build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <project name="jalviewX" default="usage" basedir=".">
  21   <target name="help" depends="usage" />
  22   <target name="usage" depends="init">
  23     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  24     <echo message="Targets include:" />
  25     <echo message="usage - default target, displays this message" />
  26     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  27     <echo message="build - compiles all necessary files for Application" />
  28     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  29     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  30     <echo message="              this needs a keystore and key. 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     <!-- locally valid proxy for signing with external time server -->
  89     <property name="proxyPort" value="80"/>
  90     <property name="proxyHost" value="sqid"/>
  91
  92     <!-- default TestNG groups to run -->
  93     <property name="testng-groups" value="Functional" />
  94
  95     <!-- Don't change anything below here unless you know what you are doing! -->
  96     <!-- Url path for WebStart in JNLP file -->
  97     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  98     <!-- Webstart Image - looked for in resources/images -->
  99     <property name="WebStartImage" value="JalviewLogo_big.png" />
 100     <!-- J2SE version needed for webstart launch -->
 101     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
 102     <property name="j2sev" value="1.7+" />
 103     <!-- Java Compilation settings - source and target javac version -->
 104     <property name="javac.source" value="1.7" />
 105     <property name="javac.target" value="1.7" />
 106
 107     <!-- Permissions for running Java applets and applications. -->
 108     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 109     <property name="application.codebase" value="*.jalview.org" />
 110     <!-- and allowing the applet to be deployed from any URL -->
 111     <!-- 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 -->
 112     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 113     <property name="applet.caller-codebase" value="${applet.codebase}" />
 114
 115     <!-- build directory configuration -->
 116     <property name="libDir" value="lib" />
 117     <property name="resourceDir" value="resources" />
 118     <property name="helpDir" value="help" />
 119     <property name="docDir" value="doc" />
 120     <property name="sourceDir" value="src" />
 121     <property name="schemaDir" value="schemas" />
 122     <property name="outputDir" value="classes" />
 123     <property name="packageDir" value="dist" />
 124     <property name="outputJar" value="jalview.jar" />
 125     <!-- Jalview Applet JMol Jar Dependency -->
 126     <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
 127     <property name="varnaJar" value="VARNAv3-93.jar" />
 128     <property name="jsoup" value="jsoup-1.8.1.jar" />
 129     <property name="jsonSimple" value="json_simple-1.1.jar" />
 130     <property name="javaJson" value="java-json.jar" />
 131     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 132     <property name="reportDir" value="test-reports" />
 133     <property name="testDir" value="test" />
 134     <property name="testOutputDir" value="tests" />
 135     <!-- switch to indicate if we should obfuscate jalviewLite -->
 136     <!-- <property name="donotobfuscate" value="true"/> -->
 137     <!-- switch to exclude associations from generated jnlp files -->
 138     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 139
 140     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 141     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 142     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 143     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 144     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 145     <property name="WSInterf" value="MsaWS" />
 146     <property name="wsdl.Namespace" value="vamsas" />
 147     <property name="wsdl.ClientNS" value="ext.vamsas" />
 148     <!-- the class path for building the application -->
 149     <path id="build.classpath">
 150       <fileset dir="utils">
 151         <include name="*.jar" />
 152         <include name="**/*.jar" />
 153       </fileset>
 154       <fileset dir="${libDir}">
 155         <include name="*.jar" />
 156         <include name="**/*.jar" />
 157       </fileset>
 158       <fileset dir="${java.home}/lib">
 159         <include name="plugin.jar" />
 160       </fileset>
 161       <fileset dir="appletlib">
 162         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 163                                 -->
 164         <include name="${jmolJar}" />
 165         <include name="${varnaJar}" />
 166       </fileset>
 167     </path>
 168     <path id="test.classpath">
 169       <pathelement path="${outputDir}" />
 170       <path refid="build.classpath" />
 171     </path>
 172     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 173     <!-- The Location of the java 1.1.8 jdk -->
