build.xml

   1 <?xml version="1.0"?>
   2   <project name="jalviewX" default="build" basedir=".">
   3 <!-- we use jalopy to format our sources -->
   4 <taskdef name="jalopy"
   5          classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
   6   <classpath>
   7     <fileset dir="utils/jalopy/lib">
   8       <include name="*.jar" />
   9     </fileset>
  10   </classpath>
  11 </taskdef>
  12
  13
  14     <!-- utils is a class path to additional utilities needed for
  15     building docs, jars and webstart stuff -->
  16
  17 <!--
  18         Userdefined build property defaults
  19
  20         wsdl.server list (plus namespace mapping info ???)  - also want
  21                 ... to make this a dynamically generatable property
  22         WebStart Location
  23         Build location - provide a temporary root for speed
  24         jarsigner keystore and info
  25         Jakarta and axis classpath ?
  26         Default argument for starting Jalview (if it exists).
  27
  28 -->
  29
  30     <target name="init">
  31       <path id="axis.classpath">
  32 <!-->        <fileset dir="/usr/local/axis/lib">
  33           <include name="**/*.jar" />
  34         </fileset>
  35         <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  36           <include name="**/*.jar"/>
  37           <include name="*.jar"/>
  38         </fileset> -->
  39       </path>
  40
  41       <property name="JALVIEW_VERSION" value="2.07"/>
  42       <property name="" value=""/>
  43       <property name="libDir" value="lib"/>
  44       <property name="resourceDir" value="resources"/>
  45       <property name="helpDir" value="help"/>
  46       <property name="docDir" value="doc"/>
  47       <property name="sourceDir" value="src" />
  48       <property name="outputDir" value="classes" />
  49       <property name="packageDir" value="dist" />
  50       <property name="outputJar" value="jalview.jar" />
  51       <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
  52       <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
  53       <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
  54       <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
  55       <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
  56         <property name="WSInterf" value="MsaWS" />
  57       <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
  58       <property name="wsdl.Namespace" value="vamsas" />
  59       <property name="wsdl.ClientNS" value="ext.vamsas" />
  60
  61       <path id="build.classpath">
  62         <fileset dir="utils">
  63           <include name="*.jar"/>
  64           <include name="**/*.jar"/>
  65         </fileset>
  66         <fileset dir="${libDir}">
  67           <include name="*.jar"/>
  68           <include name="**/*.jar"/>
  69         </fileset>
  70 <!--        <fileset dir="old_lib_signed">
  71 <include name="lib_axis.jar"/>
  72
  73         </fileset>-->
  74       </path>
  75       <!-->    <uptodate property="help.uptodate"
  76       targetfile="${helpDir}/helpIndex.xml">
  77       <srcfiles
  78                  dir="${helpDir}"
  79                  includes="**/*.html" />
  80                </uptodate>
  81       -->
  82     </target>
  83
  84
  85     <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
  86     <target name="buildPropertiesFile" depends="init">
  87       <tstamp prefix="build">
  88         <format property="date" pattern="dd MMMM yyyy"/>
  89       </tstamp>
  90       <properties file="${outputDir}/.build_properties">
  91         <header>
  92           ---Jalview Build Details---
  93         </header>
  94         <property name="VERSION" value="${JALVIEW_VERSION}"/>
  95         <property name="BUILD_DATE" value="${build.date}"/>
  96       </properties>
  97     </target>
  98
  99
 100     <target name="clean" depends="init">
 101       <!-- not efficient yet. -->
 102       <delete dir="${outputDir}"/>
 103     </target>
 104
 105     <target name="distclean" depends="init, clean">
 106
 107       <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
 108       <delete>
 109         <fileset dir=".">
 110           <include name="${outputJar}"/>
 111           <include name="#*#"/>
 112           <include name="#*.*#"/>
 113           <include name="**/#*#"/>
 114           <include name="**/#*.*#"/>
 115           <include name="*~"/>
 116           <include name="*.*~"/>
 117           <include name="**/*~"/>
 118           <include name="**/*.*~"/>
 119         </fileset>
 120       </delete>
 121     </target>
 122
 123     <target name="prepare" depends="init">
 124       <mkdir dir="${outputDir}"/>
 125       <copy todir="${outputDir}">
 126         <fileset dir=".">
 127           <include name="${docDir}/**/*.*"/>
