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" depends="init">
  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="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
  34     <echo message="      you can specify particular test groups as a list via -Dtestng-groups=" />
  35     <echo message="See docs/building.html and the comments in build file for other targets." />
  36     <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  37     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  38   </target>
  39
  40
  41   <!-- utils is a class path to additional utilities needed for
  42     building docs, jars and webstart stuff -->
  43   <!--
  44         Userdefined build property defaults
  45
  46         wsdl.server list (plus namespace mapping info ???)  - also want
  47                 ... to make this a dynamically generatable property
  48         WebStart Location
  49         Build location - provide a temporary root for speed
  50         jarsigner keystore and info
  51         Jakarta and axis classpath ?
  52         Default argument for starting Jalview (if it exists).
  53
  54 -->
  55
  56   <target name="init">
  57     <path id="axis.classpath">
  58       <!-->
  59       <fileset dir="/usr/local/axis/lib">
  60         <include name="**/*.jar" />
  61       </fileset>
  62       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  63         <include name="**/*.jar"/>
  64         <include name="*.jar"/>
  65       </fileset> -->
  66       </path>
  67
  68     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  69     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  70
  71     <property name="INSTALLATION" value="Source" />
  72
  73     <!-- 2.4 (VAMSAS)" -->
  74     <!-- Include debugging information in javac true or false -->
  75     <property name="javac.debug" value="true" />
  76
  77     <!-- JarSigner Key Store for Webstart Distribution -->
  78     <property name="jalview.keystore" value="./keys/.keystore" />
  79     <!-- Keystore Password -->
  80     <property name="jalview.keystore.pass" value="alignmentisfun" />
  81     <!-- Key Name -->
  82     <property name="jalview.key" value="jalview" />
  83     <!-- Key Password -->
  84     <property name="jalview.key.pass" value="alignmentisfun" />
  85
  86     <property name="testng-groups" value="Functional"/>
  87
  88     <!-- Don't change anything below here unless you know what you are doing! -->
  89     <!-- Url path for WebStart in JNLP file -->
  90     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  91     <!-- Webstart Image - looked for in resources/images -->
  92     <property name="WebStartImage" value="JalviewLogo_big.png"/>
  93     <!-- J2SE version needed for webstart launch -->
  94     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  95     <property name="j2sev" value="1.7+"/>
  96         <!-- Java Compilation settings - source and target javac version -->
  97         <property name="javac.source" value="1.7"/>
  98         <property name="javac.target" value="1.7"/>
  99
 100     <!-- Permissions for running Java applets and applications. -->
 101     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 102     <property name="application.codebase" value="*.jalview.org" />
 103     <!-- and allowing the applet to be deployed from any URL -->
 104     <!-- 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 -->
 105     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 106     <property name="applet.caller-codebase" value="${applet.codebase}" />
 107
 108     <!-- build directory configuration -->
 109     <property name="libDir" value="lib" />
 110     <property name="resourceDir" value="resources" />
 111     <property name="helpDir" value="help" />
 112     <property name="docDir" value="doc" />
 113     <property name="sourceDir" value="src" />
 114     <property name="schemaDir" value="schemas" />
 115     <property name="outputDir" value="classes" />
 116     <property name="packageDir" value="dist" />
 117     <property name="outputJar" value="jalview.jar" />
 118     <!-- Jalview Applet JMol Jar Dependency -->
 119     <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
 120     <property name="varnaJar" value="VARNAv3-93.jar" />
 121     <property name="jsoup" value="jsoup-1.8.1.jar" />
 122     <property name="jsonSimple" value="json_simple-1.1.jar" />
 123     <property name="javaJson" value="java-json.jar" />
 124     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 125         <property name="reportDir" value="test-reports" />
 126         <property name="testDir" value="test" />
 127         <property name="testOutputDir" value="tests" />
 128     <!-- switch to indicate if we should obfuscate jalviewLite -->
