build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <project name="jalviewX" default="usage" basedir=".">
  21   <target name="help" depends="usage" />
  22   <target name="usage" depends="init">
  23     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  24     <echo message="Targets include:" />
  25     <echo message="usage - default target, displays this message" />
  26     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  27     <echo message="build - compiles all necessary files for Application" />
  28     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  29     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  30     <echo message="              this needs a keystore and key. See docs/building.html for more information." />
  31     <echo message="compileApplet - compiles all necessary files for Applet" />
  32     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  33     <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
  34     <echo message="      you can specify particular test groups as a list via -Dtestng-groups=" />
  35     <echo message="See docs/building.html and the comments in build file for other targets." />
  36     <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  37     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  38   </target>
  39
  40
  41   <!-- utils is a class path to additional utilities needed for
  42     building docs, jars and webstart stuff -->
  43   <!--
  44         Userdefined build property defaults
  45
  46         wsdl.server list (plus namespace mapping info ???)  - also want
  47                 ... to make this a dynamically generatable property
  48         WebStart Location
  49         Build location - provide a temporary root for speed
  50         jarsigner keystore and info
  51         Jakarta and axis classpath ?
  52         Default argument for starting Jalview (if it exists).
  53
  54 -->
  55
  56   <target name="init">
  57     <path id="axis.classpath">
  58       <!-->
  59       <fileset dir="/usr/local/axis/lib">
  60         <include name="**/*.jar" />
  61       </fileset>
  62       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  63         <include name="**/*.jar"/>
  64         <include name="*.jar"/>
  65       </fileset> -->
  66       </path>
  67
  68     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  69     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  70
  71     <property name="INSTALLATION" value="Source" />
  72
  73     <!-- 2.4 (VAMSAS)" -->
  74     <!-- Include debugging information in javac true or false -->
  75     <property name="javac.debug" value="true" />
  76
  77     <!-- JarSigner Key Store for Webstart Distribution -->
  78     <property name="jalview.keystore" value="./keys/.keystore" />
  79     <!-- Keystore Password -->
  80     <property name="jalview.keystore.pass" value="alignmentisfun" />
  81     <!-- Key Name -->
  82     <property name="jalview.key" value="jalview" />
  83     <!-- Key Password -->
  84     <property name="jalview.key.pass" value="alignmentisfun" />
  85
  86     <property name="testng-groups" value="Functional"/>
  87
  88     <!-- Don't change anything below here unless you know what you are doing! -->
  89     <!-- Url path for WebStart in JNLP file -->
  90     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  91     <!-- Webstart Image - looked for in resources/images -->
  92     <property name="WebStartImage" value="JalviewLogo_big.png"/>
  93     <!-- J2SE version needed for webstart launch -->
  94     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  95     <property name="j2sev" value="1.7+"/>
  96         <!-- Java Compilation settings - source and target javac version -->
  97         <property name="javac.source" value="1.7"/>
  98         <property name="javac.target" value="1.7"/>
  99
 100     <!-- Permissions for running Java applets and applications. -->
 101     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 102     <property name="application.codebase" value="*.jalview.org" />
 103     <!-- and allowing the applet to be deployed from any URL -->
 104     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
 105     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 106     <property name="applet.caller-codebase" value="${applet.codebase}" />
 107
 108     <!-- build directory configuration -->
 109     <property name="libDir" value="lib" />
 110     <property name="resourceDir" value="resources" />
 111     <property name="helpDir" value="help" />
 112     <property name="docDir" value="doc" />
 113     <property name="sourceDir" value="src" />
 114     <property name="schemaDir" value="schemas" />
 115     <property name="outputDir" value="classes" />
 116     <property name="packageDir" value="dist" />
 117     <property name="outputJar" value="jalview.jar" />
 118     <!-- Jalview Applet JMol Jar Dependency -->
 119     <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