 174     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
 175     <property name="java118.home" value="${java.home}" />
 176     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 177                 -->
 178     <!-- jre for 1.4 version -->
 179     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
 180
 181     <!-- the classpath for building the 1.1 applet -->
 182     <path id="jalviewlite.deps">
 183       <fileset dir="${java118.home}">
 184         <include name="lib/classes.zip" />
 185       </fileset>
 186       <fileset dir="${java.home}/lib">
 187         <include name="plugin.jar" />
 188       </fileset>
 189       <pathelement location="appletlib/${jmolJar}" />
 190       <pathelement location="lib/${varnaJar}" />
 191       <pathelement location="appletlib/${jsoup}" />
 192       <pathelement location="appletlib/${jsonSimple}" />
 193       <pathelement location="appletlib/${javaJson}" />
 194
 195     </path>
 196     <!-- default location for outputting javadoc -->
 197     <property name="javadocDir" value="${packageDir}/javadoc" />
 198   </target>
 199
 200
 201   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 202   <target name="buildPropertiesFile" depends="init">
 203     <tstamp prefix="build">
 204       <format property="date" pattern="dd MMMM yyyy" />
 205     </tstamp>
 206     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 207       <arg value="rev-parse" />
 208       <arg value="--short" />
 209       <arg value="HEAD" />
 210     </exec>
 211     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 212       <arg value="rev-parse" />
 213       <arg value="--abbrev-ref" />
 214       <arg value="HEAD" />
 215     </exec>
 216     <properties file="${outputDir}/.build_properties">
 217       <header>
 218           ---Jalview Build Details---
 219         </header>
 220       <property name="VERSION" value="${JALVIEW_VERSION}" />
 221       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 222       <property name="BUILD_DATE" value="${build.date}" />
 223     </properties>
 224   </target>
 225
 226
 227   <target name="clean" depends="init">
 228     <!-- not efficient yet. -->
 229     <delete dir="${outputDir}" includes="*,**/*" />
 230   </target>
 231
 232   <target name="distclean" depends="init, clean">
 233
 234     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 235     <delete>
 236       <fileset dir=".">
 237         <include name="${outputJar}" />
 238         <include name="#*#" />
 239         <include name="#*.*#" />
 240         <include name="**/#*#" />
 241         <include name="**/#*.*#" />
 242         <include name="*~" />
 243         <include name="*.*~" />
 244         <include name="**/*~" />
 245         <include name="**/*.*~" />
 246       </fileset>
 247     </delete>
 248   </target>
 249
 250   <target name="prepare" depends="init">
 251     <mkdir dir="${outputDir}" />
 252     <copy todir="${outputDir}">
 253       <fileset dir=".">
 254         <include name="${docDir}/**/*.*" />
 255         <include name="${helpDir}/**/*.*" />
 256         <include name="${libDir}/*.jar" />
 257       </fileset>
 258       <fileset dir="${resourceDir}">
 259         <include name="**/*.*" />
 260       </fileset>
 261     </copy>
 262   </target>
 263
 264   <target name="build" depends="prepare">
 265     <!-- not efficient yet. -->
 266     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 267       <exclude name="jalview/*applet*" />
 268       <exclude name="jalview/appletgui/**" />
 269       <exclude name="com/stevesoft/**" />
 270     </javac>
 271   </target>
 272
 273
 274   <target name="testclean" depends="init">
 275     <delete dir="${testOutputDir}" includes="*,**/*" />
 276   </target>
 277
 278   <target name="prepareTests" depends="init,testclean">
 279     <mkdir dir="${testOutputDir}" />
 280   </target>
 281
 282   <target name="buildTests" depends="build,buildindices,prepareTests">
 283     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 284     </javac>
 285   </target>
 286
 287   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 288
 289   <target name="testng" depends="buildTests">
 290     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 291       verbose="2">
 292       <classpath>
 293         <pathelement location="${testOutputDir}" />
 294         <path refid="test.classpath" />
 295       </classpath>
 296       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 297     </testng>
 298   </target>
 299
 300   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 301     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 302       <arg line="html" />
 303     </java>
 304   </target>
 305
 306   <target name="preparejnlp" depends="makedist">
 307     <copy todir="${packageDir}">
 308       <fileset dir="${resourceDir}/images">
 309         <include name="${WebStartImage}" />
 310       </fileset>
 311     </copy>
 312
 313     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 314
 315     <!-- create a dummy jar which will eventually contain the jnlp template -->
