build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
   4  * Copyright (C) 2015 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. Add -Dtimestamp to timestamp signed jars"/>
  31     <echo message="              See docs/building.html for more information." />
  32     <echo message="compileApplet - compiles all necessary files for Applet" />
  33     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  34     <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
  35     <echo message="      you can specify particular test groups as a list via -Dtestng-groups=" />
  36     <echo message="See docs/building.html and the comments in build file for other targets." />
  37     <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  38     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  39   </target>
  40
  41
  42   <!-- utils is a class path to additional utilities needed for
  43     building docs, jars and webstart stuff -->
  44   <!--
  45         Userdefined build property defaults
  46
  47         wsdl.server list (plus namespace mapping info ???)  - also want
  48                 ... to make this a dynamically generatable property
  49         WebStart Location
  50         Build location - provide a temporary root for speed
  51         jarsigner keystore and info
  52         Jakarta and axis classpath ?
  53         Default argument for starting Jalview (if it exists).
  54
  55 -->
  56
  57   <target name="init">
  58     <path id="axis.classpath">
  59       <!-->
  60       <fileset dir="/usr/local/axis/lib">
  61         <include name="**/*.jar" />
  62       </fileset>
  63       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  64         <include name="**/*.jar"/>
  65         <include name="*.jar"/>
  66       </fileset> -->
  67       </path>
  68
  69     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  70     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  71
  72     <property name="INSTALLATION" value="Source" />
  73
  74     <!-- 2.4 (VAMSAS)" -->
  75     <!-- Include debugging information in javac true or false -->
  76     <property name="javac.debug" value="true" />
  77
  78     <!-- JarSigner Key Store for Webstart Distribution -->
  79     <property name="jalview.keystore" value="./keys/.keystore" />
  80     <!-- Keystore Password -->
  81     <property name="jalview.keystore.pass" value="alignmentisfun" />
  82     <!-- Key Name -->
  83     <property name="jalview.key" value="jalview" />
  84     <!-- Key Password -->
  85     <property name="jalview.key.pass" value="alignmentisfun" />
  86         <!-- time stamp server URL -->
  87     <property name="jalview.tsaurl" value="" />
  88
  89     <property name="testng-groups" value="Functional" />
  90
  91     <!-- Don't change anything below here unless you know what you are doing! -->
  92     <!-- Url path for WebStart in JNLP file -->
  93     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  94     <!-- Webstart Image - looked for in resources/images -->
  95     <property name="WebStartImage" value="JalviewLogo_big.png" />
  96     <!-- J2SE version needed for webstart launch -->
  97     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  98     <property name="j2sev" value="1.7+" />
  99     <!-- Java Compilation settings - source and target javac version -->
 100     <property name="javac.source" value="1.7" />
 101     <property name="javac.target" value="1.7" />
 102
 103     <!-- Permissions for running Java applets and applications. -->
 104     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 105     <property name="application.codebase" value="*.jalview.org" />
 106     <!-- and allowing the applet to be deployed from any URL -->
 107     <!-- 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 -->
 108     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 109     <property name="applet.caller-codebase" value="${applet.codebase}" />
 110
 111     <!-- build directory configuration -->
 112     <property name="libDir" value="lib" />
 113     <property name="resourceDir" value="resources" />
 114     <property name="helpDir" value="help" />
 115     <property name="docDir" value="doc" />
 116     <property name="sourceDir" value="src" />
 117     <property name="schemaDir" value="schemas" />
 118     <property name="outputDir" value="classes" />
 119     <property name="packageDir" value="dist" />
 120     <property name="outputJar" value="jalview.jar" />
 121     <!-- Jalview Applet JMol Jar Dependency -->
 122     <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
 123     <property name="varnaJar" value="VARNAv3-93.jar" />
 124     <property name="jsoup" value="jsoup-1.8.1.jar" />
 125     <property name="jsonSimple" value="json_simple-1.1.jar" />
 126     <property name="javaJson" value="java-json.jar" />
