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