 316     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 317       <fileset dir="${packageDir}">
 318         <include name="jalview.jar" />
 319       </fileset>
 320     </jar>
 321
 322     <mkdir dir="${packageDir}/JNLP-INF" />
 323     <antcall target="writejnlpf">
 324       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 325       <param name="inih" value="*" />
 326       <param name="maxh" value="*" />
 327     </antcall>
 328
 329     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 330       <fileset dir="${packageDir}">
 331         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 332       </fileset>
 333     </jar>
 334
 335     <antcall target="writejnlpf">
 336       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 337       <param name="inih" value="10M" />
 338       <param name="maxh" value="256M" />
 339     </antcall>
 340
 341     <antcall target="writejnlpf">
 342       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 343       <param name="inih" value="128M" />
 344       <param name="maxh" value="512M" />
 345     </antcall>
 346
 347     <antcall target="writejnlpf">
 348       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 349       <param name="inih" value="256M" />
 350       <param name="maxh" value="1024M" />
 351     </antcall>
 352
 353     <!-- finally, need to postprocess to add in associations at end of 'information' element
 354
 355                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 356
 357                 </xslt>
 358
 359
 360                         -->
 361     <!--
 362                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 363         <association mime-type="application-x/ext-file" extensions="fasta"/>
 364         <association mime-type="application-x/ext-file" extensions="mfa"/>
 365         <association mime-type="application-x/ext-file" extensions="fastq"/>
 366         <association mime-type="application-x/ext-file" extensions="blc"/>
 367         <association mime-type="application-x/ext-file" extensions="msf"/>
 368         <association mime-type="application-x/ext-file" extensions="pfam"/>
 369         <association mime-type="application-x/ext-file" extensions="aln"/>
 370         <association mime-type="application-x/ext-file" extensions="pir"/>
 371         <association mime-type="application-x/ext-file" extensions="amsa"/>
 372         <association mime-type="application-x/ext-file" extensions="stk"/>
 373         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 374   </target>
 375
 376   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
 377     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA"
 378       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 379       <fileset dir="${packageDir}">
 380         <include name="*.jar" />
 381       </fileset>
 382     </signjar>
 383   </target>
 384   <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
 385     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 386       <fileset dir="${packageDir}">
 387         <include name="*.jar" />
 388       </fileset>
 389     </signjar>
 390   </target>
 391
 392   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 393     <!-- and sign the jars -->
 394     <!-- the default keystore details might need to be edited here -->
 395   </target>
 396
 397   <target name="runenv" depends="init">
 398     <path id="run.classpath">
 399       <pathelement location="${outputDir}" />
 400       <fileset dir="${outputDir}">
 401         <include name="${libDir}/*.jar" />
 402       </fileset>
 403     </path>
 404     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 405
 406     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 407       </echo>
 408   </target>
 409
 410   <target name="-generatejnlpf">
 411     <presetdef name="jnlpf">
 412       <jnlp codebase="${WebStartLocation}">
 413         <information>
 414           <title>Jalview</title>
 415           <vendor>The Barton Group</vendor>
 416           <homepage href="http://www.jalview.org" />
 417           <description>Jalview Multiple Alignment Editor</description>
 418           <description kind="short">Jalview</description>
 419           <icon href="${WebStartImage}" />
 420           <offline_allowed />
 421         </information>
 422         <resources>
 423           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 424           <jar main="true" href="jalview.jar"/>
 425           <fileset dir="${packageDir}">
 426             <exclude name="jalview.jar" />
 427             <include name="*.jar" />
 428             <include name="*_*.jar" />
 429             <exclude name="*jnilib.jar" />
 430           </fileset>
 431           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 432         </resources>
 433         <resources os="Mac OS X">
 434           <fileset dir="${packageDir}">
 435             <include name="*quaqua*.jnilib.jar" />
 436           </fileset>
 437         </resources>
 438
 439         <application_desc main_class="jalview.bin.Jalview">
 440         </application_desc>
 441         <security>