 127     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 128     <property name="reportDir" value="test-reports" />
 129     <property name="testDir" value="test" />
 130     <property name="testOutputDir" value="tests" />
 131     <!-- switch to indicate if we should obfuscate jalviewLite -->
 132     <!-- <property name="donotobfuscate" value="true"/> -->
 133     <!-- switch to exclude associations from generated jnlp files -->
 134     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 135
 136     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 137     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 138     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 139     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 140     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 141     <property name="WSInterf" value="MsaWS" />
 142     <property name="wsdl.Namespace" value="vamsas" />
 143     <property name="wsdl.ClientNS" value="ext.vamsas" />
 144     <!-- the class path for building the application -->
 145     <path id="build.classpath">
 146       <fileset dir="utils">
 147         <include name="*.jar" />
 148         <include name="**/*.jar" />
 149       </fileset>
 150       <fileset dir="${libDir}">
 151         <include name="*.jar" />
 152         <include name="**/*.jar" />
 153       </fileset>
 154       <fileset dir="${java.home}/lib">
 155         <include name="plugin.jar" />
 156       </fileset>
 157       <fileset dir="appletlib">
 158         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 159                                 -->
 160         <include name="${jmolJar}" />
 161         <include name="${varnaJar}" />
 162       </fileset>
 163     </path>
 164     <path id="test.classpath">
 165       <pathelement path="${outputDir}" />
 166       <path refid="build.classpath" />
 167     </path>
 168     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 169     <!-- The Location of the java 1.1.8 jdk -->
 170     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
 171     <property name="java118.home" value="${java.home}" />
 172     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 173                 -->
 174     <!-- jre for 1.4 version -->
 175     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
 176
 177     <!-- the classpath for building the 1.1 applet -->
 178     <path id="jalviewlite.deps">
 179       <fileset dir="${java118.home}">
 180         <include name="lib/classes.zip" />
 181       </fileset>
 182       <fileset dir="${java.home}/lib">
 183         <include name="plugin.jar" />
 184       </fileset>
 185       <pathelement location="appletlib/${jmolJar}" />
 186       <pathelement location="lib/${varnaJar}" />
 187       <pathelement location="lib/${jsoup}" />
 188       <pathelement location="lib/${jsonSimple}" />
 189       <pathelement location="lib/${javaJson}" />
 190
 191     </path>
 192     <!-- default location for outputting javadoc -->
 193     <property name="javadocDir" value="${packageDir}/javadoc" />
 194   </target>
 195
 196
 197   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 198   <target name="buildPropertiesFile" depends="init">
 199     <tstamp prefix="build">
 200       <format property="date" pattern="dd MMMM yyyy" />
 201     </tstamp>
 202     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 203       <arg value="rev-parse" />
 204       <arg value="--short" />
 205       <arg value="HEAD" />
 206     </exec>
 207     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 208       <arg value="rev-parse" />
 209       <arg value="--abbrev-ref" />
 210       <arg value="HEAD" />
 211     </exec>
 212     <properties file="${outputDir}/.build_properties">
 213       <header>
 214           ---Jalview Build Details---
 215         </header>
 216       <property name="VERSION" value="${JALVIEW_VERSION}" />
 217       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 218       <property name="BUILD_DATE" value="${build.date}" />
 219     </properties>
 220   </target>
 221
 222
 223   <target name="clean" depends="init">
 224     <!-- not efficient yet. -->
 225     <delete dir="${outputDir}" includes="*,**/*" />
 226   </target>
 227
 228   <target name="distclean" depends="init, clean">
 229
 230     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 231     <delete>
 232       <fileset dir=".">
 233         <include name="${outputJar}" />
 234         <include name="#*#" />
 235         <include name="#*.*#" />
 236         <include name="**/#*#" />
 237         <include name="**/#*.*#" />
 238         <include name="*~" />
 239         <include name="*.*~" />
 240         <include name="**/*~" />
 241         <include name="**/*.*~" />
 242       </fileset>
 243     </delete>
 244   </target>
 245
 246   <target name="prepare" depends="init">
 247     <mkdir dir="${outputDir}" />
 248     <copy todir="${outputDir}">