 120     <property name="varnaJar" value="VARNAv3-93.jar" />
 121     <property name="jsoup" value="jsoup-1.8.1.jar" />
 122     <property name="jsonSimple" value="json_simple-1.1.jar" />
 123     <property name="javaJson" value="java-json.jar" />
 124     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 125         <property name="reportDir" value="test-reports" />
 126         <property name="testDir" value="test" />
 127         <property name="testOutputDir" value="tests" />
 128     <!-- switch to indicate if we should obfuscate jalviewLite -->
 129     <!-- <property name="donotobfuscate" value="true"/> -->
 130     <!-- switch to exclude associations from generated jnlp files -->
 131     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 132
 133     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 134     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 135     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 136     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 137     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 138     <property name="WSInterf" value="MsaWS" />
 139     <property name="wsdl.Namespace" value="vamsas" />
 140     <property name="wsdl.ClientNS" value="ext.vamsas" />
 141     <!-- the class path for building the application -->
 142     <path id="build.classpath">
 143       <fileset dir="utils">
 144         <include name="*.jar" />
 145         <include name="**/*.jar" />
 146       </fileset>
 147       <fileset dir="${libDir}">
 148         <include name="*.jar" />
 149         <include name="**/*.jar" />
 150       </fileset>
 151       <fileset dir="${java.home}/lib">
 152         <include name="plugin.jar"/>
 153       </fileset>
 154       <fileset dir="appletlib">
 155         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 156                                 -->
 157         <include name="${jmolJar}" />
 158         <include name="${varnaJar}" />
 159       </fileset>
 160
 161     </path>
 162     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 163     <!-- The Location of the java 1.1.8 jdk -->
 164     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
 165     <property name="java118.home" value="${java.home}" />
 166     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 167                 -->
 168     <!-- jre for 1.4 version -->
 169     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 170
 171     <!-- the classpath for building the 1.1 applet -->
 172     <path id="jalviewlite.deps">
 173       <fileset dir="${java118.home}">
 174         <include name="lib/classes.zip" />
 175       </fileset>
 176       <fileset dir="${java.home}/lib">
 177         <include name="plugin.jar"/>
 178       </fileset>
 179       <pathelement location="appletlib/${jmolJar}" />
 180       <pathelement location="lib/${varnaJar}" />
 181       <pathelement location="lib/${jsoup}" />
 182       <pathelement location="lib/${jsonSimple}" />
 183       <pathelement location="lib/${javaJson}" />
 184
 185     </path>
 186     <!-- default location for outputting javadoc -->
 187     <property name="javadocDir" value="${packageDir}/javadoc"/>
 188   </target>
 189
 190
 191   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 192   <target name="buildPropertiesFile" depends="init">
 193     <tstamp prefix="build">
 194       <format property="date" pattern="dd MMMM yyyy" />
 195     </tstamp>
 196     <exec executable="/usr/bin/git" outputproperty="git.commit"  failifexecutionfails="false">
 197       <arg value="rev-parse"/>
 198       <arg value="--short"/>
 199       <arg value="HEAD"/>
 200     </exec>
 201     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 202       <arg value="rev-parse"/>
 203       <arg value="--abbrev-ref"/>
 204       <arg value="HEAD"/>
 205     </exec>
 206     <properties file="${outputDir}/.build_properties">
 207       <header>
 208           ---Jalview Build Details---
 209         </header>
 210       <property name="VERSION" value="${JALVIEW_VERSION}" />
 211       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 212       <property name="BUILD_DATE" value="${build.date}" />
 213     </properties>
 214   </target>
 215
 216
 217   <target name="clean" depends="init">
 218     <!-- not efficient yet. -->
 219     <delete dir="${outputDir}" includes="*,**/*"/>
 220   </target>
 221
 222   <target name="distclean" depends="init, clean">
 223
 224     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 225     <delete>
 226       <fileset dir=".">
 227         <include name="${outputJar}" />
 228         <include name="#*#" />
 229         <include name="#*.*#" />
 230         <include name="**/#*#" />
 231         <include name="**/#*.*#" />
 232         <include name="*~" />
 233         <include name="*.*~" />
 234         <include name="**/*~" />
 235         <include name="**/*.*~" />
 236       </fileset>
 237     </delete>
 238   </target>
 239
 240   <target name="prepare" depends="init">