 442           <all_permissions />
 443         </security>
 444       </jnlp>
 445     </presetdef>
 446
 447     <jnlpf toFile="${jnlpFile}" />
 448
 449   </target>
 450
 451   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 452     <echo message="Not adding JNLP File Associations" />
 453   </target>
 454
 455   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 456     <replace file="${jnlpFile}">
 457       <replacetoken>
 458         <![CDATA[</information>]]></replacetoken>
 459       <replacevalue>
 460         <![CDATA[
 461           <association mime-type="application-x/ext-file" extensions="fa" />
 462         <association mime-type="application-x/ext-file" extensions="fasta" />
 463         <association mime-type="application-x/ext-file" extensions="mfa" />
 464         <association mime-type="application-x/ext-file" extensions="fastq" />
 465         <association mime-type="application-x/ext-file" extensions="blc" />
 466         <association mime-type="application-x/ext-file" extensions="msf" />
 467         <association mime-type="application-x/ext-file" extensions="pfam" />
 468         <association mime-type="application-x/ext-file" extensions="aln"/>
 469         <association mime-type="application-x/ext-file" extensions="pir"/>
 470         <association mime-type="application-x/ext-file" extensions="amsa"/>
 471         <association mime-type="application-x/ext-file" extensions="stk"/>
 472         <association mime-type="application-x/ext-file" extensions="jvp"/>
 473       </information>]]></replacevalue>
 474   </replace>
 475   <echo message="Added file associations to JNLP file" />
 476 </target>
 477 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 478 </target>
 479
 480 <target name="buildextclients" depends="init">
 481   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 482   <condition property="dontextbuild">
 483     <equals arg1="n" arg2="${doextbuild.response}" />
 484   </condition>
 485   <condition property="dontextbuild">
 486     <equals arg1="N" arg2="${doextbuild.response}" />
 487   </condition>
 488   <fail if="dontextbuild">
 489         Build External Client Code process aborted by user. Jalview source is unchanged.
 490       </fail>
 491   <!-- Currently, this doesn't happen automatically.
 492      1. Run WSDL2Java as below, which generates an ext.vamsas +
 493      vamsas.<datapackages> fileset.
 494      2. refactor ext.vamsas.SpecificserviceWS* to
 495      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 496      3. Update the jalview.ws.*WServices classes to reflect the
 497      interface type, and all locations of this wsdl type that Jalview
 498      might be using.
 499
 500 -->
 501   <path id="axisbuild">
 502     <path refid="build.classpath" />
 503   </path>
 504   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 505   <move todir="./bak">
 506     <fileset dir="${sourceDir}" id="client">
 507       <include name="${wsdl.ClientNS}/*.*" />
 508     </fileset>
 509   </move>
 510
 511   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 512     <mappingSet>
 513       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 514       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 515     </mappingSet>
 516   </axis-wsdl2java>
 517 </target>
 518
 519 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 520   <!-- make the package jar if not already existing -->
 521   <mkdir dir="${packageDir}" />
 522   <!-- clean dir if it already existed -->
 523   <delete>
 524     <fileset dir="${packageDir}">
 525       <include name="*.jar" />
 526     </fileset>
 527   </delete>
 528   <jar destfile="${packageDir}/${outputJar}" index="true">
 529     <manifest>
 530       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 531       <attribute name="Permissions" value="all-permissions" />
 532       <attribute name="Application-Name" value="Jalview Desktop" />
 533       <attribute name="Codebase" value="${application.codebase}" />
 534     </manifest>
 535     <fileset dir="${outputDir}/">
 536       <exclude name="cache*/**" />
 537       <exclude name="*.jar" />
 538       <exclude name="*.jar.*" />
 539       <exclude name="**/*.jar" />
 540       <exclude name="**/*.jar.*" />
 541     </fileset>
 542   </jar>
 543
 544   <copy toDir="${packageDir}" flatten="true">
 545     <fileset dir="${outputDir}">
 546       <include name="*.jar" />
 547       <include name="**/*.jar" />
 548     </fileset>
 549   </copy>
 550 </target>
 551
 552
 553 <!-- jalopy code reformatter -->
 554 <target name="sourcescrub" depends="init,build">
 555   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 556     <fileset dir="${sourceDir}">
 557       <include name="*.java" />
 558       <include name="**/*.java" />
 559       <include name="**/**/*.java" />
 560     </fileset>
 561   </jalopy>
 562 </target>
 563
 564
 565
 566 <!-- Compile, package and obfuscate Jalview Applet -->
 567 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 568
 569 <target name="compileApplet" depends="init,clean">
 570   <mkdir dir="${outputDir}" />
 571   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so" />