 249       <fileset dir=".">
 250         <include name="${docDir}/**/*.*" />
 251         <include name="${helpDir}/**/*.*" />
 252         <include name="${libDir}/*.jar" />
 253       </fileset>
 254       <fileset dir="${resourceDir}">
 255         <include name="**/*.*" />
 256       </fileset>
 257     </copy>
 258   </target>
 259
 260   <target name="build" depends="prepare">
 261     <!-- not efficient yet. -->
 262     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 263       <exclude name="jalview/*applet*" />
 264       <exclude name="jalview/appletgui/**" />
 265       <exclude name="com/stevesoft/**" />
 266     </javac>
 267   </target>
 268
 269
 270   <target name="testclean" depends="init">
 271     <delete dir="${testOutputDir}" includes="*,**/*" />
 272   </target>
 273
 274   <target name="prepareTests" depends="init,testclean">
 275     <mkdir dir="${testOutputDir}" />
 276   </target>
 277
 278   <target name="buildTests" depends="build,buildindices,prepareTests">
 279     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 280     </javac>
 281   </target>
 282
 283   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 284
 285   <target name="testng" depends="buildTests">
 286     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 287       verbose="2">
 288       <classpath>
 289         <pathelement location="${testOutputDir}" />
 290         <path refid="test.classpath" />
 291       </classpath>
 292       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 293     </testng>
 294   </target>
 295
 296   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 297     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 298       <arg line="html" />
 299     </java>
 300   </target>
 301
 302     <target name="preparejnlp" depends="makedist">
 303     <copy todir="${packageDir}">
 304       <fileset dir="${resourceDir}/images">
 305         <include name="${WebStartImage}" />
 306       </fileset>
 307     </copy>
 308
 309     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 310
 311     <!-- create a dummy jar which will eventually contain the jnlp template -->
 312     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 313       <fileset dir="${packageDir}">
 314         <include name="jalview.jar" />
 315       </fileset>
 316     </jar>
 317
 318     <mkdir dir="${packageDir}/JNLP-INF" />
 319     <antcall target="writejnlpf">
 320       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 321       <param name="inih" value="*" />
 322       <param name="maxh" value="*" />
 323     </antcall>
 324
 325     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 326       <fileset dir="${packageDir}">
 327         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 328       </fileset>
 329     </jar>
 330
 331     <antcall target="writejnlpf">
 332       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 333       <param name="inih" value="10M" />
 334       <param name="maxh" value="256M" />
 335     </antcall>
 336
 337     <antcall target="writejnlpf">
 338       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 339       <param name="inih" value="128M" />
 340       <param name="maxh" value="512M" />
 341     </antcall>
 342
 343     <antcall target="writejnlpf">
 344       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 345       <param name="inih" value="256M" />
 346       <param name="maxh" value="1024M" />
 347     </antcall>
 348
 349     <!-- finally, need to postprocess to add in associations at end of 'information' element
 350
 351                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 352
 353                 </xslt>
 354
 355
 356                         -->
 357     <!--
 358                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 359         <association mime-type="application-x/ext-file" extensions="fasta"/>
 360         <association mime-type="application-x/ext-file" extensions="mfa"/>
 361         <association mime-type="application-x/ext-file" extensions="fastq"/>
 362         <association mime-type="application-x/ext-file" extensions="blc"/>
 363         <association mime-type="application-x/ext-file" extensions="msf"/>
 364         <association mime-type="application-x/ext-file" extensions="pfam"/>
 365         <association mime-type="application-x/ext-file" extensions="aln"/>
 366         <association mime-type="application-x/ext-file" extensions="pir"/>
 367         <association mime-type="application-x/ext-file" extensions="amsa"/>
 368         <association mime-type="application-x/ext-file" extensions="stk"/>
 369         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 370       </target>
 371
 372   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
 373     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA"
 374       tsaproxyhost="squid" tsaproxyport="80" tsaurl="${jalview.tsaurl}">