 241     <mkdir dir="${outputDir}" />
 242     <copy todir="${outputDir}">
 243       <fileset dir=".">
 244         <include name="${docDir}/**/*.*" />
 245         <include name="${helpDir}/**/*.*" />
 246         <include name="${libDir}/*.jar" />
 247       </fileset>
 248       <fileset dir="${resourceDir}">
 249         <include name="**/*.*" />
 250       </fileset>
 251     </copy>
 252   </target>
 253
 254   <target name="build" depends="prepare">
 255     <!-- not efficient yet. -->
 256     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 257       <exclude name="jalview/*applet*" />
 258       <exclude name="jalview/appletgui/**" />
 259       <exclude name="com/stevesoft/**" />
 260     </javac>
 261   </target>
 262
 263
 264   <target name="testclean" depends="init">
 265     <delete dir="${testOutputDir}" includes="*,**/*"/>
 266   </target>
 267
 268   <target name="prepareTests" depends="init">
 269         <mkdir dir="${testOutputDir}" />
 270         <copy todir="${testOutputDir}">
 271                 <fileset dir=".">
 272                         <include name="${docDir}/**/*.*" />
 273                         <include name="${helpDir}/**/*.*" />
 274                         <include name="${libDir}/*.jar" />
 275                 </fileset>
 276                 <fileset dir="${resourceDir}">
 277                         <include name="**/*.*" />
 278                 </fileset>
 279         </copy>
 280   </target>
 281
 282   <target name="buildTests" depends="prepareTests">
 283         <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${testOutputDir}"
 284                 debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
 285         </javac>
 286         <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}"
 287                 debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
 288         </javac>
 289   </target>
 290
 291   <taskdef name="testng" classname="org.testng.TestNGAntTask" >
 292         <classpath location="utils/testnglibs/testng.jar" />
 293   </taskdef>
 294
 295   <target name="testng" depends="buildTests">
 296         <testng classpathref="build.classpath" outputDir="${reportDir}"
 297                 haltOnFailure="false">
 298                 <classpath location="${testOutputDir}" />
 299                 <xmlfileset dir="utils" includes="jalview_testng.xml" />
 300         </testng>
 301   </target>
 302
 303   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 304     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 305       <arg line="html" />
 306     </java>
 307   </target>
 308
 309   <target name="makefulldist" depends="makedist">
 310     <copy todir="${packageDir}">
 311       <fileset dir="${resourceDir}/images">
 312         <include name="${WebStartImage}"/>
 313       </fileset>
 314     </copy>
 315
 316     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 317
 318     <!-- create a dummy jar which will eventually contain the jnlp template -->
 319     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 320       <fileset dir="${packageDir}">
 321         <include name="jalview.jar" />
 322       </fileset>
 323     </jar>
 324
 325     <mkdir dir="${packageDir}/JNLP-INF"/>
 326     <antcall target="writejnlpf">
 327       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 328       <param name="inih" value="*" />
 329       <param name="maxh" value="*"/>
 330     </antcall>
 331
 332     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 333       <fileset dir="${packageDir}">
 334         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 335       </fileset>
 336     </jar>
 337
 338     <antcall target="writejnlpf">
 339       <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 340       <param name="inih" value="10M" />
 341       <param name="maxh" value="256M"/>
 342     </antcall>
 343
 344     <antcall target="writejnlpf">
 345       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 346       <param name="inih" value="128M" />
 347       <param name="maxh" value="512M"/>
 348     </antcall>
 349
 350     <antcall target="writejnlpf">
 351       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 352       <param name="inih" value="256M" />
 353       <param name="maxh" value="1024M"/>
 354     </antcall>
 355
 356     <!-- finally, need to postprocess to add in associations at end of 'information' element
 357
 358                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 359
 360                 </xslt>
 361
 362
 363                         -->
 364     <!--
 365                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 366         <association mime-type="application-x/ext-file" extensions="fasta"/>
 367         <association mime-type="application-x/ext-file" extensions="mfa"/>
 368         <association mime-type="application-x/ext-file" extensions="fastq"/>
 369         <association mime-type="application-x/ext-file" extensions="blc"/>
