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="2.01"/>
  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="${helpDir}"
  79                  includes="**/*.html" />
  80                </uptodate>
  81       -->
  82     </target>
  83
  84
  85     <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
  86     <target name="buildPropertiesFile" depends="init">
  87       <tstamp prefix="build">
  88         <format property="date" pattern="dd MMMM yyyy hh.mm aa"/>
  89       </tstamp>
  90       <properties file="${outputDir}/.build_properties">
  91         <header>
  92           ---Jalview Application Properties---
  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}/${outputJar}">
 164         <fileset dir="${outputDir}/">
 165           <exclude name="cache*/**"/>
 166           <exclude name="*.jar" />
 167           <exclude name="*.jar.*" />
 168           <exclude name="**/*.jar" />
 169           <exclude name="**/*.jar.*" />
 170         </fileset>
 171       </jar>
 172
 173       <copy toDir="${packageDir}" flatten="true">
 174         <fileset dir="${outputDir}">
 175           <include name="*.jar"/>
 176           <include name="**/*.jar"/>
 177         </fileset>
 178       </copy>
 179 <!-- the default keystore details might need to be edited here -->
 180       <signjar
 181       storepass="alignmentisfun"
 182       keypass="alignmentisfun"
 183       keystore="keys/.keystore"
 184       alias="jalview"
 185       lazy="false"
 186       verbose="false"
 187       >
 188
 189       <fileset dir="${packageDir}">
 190         <include name="*.jar"/>
 191       </fileset>
 192       </signjar>
 193       <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
 194
 195       <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 196       <jnlp toFile="${packageDir}/Jalview.jnlp" href="Jalview.jnlp"
 197       codebase="${WebStartLocation}">
 198       <information>
 199         <title>Jalview</title>
 200         <vendor>The Barton Group</vendor>
 201         <homepage href="www.jalview.org"/>
 202         <description>Jalview Multiple Alignment Editor</description>
 203         <description kind="short">Jalview</description>
 204         <icon href="logo_big.gif"/>
 205         <!--
 206         <association mime-type="application-x/ext-file" extensions="fa"/>
 207         <association mime-type="application-x/ext-file" extensions="fasta"/>
 208         <association mime-type="application-x/ext-file" extensions="fastq"/>
 209         <association mime-type="application-x/ext-file" extensions="blc"/>
 210         <association mime-type="application-x/ext-file" extensions="msf"/>
 211         <association mime-type="application-x/ext-file" extensions="pfam"/>
 212         <association mime-type="application-x/ext-file" extensions="aln"/>
 213         <association mime-type="application-x/ext-file" extensions="pir"/>
 214         -->
 215        </information>
 216         <resources>
 217           <j2se version="1.4+"/>
 218           <fileset dir="${packageDir}">
 219             <include name="jalview.jar"/>
 220           </fileset>
 221           <fileset dir="${packageDir}">
 222             <include name="*.jar"/>
 223             <exclude name="jalview.jar"/>
 224           </fileset>
 225         </resources>
 226         <application_desc main_class="jalview.bin.Jalview">
 227           </application_desc>
 228         <security>
 229           <all_permissions/>
 230         </security>
 231       </jnlp>
 232     </target>
 233     <target name="runenv" depends="init">
 234       <path id="run.classpath">
 235         <pathelement location="${outputDir}"/>
 236         <fileset dir="${outputDir}">
 237           <include name="${libDir}/*.jar"/>
 238         </fileset>
 239       </path>
 240       <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
 241
 242       <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 243       </echo>
 244     </target>
 245
 246     <target name="buildextclients" depends="init">
 247 <!-- Currently, this doesn't happen automatically.
 248      1. Run WSDL2Java as below, which generates an ext.vamsas +
 249      vamsas.<datapackages> fileset.
 250      2. refactor ext.vamsas.SpecificserviceWS* to
 251      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 252      3. Update the jalview.ws.*WServices classes to reflect the
 253      interface type, and all locations of this wsdl type that Jalview
 254      might be using.
 255
 256 -->
 257       <path id="axisbuild">
 258         <!--        <path refid="axis.classpath"/> -->
 259         <path refid="build.classpath"/>
 260       </path>
 261       <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
 262       <move todir="./bak">
 263         <fileset dir="${sourceDir}" id="client">
 264           <include name="${wsdl.ClientNS}/*.*"/>
 265         </fileset>
 266       </move>
 267
 268       <axis-wsdl2java
 269       output="${sourceDir}"
 270       verbose="true"
 271       url="${wsdl.MsaWS2}"
 272       serverside="false"
 273       deployscope="Request"
 274       debug="false"
 275       helpergen="true"
 276       all="true"
 277       >
 278       <mappingSet>
 279         <mapping
 280         namespace="${wsdl.Namespace}"
 281         package="${wsdl.ClientNS}"
 282         />
 283         <mapping namespace="http://dataTypes.vamsas"
 284         package="${wsdl.ClientNS}"/>
 285         </mappingSet>
 286     </axis-wsdl2java>
 287
 288   </target>
 289   <target name="package" depends="init, build">
 290
 291   </target>
 292   <!-- jalopy code reformatter -->
 293   <target name="sourcescrub" depends="init,build">
 294     <jalopy destdir="jsrc" classpathref="run.classpath"
 295       convention="jalview-jalopy.xml">
 296       <fileset dir="${sourceDir}">
 297         <include name="*.java"/>
 298         <include name="**/*.java"/>
 299         <include name="**/**/*.java"/>
 300       </fileset>
 301       </jalopy>
 302   </target>
 303
 304
 305
 306   <!-- Compile, package and obfuscate Jalview Applet -->
 307   <target name="makeApplet" depends="obfuscate"/>
 308
 309   <target name="compileApplet" depends="init,clean">
 310     <mkdir dir="${outputDir}"/>
 311     <javac source="1.2" target="1.1" srcdir="${sourceDir}" destdir="${outputDir}"
 312        includes="jalview/analysis/**,jalview/appletgui/**,jalview/datamodel/**jalview/jbappletgui/**,jalview/math/**,jalview/schemes/**"
 313        excludes="ext/**,MCview/**,org/**,vamsas/**"/>
 314   </target>
 315
 316   <target name="packageApplet" depends="compileApplet">
 317        <jar destfile="in.jar">
 318         <fileset dir="${outputDir}">
 319           <include name="com/**"/>
 320           <include name="jalview/**"/>
 321           <include name="${resourceDir}/images/idwidth.gif"/>
 322         </fileset>
 323       </jar>
 324   </target>
 325
 326   <target name="obfuscate" depends="packageApplet">
 327     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 328     <proguard>
 329       -libraryjars "${java.home}/lib/rt.jar"
 330       -injars      in.jar
 331       -outjars     jalviewApplet.jar
 332       -keep public class jalview.bin.JalviewLite
 333     </proguard>
 334     <delete file="in.jar"/>
 335   </target>
 336
 337
 338 </project>