 572 </target>
 573
 574 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 575   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 576   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 577   <copy todir="${outputDir}/lang">
 578     <fileset dir="${resourceDir}/lang">
 579       <include name="**.*" />
 580     </fileset>
 581   </copy>
 582   <jar destfile="in.jar" index="true">
 583     <manifest>
 584       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 585       <attribute name="Application-Name" value="JalviewLite" />
 586       <attribute name="Codebase" value="${applet.codebase}" />
 587     </manifest>
 588     <fileset dir="${outputDir}">
 589       <include name="com/**" />
 590       <include name="MCview/**" />
 591       <include name="jalview/**" />
 592       <include name=".build_properties" />
 593       <include name="images/idwidth.gif" />
 594       <include name="images/link.gif" />
 595       <include name="lang/**" />
 596     </fileset>
 597   </jar>
 598 </target>
 599 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 600 </target>
 601 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 602   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 603   <delete file="in.jar" />
 604 </target>
 605 <target name="-obfuscatereally" unless="donotobfuscate">
 606
 607   <path id="obfuscateDeps.path">
 608     <pathelement location="${applet.jre.tools}" />
 609     <pathelement location="appletlib/${jmolJar}" />
 610     <pathelement location="lib/${varnaJar}" />
 611     <pathelement location="appletlib/${jsoup}" />
 612     <pathelement location="appletlib/${jsonSimple}" />
 613     <pathelement location="appletlib/${javaJson}" />
 614         <fileset dir="${java.home}/lib">
 615         <include name="plugin.jar" />
 616     </fileset>
 617   </path>
 618   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 619
 620   <proguard verbose="true" >
 621     <injar file="in.jar" />
 622     <outjar file="${jalviewLiteJar}" />
 623     <libraryjar refid="obfuscateDeps.path" />
 624     <dontwarn />
 625     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 626       <field access="public" />
 627       <method access="public" />
 628       <constructor access="public" />
 629     </keep>
 630     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 631       <field access="public" />
 632       <method access="public" />
 633       <constructor access="public" />
 634     </keep>
 635
 636     <keep name="jalview.json.binding**">
 637       <constructor/>
 638       <method name="*"/>
 639     </keep>
 640
 641     <keep access="public" type="class" name="MCview.PDBfile">
 642       <field access="public" />
 643       <method access="public" />
 644       <constructor access="public" />
 645     </keep>
 646
 647     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 648       <field access="public" />
 649       <method access="public" />
 650       <constructor access="public" />
 651     </keep>
 652
 653     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 654       <field access="public" />
 655       <method access="public" />
 656       <constructor access="public" />
 657     </keep>
 658
 659
 660     <!--      -libraryjars "${obfuscateDeps}"
 661       -injars      in.jar
 662       -outjars     jalviewApplet.jar
 663       -keep public class jalview.bin.JalviewLite
 664        { public * ; } -->
 665   </proguard>
 666   <delete file="in.jar" />
 667 </target>
 668
 669 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 670   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 671   <delete>
 672     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 673       <include name="*.java" />
 674       <include name="descriptors/*.java" />
 675     </fileset>
 676   </delete>
 677   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 678   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 679   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 680   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 681   <!--
 682                 now build the jalview.binding package with the old schema set
 683                 -->
 684   <delete>
 685     <fileset dir="${sourceDir}/jalview/binding/">
 686       <include name="**" />
 687     </fileset>
 688   </delete>
 689   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 690   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 691   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 692 </target>
 693 <target name="sourcedist" description="create jalview source distribution" depends="init">
 694   <delete file="${source.dist.name}" />
 695   <tar destfile="${source.dist.name}" compression="gzip">
 696     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 697       <include name="LICENSE" />
 698       <include name="README" />
 699       <include name="build.xml" />
 700       <include name="jalview-jalopy.xml" />
 701       <include name="JalviewApplet.jpx" />
 702       <include name="JalviewX.jpx" />
 703       <include name="nbbuild.xml" />