 370         <association mime-type="application-x/ext-file" extensions="msf"/>
 371         <association mime-type="application-x/ext-file" extensions="pfam"/>
 372         <association mime-type="application-x/ext-file" extensions="aln"/>
 373         <association mime-type="application-x/ext-file" extensions="pir"/>
 374         <association mime-type="application-x/ext-file" extensions="amsa"/>
 375         <association mime-type="application-x/ext-file" extensions="stk"/>
 376         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 377     <!-- and sign the jars -->
 378     <!-- the default keystore details might need to be edited here -->
 379     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 380       <fileset dir="${packageDir}">
 381         <include name="*.jar" />
 382       </fileset>
 383     </signjar>
 384   </target>
 385
 386   <target name="runenv" depends="init">
 387     <path id="run.classpath">
 388       <pathelement location="${outputDir}" />
 389       <fileset dir="${outputDir}">
 390         <include name="${libDir}/*.jar" />
 391       </fileset>
 392     </path>
 393     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 394
 395     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 396       </echo>
 397   </target>
 398
 399   <target name="-generatejnlpf">
 400     <presetdef name="jnlpf">
 401       <jnlp codebase="${WebStartLocation}">
 402         <information>
 403           <title>Jalview</title>
 404           <vendor>The Barton Group</vendor>
 405           <homepage href="http://www.jalview.org" />
 406           <description>Jalview Multiple Alignment Editor</description>
 407           <description kind="short">Jalview</description>
 408           <icon href="${WebStartImage}" />
 409           <offline_allowed />
 410         </information>
 411         <resources>
 412           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 413           <fileset dir="${packageDir}">
 414             <include name="jalview.jar" />
 415           </fileset>
 416           <fileset dir="${packageDir}">
 417             <include name="*.jar" />
 418             <include name="*_*.jar" />
 419             <exclude name="jalview.jar" />
 420                 <exclude name="*jnilib.jar"/>
 421           </fileset>
 422         </resources>
 423         <resources os="Mac OS X">
 424           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 425                 <fileset dir="${packageDir}">
 426                         <include name="*quaqua*.jnilib.jar"/>
 427                 </fileset>
 428         </resources>
 429
 430         <application_desc main_class="jalview.bin.Jalview">
 431         </application_desc>
 432         <security>
 433           <all_permissions />
 434         </security>
 435       </jnlp>
 436     </presetdef>
 437
 438     <jnlpf toFile="${jnlpFile}"/>
 439
 440   </target>
 441
 442   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 443     <echo message="Not adding JNLP File Associations"/>
 444   </target>
 445
 446   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 447     <replace file="${jnlpFile}">
 448       <replacetoken>
 449         <![CDATA[</information>]]></replacetoken>
 450       <replacevalue>
 451         <![CDATA[
 452           <association mime-type="application-x/ext-file" extensions="fa" />
 453         <association mime-type="application-x/ext-file" extensions="fasta" />
 454         <association mime-type="application-x/ext-file" extensions="mfa" />
 455         <association mime-type="application-x/ext-file" extensions="fastq" />
 456         <association mime-type="application-x/ext-file" extensions="blc" />
 457         <association mime-type="application-x/ext-file" extensions="msf" />
 458         <association mime-type="application-x/ext-file" extensions="pfam" />
 459         <association mime-type="application-x/ext-file" extensions="aln"/>
 460         <association mime-type="application-x/ext-file" extensions="pir"/>
 461         <association mime-type="application-x/ext-file" extensions="amsa"/>
 462         <association mime-type="application-x/ext-file" extensions="stk"/>
 463         <association mime-type="application-x/ext-file" extensions="jvp"/>
 464       </information>]]></replacevalue>
 465   </replace>
 466   <echo message="Added file associations to JNLP file"/>
 467 </target>
 468 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 469 </target>
 470
 471 <target name="buildextclients" depends="init">
 472   <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" />
 473   <condition property="dontextbuild">
 474     <equals arg1="n" arg2="${doextbuild.response}" />
 475   </condition>
 476   <condition property="dontextbuild">
 477     <equals arg1="N" arg2="${doextbuild.response}" />
 478   </condition>
 479   <fail if="dontextbuild">
 480         Build External Client Code process aborted by user. Jalview source is unchanged.
 481       </fail>
 482   <!-- Currently, this doesn't happen automatically.