 375       <fileset dir="${packageDir}">
 376         <include name="*.jar" />
 377       </fileset>
 378     </signjar>
 379   </target>
 380   <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
 381     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 382       <fileset dir="${packageDir}">
 383         <include name="*.jar" />
 384       </fileset>
 385     </signjar>
 386   </target>
 387
 388   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 389     <!-- and sign the jars -->
 390     <!-- the default keystore details might need to be edited here -->
 391   </target>
 392
 393   <target name="runenv" depends="init">
 394     <path id="run.classpath">
 395       <pathelement location="${outputDir}" />
 396       <fileset dir="${outputDir}">
 397         <include name="${libDir}/*.jar" />
 398       </fileset>
 399     </path>
 400     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 401
 402     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 403       </echo>
 404   </target>
 405
 406   <target name="-generatejnlpf">
 407     <presetdef name="jnlpf">
 408       <jnlp codebase="${WebStartLocation}">
 409         <information>
 410           <title>Jalview</title>
 411           <vendor>The Barton Group</vendor>
 412           <homepage href="http://www.jalview.org" />
 413           <description>Jalview Multiple Alignment Editor</description>
 414           <description kind="short">Jalview</description>
 415           <icon href="${WebStartImage}" />
 416           <offline_allowed />
 417         </information>
 418         <resources>
 419           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 420           <fileset dir="${packageDir}">
 421             <include name="jalview.jar" />
 422           </fileset>
 423           <fileset dir="${packageDir}">
 424             <include name="*.jar" />
 425             <include name="*_*.jar" />
 426             <exclude name="jalview.jar" />
 427             <exclude name="*jnilib.jar" />
 428           </fileset>
 429         </resources>
 430         <resources os="Mac OS X">
 431           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 432           <fileset dir="${packageDir}">
 433             <include name="*quaqua*.jnilib.jar" />
 434           </fileset>
 435         </resources>
 436
 437         <application_desc main_class="jalview.bin.Jalview">
 438         </application_desc>
 439         <security>
 440           <all_permissions />
 441         </security>
 442       </jnlp>
 443     </presetdef>
 444
 445     <jnlpf toFile="${jnlpFile}" />
 446
 447   </target>
 448
 449   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 450     <echo message="Not adding JNLP File Associations" />
 451   </target>
 452
 453   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 454     <replace file="${jnlpFile}">
 455       <replacetoken>
 456         <![CDATA[</information>]]></replacetoken>
 457       <replacevalue>
 458         <![CDATA[
 459           <association mime-type="application-x/ext-file" extensions="fa" />
 460         <association mime-type="application-x/ext-file" extensions="fasta" />
 461         <association mime-type="application-x/ext-file" extensions="mfa" />
 462         <association mime-type="application-x/ext-file" extensions="fastq" />
 463         <association mime-type="application-x/ext-file" extensions="blc" />
 464         <association mime-type="application-x/ext-file" extensions="msf" />
 465         <association mime-type="application-x/ext-file" extensions="pfam" />
 466         <association mime-type="application-x/ext-file" extensions="aln"/>
 467         <association mime-type="application-x/ext-file" extensions="pir"/>
 468         <association mime-type="application-x/ext-file" extensions="amsa"/>
 469         <association mime-type="application-x/ext-file" extensions="stk"/>
 470         <association mime-type="application-x/ext-file" extensions="jvp"/>
 471       </information>]]></replacevalue>
 472   </replace>
 473   <echo message="Added file associations to JNLP file" />
 474 </target>
 475 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 476 </target>
 477
 478 <target name="buildextclients" depends="init">
 479   <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" />
 480   <condition property="dontextbuild">
 481     <equals arg1="n" arg2="${doextbuild.response}" />
 482   </condition>
 483   <condition property="dontextbuild">
 484     <equals arg1="N" arg2="${doextbuild.response}" />
 485   </condition>
 486   <fail if="dontextbuild">
 487         Build External Client Code process aborted by user. Jalview source is unchanged.
 488       </fail>
 489   <!-- Currently, this doesn't happen automatically.
 490      1. Run WSDL2Java as below, which generates an ext.vamsas +
 491      vamsas.<datapackages> fileset.