 704       <include name="nbproject/genfiles.properties" />
 705       <include name="nbproject/project.properties" />
 706       <include name="nbproject/project.xml" />
 707       <include name="${sourceDir}/*.java" />
 708       <include name="${sourceDir}/**/*.java" />
 709       <include name="${sourceDir}/**/*.cdr" />
 710       <include name="${libDir}/**/*" />
 711       <include name="${resourceDir}/**/*" />
 712       <include name="${helpDir}/**/*" />
 713       <include name="appletlib/${jmolJar}" />
 714       <include name="appletlib/${jsonSimple}" />
 715       <include name="appletlib/${javaJson}" />
 716       <exclude name="**/*locales" />
 717       <exclude name="*locales/**" />
 718       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 719       <exclude name="utils/InstallAnywhere/**Build*/**" />
 720       <exclude name="utils/InstallAnywhere/**Build*/**" />
 721       <exclude name="utils/InstallAnywhere/**locale*" />
 722       <exclude name="utils/InstallAnywhere/**locale*/**" />
 723       <include name="${schemaDir}/**/*" />
 724       <include name="utils/**/*" />
 725       <include name="${docDir}/**/*" />
 726       <include name="examples/**/*" />
 727     </tarfileset>
 728   </tar>
 729 </target>
 730 <target name="prepubapplet_1" depends="makeApplet">
 731   <copy todir="${packageDir}/examples">
 732     <fileset dir="examples">
 733       <include name="**/*" />
 734       <include name="javascript/*" />
 735       <include name="jmol/*" />
 736     </fileset>
 737     <fileset dir=".">
 738       <include name="${jalviewLiteJar}" />
 739     </fileset>
 740     <fileset dir="appletlib">
 741       <include name="**/*" />
 742     </fileset>
 743   </copy>
 744   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 745   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 746   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 747   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 748     <manifest>
 749       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 750       <!--          <attribute name="Permissions" value="sandbox" /> -->
 751       <!--<attribute name="Trusted-Lib" value="true" /> -->
 752       <attribute name="Codebase" value="${applet.codebase}" />
 753       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 754     </manifest>
 755   </jar>
 756
 757   <presetdef name="ap_applet.jar">
 758     <!-- build a signed applet with 'all-permissions' -
 759                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 760                           JalviewLite+JmolApplet linked sequence/structure fails
 761                           Mixed code warnings are raised
 762                           -->
 763     <jar update="true" index="true">
 764       <manifest>
 765         <attribute name="Application-Name" value="JalviewLite" />
 766         <attribute name="Permissions" value="all-permissions" />
 767         <attribute name="Codebase" value="${applet.codebase}" />
 768         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 769         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 770       </manifest>
 771     </jar>
 772   </presetdef>
 773   <presetdef name="applet.jar">
 774     <!-- build signed applet with sandbox permissions -
 775                           Needs 'param name="permissions' value="sandbox"' in applet tag
 776                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 777                         -->
 778
 779     <jar update="true" index="true">
 780       <manifest>
 781         <attribute name="Application-Name" value="JalviewLite" />
 782         <attribute name="Permissions" value="sandbox" />
 783         <attribute name="Codebase" value="${applet.codebase}" />
 784         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 785         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 786       </manifest>
 787     </jar>
 788   </presetdef>
 789   <presetdef name="tl_applet.jar">
 790     <!-- build signed applet with trusted library/trusted permissions -
 791                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 792                                j1.7_45:
 793                                No mixed code warnings raised
 794                                Jmol/JalviewLite sequence/structure example doesn't link structures
 795                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 796
 797                               -->
 798
 799     <jar update="true" index="true">
 800       <manifest>
 801         <attribute name="Application-Name" value="JalviewLite" />
 802         <attribute name="Permissions" value="all-permissions" />
 803         <attribute name="Codebase" value="${applet.codebase}" />
 804         <attribute name="Trusted-Only" value="true" />
 805         <attribute name="Trusted-Library" value="true" />
 806       </manifest>
 807     </jar>
 808   </presetdef>
 809   <presetdef name="to_applet.jar">
 810     <!-- not fully test variant (yet) -->
 811     <jar update="true" index="true">
 812       <manifest>
 813         <attribute name="Application-Name" value="JalviewLite" />
