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_2015.06.11.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="${packageDir}/javadoc"/>
 184   </target>
 185
 186
 187   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 188   <target name="buildPropertiesFile" depends="init">
 189     <tstamp prefix="build">
 190       <format property="date" pattern="dd MMMM yyyy" />
 191     </tstamp>
 192     <exec executable="/usr/bin/git" outputproperty="git.commit"  failifexecutionfails="false">
 193       <arg value="rev-parse"/>
 194       <arg value="--short"/>
 195       <arg value="HEAD"/>
 196     </exec>
 197     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 198       <arg value="rev-parse"/>
 199       <arg value="--abbrev-ref"/>
 200       <arg value="HEAD"/>
 201     </exec>
 202     <properties file="${outputDir}/.build_properties">
 203       <header>
 204           ---Jalview Build Details---
 205         </header>
 206       <property name="VERSION" value="${JALVIEW_VERSION}" />
 207       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 208       <property name="BUILD_DATE" value="${build.date}" />
 209     </properties>
 210   </target>
 211
 212
 213   <target name="clean" depends="init">
 214     <!-- not efficient yet. -->
 215     <delete dir="${outputDir}" includes="*,**/*"/>
 216   </target>
 217
 218   <target name="distclean" depends="init, clean">
 219
 220     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 221     <delete>
 222       <fileset dir=".">
 223         <include name="${outputJar}" />
 224         <include name="#*#" />
 225         <include name="#*.*#" />
 226         <include name="**/#*#" />
 227         <include name="**/#*.*#" />
 228         <include name="*~" />
 229         <include name="*.*~" />
 230         <include name="**/*~" />
 231         <include name="**/*.*~" />
 232       </fileset>
 233     </delete>
 234   </target>
 235
 236   <target name="prepare" depends="init">
 237     <mkdir dir="${outputDir}" />
 238     <copy todir="${outputDir}">
 239       <fileset dir=".">
 240         <include name="${docDir}/**/*.*" />
 241         <include name="${helpDir}/**/*.*" />
 242         <include name="${libDir}/*.jar" />
 243       </fileset>
 244       <fileset dir="${resourceDir}">
 245         <include name="**/*.*" />
 246       </fileset>
 247     </copy>
 248   </target>
 249
 250   <target name="build" depends="prepare">
 251     <!-- not efficient yet. -->
 252     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 253       <exclude name="jalview/*applet*" />
 254       <exclude name="jalview/appletgui/**" />
 255       <exclude name="com/stevesoft/**" />
 256     </javac>
 257   </target>
 258
 259
 260   <target name="testclean" depends="init">
 261     <delete dir="${testOutputDir}" includes="*,**/*"/>
 262   </target>
 263
 264   <target name="prepareTests" depends="init">
 265         <mkdir dir="${testOutputDir}" />
 266         <copy todir="${testOutputDir}">
 267                 <fileset dir=".">
 268                         <include name="${docDir}/**/*.*" />
 269                         <include name="${helpDir}/**/*.*" />
 270                         <include name="${libDir}/*.jar" />
 271                 </fileset>
 272                 <fileset dir="${resourceDir}">
 273                         <include name="**/*.*" />
 274                 </fileset>
 275         </copy>
 276   </target>
 277
 278   <target name="buildTests" depends="prepareTests">
 279         <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${testOutputDir}"
 280                 debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
 281         </javac>
 282         <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}"
 283                 debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
 284         </javac>
 285   </target>
 286
 287   <taskdef name="testng" classname="org.testng.TestNGAntTask" >
 288         <classpath location="utils/testnglibs/testng.jar" />
 289   </taskdef>
 290
 291   <target name="testng" depends="buildTests">
 292         <testng classpathref="build.classpath" outputDir="${reportDir}"
 293                 haltOnFailure="false">
 294                 <classpath location="${testOutputDir}" />
 295                 <xmlfileset dir="utils" includes="jalview_testng.xml" />
 296         </testng>
 297   </target>
 298
 299   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 300     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 301       <arg line="html" />
 302     </java>
 303   </target>
 304
 305   <target name="makefulldist" depends="makedist">
 306     <copy todir="${packageDir}">
 307       <fileset dir="${resourceDir}/images">
 308         <include name="${WebStartImage}"/>
 309       </fileset>
 310     </copy>
 311
 312     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 313
 314     <!-- create a dummy jar which will eventually contain the jnlp template -->
 315     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 316       <fileset dir="${packageDir}">
 317         <include name="jalview.jar" />
 318       </fileset>
 319     </jar>
 320
 321     <mkdir dir="${packageDir}/JNLP-INF"/>
 322     <antcall target="writejnlpf">
