build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3   Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
   4   Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   5
   6   This program is free software; you can redistribute it and/or
   7   modify it under the terms of the GNU General Public License
   8   as published by the Free Software Foundation; either version 2
   9   of the License, or (at your option) any later version.
  10
  11   This program is distributed in the hope that it will be useful,
  12   but WITHOUT ANY WARRANTY; without even the implied warranty of
  13   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  14   GNU General Public License for more details.
  15
  16   You should have received a copy of the GNU General Public License
  17   along with this program; if not, write to the Free Software
  18   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  19 -->
  20 <project name="jalviewX" default="usage" basedir=".">
  21         <!-- we use jalopy to format our sources -->
  22         <taskdef name="jalopy"
  23          classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
  24                 <classpath>
  25                         <fileset dir="utils/jalopy/lib">
  26                                 <include name="*.jar" />
  27                         </fileset>
  28                 </classpath>
  29         </taskdef>
  30
  31         <target name="help" depends="usage"/>
  32         <target name="usage">
  33                 <echo message="~~~Jalview Ant build.xml Usage~~~~"/>
  34                 <echo message="Targets include:"/>
  35                 <echo message="usage - default target, displays this message"/>
  36                 <echo message="buildindices - generates JavaHelpSearch from the help files"/>
  37                 <echo message="build - compiles all necessary files for Application"/>
  38                 <echo message="makedist - compiles and places all necessary jar files into directory dist"/>
  39                 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution"/>
  40                 <echo message="              this needs a keystore and key. See docs/building.html for more information."/>
  41                 <echo message="compileApplet - compiles all necessary files for Applet"/>
  42                 <echo message="makeApplet - compiles, then packages and obfuscates the Applet"/>
  43                 <echo message="See docs/building.html and the comments in build file for other targets."/>
  44             <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk."/>
  45             <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation"/>
  46         </target>
  47
  48
  49         <!-- utils is a class path to additional utilities needed for
  50     building docs, jars and webstart stuff -->
  51         <!--
  52         Userdefined build property defaults
  53
  54         wsdl.server list (plus namespace mapping info ???)  - also want
  55                 ... to make this a dynamically generatable property
  56         WebStart Location
  57         Build location - provide a temporary root for speed
  58         jarsigner keystore and info
  59         Jakarta and axis classpath ?
  60         Default argument for starting Jalview (if it exists).
  61
  62 -->
  63
  64         <target name="init">
  65                 <path id="axis.classpath">
  66                         <!-->
  67                         <fileset dir="/usr/local/axis/lib">
  68                                 <include name="**/*.jar" />
  69                         </fileset>
  70                         <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  71                                 <include name="**/*.jar"/>
  72                                 <include name="*.jar"/>
  73                         </fileset> -->
  74       </path>
  75                 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  76     <property name="JALVIEW_VERSION" value="DEVELOPMENT"/> <!-- 2.4 (VAMSAS)" -->
  77                 <!-- Include debugging information in javac true or false -->
  78                 <property name="javac.debug" value="true"/>
  79
  80                 <!-- JarSigner Key Store for Webstart Distribution -->
  81                 <property name="jalview.keystore" value="./keys/.keystore"/>
  82                 <!-- Keystore Password -->
  83                 <property name="jalview.keystore.pass" value="alignmentisfun"/>
  84                 <!-- Key Name -->
  85                 <property name="jalview.key" value="jalview"/>
  86                 <!-- Key Password -->
  87                 <property name="jalview.key.pass" value="alignmentisfun"/>
  88
  89                 <!-- Don't change anything below here unless you know what you are doing! -->
  90                 <!-- Url path for WebStart in JNLP file -->
  91                 <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
  92                 <!-- build directory configuration -->
  93                 <property name="libDir" value="lib"/>
  94                 <property name="resourceDir" value="resources"/>
  95                 <property name="helpDir" value="help"/>
  96                 <property name="docDir" value="doc"/>
  97                 <property name="sourceDir" value="src" />
  98                 <property name="schemaDir" value="schemas" />
  99                 <property name="outputDir" value="classes" />