 492      2. refactor ext.vamsas.SpecificserviceWS* to
 493      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 494      3. Update the jalview.ws.*WServices classes to reflect the
 495      interface type, and all locations of this wsdl type that Jalview
 496      might be using.
 497
 498 -->
 499   <path id="axisbuild">
 500     <path refid="build.classpath" />
 501   </path>
 502   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 503   <move todir="./bak">
 504     <fileset dir="${sourceDir}" id="client">
 505       <include name="${wsdl.ClientNS}/*.*" />
 506     </fileset>
 507   </move>
 508
 509   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 510     <mappingSet>
 511       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 512       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 513     </mappingSet>
 514   </axis-wsdl2java>
 515 </target>
 516
 517 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 518   <!-- make the package jar if not already existing -->
 519   <mkdir dir="${packageDir}" />
 520   <!-- clean dir if it already existed -->
 521   <delete>
 522     <fileset dir="${packageDir}">
 523       <include name="*.jar" />
 524     </fileset>
 525   </delete>
 526   <jar destfile="${packageDir}/${outputJar}" index="true">
 527     <manifest>
 528       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 529       <attribute name="Permissions" value="all-permissions" />
 530       <attribute name="Application-Name" value="Jalview Desktop" />
 531       <attribute name="Codebase" value="${application.codebase}" />
 532     </manifest>
 533     <fileset dir="${outputDir}/">
 534       <exclude name="cache*/**" />
 535       <exclude name="*.jar" />
 536       <exclude name="*.jar.*" />
 537       <exclude name="**/*.jar" />
 538       <exclude name="**/*.jar.*" />
 539     </fileset>
 540   </jar>
 541
 542   <copy toDir="${packageDir}" flatten="true">
 543     <fileset dir="${outputDir}">
 544       <include name="*.jar" />
 545       <include name="**/*.jar" />
 546     </fileset>
 547   </copy>
 548 </target>
 549
 550
 551 <!-- jalopy code reformatter -->
 552 <target name="sourcescrub" depends="init,build">
 553   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 554     <fileset dir="${sourceDir}">
 555       <include name="*.java" />
 556       <include name="**/*.java" />
 557       <include name="**/**/*.java" />
 558     </fileset>
 559   </jalopy>
 560 </target>
 561
 562
 563
 564 <!-- Compile, package and obfuscate Jalview Applet -->
 565 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 566
 567 <target name="compileApplet" depends="init,clean">
 568   <mkdir dir="${outputDir}" />
 569   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
 570 </target>
 571
 572 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 573   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 574   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 575   <copy todir="${outputDir}/lang">
 576     <fileset dir="${resourceDir}/lang">
 577       <include name="**.*" />
 578     </fileset>
 579   </copy>
 580   <jar destfile="in.jar" index="true">
 581     <manifest>
 582       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 583       <attribute name="Application-Name" value="JalviewLite" />
 584       <attribute name="Codebase" value="${applet.codebase}" />
 585     </manifest>
 586     <fileset dir="${outputDir}">
 587       <include name="com/**" />
 588       <include name="MCview/**" />
 589       <include name="jalview/**" />
 590       <include name=".build_properties" />
 591       <include name="images/idwidth.gif" />
 592       <include name="images/link.gif" />
 593       <include name="lang/**" />
 594     </fileset>
 595   </jar>
 596 </target>
 597 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 598 </target>
 599 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 600   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 601   <delete file="in.jar" />
 602 </target>
 603 <target name="-obfuscatereally" unless="donotobfuscate">
 604
 605   <path id="obfuscateDeps.path">
 606     <pathelement location="${applet.jre.tools}" />
 607     <pathelement location="appletlib/${jmolJar}" />
 608     <pathelement location="appletlib/${jsonSimple}" />
 609     <pathelement location="appletlib/${javaJson}" />
 610   </path>
 611   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 612
 613   <proguard>
 614     <injar file="in.jar" />
 615     <outjar file="${jalviewLiteJar}" />
 616     <libraryjar refid="obfuscateDeps.path" />
 617     <dontwarn />
 618     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 619       <field access="public" />
 620       <method access="public" />
 621       <constructor access="public" />
 622     </keep>
 623     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 624       <field access="public" />
 625       <method access="public" />
 626       <constructor access="public" />
 627     </keep>
 628     <!--      -libraryjars "${obfuscateDeps}"
 629       -injars      in.jar
 630       -outjars     jalviewApplet.jar
 631       -keep public class jalview.bin.JalviewLite
 632        { public * ; } -->
 633   </proguard>
 634   <delete file="in.jar" />
 635 </target>
 636
 637 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 638   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 639   <delete>