 323       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 324       <param name="inih" value="*" />
 325       <param name="maxh" value="*"/>
 326     </antcall>
 327
 328     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 329       <fileset dir="${packageDir}">
 330         <include name="JNLP-INF"/>
 331       </fileset>
 332     </jar>
 333
 334     <antcall target="writejnlpf">
 335       <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 336       <param name="inih" value="10M" />
 337       <param name="maxh" value="256M"/>
 338     </antcall>
 339
 340     <antcall target="writejnlpf">
 341       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 342       <param name="inih" value="128M" />
 343       <param name="maxh" value="512M"/>
 344     </antcall>
 345
 346     <antcall target="writejnlpf">
 347       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 348       <param name="inih" value="256M" />
 349       <param name="maxh" value="1024M"/>
 350     </antcall>
 351
 352     <!-- finally, need to postprocess to add in associations at end of 'information' element
 353
 354                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 355
 356                 </xslt>
 357
 358
 359                         -->
 360     <!--
 361                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 362         <association mime-type="application-x/ext-file" extensions="fasta"/>
 363         <association mime-type="application-x/ext-file" extensions="mfa"/>
 364         <association mime-type="application-x/ext-file" extensions="fastq"/>
 365         <association mime-type="application-x/ext-file" extensions="blc"/>
 366         <association mime-type="application-x/ext-file" extensions="msf"/>
 367         <association mime-type="application-x/ext-file" extensions="pfam"/>
 368         <association mime-type="application-x/ext-file" extensions="aln"/>
 369         <association mime-type="application-x/ext-file" extensions="pir"/>
 370         <association mime-type="application-x/ext-file" extensions="amsa"/>
 371         <association mime-type="application-x/ext-file" extensions="stk"/>
 372         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 373     <!-- and sign the jars -->
 374     <!-- the default keystore details might need to be edited here -->
 375     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 376       <fileset dir="${packageDir}">
 377         <include name="*.jar" />
 378       </fileset>
 379     </signjar>
 380   </target>
 381
 382   <target name="runenv" depends="init">
 383     <path id="run.classpath">
 384       <pathelement location="${outputDir}" />
 385       <fileset dir="${outputDir}">
 386         <include name="${libDir}/*.jar" />
 387       </fileset>
 388     </path>
 389     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 390
 391     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 392       </echo>
 393   </target>
 394
 395   <target name="-generatejnlpf">
 396     <presetdef name="jnlpf">
 397       <jnlp codebase="${WebStartLocation}">
 398         <information>
 399           <title>Jalview</title>
 400           <vendor>The Barton Group</vendor>
 401           <homepage href="http://www.jalview.org" />
 402           <description>Jalview Multiple Alignment Editor</description>
 403           <description kind="short">Jalview</description>
 404           <icon href="${WebStartImage}" />
 405           <offline_allowed />
 406         </information>
 407         <resources>
 408           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 409           <fileset dir="${packageDir}">
 410             <include name="jalview.jar" />
 411           </fileset>
 412           <fileset dir="${packageDir}">
 413             <include name="*.jar" />
 414             <include name="*_*.jar" />
 415             <exclude name="jalview.jar" />
 416                 <exclude name="*jnilib.jar"/>
 417           </fileset>
 418         </resources>
 419         <resources os="Mac OS X">
 420           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 421                 <fileset dir="${packageDir}">
 422                         <include name="*quaqua*.jnilib.jar"/>
 423                 </fileset>
 424         </resources>
 425
 426         <application_desc main_class="jalview.bin.Jalview">
 427         </application_desc>
 428         <security>
 429           <all_permissions />
 430         </security>
 431       </jnlp>
 432     </presetdef>
 433
 434     <jnlpf toFile="${jnlpFile}"/>
 435
 436   </target>
 437
 438   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 439     <echo message="Not adding JNLP File Associations"/>
 440   </target>
 441
 442   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 443     <replace file="${jnlpFile}">
 444       <replacetoken>
 445         <![CDATA[</information>]]></replacetoken>
 446       <replacevalue>
 447         <![CDATA[
 448           <association mime-type="application-x/ext-file" extensions="fa" />
 449         <association mime-type="application-x/ext-file" extensions="fasta" />
 450         <association mime-type="application-x/ext-file" extensions="mfa" />
 451         <association mime-type="application-x/ext-file" extensions="fastq" />