 100                 <property name="packageDir" value="dist" />
 101                 <property name="outputJar" value="jalview.jar" />
 102           <!-- Jalview Applet JMol Jar Dependency -->
 103     <property name="jmolJar" value="Jmol-11.0.2.jar" />
 104                 <property name="jalviewLiteJar" value="jalviewApplet.jar"/>
 105                 <!-- switch to indicate if we should obfuscate jalviewLite -->
 106                 <!--<property name="donotobfuscate" value="true"/> -->
 107
 108                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 109                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 110                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 111                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 112                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 113                 <property name="WSInterf" value="MsaWS" />
 114                 <property name="wsdl.Namespace" value="vamsas" />
 115                 <property name="wsdl.ClientNS" value="ext.vamsas" />
 116                 <!-- the class path for building the application -->
 117                 <path id="build.classpath">
 118                         <fileset dir="utils">
 119                                 <include name="*.jar"/>
 120                                 <include name="**/*.jar"/>
 121                         </fileset>
 122                         <fileset dir="${libDir}">
 123                                 <include name="*.jar"/>
 124                                 <include name="**/*.jar"/>
 125                         </fileset>
 126
 127                 </path>
 128                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz"/>
 129                 <!-- The Location of the java 1.1.8 jdk -->
 130                 <property name="java118.home" value="C:\Sun\jdk1.1.8" />
 131                 <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip"/>
 132                 <!-- jre for 1.4 version
 133                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 134                 -->
 135                 <!-- the classpath for building the 1.1 applet -->
 136                 <path id="jalviewlite.deps">
 137                         <fileset dir="${java118.home}">
 138                                 <include name="lib/classes.zip"/>
 139                         </fileset>
 140                 <pathelement location="lib/${jmolJar}"/>
 141           </path>
 142         </target>
 143
 144
 145         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
 146         <target name="buildPropertiesFile" depends="init">
 147                 <tstamp prefix="build">
 148                         <format property="date" pattern="dd MMMM yyyy"/>
 149                 </tstamp>
 150                 <properties file="${outputDir}/.build_properties">
 151                         <header>
 152           ---Jalview Build Details---
 153         </header>
 154                         <property name="VERSION" value="${JALVIEW_VERSION}"/>
 155                         <property name="BUILD_DATE" value="${build.date}"/>
 156                 </properties>
 157         </target>
 158
 159
 160         <target name="clean" depends="init">
 161                 <!-- not efficient yet. -->
 162                 <delete dir="${outputDir}"/>
 163         </target>
 164
 165         <target name="distclean" depends="init, clean">
 166
 167                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
 168                 <delete>
 169                         <fileset dir=".">
 170                                 <include name="${outputJar}"/>
 171                                 <include name="#*#"/>
 172                                 <include name="#*.*#"/>
 173                                 <include name="**/#*#"/>
 174                                 <include name="**/#*.*#"/>
 175                                 <include name="*~"/>
 176                                 <include name="*.*~"/>
 177                                 <include name="**/*~"/>
 178                                 <include name="**/*.*~"/>
 179                         </fileset>
 180                 </delete>
 181         </target>
 182
 183         <target name="prepare" depends="init">
 184                 <mkdir dir="${outputDir}"/>
 185                 <copy todir="${outputDir}">
 186                         <fileset dir=".">
 187                                 <include name="${docDir}/**/*.*"/>
 188                                 <include name="${helpDir}/**/*.*"/>
 189                                 <include name="${libDir}/*.jar"/>
 190                         </fileset>
 191                         <fileset dir="${resourceDir}">
 192                                 <include name="**/*.*"/>
 193                         </fileset>
 194                 </copy>
 195         </target>
 196
 197         <target name="build" depends="prepare">
 198                 <!-- not efficient yet. -->
 199                 <javac source="1.4" target="1.4"
 200         srcdir ="${sourceDir}"
 201         destdir="${outputDir}"
 202                                 debug="${javac.debug}"
 203       classpathref="build.classpath">
 204                         <exclude name="jalview/*applet*"/>
 205                         <exclude name="com/stevesoft/**"/>
 206                 </javac>
 207         </target>
 208         <target name="buildindices" depends="init, prepare"