 483      1. Run WSDL2Java as below, which generates an ext.vamsas +
 484      vamsas.<datapackages> fileset.
 485      2. refactor ext.vamsas.SpecificserviceWS* to
 486      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 487      3. Update the jalview.ws.*WServices classes to reflect the
 488      interface type, and all locations of this wsdl type that Jalview
 489      might be using.
 490
 491 -->
 492   <path id="axisbuild">
 493     <path refid="build.classpath" />
 494   </path>
 495   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 496   <move todir="./bak">
 497     <fileset dir="${sourceDir}" id="client">
 498       <include name="${wsdl.ClientNS}/*.*" />
 499     </fileset>
 500   </move>
 501
 502   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 503     <mappingSet>
 504       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 505       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 506     </mappingSet>
 507   </axis-wsdl2java>
 508 </target>
 509
 510 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 511   <!-- make the package jar if not already existing -->
 512   <mkdir dir="${packageDir}" />
 513   <!-- clean dir if it already existed -->
 514   <delete>
 515     <fileset dir="${packageDir}">
 516       <include name="*.jar"/>
 517     </fileset>
 518   </delete>
 519   <jar destfile="${packageDir}/${outputJar}" index="true">
 520     <manifest>
 521       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 522       <attribute name="Permissions" value="all-permissions" />
 523       <attribute name="Application-Name" value="Jalview Desktop" />
 524       <attribute name="Codebase" value="${application.codebase}" />
 525     </manifest>
 526     <fileset dir="${outputDir}/">
 527       <exclude name="cache*/**" />
 528       <exclude name="*.jar" />
 529       <exclude name="*.jar.*" />
 530       <exclude name="**/*.jar" />
 531       <exclude name="**/*.jar.*" />
 532     </fileset>
 533   </jar>
 534
 535   <copy toDir="${packageDir}" flatten="true">
 536     <fileset dir="${outputDir}">
 537       <include name="*.jar" />
 538       <include name="**/*.jar" />
 539     </fileset>
 540   </copy>
 541 </target>
 542
 543
 544 <!-- jalopy code reformatter -->
 545 <target name="sourcescrub" depends="init,build">
 546   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 547     <fileset dir="${sourceDir}">
 548       <include name="*.java" />
 549       <include name="**/*.java" />
 550       <include name="**/**/*.java" />
 551     </fileset>
 552   </jalopy>
 553 </target>
 554
 555
 556
 557 <!-- Compile, package and obfuscate Jalview Applet -->
 558 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 559
 560 <target name="compileApplet" depends="init,clean">
 561   <mkdir dir="${outputDir}" />
 562   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 563                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 564                         excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
 565 </target>
 566
 567 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 568   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 569   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 570   <copy todir="${outputDir}/lang">
 571     <fileset dir="${resourceDir}/lang">
 572       <include name="**.*"/>
 573     </fileset>
 574   </copy>
 575   <jar destfile="in.jar" index="true">
 576     <manifest>
 577       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 578       <attribute name="Application-Name" value="JalviewLite" />
 579       <attribute name="Codebase" value="${applet.codebase}" />
 580     </manifest>
 581     <fileset dir="${outputDir}">
 582       <include name="com/**" />
 583       <include name="MCview/**" />
 584       <include name="jalview/**" />
 585       <include name=".build_properties" />
 586       <include name="images/idwidth.gif" />
 587       <include name="images/link.gif" />
 588       <include name="lang/**" />
 589     </fileset>
 590   </jar>
 591 </target>
 592 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 593 </target>
 594 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 595   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 596   <delete file="in.jar" />
 597 </target>
 598 <target name="-obfuscatereally" unless="donotobfuscate">
 599
 600   <path id="obfuscateDeps.path">
 601     <pathelement location="${applet.jre.tools}" />
 602     <pathelement location="appletlib/${jmolJar}" />
 603     <pathelement location="appletlib/${jsonSimple}" />
 604     <pathelement location="appletlib/${javaJson}" />
 605   </path>
 606   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 607
 608   <proguard>
 609     <injar file="in.jar" />
 610     <outjar file="${jalviewLiteJar}" />
 611     <libraryjar refid="obfuscateDeps.path" />
 612     <dontwarn/>
 613     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 614       <field access="public" />
 615       <method access="public" />
 616       <constructor access="public" />
 617     </keep>
 618     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 619       <field access="public" />
 620       <method access="public" />
 621       <constructor access="public" />
 622     </keep>
 623     <!--      -libraryjars "${obfuscateDeps}"
 624       -injars      in.jar
 625       -outjars     jalviewApplet.jar
 626       -keep public class jalview.bin.JalviewLite
 627        { public * ; } -->
 628   </proguard>
 629   <delete file="in.jar" />
 630 </target>
 631