 129     <!-- <property name="donotobfuscate" value="true"/> -->
 130     <!-- switch to exclude associations from generated jnlp files -->
 131     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 132
 133     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 134     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 135     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 136     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 137     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 138     <property name="WSInterf" value="MsaWS" />
 139     <property name="wsdl.Namespace" value="vamsas" />
 140     <property name="wsdl.ClientNS" value="ext.vamsas" />
 141     <!-- the class path for building the application -->
 142     <path id="build.classpath">
 143       <fileset dir="utils">
 144         <include name="*.jar" />
 145         <include name="**/*.jar" />
 146       </fileset>
 147       <fileset dir="${libDir}">
 148         <include name="*.jar" />
 149         <include name="**/*.jar" />
 150       </fileset>
 151       <fileset dir="${java.home}/lib">
 152         <include name="plugin.jar"/>
 153       </fileset>
 154       <fileset dir="appletlib">
 155         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 156                                 -->
 157         <include name="${jmolJar}" />
 158         <include name="${varnaJar}" />
 159       </fileset>
 160     </path>
 161     <path id="test.classpath">
 162       <pathelement path="${outputDir}" />
 163       <path refid="build.classpath" />
 164     </path>
 165     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 166     <!-- The Location of the java 1.1.8 jdk -->
 167     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
 168     <property name="java118.home" value="${java.home}" />
 169     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 170                 -->
 171     <!-- jre for 1.4 version -->
 172     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 173
 174     <!-- the classpath for building the 1.1 applet -->
 175     <path id="jalviewlite.deps">
 176       <fileset dir="${java118.home}">
 177         <include name="lib/classes.zip" />
 178       </fileset>
 179       <fileset dir="${java.home}/lib">
 180         <include name="plugin.jar"/>
 181       </fileset>
 182       <pathelement location="appletlib/${jmolJar}" />
 183       <pathelement location="lib/${varnaJar}" />
 184       <pathelement location="lib/${jsoup}" />
 185       <pathelement location="lib/${jsonSimple}" />
 186       <pathelement location="lib/${javaJson}" />
 187
 188     </path>
 189     <!-- default location for outputting javadoc -->
 190     <property name="javadocDir" value="${packageDir}/javadoc"/>
 191   </target>
 192
 193
 194   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 195   <target name="buildPropertiesFile" depends="init">
 196     <tstamp prefix="build">
 197       <format property="date" pattern="dd MMMM yyyy" />
 198     </tstamp>
 199     <exec executable="/usr/bin/git" outputproperty="git.commit"  failifexecutionfails="false">
 200       <arg value="rev-parse"/>
 201       <arg value="--short"/>
 202       <arg value="HEAD"/>
 203     </exec>
 204     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 205       <arg value="rev-parse"/>
 206       <arg value="--abbrev-ref"/>
 207       <arg value="HEAD"/>
 208     </exec>
 209     <properties file="${outputDir}/.build_properties">
 210       <header>
 211           ---Jalview Build Details---
 212         </header>
 213       <property name="VERSION" value="${JALVIEW_VERSION}" />
 214       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 215       <property name="BUILD_DATE" value="${build.date}" />
 216     </properties>
 217   </target>
 218
 219
 220   <target name="clean" depends="init">
 221     <!-- not efficient yet. -->
 222     <delete dir="${outputDir}" includes="*,**/*"/>
 223   </target>
 224
 225   <target name="distclean" depends="init, clean">
 226
 227     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 228     <delete>
 229       <fileset dir=".">
 230         <include name="${outputJar}" />
 231         <include name="#*#" />
 232         <include name="#*.*#" />
 233         <include name="**/#*#" />
 234         <include name="**/#*.*#" />
 235         <include name="*~" />
 236         <include name="*.*~" />
 237         <include name="**/*~" />
 238         <include name="**/*.*~" />
 239       </fileset>
 240     </delete>
 241   </target>
 242
 243   <target name="prepare" depends="init">
 244     <mkdir dir="${outputDir}" />
 245     <copy todir="${outputDir}">
 246       <fileset dir=".">