 452         <association mime-type="application-x/ext-file" extensions="blc" />
 453         <association mime-type="application-x/ext-file" extensions="msf" />
 454         <association mime-type="application-x/ext-file" extensions="pfam" />
 455         <association mime-type="application-x/ext-file" extensions="aln"/>
 456         <association mime-type="application-x/ext-file" extensions="pir"/>
 457         <association mime-type="application-x/ext-file" extensions="amsa"/>
 458         <association mime-type="application-x/ext-file" extensions="stk"/>
 459         <association mime-type="application-x/ext-file" extensions="jvp"/>
 460       </information>]]></replacevalue>
 461   </replace>
 462   <echo message="Added file associations to JNLP file"/>
 463 </target>
 464 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 465 </target>
 466
 467 <target name="buildextclients" depends="init">
 468   <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" />
 469   <condition property="dontextbuild">
 470     <equals arg1="n" arg2="${doextbuild.response}" />
 471   </condition>
 472   <condition property="dontextbuild">
 473     <equals arg1="N" arg2="${doextbuild.response}" />
 474   </condition>
 475   <fail if="dontextbuild">
 476         Build External Client Code process aborted by user. Jalview source is unchanged.
 477       </fail>
 478   <!-- Currently, this doesn't happen automatically.
 479      1. Run WSDL2Java as below, which generates an ext.vamsas +
 480      vamsas.<datapackages> fileset.
 481      2. refactor ext.vamsas.SpecificserviceWS* to
 482      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 483      3. Update the jalview.ws.*WServices classes to reflect the
 484      interface type, and all locations of this wsdl type that Jalview
 485      might be using.
 486
 487 -->
 488   <path id="axisbuild">
 489     <path refid="build.classpath" />
 490   </path>
 491   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 492   <move todir="./bak">
 493     <fileset dir="${sourceDir}" id="client">
 494       <include name="${wsdl.ClientNS}/*.*" />
 495     </fileset>
 496   </move>
 497
 498   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 499     <mappingSet>
 500       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 501       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 502     </mappingSet>
 503   </axis-wsdl2java>
 504 </target>
 505
 506 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 507   <!-- make the package jar if not already existing -->
 508   <mkdir dir="${packageDir}" />
 509   <!-- clean dir if it already existed -->
 510   <delete>
 511     <fileset dir="${packageDir}">
 512       <include name="*.jar"/>
 513     </fileset>
 514   </delete>
 515   <jar destfile="${packageDir}/${outputJar}" index="true">
 516     <manifest>
 517       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 518       <attribute name="Permissions" value="all-permissions" />
 519       <attribute name="Application-Name" value="Jalview Desktop" />
 520       <attribute name="Codebase" value="${application.codebase}" />
 521     </manifest>
 522     <fileset dir="${outputDir}/">
 523       <exclude name="cache*/**" />
 524       <exclude name="*.jar" />
 525       <exclude name="*.jar.*" />
 526       <exclude name="**/*.jar" />
 527       <exclude name="**/*.jar.*" />
 528     </fileset>
 529   </jar>
 530
 531   <copy toDir="${packageDir}" flatten="true">
 532     <fileset dir="${outputDir}">
 533       <include name="*.jar" />
 534       <include name="**/*.jar" />
 535     </fileset>
 536   </copy>
 537 </target>
 538
 539
 540 <!-- jalopy code reformatter -->
 541 <target name="sourcescrub" depends="init,build">
 542   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 543     <fileset dir="${sourceDir}">
 544       <include name="*.java" />
 545       <include name="**/*.java" />
 546       <include name="**/**/*.java" />
 547     </fileset>
 548   </jalopy>
 549 </target>
 550
 551
 552
 553 <!-- Compile, package and obfuscate Jalview Applet -->
 554 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 555
 556 <target name="compileApplet" depends="init,clean">
 557   <mkdir dir="${outputDir}" />
 558   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 559                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 560                         excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
 561 </target>
 562
 563 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 564   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 565   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 566   <copy todir="${outputDir}/lang">
 567     <fileset dir="${resourceDir}/lang">
 568       <include name="**.*"/>
 569     </fileset>
 570   </copy>
 571   <jar destfile="in.jar" index="true">
 572     <manifest>
 573       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 574       <attribute name="Application-Name" value="JalviewLite" />
 575       <attribute name="Codebase" value="${applet.codebase}" />
 576     </manifest>
 577     <fileset dir="${outputDir}">
 578       <include name="com/**" />
 579       <include name="MCview/**" />
 580       <include name="jalview/**" />
 581       <include name=".build_properties" />
 582       <include name="images/idwidth.gif" />
 583       <include name="images/link.gif" />
 584       <include name="lang/**" />
 585     </fileset>
 586   </jar>
 587 </target>
 588 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 589 </target>
 590 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 591   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 592   <delete file="in.jar" />
 593 </target>
 594 <target name="-obfuscatereally" unless="donotobfuscate">
 595
 596   <path id="obfuscateDeps.path">
 597     <pathelement location="${applet.jre.tools}" />
 598     <pathelement location="appletlib/${jmolJar}" />
 599     <pathelement location="appletlib/${jsonSimple}" />
 600     <pathelement location="appletlib/${javaJson}" />
 601   </path>
