jsonSimple}" />
 818       <include name="tl_${jalviewLiteJar}" />
 819       <include name="tl_${jmolJar}" />
 820       <include name="tl_${javaJson}" />
 821       <include name="tl_${jsonSimple}" />
 822       <include name="ap_${jalviewLiteJar}" />
 823       <include name="ap_${jmolJar}" />
 824       <include name="ap_${javaJson}" />
 825       <include name="ap_${jsonSimple}" />
 826     </fileset>
 827   </signjar>
 828   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 829   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 830         <!-- finally, replace any launchApp servlet tags with a version specification -->
 831         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 832                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
 833                 <fileset dir="${packageDir}/examples">
 834                         <include name="**/*.html"/>
 835                 </fileset>
 836         </replace>
 837         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 838                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
 839                 <fileset dir="${packageDir}/examples">
 840                         <include name="**/*.html"/>
 841                 </fileset>
 842         </replace>
 843
 844 </target>
 845 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 846   <javadoc destdir="${javadocDir}">
 847     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 848     </packageset>
 849   </javadoc>
 850 </target>
 851 </project>