 128           <include name="${helpDir}/**/*.*"/>
 129           <include name="${libDir}/*.jar"/>
 130         </fileset>
 131         <fileset dir="${resourceDir}">
 132           <include name="**/*.*"/>
 133         </fileset>
 134       </copy>
 135     </target>
 136
 137     <target name="build" depends="prepare">
 138       <!-- not efficient yet. -->
 139       <javac source="1.4" target="1.4"
 140         srcdir ="${sourceDir}"
 141         destdir="${outputDir}"
 142       classpathref="build.classpath">
 143       <exclude name="jalview/*applet*"/>
 144        <exclude name="com/stevesoft/**"/>
 145       </javac>
 146     </target>
 147     <target name="buildindices" depends="init, prepare"
 148     unless="help.uptodate">
 149     <java
 150       classname="com.sun.java.help.search.Indexer"
 151       classpathref="build.classpath"
 152       fork="true"
 153       dir="${outputDir}/${helpDir}"
 154       >
 155       <arg line="html"/>
 156     </java>
 157     </target>
 158
 159     <target name="makejars" depends="build, buildPropertiesFile, buildindices">
 160       <!-- make the package jar -->
 161       <mkdir dir="${packageDir}"/>
 162
 163       <jar destfile="${packageDir}/${outputJar}">
 164         <manifest>
 165              <attribute name="Main-Class" value="jalview.bin.Jalview"/>
 166         </manifest>
 167         <fileset dir="${outputDir}/">
 168           <exclude name="cache*/**"/>
 169           <exclude name="*.jar" />
 170           <exclude name="*.jar.*" />
 171           <exclude name="**/*.jar" />
 172           <exclude name="**/*.jar.*" />
 173         </fileset>
 174       </jar>
 175
 176       <copy toDir="${packageDir}" flatten="true">
 177         <fileset dir="${outputDir}">
 178           <include name="*.jar"/>
 179           <include name="**/*.jar"/>
 180         </fileset>
 181       </copy>
 182 <!-- the default keystore details might need to be edited here -->
 183       <signjar
 184       storepass="alignmentisfun"
 185       keypass="alignmentisfun"
 186       keystore="keys/.keystore"
 187       alias="jalview"
 188       lazy="false"
 189       verbose="false"
 190       >
 191
 192       <fileset dir="${packageDir}">
 193         <include name="*.jar"/>
 194       </fileset>
 195       </signjar>
 196       <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
 197
 198       <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 199       <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
 200       codebase="${WebStartLocation}">
 201       <information>
 202         <title>Jalview</title>
 203         <vendor>The Barton Group</vendor>
 204         <homepage href="http://www.jalview.org"/>
 205         <description>Jalview Multiple Alignment Editor</description>
 206         <description kind="short">Jalview</description>
 207         <icon href="logo_big.gif"/>
 208         <offline_allowed/>
 209         <!--
 210         <association mime-type="application-x/ext-file" extensions="fa"/>
 211         <association mime-type="application-x/ext-file" extensions="fasta"/>
 212         <association mime-type="application-x/ext-file" extensions="fastq"/>
 213         <association mime-type="application-x/ext-file" extensions="blc"/>
 214         <association mime-type="application-x/ext-file" extensions="msf"/>
 215         <association mime-type="application-x/ext-file" extensions="pfam"/>
 216         <association mime-type="application-x/ext-file" extensions="aln"/>
 217         <association mime-type="application-x/ext-file" extensions="pir"/>
 218         -->
 219        </information>
 220         <resources>
 221           <j2se version="1.4+"/>
 222           <fileset dir="${packageDir}">
 223             <include name="jalview.jar"/>
 224           </fileset>
 225           <fileset dir="${packageDir}">
 226             <include name="*.jar"/>
 227             <exclude name="jalview.jar"/>
 228           </fileset>
 229           <property name="jalview.version" value="${JALVIEW_VERSION}"/>
 230         </resources>
 231         <application_desc main_class="jalview.bin.Jalview">
 232           </application_desc>
 233         <security>
 234           <all_permissions/>
 235         </security>
 236       </jnlp>
 237     </target>
 238     <target name="runenv" depends="init">
 239       <path id="run.classpath">
 240         <pathelement location="${outputDir}"/>
 241         <fileset dir="${outputDir}">
 242           <include name="${libDir}/*.jar"/>
 243         </fileset>
 244       </path>
 245       <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
 246
 247       <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 248       </echo>
 249     </target>
 250
 251     <target name="buildextclients" depends="init">
 252 <!-- Currently, this doesn't happen automatically.