 247         <include name="${docDir}/**/*.*" />
 248         <include name="${helpDir}/**/*.*" />
 249         <include name="${libDir}/*.jar" />
 250       </fileset>
 251       <fileset dir="${resourceDir}">
 252         <include name="**/*.*" />
 253       </fileset>
 254     </copy>
 255   </target>
 256
 257   <target name="build" depends="prepare">
 258     <!-- not efficient yet. -->
 259     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 260       <exclude name="jalview/*applet*" />
 261       <exclude name="jalview/appletgui/**" />
 262       <exclude name="com/stevesoft/**" />
 263     </javac>
 264   </target>
 265
 266
 267   <target name="testclean" depends="init">
 268     <delete dir="${testOutputDir}" includes="*,**/*"/>
 269   </target>
 270
 271   <target name="prepareTests" depends="init,clean">
 272     <mkdir dir="${testOutputDir}" />
 273   </target>
 274
 275   <target name="buildTests" depends="build,buildindices,prepareTests">
 276     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 277     </javac>
 278   </target>
 279
 280   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 281
 282   <target name="testng" depends="buildTests">
 283     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng">
 284       <classpath>
 285         <pathelement location="${testOutputDir}" />
 286         <path refid="test.classpath" />
 287       </classpath>
 288       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 289     </testng>
 290   </target>
 291
 292   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 293     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 294       <arg line="html" />
 295     </java>
 296   </target>
 297
 298   <target name="makefulldist" depends="makedist">
 299     <copy todir="${packageDir}">
 300       <fileset dir="${resourceDir}/images">
 301         <include name="${WebStartImage}"/>
 302       </fileset>
 303     </copy>
 304
 305     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 306
 307     <!-- create a dummy jar which will eventually contain the jnlp template -->
 308     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 309       <fileset dir="${packageDir}">
 310         <include name="jalview.jar" />
 311       </fileset>
 312     </jar>
 313
 314     <mkdir dir="${packageDir}/JNLP-INF"/>
 315     <antcall target="writejnlpf">
 316       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 317       <param name="inih" value="*" />
 318       <param name="maxh" value="*"/>
 319     </antcall>
 320
 321     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 322       <fileset dir="${packageDir}">
 323         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 324       </fileset>
 325     </jar>
 326
 327     <antcall target="writejnlpf">
 328       <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 329       <param name="inih" value="10M" />
 330       <param name="maxh" value="256M"/>
 331     </antcall>
 332
 333     <antcall target="writejnlpf">
 334       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 335       <param name="inih" value="128M" />
 336       <param name="maxh" value="512M"/>
 337     </antcall>
 338
 339     <antcall target="writejnlpf">
 340       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 341       <param name="inih" value="256M" />
 342       <param name="maxh" value="1024M"/>
 343     </antcall>
 344
 345     <!-- finally, need to postprocess to add in associations at end of 'information' element
 346
 347                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 348
 349                 </xslt>
 350
 351
 352                         -->
 353     <!--
 354                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 355         <association mime-type="application-x/ext-file" extensions="fasta"/>
 356         <association mime-type="application-x/ext-file" extensions="mfa"/>
 357         <association mime-type="application-x/ext-file" extensions="fastq"/>
 358         <association mime-type="application-x/ext-file" extensions="blc"/>
 359         <association mime-type="application-x/ext-file" extensions="msf"/>
 360         <association mime-type="application-x/ext-file" extensions="pfam"/>
 361         <association mime-type="application-x/ext-file" extensions="aln"/>
 362         <association mime-type="application-x/ext-file" extensions="pir"/>
 363         <association mime-type="application-x/ext-file" extensions="amsa"/>
 364         <association mime-type="application-x/ext-file" extensions="stk"/>
 365         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 366     <!-- and sign the jars -->
 367     <!-- the default keystore details might need to be edited here -->