 209     unless="help.uptodate">
 210                 <java
 211       classname="com.sun.java.help.search.Indexer"
 212       classpathref="build.classpath"
 213       fork="true"
 214       dir="${outputDir}/${helpDir}"
 215       >
 216                         <arg line="html"/>
 217                 </java>
 218         </target>
 219
 220         <target name="makefulldist" depends="makedist">
 221                 <!-- the default keystore details might need to be edited here -->
 222                 <signjar
 223       storepass="${jalview.keystore.pass}"
 224       keypass="${jalview.key.pass}"
 225       keystore="${jalview.keystore}"
 226       alias="${jalview.key}"
 227       lazy="false"
 228       verbose="false"
 229       >
 230
 231                         <fileset dir="${packageDir}">
 232                                 <include name="*.jar"/>
 233                         </fileset>
 234                 </signjar>
 235                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
 236
 237                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 238                 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 239                 <jnlp toFile="${packageDir}/jalview.jnlp"
 240       codebase="${WebStartLocation}">
 241                         <information>
 242                                 <title>Jalview</title>
 243                                 <vendor>The Barton Group</vendor>
 244                                 <homepage href="http://www.jalview.org"/>
 245                                 <description>Jalview Multiple Alignment Editor</description>
 246                                 <description kind="short">Jalview</description>
 247                                 <icon href="logo_big.gif"/>
 248                                 <offline_allowed/>
 249                                 <!--
 250         <association mime-type="application-x/ext-file" extensions="fa"/>
 251         <association mime-type="application-x/ext-file" extensions="fasta"/>
 252         <association mime-type="application-x/ext-file" extensions="fastq"/>
 253         <association mime-type="application-x/ext-file" extensions="blc"/>
 254         <association mime-type="application-x/ext-file" extensions="msf"/>
 255         <association mime-type="application-x/ext-file" extensions="pfam"/>
 256         <association mime-type="application-x/ext-file" extensions="aln"/>
 257         <association mime-type="application-x/ext-file" extensions="pir"/>
 258         <association mime-type="application-x/ext-file" extensions="amsa"/>
 259         -->
 260                         </information>
 261                         <resources>
 262                                 <j2se version="1.4+"/>
 263                                 <fileset dir="${packageDir}">
 264                                         <include name="jalview.jar"/>
 265                                 </fileset>
 266                                 <fileset dir="${packageDir}">
 267                                         <include name="*.jar"/>
 268                                         <include name="*_*.jar"/>
 269                                         <exclude name="jalview.jar"/>
 270                                 </fileset>
 271                                 <property name="jalview.version" value="${JALVIEW_VERSION}"/>
 272                         </resources>
 273                         <application_desc main_class="jalview.bin.Jalview">
 274                         </application_desc>
 275                         <security>
 276                                 <all_permissions/>
 277                         </security>
 278                 </jnlp>
 279         </target>
 280         <target name="runenv" depends="init">
 281                 <path id="run.classpath">
 282                         <pathelement location="${outputDir}"/>
 283                         <fileset dir="${outputDir}">
 284                                 <include name="${libDir}/*.jar"/>
 285                         </fileset>
 286                 </path>
 287                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
 288
 289                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 290       </echo>
 291         </target>
 292
 293         <target name="buildextclients" depends="init">
 294                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
 295       validargs="Y,y,n,N" defaultvalue="N"
 296       addproperty="doextbuild.response"/>
 297                 <condition property="dontextbuild">
 298                         <equals arg1="n" arg2="${doextbuild.response}"/>
 299                 </condition>
 300                 <condition property="dontextbuild">
 301                         <equals arg1="N" arg2="${doextbuild.response}"/>
 302                 </condition>
 303                 <fail if="dontextbuild">
 304         Build External Client Code process aborted by user. Jalview source is unchanged.
 305       </fail>
 306                 <!-- Currently, this doesn't happen automatically.
 307      1. Run WSDL2Java as below, which generates an ext.vamsas +
 308      vamsas.<datapackages> fileset.
 309      2. refactor ext.vamsas.SpecificserviceWS* to
 310      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 311      3. Update the jalview.ws.*WServices classes to reflect the
 312      interface type, and all locations of this wsdl type that Jalview
 313      might be using.