 253      1. Run WSDL2Java as below, which generates an ext.vamsas +
 254      vamsas.<datapackages> fileset.
 255      2. refactor ext.vamsas.SpecificserviceWS* to
 256      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 257      3. Update the jalview.ws.*WServices classes to reflect the
 258      interface type, and all locations of this wsdl type that Jalview
 259      might be using.
 260
 261 -->
 262       <path id="axisbuild">
 263         <!--        <path refid="axis.classpath"/> -->
 264         <path refid="build.classpath"/>
 265       </path>
 266       <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
 267       <move todir="./bak">
 268         <fileset dir="${sourceDir}" id="client">
 269           <include name="${wsdl.ClientNS}/*.*"/>
 270         </fileset>
 271       </move>
 272
 273       <axis-wsdl2java
 274       output="${sourceDir}"
 275       verbose="true"
 276       url="${wsdl.MsaWS2}"
 277       serverside="false"
 278       deployscope="Request"
 279       debug="false"
 280       helpergen="true"
 281       all="true"
 282       >
 283       <mappingSet>
 284         <mapping
 285         namespace="${wsdl.Namespace}"
 286         package="${wsdl.ClientNS}"
 287         />
 288         <mapping namespace="http://dataTypes.vamsas"
 289         package="${wsdl.ClientNS}"/>
 290         </mappingSet>
 291     </axis-wsdl2java>
 292
 293   </target>
 294   <target name="package" depends="init, build">
 295
 296   </target>
 297   <!-- jalopy code reformatter -->
 298   <target name="sourcescrub" depends="init,build">
 299     <jalopy destdir="jsrc" classpathref="run.classpath"
 300       convention="jalview-jalopy.xml">
 301       <fileset dir="${sourceDir}">
 302         <include name="*.java"/>
 303         <include name="**/*.java"/>
 304         <include name="**/**/*.java"/>
 305       </fileset>
 306       </jalopy>
 307   </target>
 308
 309
 310
 311   <!-- Compile, package and obfuscate Jalview Applet -->
 312   <target name="makeApplet" depends="obfuscate"/>
 313
 314   <target name="compileApplet" depends="init,clean">
 315     <mkdir dir="${outputDir}"/>
 316     <javac source="1.2" target="1.1" srcdir="${sourceDir}" destdir="${outputDir}"
 317        includes="jalview/analysis/**,jalview/appletgui/**,jalview/datamodel/**jalview/jbappletgui/**,jalview/math/**,jalview/schemes/**"
 318        excludes="ext/**,MCview/**,org/**,vamsas/**"/>
 319   </target>
 320
 321   <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 322   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
 323        <jar destfile="in.jar">
 324         <manifest>
 325             <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
 326         </manifest>
 327         <fileset dir="${outputDir}">
 328           <include name="com/**"/>
 329           <include name="jalview/**"/>
 330           <include name=".build_properties"/>
 331           <include name="images/idwidth.gif"/>
 332         </fileset>
 333       </jar>
 334   </target>
 335
 336   <target name="obfuscate" depends="packageApplet">
 337     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 338     <proguard>
 339       -libraryjars "${java.home}/lib/rt.jar"
 340       -injars      in.jar
 341       -outjars     jalviewApplet.jar
 342       -keep public class jalview.bin.JalviewLite
 343                 { public static void main(java.lang.String[]);}
 344     </proguard>
 345     <delete file="in.jar"/>
 346   </target>
 347
 348
 349 </project>