 640     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 641       <include name="*.java" />
 642       <include name="descriptors/*.java" />
 643     </fileset>
 644   </delete>
 645   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 646   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 647   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 648   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 649   <!--
 650                 now build the jalview.binding package with the old schema set
 651                 -->
 652   <delete>
 653     <fileset dir="${sourceDir}/jalview/binding/">
 654       <include name="**" />
 655     </fileset>
 656   </delete>
 657   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 658   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 659   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 660 </target>
 661 <target name="sourcedist" description="create jalview source distribution" depends="init">
 662   <delete file="${source.dist.name}" />
 663   <tar destfile="${source.dist.name}" compression="gzip">
 664     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 665       <include name="LICENSE" />
 666       <include name="README" />
 667       <include name="build.xml" />
 668       <include name="jalview-jalopy.xml" />
 669       <include name="JalviewApplet.jpx" />
 670       <include name="JalviewX.jpx" />
 671       <include name="nbbuild.xml" />
 672       <include name="nbproject/genfiles.properties" />
 673       <include name="nbproject/project.properties" />
 674       <include name="nbproject/project.xml" />
 675       <include name="${sourceDir}/*.java" />
 676       <include name="${sourceDir}/**/*.java" />
 677       <include name="${sourceDir}/**/*.cdr" />
 678       <include name="${libDir}/**/*" />
 679       <include name="${resourceDir}/**/*" />
 680       <include name="${helpDir}/**/*" />
 681       <include name="appletlib/${jmolJar}" />
 682       <exclude name="**/*locales" />
 683       <exclude name="*locales/**" />
 684       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 685       <exclude name="utils/InstallAnywhere/**Build*/**" />
 686       <exclude name="utils/InstallAnywhere/**Build*/**" />
 687       <exclude name="utils/InstallAnywhere/**locale*" />
 688       <exclude name="utils/InstallAnywhere/**locale*/**" />
 689       <include name="${schemaDir}/**/*" />
 690       <include name="utils/**/*" />
 691       <include name="${docDir}/**/*" />
 692       <include name="examples/**/*" />
 693     </tarfileset>
 694   </tar>
 695 </target>
 696 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 697   <copy todir="${packageDir}/examples">
 698     <fileset dir="examples">
 699       <include name="**/*" />
 700       <include name="javascript/*" />
 701       <include name="jmol/*" />
 702     </fileset>
 703     <fileset dir=".">
 704       <include name="${jalviewLiteJar}" />
 705     </fileset>
 706     <fileset dir="appletlib">
 707       <include name="**/*" />
 708     </fileset>
 709   </copy>
 710   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 711   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 712   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 713   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 714     <manifest>
 715       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 716       <!--          <attribute name="Permissions" value="sandbox" /> -->
 717       <!--<attribute name="Trusted-Lib" value="true" /> -->
 718       <attribute name="Codebase" value="${applet.codebase}" />
 719       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 720     </manifest>
 721   </jar>
 722   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 723     <fileset dir="${packageDir}/examples">
 724       <include name="*.jar" />
 725     </fileset>
 726   </signjar>
 727   <presetdef name="ap_applet.jar">
 728     <!-- build a signed applet with 'all-permissions' -
 729                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 730                           JalviewLite+JmolApplet linked sequence/structure fails
 731                           Mixed code warnings are raised
 732                           -->
 733     <jar update="true" index="true">
 734       <manifest>
 735         <attribute name="Application-Name" value="JalviewLite" />
 736         <attribute name="Permissions" value="all-permissions" />
 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="${applet.codebase}" />
 740       </manifest>
 741     </jar>
 742   </presetdef>
 743   <presetdef name="applet.jar">
 744     <!-- build signed applet with sandbox permissions -
 745                           Needs 'param name="permissions' value="sandbox"' in applet tag
 746                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 747                         -->
 748
 749     <jar update="true" index="true">
 750       <manifest>
 751         <attribute name="Application-Name" value="JalviewLite" />
 752         <attribute name="Permissions" value="sandbox" />
 753         <attribute name="Codebase" value="${applet.codebase}" />
 754         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 755         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 756       </manifest>
 757     </jar>
 758   </presetdef>
 759   <presetdef name="tl_applet.jar">
 760     <!-- build signed applet with trusted library/trusted permissions -