 602   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 603
 604   <proguard>
 605     <injar file="in.jar" />
 606     <outjar file="${jalviewLiteJar}" />
 607     <libraryjar refid="obfuscateDeps.path" />
 608     <dontwarn/>
 609     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 610       <field access="public" />
 611       <method access="public" />
 612       <constructor access="public" />
 613     </keep>
 614     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 615       <field access="public" />
 616       <method access="public" />
 617       <constructor access="public" />
 618     </keep>
 619     <!--      -libraryjars "${obfuscateDeps}"
 620       -injars      in.jar
 621       -outjars     jalviewApplet.jar
 622       -keep public class jalview.bin.JalviewLite
 623        { public * ; } -->
 624   </proguard>
 625   <delete file="in.jar" />
 626 </target>
 627
 628 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 629   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 630   <delete>
 631     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 632       <include name="*.java" />
 633       <include name="descriptors/*.java" />
 634     </fileset>
 635   </delete>
 636   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 637   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 638   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 639   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 640   <!--
 641                 now build the jalview.binding package with the old schema set
 642                 -->
 643   <delete>
 644     <fileset dir="${sourceDir}/jalview/binding/">
 645       <include name="**" />
 646     </fileset>
 647   </delete>
 648   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 649   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 650   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 651 </target>
 652 <target name="sourcedist" description="create jalview source distribution" depends="init">
 653   <delete file="${source.dist.name}" />
 654   <tar destfile="${source.dist.name}" compression="gzip">
 655     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 656       <include name="LICENSE" />
 657       <include name="README" />
 658       <include name="build.xml" />
 659       <include name="jalview-jalopy.xml" />
 660       <include name="JalviewApplet.jpx" />
 661       <include name="JalviewX.jpx" />
 662       <include name="nbbuild.xml"/>
 663       <include name="nbproject/genfiles.properties"/>
 664       <include name="nbproject/project.properties"/>
 665       <include name="nbproject/project.xml"/>
 666       <include name="${sourceDir}/*.java" />
 667       <include name="${sourceDir}/**/*.java" />
 668       <include name="${sourceDir}/**/*.cdr" />
 669       <include name="${libDir}/**/*" />
 670       <include name="${resourceDir}/**/*" />
 671       <include name="${helpDir}/**/*" />
 672       <include name="appletlib/${jmolJar}" />
 673       <exclude name="**/*locales" />
 674       <exclude name="*locales/**" />
 675       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 676       <exclude name="utils/InstallAnywhere/**Build*/**" />
 677       <exclude name="utils/InstallAnywhere/**Build*/**" />
 678       <exclude name="utils/InstallAnywhere/**locale*" />
 679       <exclude name="utils/InstallAnywhere/**locale*/**" />
 680       <include name="${schemaDir}/**/*" />
 681       <include name="utils/**/*" />
 682       <include name="${docDir}/**/*" />
 683       <include name="examples/**/*" />
 684     </tarfileset>
 685   </tar>
 686 </target>
 687 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 688   <copy todir="${packageDir}/examples">
 689     <fileset dir="examples">
 690       <include name="**/*"/>
 691       <include name="javascript/*"/>
 692       <include name="jmol/*"/>
 693     </fileset>
 694     <fileset dir=".">
 695       <include name="${jalviewLiteJar}" />
 696     </fileset>
 697     <fileset dir="appletlib">
 698       <include name="**/*"/>
 699     </fileset>
 700   </copy>
 701   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 702   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
 703   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
 704   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 705     <manifest>
 706       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 707       <!--          <attribute name="Permissions" value="sandbox" /> -->
 708       <!--<attribute name="Trusted-Lib" value="true" /> -->
 709       <attribute name="Codebase" value="${applet.codebase}"/>
 710       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 711     </manifest>
 712   </jar>
 713   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 714     <fileset dir="${packageDir}/examples">
 715       <include name="*.jar" />
 716     </fileset>
 717   </signjar>
 718   <presetdef name="ap_applet.jar">
 719     <!-- build a signed applet with 'all-permissions' -
 720                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 721                           JalviewLite+JmolApplet linked sequence/structure fails
 722                           Mixed code warnings are raised
 723                           -->
 724     <jar update="true" index="true">
 725       <manifest>
 726         <attribute name="Application-Name" value="JalviewLite" />
 727         <attribute name="Permissions" value="all-permissions" />
 728         <attribute name="Codebase" value="${applet.codebase}" />
 729         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 730         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 731       </manifest>
 732     </jar>
 733   </presetdef>
 734   <presetdef name="applet.jar">
 735     <!-- build signed applet with sandbox permissions -
 736                           Needs 'param name="permissions' value="sandbox"' in applet tag
 737                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 738                         -->
 739
