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="" value=""/>
  42       <property name="libDir" value="lib"/>
  43       <property name="resourceDir" value="resources"/>
  44       <property name="helpDir" value="help"/>
  45       <property name="docDir" value="doc"/>
  46       <property name="sourceDir" value="src" />
  47       <property name="outputDir" value="classes" />
  48       <property name="packageDir" value="dist" />
  49       <property name="outputJar" value="jalview.jar" />
  50       <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
  51       <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
  52       <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
  53       <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
  54       <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
  55         <property name="WSInterf" value="MsaWS" />
  56       <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
  57       <property name="wsdl.Namespace" value="vamsas" />
  58       <property name="wsdl.ClientNS" value="ext.vamsas" />
  59
  60       <path id="build.classpath">
  61         <fileset dir="utils">
  62           <include name="*.jar"/>
  63           <include name="**/*.jar"/>
  64         </fileset>
  65         <fileset dir="${libDir}">
  66           <include name="*.jar"/>
  67           <include name="**/*.jar"/>
  68         </fileset>
  69 <!--        <fileset dir="old_lib_signed">
  70 <include name="lib_axis.jar"/>
  71
  72         </fileset>-->
  73       </path>
  74       <!-->    <uptodate property="help.uptodate"
  75       targetfile="${helpDir}/helpIndex.xml">
  76       <srcfiles
  77                  dir="${helpDir}"
  78                  includes="**/*.html" />
  79                </uptodate>
  80       -->
  81     </target>
  82
  83     <target name="clean" depends="init">
  84       <!-- not efficient yet. -->
  85       <delete dir="${outputDir}"/>
  86     </target>
  87
  88     <target name="distclean" depends="init, clean">
  89
  90       <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
  91       <delete>
  92         <fileset dir=".">
  93           <include name="${outputJar}"/>
  94           <include name="#*#"/>
  95           <include name="#*.*#"/>
  96           <include name="**/#*#"/>
  97           <include name="**/#*.*#"/>
  98           <include name="*~"/>
  99           <include name="*.*~"/>
 100           <include name="**/*~"/>
 101           <include name="**/*.*~"/>
 102         </fileset>
 103       </delete>
 104     </target>
 105
 106     <target name="prepare" depends="init">
 107       <mkdir dir="${outputDir}"/>
 108       <copy todir="${outputDir}">
 109         <fileset dir=".">
 110           <include name="${docDir}/**/*.*"/>
 111           <include name="${helpDir}/**/*.*"/>
 112           <include name="${libDir}/*.jar"/>
 113         </fileset>
 114         <fileset dir="${resourceDir}">
 115           <include name="**/*.*"/>
 116         </fileset>
 117       </copy>
 118     </target>
 119
 120     <target name="build" depends="prepare">
 121       <!-- not efficient yet. -->
 122       <javac source="1.4" target="1.4"
 123         srcdir ="${sourceDir}"
 124         destdir="${outputDir}"
 125       classpathref="build.classpath">
 126       <exclude name="jalview/*applet*"/>
 127        <exclude name="com/stevesoft/**"/>
 128       </javac>
 129     </target>
 130     <target name="buildindices" depends="init, prepare"
 131     unless="help.uptodate">
 132     <java
 133       classname="com.sun.java.help.search.Indexer"
 134       classpathref="build.classpath"
 135       fork="true"
 136       dir="${outputDir}/${helpDir}"
 137       >
 138       <arg line="html"/>
 139     </java>
 140     </target>
 141
 142     <target name="makejars" depends="build, buildindices">
 143       <!-- make the package jar -->
 144       <mkdir dir="${packageDir}"/>
 145
 146       <jar destfile="${packageDir}/${outputJar}">
 147         <fileset dir="${outputDir}/">
 148           <exclude name="cache*/**"/>
 149           <exclude name="*.jar" />
 150           <exclude name="*.jar.*" />
 151           <exclude name="**/*.jar" />
 152           <exclude name="**/*.jar.*" />
 153         </fileset>
 154       </jar>
 155
 156       <copy toDir="${packageDir}" flatten="true">
 157         <fileset dir="${outputDir}">
 158           <include name="*.jar"/>
 159           <include name="**/*.jar"/>
 160         </fileset>
 161       </copy>
 162 <!-- the default keystore details might need to be edited here -->
 163       <signjar
 164       storepass="alignmentisfun"
 165       keypass="alignmentisfun"
 166       keystore="keys/.keystore"
 167       alias="jalview"
 168       lazy="false"
 169       verbose="false"
 170       >
 171
 172       <fileset dir="${packageDir}">
 173         <include name="*.jar"/>
 174       </fileset>
 175       </signjar>
 176       <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
 177
 178       <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 179       <jnlp toFile="${packageDir}/Jalview.jnlp" href="Jalview.jnlp"
 180       codebase="${WebStartLocation}">
 181       <information>
 182         <title>Jalview</title>
 183         <vendor>The Barton Group</vendor>
