2 <project name="jalviewX" default="usage" basedir=".">
3 <!-- we use jalopy to format our sources -->
5 classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
7 <fileset dir="utils/jalopy/lib">
8 <include name="*.jar" />
13 <target name="help" depends="usage"/>
15 <echo message="~~~Jalview Ant build.xml Usage~~~~"/>
16 <echo message="Targets include:"/>
17 <echo message="usage - default target, displays this message"/>
18 <echo message="buildindices - generates JavaHelpSearch from the help files"/>
19 <echo message="build - compiles all necessary files for Application"/>
20 <echo message="makedist - compiles and places all necessary jar files into directory dist"/>
21 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution"/>
22 <echo message=" this needs a keystore and key. See docs/building.html for more information."/>
23 <echo message="compileApplet - compiles all necessary files for Applet"/>
24 <echo message="makeApplet - compiles, then packages and obfuscates the Applet"/>
25 <echo message="See docs/building.html and the comments in build file for other targets."/>
26 <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk."/>
30 <!-- utils is a class path to additional utilities needed for
31 building docs, jars and webstart stuff -->
33 Userdefined build property defaults
35 wsdl.server list (plus namespace mapping info ???) - also want
36 ... to make this a dynamically generatable property
38 Build location - provide a temporary root for speed
39 jarsigner keystore and info
40 Jakarta and axis classpath ?
41 Default argument for starting Jalview (if it exists).
46 <path id="axis.classpath">
48 <fileset dir="/usr/local/axis/lib">
49 <include name="**/*.jar" />
51 <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
52 <include name="**/*.jar"/>
53 <include name="*.jar"/>
56 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
57 <property name="JALVIEW_VERSION" value="DEVELOPMENT"/> <!-- 2.4 (VAMSAS)" -->
58 <!-- Include debugging information in javac true or false -->
59 <property name="javac.debug" value="true"/>
60 <!-- Don't change anything below here unless you know what you are doing! -->
61 <!-- Url path for WebStart in JNLP file -->
62 <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
63 <!-- build directory configuration -->
64 <property name="libDir" value="lib"/>
65 <property name="resourceDir" value="resources"/>
66 <property name="helpDir" value="help"/>
67 <property name="docDir" value="doc"/>
68 <property name="sourceDir" value="src" />
69 <property name="schemaDir" value="schemas" />
70 <property name="outputDir" value="classes" />
71 <property name="packageDir" value="dist" />
72 <property name="outputJar" value="jalview.jar" />
73 <!-- Jalview Applet JMol Jar Dependency -->
74 <property name="jmolJar" value="Jmol-11.0.2.jar" />
75 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
76 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
77 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
78 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
79 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
80 <property name="WSInterf" value="MsaWS" />
81 <property name="wsdl.Namespace" value="vamsas" />
82 <property name="wsdl.ClientNS" value="ext.vamsas" />
83 <!-- the class path for building the application -->
84 <path id="build.classpath">
86 <include name="*.jar"/>
87 <include name="**/*.jar"/>
89 <fileset dir="${libDir}">
90 <include name="*.jar"/>
91 <include name="**/*.jar"/>
95 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz"/>
96 <!-- The Location of the java 1.1.8 jdk -->
97 <property name="java118.home" value="C:\Sun\jdk1.1.8" />
98 <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip"/>
99 <!-- jre for 1.4 version
100 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
102 <!-- the classpath for building the 1.1 applet -->
103 <path id="jalviewlite.deps">
104 <fileset dir="${java118.home}">
105 <include name="lib/classes.zip"/>
107 <pathelement location="lib/${jmolJar}"/>
112 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
113 <target name="buildPropertiesFile" depends="init">