 740     <jar update="true" index="true">
 741       <manifest>
 742         <attribute name="Application-Name" value="JalviewLite" />
 743         <attribute name="Permissions" value="sandbox" />
 744         <attribute name="Codebase" value="${applet.codebase}" />
 745         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 746         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 747       </manifest>
 748     </jar>
 749   </presetdef>
 750   <presetdef name="tl_applet.jar">
 751     <!-- build signed applet with trusted library/trusted permissions -
 752                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 753                                j1.7_45:
 754                                No mixed code warnings raised
 755                                Jmol/JalviewLite sequence/structure example doesn't link structures
 756                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 757
 758                               -->
 759
 760     <jar update="true" index="true">
 761       <manifest>
 762         <attribute name="Application-Name" value="JalviewLite" />
 763         <attribute name="Permissions" value="all-permissions" />
 764         <attribute name="Codebase" value="${applet.codebase}" />
 765         <attribute name="Trusted-Only" value="true" />
 766         <attribute name="Trusted-Library" value="true" />
 767       </manifest>
 768     </jar>
 769   </presetdef>
 770   <presetdef name="to_applet.jar">
 771     <!-- not fully test variant (yet) -->
 772     <jar update="true" index="true">
 773       <manifest>
 774         <attribute name="Application-Name" value="JalviewLite" />
 775         <attribute name="Permissions" value="all-permissions" />
 776         <attribute name="Codebase" value="${applet.codebase}" />
 777         <attribute name="Trusted-Only" value="true" />
 778       </manifest>
 779     </jar>
 780   </presetdef>
 781   <!-- create differently privileged artefacts -->
 782   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 783   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 784   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
 785   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
 786   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 787   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 788   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
 789   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
 790   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 791   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 792   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 793   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 794   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 795   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 796   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 797   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 798   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 799   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 800   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 801   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 802   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 803   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 804   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 805   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 806   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 807   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 808   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 809   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 810   <!-- finally, create manifest for original jars -->
 811   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 812   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 813   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 814   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 815
 816   <!-- todo - write examples/downloads for alternate versions of the applet -->
 817   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 818
 819     <fileset dir="${packageDir}/examples">
 820       <exclude name="u_*.jar"/>
 821       <include name="${jalviewLiteJar}" />
 822       <include name="${jmolJar}" />
 823       <include name="${javaJson}" />
 824       <include name="${jsonSimple}" />
 825       <include name="to_${jalviewLiteJar}" />
 826       <include name="to_${jmolJar}" />
 827       <include name="to_${javaJson}" />
 828       <include name="to_${jsonSimple}" />
 829       <include name="tl_${jalviewLiteJar}" />
 830       <include name="tl_${jmolJar}" />
 831       <include name="tl_${javaJson}" />
 832       <include name="tl_${jsonSimple}" />
 833       <include name="ap_${jalviewLiteJar}" />
 834       <include name="ap_${jmolJar}" />
 835       <include name="ap_${javaJson}" />
 836       <include name="ap_${jsonSimple}" />
 837     </fileset>
 838   </signjar>
 839   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 840   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 841         <!-- finally, replace any launchApp servlet tags with a version specification -->
 842         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 843                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
 844                 <fileset dir="${packageDir}/examples">
 845                         <include name="**/*.html"/>
 846                 </fileset>
 847         </replace>
 848         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 849                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
 850                 <fileset dir="${packageDir}/examples">
 851                         <include name="**/*.html"/>
 852                 </fileset>
 853         </replace>
 854
 855 </target>
 856 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 857   <javadoc destdir="${javadocDir}">
 858     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 859     </packageset>
 860   </javadoc>
 861 </target>
 862 </project>