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