 368     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 369       <fileset dir="${packageDir}">
 370         <include name="*.jar" />
 371       </fileset>
 372     </signjar>
 373   </target>
 374
 375   <target name="runenv" depends="init">
 376     <path id="run.classpath">
 377       <pathelement location="${outputDir}" />
 378       <fileset dir="${outputDir}">
 379         <include name="${libDir}/*.jar" />
 380       </fileset>
 381     </path>
 382     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 383
 384     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 385       </echo>
 386   </target>
 387
 388   <target name="-generatejnlpf">
 389     <presetdef name="jnlpf">
 390       <jnlp codebase="${WebStartLocation}">
 391         <information>
 392           <title>Jalview</title>
 393           <vendor>The Barton Group</vendor>
 394           <homepage href="http://www.jalview.org" />
 395           <description>Jalview Multiple Alignment Editor</description>
 396           <description kind="short">Jalview</description>
 397           <icon href="${WebStartImage}" />
 398           <offline_allowed />
 399         </information>
 400         <resources>
 401           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 402           <fileset dir="${packageDir}">
 403             <include name="jalview.jar" />
 404           </fileset>
 405           <fileset dir="${packageDir}">
 406             <include name="*.jar" />
 407             <include name="*_*.jar" />
 408             <exclude name="jalview.jar" />
 409                 <exclude name="*jnilib.jar"/>
 410           </fileset>
 411         </resources>
 412         <resources os="Mac OS X">
 413           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 414                 <fileset dir="${packageDir}">
 415                         <include name="*quaqua*.jnilib.jar"/>
 416                 </fileset>
 417         </resources>
 418
 419         <application_desc main_class="jalview.bin.Jalview">
 420         </application_desc>
 421         <security>
 422           <all_permissions />
 423         </security>
 424       </jnlp>
 425     </presetdef>
 426
 427     <jnlpf toFile="${jnlpFile}"/>
 428
 429   </target>
 430
 431   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 432     <echo message="Not adding JNLP File Associations"/>
 433   </target>
 434
 435   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 436     <replace file="${jnlpFile}">
 437       <replacetoken>
 438         <![CDATA[</information>]]></replacetoken>
 439       <replacevalue>
 440         <![CDATA[
 441           <association mime-type="application-x/ext-file" extensions="fa" />
 442         <association mime-type="application-x/ext-file" extensions="fasta" />
 443         <association mime-type="application-x/ext-file" extensions="mfa" />
 444         <association mime-type="application-x/ext-file" extensions="fastq" />
 445         <association mime-type="application-x/ext-file" extensions="blc" />
 446         <association mime-type="application-x/ext-file" extensions="msf" />
 447         <association mime-type="application-x/ext-file" extensions="pfam" />
 448         <association mime-type="application-x/ext-file" extensions="aln"/>
 449         <association mime-type="application-x/ext-file" extensions="pir"/>
 450         <association mime-type="application-x/ext-file" extensions="amsa"/>
 451         <association mime-type="application-x/ext-file" extensions="stk"/>
 452         <association mime-type="application-x/ext-file" extensions="jvp"/>
 453       </information>]]></replacevalue>
 454   </replace>
 455   <echo message="Added file associations to JNLP file"/>
 456 </target>
 457 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 458 </target>
 459
 460 <target name="buildextclients" depends="init">
 461   <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" />
 462   <condition property="dontextbuild">
 463     <equals arg1="n" arg2="${doextbuild.response}" />
 464   </condition>
 465   <condition property="dontextbuild">
 466     <equals arg1="N" arg2="${doextbuild.response}" />
 467   </condition>
 468   <fail if="dontextbuild">
 469         Build External Client Code process aborted by user. Jalview source is unchanged.
 470       </fail>
 471   <!-- Currently, this doesn't happen automatically.
 472      1. Run WSDL2Java as below, which generates an ext.vamsas +
 473      vamsas.<datapackages> fileset.
 474      2. refactor ext.vamsas.SpecificserviceWS* to
 475      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 476      3. Update the jalview.ws.*WServices classes to reflect the
 477      interface type, and all locations of this wsdl type that Jalview
 478      might be using.