 314
 315 -->
 316                 <path id="axisbuild">
 317                         <path refid="build.classpath"/>
 318                 </path>
 319                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
 320                 <move todir="./bak">
 321                         <fileset dir="${sourceDir}" id="client">
 322                                 <include name="${wsdl.ClientNS}/*.*"/>
 323                         </fileset>
 324                 </move>
 325
 326                 <axis-wsdl2java
 327       output="${sourceDir}"
 328       verbose="true"
 329       url="${wsdl.MsaWS2}"
 330       serverside="false"
 331       deployscope="Request"
 332       debug="false"
 333       helpergen="true"
 334       all="true"
 335       >
 336                         <mappingSet>
 337                                 <mapping
 338         namespace="${wsdl.Namespace}"
 339         package="${wsdl.ClientNS}"
 340         />
 341                                 <mapping namespace="http://dataTypes.vamsas"
 342         package="${wsdl.ClientNS}"/>
 343                         </mappingSet>
 344                 </axis-wsdl2java>
 345         </target>
 346
 347         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 348                 <!-- make the package jar -->
 349                 <mkdir dir="${packageDir}"/>
 350
 351                 <jar destfile="${packageDir}/${outputJar}">
 352                         <manifest>
 353                                 <attribute name="Main-Class" value="jalview.bin.Jalview"/>
 354                         </manifest>
 355                         <fileset dir="${outputDir}/">
 356                                 <exclude name="cache*/**"/>
 357                                 <exclude name="*.jar" />
 358                                 <exclude name="*.jar.*" />
 359                                 <exclude name="**/*.jar" />
 360                                 <exclude name="**/*.jar.*" />
 361                         </fileset>
 362                 </jar>
 363
 364                 <copy toDir="${packageDir}" flatten="true">
 365                         <fileset dir="${outputDir}">
 366                                 <include name="*.jar"/>
 367                                 <include name="**/*.jar"/>
 368                         </fileset>
 369                 </copy>
 370         </target>
 371
 372
 373         <!-- jalopy code reformatter -->
 374         <target name="sourcescrub" depends="init,build">
 375                 <jalopy destdir="jsrc" classpathref="run.classpath"
 376       convention="jalview-jalopy.xml">
 377                         <fileset dir="${sourceDir}">
 378                                 <include name="*.java"/>
 379                                 <include name="**/*.java"/>
 380                                 <include name="**/**/*.java"/>
 381                         </fileset>
 382                 </jalopy>
 383         </target>
 384
 385
 386
 387   <!-- Compile, package and obfuscate Jalview Applet -->
 388   <target name="makeApplet" depends="obfuscate"/>
 389
 390   <target name="compileApplet" depends="init,clean">
 391     <mkdir dir="${outputDir}"/>
 392     <javac source="1.2"
 393     target="1.1"
 394     srcdir="${sourceDir}"
 395     destdir="${outputDir}"
 396         debug="${javac.debug}"
 397     classpath="lib/${jmolJar}"
 398        includes="jalview/appletgui/**"
 399        excludes="ext/**,MCview/**,org/**,vamsas/**"
 400        />
 401   </target>
 402
 403   <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 404   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
 405   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
 406        <jar destfile="in.jar">
 407         <manifest>
 408             <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
 409         </manifest>
 410         <fileset dir="${outputDir}">
 411           <include name="com/**"/>
 412           <include name="MCview/**"/>
 413           <include name="jalview/**"/>
 414           <include name=".build_properties"/>
 415           <include name="images/idwidth.gif"/>
 416           <include name="images/link.gif"/>
 417         </fileset>
 418       </jar>
 419   </target>
 420   <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
 421   </target>
 422         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 423         <copy file="in.jar" tofile="${jalviewLiteJar}" />
 424     <delete file="in.jar"/>
 425   </target>
 426         <target name="-obfuscatereally" unless="donotobfuscate">
 427
 428         <path id="obfuscateDeps.path">
 429     <pathelement location="${applet.jre.tools}"/>
 430     <pathelement location="lib/${jmolJar}"/>
 431     </path>
 432     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 433
 434     <proguard>
 435       <injar file="in.jar"/>
 436       <outjar file="${jalviewLiteJar}"/>
 437       <libraryjar refid="obfuscateDeps.path"/>
 438       <keep access="public" type="class"
 439       name="jalview.bin.JalviewLite">
 440         <field access="public"/>
 441         <method access="public"/>
 442         <constructor access="public"/>
 443       </keep>
 444 <!--      -libraryjars "${obfuscateDeps}"
 445       -injars      in.jar
 446       -outjars     jalviewApplet.jar
 447       -keep public class jalview.bin.JalviewLite
 448        { public * ; } -->
 449       </proguard>
 450     <delete file="in.jar"/>
 451   </target>
 452
 453         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 454                 <taskdef name="castor-srcgen"
 455                           classname="org.castor.anttask.CastorCodeGenTask"
 456                       classpathref="build.classpath" />