 632 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 633   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 634   <delete>
 635     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 636       <include name="*.java" />
 637       <include name="descriptors/*.java" />
 638     </fileset>
 639   </delete>
 640   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 641   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 642   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 643   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 644   <!--
 645                 now build the jalview.binding package with the old schema set
 646                 -->
 647   <delete>
 648     <fileset dir="${sourceDir}/jalview/binding/">
 649       <include name="**" />
 650     </fileset>
 651   </delete>
 652   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 653   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 654   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 655 </target>
 656 <target name="sourcedist" description="create jalview source distribution" depends="init">
 657   <delete file="${source.dist.name}" />
 658   <tar destfile="${source.dist.name}" compression="gzip">
 659     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 660       <include name="LICENSE" />
 661       <include name="README" />
 662       <include name="build.xml" />
 663       <include name="jalview-jalopy.xml" />
 664       <include name="JalviewApplet.jpx" />
 665       <include name="JalviewX.jpx" />
 666       <include name="nbbuild.xml"/>
 667       <include name="nbproject/genfiles.properties"/>
 668       <include name="nbproject/project.properties"/>
 669       <include name="nbproject/project.xml"/>
 670       <include name="${sourceDir}/*.java" />
 671       <include name="${sourceDir}/**/*.java" />
 672       <include name="${sourceDir}/**/*.cdr" />
 673       <include name="${libDir}/**/*" />
 674       <include name="${resourceDir}/**/*" />
 675       <include name="${helpDir}/**/*" />
 676       <include name="appletlib/${jmolJar}" />
 677       <exclude name="**/*locales" />
 678       <exclude name="*locales/**" />
 679       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 680       <exclude name="utils/InstallAnywhere/**Build*/**" />
 681       <exclude name="utils/InstallAnywhere/**Build*/**" />
 682       <exclude name="utils/InstallAnywhere/**locale*" />
 683       <exclude name="utils/InstallAnywhere/**locale*/**" />
 684       <include name="${schemaDir}/**/*" />
 685       <include name="utils/**/*" />
 686       <include name="${docDir}/**/*" />
 687       <include name="examples/**/*" />
 688     </tarfileset>
 689   </tar>
 690 </target>
 691 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 692   <copy todir="${packageDir}/examples">
 693     <fileset dir="examples">
 694       <include name="**/*"/>
 695       <include name="javascript/*"/>
 696       <include name="jmol/*"/>
 697     </fileset>
 698     <fileset dir=".">
 699       <include name="${jalviewLiteJar}" />
 700     </fileset>
 701     <fileset dir="appletlib">
 702       <include name="**/*"/>
 703     </fileset>
 704   </copy>
 705   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 706   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
 707   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
 708   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 709     <manifest>
 710       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 711       <!--          <attribute name="Permissions" value="sandbox" /> -->
 712       <!--<attribute name="Trusted-Lib" value="true" /> -->
 713       <attribute name="Codebase" value="${applet.codebase}"/>
 714       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 715     </manifest>
 716   </jar>
 717   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 718     <fileset dir="${packageDir}/examples">
 719       <include name="*.jar" />
 720     </fileset>
 721   </signjar>
 722   <presetdef name="ap_applet.jar">
 723     <!-- build a signed applet with 'all-permissions' -
 724                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 725                           JalviewLite+JmolApplet linked sequence/structure fails
 726                           Mixed code warnings are raised
 727                           -->
 728     <jar update="true" index="true">
 729       <manifest>
 730         <attribute name="Application-Name" value="JalviewLite" />
 731         <attribute name="Permissions" value="all-permissions" />
 732         <attribute name="Codebase" value="${applet.codebase}" />
 733         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 734         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 735       </manifest>
 736     </jar>
 737   </presetdef>
 738   <presetdef name="applet.jar">
 739     <!-- build signed applet with sandbox permissions -
 740                           Needs 'param name="permissions' value="sandbox"' in applet tag
 741                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 742                         -->
 743
 744     <jar update="true" index="true">
 745       <manifest>
 746         <attribute name="Application-Name" value="JalviewLite" />
 747         <attribute name="Permissions" value="sandbox" />
 748         <attribute name="Codebase" value="${applet.codebase}" />
 749         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 750         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 751       </manifest>
 752     </jar>
 753   </presetdef>
 754   <presetdef name="tl_applet.jar">