 479
 480 -->
 481   <path id="axisbuild">
 482     <path refid="build.classpath" />
 483   </path>
 484   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 485   <move todir="./bak">
 486     <fileset dir="${sourceDir}" id="client">
 487       <include name="${wsdl.ClientNS}/*.*" />
 488     </fileset>
 489   </move>
 490
 491   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 492     <mappingSet>
 493       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 494       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 495     </mappingSet>
 496   </axis-wsdl2java>
 497 </target>
 498
 499 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 500   <!-- make the package jar if not already existing -->
 501   <mkdir dir="${packageDir}" />
 502   <!-- clean dir if it already existed -->
 503   <delete>
 504     <fileset dir="${packageDir}">
 505       <include name="*.jar"/>
 506     </fileset>
 507   </delete>
 508   <jar destfile="${packageDir}/${outputJar}" index="true">
 509     <manifest>
 510       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 511       <attribute name="Permissions" value="all-permissions" />
 512       <attribute name="Application-Name" value="Jalview Desktop" />
 513       <attribute name="Codebase" value="${application.codebase}" />
 514     </manifest>
 515     <fileset dir="${outputDir}/">
 516       <exclude name="cache*/**" />
 517       <exclude name="*.jar" />
 518       <exclude name="*.jar.*" />
 519       <exclude name="**/*.jar" />
 520       <exclude name="**/*.jar.*" />
 521     </fileset>
 522   </jar>
 523
 524   <copy toDir="${packageDir}" flatten="true">
 525     <fileset dir="${outputDir}">
 526       <include name="*.jar" />
 527       <include name="**/*.jar" />
 528     </fileset>
 529   </copy>
 530 </target>
 531
 532
 533 <!-- jalopy code reformatter -->
 534 <target name="sourcescrub" depends="init,build">
 535   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 536     <fileset dir="${sourceDir}">
 537       <include name="*.java" />
 538       <include name="**/*.java" />
 539       <include name="**/**/*.java" />
 540     </fileset>
 541   </jalopy>
 542 </target>
 543
 544
 545
 546 <!-- Compile, package and obfuscate Jalview Applet -->
 547 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 548
 549 <target name="compileApplet" depends="init,clean">
 550   <mkdir dir="${outputDir}" />
 551   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 552                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 553                         excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
 554 </target>
 555
 556 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 557   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 558   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 559   <copy todir="${outputDir}/lang">
 560     <fileset dir="${resourceDir}/lang">
 561       <include name="**.*"/>
 562     </fileset>
 563   </copy>
 564   <jar destfile="in.jar" index="true">
 565     <manifest>
 566       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 567       <attribute name="Application-Name" value="JalviewLite" />
 568       <attribute name="Codebase" value="${applet.codebase}" />
 569     </manifest>
 570     <fileset dir="${outputDir}">
 571       <include name="com/**" />
 572       <include name="MCview/**" />
 573       <include name="jalview/**" />
 574       <include name=".build_properties" />
 575       <include name="images/idwidth.gif" />
 576       <include name="images/link.gif" />
 577       <include name="lang/**" />
 578     </fileset>
 579   </jar>
 580 </target>
 581 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 582 </target>
 583 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 584   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 585   <delete file="in.jar" />
 586 </target>
 587 <target name="-obfuscatereally" unless="donotobfuscate">
 588
 589   <path id="obfuscateDeps.path">
 590     <pathelement location="${applet.jre.tools}" />
 591     <pathelement location="appletlib/${jmolJar}" />
 592     <pathelement location="appletlib/${jsonSimple}" />
 593     <pathelement location="appletlib/${javaJson}" />
 594   </path>
 595   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 596
 597   <proguard>
 598     <injar file="in.jar" />
 599     <outjar file="${jalviewLiteJar}" />
 600     <libraryjar refid="obfuscateDeps.path" />
 601     <dontwarn/>
 602     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 603       <field access="public" />
 604       <method access="public" />
 605       <constructor access="public" />
 606     </keep>
 607     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 608       <field access="public" />
 609       <method access="public" />
 610       <constructor access="public" />
 611     </keep>
 612     <!--      -libraryjars "${obfuscateDeps}"
 613       -injars      in.jar
 614       -outjars     jalviewApplet.jar
 615       -keep public class jalview.bin.JalviewLite
 616        { public * ; } -->
 617   </proguard>
 618   <delete file="in.jar" />
 619 </target>
 620
 621 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 622   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 623   <delete>
 624     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 625       <include name="*.java" />
 626       <include name="descriptors/*.java" />
 627     </fileset>