 457                 <delete>
 458                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 459                                 <include name="*.java"/>
 460                                 <include name="descriptors/*.java"/>
 461                         </fileset>
 462                 </delete>
 463                 <castor-srcgen file="${schemaDir}/vamsas.xsd"
 464                               todir="${sourceDir}"
 465                               package="jalview.schemabinding.version2"
 466                               warnings="false"
 467                                         nodesc="false"
 468                                                 verbose="true"
 469                                                 properties="${schemaDir}/jalview.properties"
 470                 />
 471                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
 472                               todir="${sourceDir}"
 473                               package="jalview.schemabinding.version2"
 474                               warnings="false"
 475                                         nodesc="false"
 476                                                 verbose="true"
 477                                                 properties="${schemaDir}/jalview.properties"
 478                 />
 479                 <castor-srcgen file="${schemaDir}/jalview.xsd"
 480                               todir="${sourceDir}"
 481                               package="jalview.schemabinding.version2"
 482                               warnings="false"
 483                                           nodesc="false"
 484                                                 verbose="true"
 485                                                 properties="${schemaDir}/jalview.properties"
 486
 487                 />
 488                 <!--
 489                 now build the jalview.binding package with the old schema set
 490                 -->
 491                 <delete>
 492                         <fileset dir="${sourceDir}/jalview/binding/">
 493                                 <include name="**"/>
 494                         </fileset>
 495                 </delete>
 496                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd"
 497                               todir="${sourceDir}"
 498                               package="jalview.binding"
 499                               warnings="false"
 500                                         nodesc="true"
 501                                                 verbose="true"
 502                                                 properties="${schemaDir}/jalview.nodesc.properties"
 503                 />
 504                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
 505                               todir="${sourceDir}"
 506                               package="jalview.binding"
 507                               warnings="false"
 508                                         nodesc="true"
 509                                                 verbose="true"
 510                                                 properties="${schemaDir}/jalview.nodesc.properties"
 511                 />
 512                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
 513                               todir="${sourceDir}"
 514                               package="jalview.binding"
 515                               warnings="false"
 516                                           nodesc="true"
 517                                                 verbose="true"
 518                                                 properties="${schemaDir}/jalview.nodesc.properties"
 519         />
 520         </target>
 521         <target name="sourcedist" description="create jalview source distribution" depends="init">
 522                 <delete file="${source.dist.name}"/>
 523                 <tar destfile="${source.dist.name}" compression="gzip">
 524                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 525                                 <include name="LICENSE"/>
 526                                 <include name="README"/>
 527                                 <include name="build.xml"/>
 528                                 <include name="jalview-jalopy.xml"/>
 529                                 <include name="JalviewApplet.jpx"/>
 530                                 <include name="JalviewX.jpx"/>
 531                                 <include name="${sourceDir}/*.java"/>
 532                                 <include name="${sourceDir}/**/*.java"/>
 533                                 <include name="${sourceDir}/**/*.cdr"/>
 534                                 <include name="${libDir}/**/*"/>
 535                                 <include name="${resourceDir}/**/*"/>
 536                                 <include name="${helpDir}/**/*"/>
 537                                 <exclude name="**/*locales"/>
 538                                 <exclude name="*locales/**"/>
 539                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml"/>
 540                                 <exclude name="utils/InstallAnywhere/**Build*/**"/>
 541                                 <exclude name="utils/InstallAnywhere/**Build*/**"/>
 542                                 <exclude name="utils/InstallAnywhere/**locale*"/>
 543                                 <exclude name="utils/InstallAnywhere/**locale*/**"/>
 544                                 <include name="${schemaDir}/**/*"/>
 545                                 <include name="utils/**/*"/>
 546                                 <include name="${docDir}/**/*"/>
 547                         </tarfileset>
 548                 </tar>
 549         </target>
 550 </project>