 761                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 762                                j1.7_45:
 763                                No mixed code warnings raised
 764                                Jmol/JalviewLite sequence/structure example doesn't link structures
 765                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 766
 767                               -->
 768
 769     <jar update="true" index="true">
 770       <manifest>
 771         <attribute name="Application-Name" value="JalviewLite" />
 772         <attribute name="Permissions" value="all-permissions" />
 773         <attribute name="Codebase" value="${applet.codebase}" />
 774         <attribute name="Trusted-Only" value="true" />
 775         <attribute name="Trusted-Library" value="true" />
 776       </manifest>
 777     </jar>
 778   </presetdef>
 779   <presetdef name="to_applet.jar">
 780     <!-- not fully test variant (yet) -->
 781     <jar update="true" index="true">
 782       <manifest>
 783         <attribute name="Application-Name" value="JalviewLite" />
 784         <attribute name="Permissions" value="all-permissions" />
 785         <attribute name="Codebase" value="${applet.codebase}" />
 786         <attribute name="Trusted-Only" value="true" />
 787       </manifest>
 788     </jar>
 789   </presetdef>
 790   <!-- create differently privileged artefacts -->
 791   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 792   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 793   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 794   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 795   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 796   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 797   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 798   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 799   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 800   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 801   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 802   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 803   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 804   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 805   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 806   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 807   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 808   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 809   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 810   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 811   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 812   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 813   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 814   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 815   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 816   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 817   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 818   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 819   <!-- finally, create manifest for original jars -->
 820   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 821   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 822   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 823   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 824
 825   <!-- todo - write examples/downloads for alternate versions of the applet -->
 826   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 827
 828     <fileset dir="${packageDir}/examples">
 829       <exclude name="u_*.jar" />
 830       <include name="${jalviewLiteJar}" />
 831       <include name="${jmolJar}" />
 832       <include name="${javaJson}" />
 833       <include name="${jsonSimple}" />
 834       <include name="to_${jalviewLiteJar}" />
 835       <include name="to_${jmolJar}" />
 836       <include name="to_${javaJson}" />
 837       <include name="to_${jsonSimple}" />
 838       <include name="tl_${jalviewLiteJar}" />
 839       <include name="tl_${jmolJar}" />
 840       <include name="tl_${javaJson}" />
 841       <include name="tl_${jsonSimple}" />
 842       <include name="ap_${jalviewLiteJar}" />
 843       <include name="ap_${jmolJar}" />
 844       <include name="ap_${javaJson}" />
 845       <include name="ap_${jsonSimple}" />
 846     </fileset>
 847   </signjar>
 848   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 849   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 850   <!-- finally, replace any launchApp servlet tags with a version specification -->
 851   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 852     <replacetoken>
 853       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 854     </replacetoken>
 855     <fileset dir="${packageDir}/examples">
 856       <include name="**/*.html" />
 857     </fileset>
 858   </replace>
 859   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 860     <replacetoken>
 861       <![CDATA[http://www.jalview.org/services/launchApp']]>
 862     </replacetoken>
 863     <fileset dir="${packageDir}/examples">
 864       <include name="**/*.html" />
 865     </fileset>
 866   </replace>
 867
 868 </target>
 869 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 870   <javadoc destdir="${javadocDir}">
 871     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 872     </packageset>
 873   </javadoc>
 874 </target>
 875 </project>