114 <tstamp prefix="build">
115 <format property="date" pattern="dd MMMM yyyy"/>
117 <properties file="${outputDir}/.build_properties">
119 ---Jalview Build Details---
121 <property name="VERSION" value="${JALVIEW_VERSION}"/>
122 <property name="BUILD_DATE" value="${build.date}"/>
127 <target name="clean" depends="init">
128 <!-- not efficient yet. -->
129 <delete dir="${outputDir}"/>
132 <target name="distclean" depends="init, clean">
134 <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
137 <include name="${outputJar}"/>
138 <include name="#*#"/>
139 <include name="#*.*#"/>
140 <include name="**/#*#"/>
141 <include name="**/#*.*#"/>
143 <include name="*.*~"/>
144 <include name="**/*~"/>
145 <include name="**/*.*~"/>
150 <target name="prepare" depends="init">
151 <mkdir dir="${outputDir}"/>
152 <copy todir="${outputDir}">
154 <include name="${docDir}/**/*.*"/>
155 <include name="${helpDir}/**/*.*"/>
156 <include name="${libDir}/*.jar"/>
158 <fileset dir="${resourceDir}">
159 <include name="**/*.*"/>
164 <target name="build" depends="prepare">
165 <!-- not efficient yet. -->
166 <javac source="1.4" target="1.4"
167 srcdir ="${sourceDir}"
168 destdir="${outputDir}"
169 debug="${javac.debug}"
170 classpathref="build.classpath">
171 <exclude name="jalview/*applet*"/>
172 <exclude name="com/stevesoft/**"/>
175 <target name="buildindices" depends="init, prepare"
176 unless="help.uptodate">
178 classname="com.sun.java.help.search.Indexer"
179 classpathref="build.classpath"
181 dir="${outputDir}/${helpDir}"
187 <target name="makefulldist" depends="makedist">
188 <!-- the default keystore details might need to be edited here -->
190 storepass="alignmentisfun"
191 keypass="alignmentisfun"
192 keystore="keys/.keystore"
198 <fileset dir="${packageDir}">
199 <include name="*.jar"/>
202 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
204 <!-- codebase="http://www.jalview.org/jalview/webstart" -->
205 <jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
206 codebase="${WebStartLocation}">
208 <title>Jalview</title>
209 <vendor>The Barton Group</vendor>
210 <homepage href="http://www.jalview.org"/>
211 <description>Jalview Multiple Alignment Editor</description>
212 <description kind="short">Jalview</description>
213 <icon href="logo_big.gif"/>
216 <association mime-type="application-x/ext-file" extensions="fa"/>
217 <association mime-type="application-x/ext-file" extensions="fasta"/>
218 <association mime-type="application-x/ext-file" extensions="fastq"/>
219 <association mime-type="application-x/ext-file" extensions="blc"/>
220 <association mime-type="application-x/ext-file" extensions="msf"/>
221 <association mime-type="application-x/ext-file" extensions="pfam"/>
222 <association mime-type="application-x/ext-file" extensions="aln"/>
223 <association mime-type="application-x/ext-file" extensions="pir"/>
227 <j2se version="1.4+"/>
228 <fileset dir="${packageDir}">
229 <include name="jalview.jar"/>
231 <fileset dir="${packageDir}">
232 <include name="*.jar"/>
233 <exclude name="jalview.jar"/>
235 <property name="jalview.version" value="${JALVIEW_VERSION}"/>
237 <application_desc main_class="jalview.bin.Jalview">
244 <target name="runenv" depends="init">
245 <path id="run.classpath">
246 <pathelement location="${outputDir}"/>
247 <fileset dir="${outputDir}">
248 <include name="${libDir}/*.jar"/>
251 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
253 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
257 <target name="buildextclients" depends="init">
258 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
259 validargs="Y,y,n,N" defaultvalue="N"
260 addproperty="doextbuild.response"/>
261 <condition property="dontextbuild">
262 <equals arg1="n" arg2="${doextbuild.response}"/>
264 <condition property="dontextbuild">
265 <equals arg1="N" arg2="${doextbuild.response}"/>
267 <fail if="dontextbuild">
268 Build External Client Code process aborted by user. Jalview source is unchanged.
270 <!-- Currently, this doesn't happen automatically.
271 1. Run WSDL2Java as below, which generates an ext.vamsas +
272 vamsas.<datapackages> fileset.