 184         <homepage href="www.jalview.org"/>
 185         <description>Jalview Multiple Alignment Editor</description>
 186         <description kind="short">Jalview</description>
 187         <icon href="logo_big.gif"/>
 188         <!--
 189         <association mime-type="application-x/ext-file" extensions="fa"/>
 190         <association mime-type="application-x/ext-file" extensions="fasta"/>
 191         <association mime-type="application-x/ext-file" extensions="fastq"/>
 192         <association mime-type="application-x/ext-file" extensions="blc"/>
 193         <association mime-type="application-x/ext-file" extensions="msf"/>
 194         <association mime-type="application-x/ext-file" extensions="pfam"/>
 195         <association mime-type="application-x/ext-file" extensions="aln"/>
 196         <association mime-type="application-x/ext-file" extensions="pir"/>
 197         -->
 198        </information>
 199         <resources>
 200           <j2se version="1.3+"/>
 201           <fileset dir="${packageDir}">
 202             <include name="jalview.jar"/>
 203           </fileset>
 204           <fileset dir="${packageDir}">
 205             <include name="*.jar"/>
 206             <exclude name="jalview.jar"/>
 207           </fileset>
 208         </resources>
 209         <application_desc main_class="jalview.bin.Jalview">
 210           </application_desc>
 211         <security>
 212           <all_permissions/>
 213         </security>
 214       </jnlp>
 215     </target>
 216     <target name="runenv" depends="init">
 217       <path id="run.classpath">
 218         <pathelement location="${outputDir}"/>
 219         <fileset dir="${outputDir}">
 220           <include name="${libDir}/*.jar"/>
 221         </fileset>
 222       </path>
 223       <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
 224
 225       <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 226       </echo>
 227     </target>
 228
 229     <target name="buildextclients" depends="init">
 230 <!-- Currently, this doesn't happen automatically.
 231      1. Run WSDL2Java as below, which generates an ext.vamsas +
 232      vamsas.<datapackages> fileset.
 233      2. refactor ext.vamsas.SpecificserviceWS* to
 234      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 235      3. Update the jalview.ws.*WServices classes to reflect the
 236      interface type, and all locations of this wsdl type that Jalview
 237      might be using.
 238
 239 -->
 240       <path id="axisbuild">
 241         <!--        <path refid="axis.classpath"/> -->
 242         <path refid="build.classpath"/>
 243       </path>
 244       <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
 245       <move todir="./bak">
 246         <fileset dir="${sourceDir}" id="client">
 247           <include name="${wsdl.ClientNS}/*.*"/>
 248         </fileset>
 249       </move>
 250
 251       <axis-wsdl2java
 252       output="${sourceDir}"
 253       verbose="true"
 254       url="${wsdl.MsaWS2}"
 255       serverside="false"
 256       deployscope="Request"
 257       debug="false"
 258       helpergen="true"
 259       all="true"
 260       >
 261       <mappingSet>
 262         <mapping
 263         namespace="${wsdl.Namespace}"
 264         package="${wsdl.ClientNS}"
 265         />
 266         <mapping namespace="http://dataTypes.vamsas"
 267         package="${wsdl.ClientNS}"/>
 268         </mappingSet>
 269     </axis-wsdl2java>
 270
 271   </target>
 272   <target name="package" depends="init, build">
 273
 274   </target>
 275   <!-- jalopy code reformatter -->
 276   <target name="sourcescrub" depends="init,build">
 277     <jalopy destdir="jsrc" classpathref="run.classpath"
 278       convention="jalview-jalopy.xml">
 279       <fileset dir="${sourceDir}">
 280         <include name="*.java"/>
 281         <include name="**/*.java"/>
 282         <include name="**/**/*.java"/>
 283       </fileset>
 284       </jalopy>
 285   </target>
 286
 287
 288
 289   <!-- Compile, package and obfuscate Jalview Applet -->
 290   <target name="makeApplet" depends="obfuscate"/>
 291
 292   <target name="compileApplet" depends="init,clean">
 293     <mkdir dir="${outputDir}"/>
 294     <javac source="1.2" target="1.1" srcdir="${sourceDir}" destdir="${outputDir}"
 295        includes="jalview/analysis/**,jalview/appletgui/**,jalview/datamodel/**jalview/jbappletgui/**,jalview/math/**,jalview/schemes/**"
 296        excludes="ext/**,MCview/**,org/**,vamsas/**"/>
 297   </target>
 298
 299   <target name="packageApplet" depends="compileApplet">
 300        <jar destfile="in.jar">
 301         <fileset dir="${outputDir}">
 302           <include name="com/**"/>
 303           <include name="jalview/**"/>
 304           <include name="${resourceDir}/images/idwidth.gif"/>
 305         </fileset>
 306       </jar>
 307   </target>
 308
 309   <target name="obfuscate" depends="packageApplet">
 310     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 311     <proguard>
 312       -libraryjars "${java.home}/lib/rt.jar"
 313       -injars      in.jar
 314       -outjars     jalviewApplet.jar
 315       -keep public class jalview.bin.JalviewLite
 316     </proguard>
 317     <delete file="in.jar"/>
 318   </target>
 319
 320
 321 </project>