 755     <!-- build signed applet with trusted library/trusted permissions -
 756                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 757                                j1.7_45:
 758                                No mixed code warnings raised
 759                                Jmol/JalviewLite sequence/structure example doesn't link structures
 760                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 761
 762                               -->
 763
 764     <jar update="true" index="true">
 765       <manifest>
 766         <attribute name="Application-Name" value="JalviewLite" />
 767         <attribute name="Permissions" value="all-permissions" />
 768         <attribute name="Codebase" value="${applet.codebase}" />
 769         <attribute name="Trusted-Only" value="true" />
 770         <attribute name="Trusted-Library" value="true" />
 771       </manifest>
 772     </jar>
 773   </presetdef>
 774   <presetdef name="to_applet.jar">
 775     <!-- not fully test variant (yet) -->
 776     <jar update="true" index="true">
 777       <manifest>
 778         <attribute name="Application-Name" value="JalviewLite" />
 779         <attribute name="Permissions" value="all-permissions" />
 780         <attribute name="Codebase" value="${applet.codebase}" />
 781         <attribute name="Trusted-Only" value="true" />
 782       </manifest>
 783     </jar>
 784   </presetdef>
 785   <!-- create differently privileged artefacts -->
 786   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 787   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 788   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
 789   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
 790   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 791   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 792   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
 793   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
 794   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 795   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 796   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 797   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 798   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 799   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 800   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 801   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 802   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 803   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 804   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 805   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 806   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 807   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 808   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 809   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 810   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 811   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 812   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 813   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 814   <!-- finally, create manifest for original jars -->
 815   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 816   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 817   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 818   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 819
 820   <!-- todo - write examples/downloads for alternate versions of the applet -->
 821   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 822
 823     <fileset dir="${packageDir}/examples">
 824       <exclude name="u_*.jar"/>
 825       <include name="${jalviewLiteJar}" />
 826       <include name="${jmolJar}" />
 827       <include name="${javaJson}" />
 828       <include name="${jsonSimple}" />
 829       <include name="to_${jalviewLiteJar}" />
 830       <include name="to_${jmolJar}" />
 831       <include name="to_${javaJson}" />
 832       <include name="to_${jsonSimple}" />
 833       <include name="tl_${jalviewLiteJar}" />
 834       <include name="tl_${jmolJar}" />
 835       <include name="tl_${javaJson}" />
 836       <include name="tl_${jsonSimple}" />
 837       <include name="ap_${jalviewLiteJar}" />
 838       <include name="ap_${jmolJar}" />
 839       <include name="ap_${javaJson}" />
 840       <include name="ap_${jsonSimple}" />
 841     </fileset>
 842   </signjar>
 843   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 844   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 845         <!-- finally, replace any launchApp servlet tags with a version specification -->
 846         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 847                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
 848                 <fileset dir="${packageDir}/examples">
 849                         <include name="**/*.html"/>
 850                 </fileset>
 851         </replace>
 852         <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 853                 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
 854                 <fileset dir="${packageDir}/examples">
 855                         <include name="**/*.html"/>
 856                 </fileset>
 857         </replace>
 858
 859 </target>
 860 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 861   <javadoc destdir="${javadocDir}">
 862     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 863     </packageset>
 864   </javadoc>
 865 </target>
 866 </project>