 814         <attribute name="Permissions" value="all-permissions" />
 815         <attribute name="Codebase" value="${applet.codebase}" />
 816         <attribute name="Trusted-Only" value="true" />
 817       </manifest>
 818     </jar>
 819   </presetdef>
 820   <!-- create differently privileged artefacts -->
 821   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 822   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 823   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 824   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 825   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 826   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 827   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 828   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 829   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 830   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 831   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 832   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 833   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 834   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 835   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 836   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 837   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 838   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 839   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 840   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 841   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 842   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 843   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 844   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 845   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 846   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 847   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 848   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 849   <!-- finally, create manifest for original jars -->
 850   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 851   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 852   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 853   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 854
 855   <!-- todo - write examples/downloads for alternate versions of the applet
 856     probably don't need to do this now since we don't have alternate versions anymore !-->
 857 </target>
 858 <target name="-signapplet" depends="prepubapplet_1">
 859   <fileset id="signappletjarset" dir="${packageDir}/examples">
 860     <exclude name="u_*.jar" />
 861     <include name="${jalviewLiteJar}" />
 862     <include name="${jmolJar}" />
 863     <include name="${javaJson}" />
 864     <include name="${jsonSimple}" />
 865     <include name="to_${jalviewLiteJar}" />
 866     <include name="to_${jmolJar}" />
 867     <include name="to_${javaJson}" />
 868     <include name="to_${jsonSimple}" />
 869     <include name="tl_${jalviewLiteJar}" />
 870     <include name="tl_${jmolJar}" />
 871     <include name="tl_${javaJson}" />
 872     <include name="tl_${jsonSimple}" />
 873     <include name="ap_${jalviewLiteJar}" />
 874     <include name="ap_${jmolJar}" />
 875     <include name="ap_${javaJson}" />
 876     <include name="ap_${jsonSimple}" />
 877   </fileset>
 878 </target>
 879 <target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
 880   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 881     <fileset refid="signappletjarset" />
 882   </signjar>
 883 </target>
 884
 885 <target name="-signapplettsa" if="timestamp" depends="-signapplet">
 886   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 887     <fileset refid="signappletjarset" />
 888   </signjar>
 889 </target>
 890
 891 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
 892
 893 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 894
 895   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 896   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 897   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 898   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 899   <!-- finally, replace any launchApp servlet tags with a version specification -->
 900   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 901     <replacetoken>
 902       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 903     </replacetoken>
 904     <fileset dir="${packageDir}/examples">
 905       <include name="**/*.html" />
 906     </fileset>
 907   </replace>
 908   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 909     <replacetoken>
 910       <![CDATA[http://www.jalview.org/services/launchApp']]>
 911     </replacetoken>
 912     <fileset dir="${packageDir}/examples">
 913       <include name="**/*.html" />
 914     </fileset>
 915   </replace>
 916
 917 </target>
 918 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 919   <javadoc destdir="${javadocDir}">
 920     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 921     </packageset>
 922   </javadoc>
 923 </target>
 924 </project>