 628   </delete>
 629   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 630   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 631   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 632   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 633   <!--
 634                 now build the jalview.binding package with the old schema set
 635                 -->
 636   <delete>
 637     <fileset dir="${sourceDir}/jalview/binding/">
 638       <include name="**" />
 639     </fileset>
 640   </delete>
 641   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 642   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 643   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 644 </target>
 645 <target name="sourcedist" description="create jalview source distribution" depends="init">
 646   <delete file="${source.dist.name}" />
 647   <tar destfile="${source.dist.name}" compression="gzip">
 648     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 649       <include name="LICENSE" />
 650       <include name="README" />
 651       <include name="build.xml" />
 652       <include name="jalview-jalopy.xml" />
 653       <include name="JalviewApplet.jpx" />
 654       <include name="JalviewX.jpx" />
 655       <include name="nbbuild.xml"/>
 656       <include name="nbproject/genfiles.properties"/>
 657       <include name="nbproject/project.properties"/>
 658       <include name="nbproject/project.xml"/>
 659       <include name="${sourceDir}/*.java" />
 660       <include name="${sourceDir}/**/*.java" />
 661       <include name="${sourceDir}/**/*.cdr" />
 662       <include name="${libDir}/**/*" />
 663       <include name="${resourceDir}/**/*" />
 664       <include name="${helpDir}/**/*" />
 665       <include name="appletlib/${jmolJar}" />
 666       <exclude name="**/*locales" />
 667       <exclude name="*locales/**" />
 668       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 669       <exclude name="utils/InstallAnywhere/**Build*/**" />
 670       <exclude name="utils/InstallAnywhere/**Build*/**" />
 671       <exclude name="utils/InstallAnywhere/**locale*" />
 672       <exclude name="utils/InstallAnywhere/**locale*/**" />
 673       <include name="${schemaDir}/**/*" />
 674       <include name="utils/**/*" />
 675       <include name="${docDir}/**/*" />
 676       <include name="examples/**/*" />
 677     </tarfileset>
 678   </tar>
 679 </target>
 680 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 681   <copy todir="${packageDir}/examples">
 682     <fileset dir="examples">
 683       <include name="**/*"/>
 684       <include name="javascript/*"/>
 685       <include name="jmol/*"/>
 686     </fileset>
 687     <fileset dir=".">
 688       <include name="${jalviewLiteJar}" />
 689     </fileset>
 690     <fileset dir="appletlib">
 691       <include name="**/*"/>
 692     </fileset>
 693   </copy>
 694   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 695   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
 696   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
 697   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 698     <manifest>
 699       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 700       <!--          <attribute name="Permissions" value="sandbox" /> -->
 701       <!--<attribute name="Trusted-Lib" value="true" /> -->
 702       <attribute name="Codebase" value="${applet.codebase}"/>
 703       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 704     </manifest>
 705   </jar>
 706   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 707     <fileset dir="${packageDir}/examples">
 708       <include name="*.jar" />
 709     </fileset>
 710   </signjar>
 711   <presetdef name="ap_applet.jar">
 712     <!-- build a signed applet with 'all-permissions' -
 713                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 714                           JalviewLite+JmolApplet linked sequence/structure fails
 715                           Mixed code warnings are raised
 716                           -->
 717     <jar update="true" index="true">
 718       <manifest>
 719         <attribute name="Application-Name" value="JalviewLite" />
 720         <attribute name="Permissions" value="all-permissions" />
 721         <attribute name="Codebase" value="${applet.codebase}" />
 722         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 723         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 724       </manifest>
 725     </jar>
 726   </presetdef>
 727   <presetdef name="applet.jar">
 728     <!-- build signed applet with sandbox permissions -
 729                           Needs 'param name="permissions' value="sandbox"' in applet tag
 730                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 731                         -->
 732
 733     <jar update="true" index="true">
 734       <manifest>
 735         <attribute name="Application-Name" value="JalviewLite" />
 736         <attribute name="Permissions" value="sandbox" />
 737         <attribute name="Codebase" value="${applet.codebase}" />
 738         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 739         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 740       </manifest>
 741     </jar>
 742   </presetdef>
 743   <presetdef name="tl_applet.jar">
 744     <!-- build signed applet with trusted library/trusted permissions -
 745                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 746                                j1.7_45:
 747                                No mixed code warnings raised
 748                                Jmol/JalviewLite sequence/structure example doesn't link structures
 749                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 750
 751                               -->
 752
 753     <jar update="true" index="true">
 754       <manifest>
 755         <attribute name="Application-Name" value="JalviewLite" />
 756         <attribute name="Permissions" value="all-permissions" />
 757         <attribute name="Codebase" value="${applet.codebase}" />
 758         <attribute name="Trusted-Only" value="true" />
 759         <attribute name="Trusted-Library" value="true" />
 760       </manifest>
 761     </jar>
 762   </presetdef>
 763   <presetdef name="to_applet.jar">
 764     <!-- not fully test variant (yet) -->
 765     <jar update="true" index="true">
 766       <manifest>
 767         <attribute name="Application-Name" value="JalviewLite" />
 768         <attribute name="Permissions" value="all-permissions" />
 769         <attribute name="Codebase" value="${applet.codebase}" />
 770         <attribute name="Trusted-Only" value="true" />
 771       </manifest>
 772     </jar>
 773   </presetdef>
 774   <!-- create differently privileged artefacts -->
 775   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 776   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 777   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
 778   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
 779   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 780   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 781   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
 782   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
 783   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 784   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 785   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 786   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 787   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 788   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 789   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 790   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 791   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 792   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 793   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 794   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 795   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 796   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 797   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 798   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 799   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 800   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 801   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 802   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 803   <!-- finally, create manifest for original jars -->
 804   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 805   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 806   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 807   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 808
 809   <!-- todo - write examples/downloads for alternate versions of the applet -->
 810   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 811
 812     <fileset dir="${packageDir}/examples">
 813       <exclude name="u_*.jar"/>
 814       <include name="${jalviewLiteJar}" />
 815       <include name="${jmolJar}" />
 816       <include name="${javaJson}" />
 817       <include name="${jsonSimple}" />
 818       <include name="to_${jalviewLiteJar}" />
 819       <include name="to_${jmolJar}" />
 820       <include name="to_${javaJson}" />
 821       <include name="to_${jsonSimple}" />
 822       <include name="tl_${jalviewLiteJar}" />
 823       <include name="tl_${jmolJar}" />
 824       <include name="tl_${javaJson}" />
 825       <include name="tl_${jsonSimple}" />
 826       <include name="ap_${jalviewLiteJar}" />
 827       <include name="ap_${jmolJar}" />
 828       <include name="ap_${javaJson}" />
 829       <include name="ap_${jsonSimple}" />
 830     </fileset>
 831   </signjar>
 832   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 833   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 834         <!-- finally, replace any launchApp servlet tags with a version specification -->
 835         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 836                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
 837                 <fileset dir="${packageDir}/examples">
 838                         <include name="**/*.html"/>
 839                 </fileset>
 840         </replace>
 841         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 842                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
 843                 <fileset dir="${packageDir}/examples">
 844                         <include name="**/*.html"/>
 845                 </fileset>
 846         </replace>
 847
 848 </target>
 849 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 850   <javadoc destdir="${javadocDir}">
 851     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 852     </packageset>
 853   </javadoc>
 854 </target>
 855 </project>