273 2. refactor ext.vamsas.SpecificserviceWS* to
274 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
275 3. Update the jalview.ws.*WServices classes to reflect the
276 interface type, and all locations of this wsdl type that Jalview
280 <path id="axisbuild">
281 <path refid="build.classpath"/>
283 <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
285 <fileset dir="${sourceDir}" id="client">
286 <include name="${wsdl.ClientNS}/*.*"/>
291 output="${sourceDir}"
295 deployscope="Request"
302 namespace="${wsdl.Namespace}"
303 package="${wsdl.ClientNS}"
305 <mapping namespace="http://dataTypes.vamsas"
306 package="${wsdl.ClientNS}"/>
311 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
312 <!-- make the package jar -->
313 <mkdir dir="${packageDir}"/>
315 <jar destfile="${packageDir}/${outputJar}">
317 <attribute name="Main-Class" value="jalview.bin.Jalview"/>
319 <fileset dir="${outputDir}/">
320 <exclude name="cache*/**"/>
321 <exclude name="*.jar" />
322 <exclude name="*.jar.*" />
323 <exclude name="**/*.jar" />
324 <exclude name="**/*.jar.*" />
328 <copy toDir="${packageDir}" flatten="true">
329 <fileset dir="${outputDir}">
330 <include name="*.jar"/>
331 <include name="**/*.jar"/>
337 <!-- jalopy code reformatter -->
338 <target name="sourcescrub" depends="init,build">
339 <jalopy destdir="jsrc" classpathref="run.classpath"
340 convention="jalview-jalopy.xml">
341 <fileset dir="${sourceDir}">
342 <include name="*.java"/>
343 <include name="**/*.java"/>
344 <include name="**/**/*.java"/>
351 <!-- Compile, package and obfuscate Jalview Applet -->
352 <target name="makeApplet" depends="obfuscate"/>
354 <target name="compileApplet" depends="init,clean">
355 <mkdir dir="${outputDir}"/>
358 srcdir="${sourceDir}"
359 destdir="${outputDir}"
360 classpath="lib/${jmolJar}"
361 includes="jalview/appletgui/**"
362 excludes="ext/**,MCview/**,org/**,vamsas/**"
366 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
367 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
368 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
369 <jar destfile="in.jar">
371 <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
373 <fileset dir="${outputDir}">
374 <include name="com/**"/>
375 <include name="MCview/**"/>
376 <include name="jalview/**"/>
377 <include name=".build_properties"/>
378 <include name="images/idwidth.gif"/>
379 <include name="images/link.gif"/>
384 <target name="obfuscate" depends="packageApplet">
385 <path id="obfuscateDeps.path">
386 <pathelement location="${applet.jre.tools}"/>
387 <pathelement location="lib/${jmolJar}"/>
389 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
391 <injar file="in.jar"/>
392 <outjar file="jalviewApplet.jar"/>
393 <libraryjar refid="obfuscateDeps.path"/>
394 <keep access="public" type="class"
395 name="jalview.bin.JalviewLite">
396 <field access="public"/>
397 <method access="public"/>
398 <constructor access="public"/>
400 <!-- -libraryjars "${obfuscateDeps}"
402 -outjars jalviewApplet.jar
403 -keep public class jalview.bin.JalviewLite
407 <delete file="in.jar"/>
410 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
411 <taskdef name="castor-srcgen"
412 classname="org.castor.anttask.CastorCodeGenTask"
413 classpathref="build.classpath" />
415 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
416 <include name="*.java"/>
417 <include name="descriptors/*.java"/>
420 <castor-srcgen file="${schemaDir}/vamsas.xsd"
422 package="jalview.schemabinding.version2"
426 properties="${schemaDir}/jalview.properties"
428 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
430 package="jalview.schemabinding.version2"
434 properties="${schemaDir}/jalview.properties"
436 <castor-srcgen file="${schemaDir}/jalview.xsd"
438 package="jalview.schemabinding.version2"
442 properties="${schemaDir}/jalview.properties"
446 now build the jalview.binding package with the old schema set
449 <fileset dir="${sourceDir}/jalview/binding/">
453 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd"
455 package="jalview.binding"
459 properties="${schemaDir}/jalview.nodesc.properties"
461 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
463 package="jalview.binding"
467 properties="${schemaDir}/jalview.nodesc.properties"
469 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
471 package="jalview.binding"
475 properties="${schemaDir}/jalview.nodesc.properties"
478 <target name="sourcedist" description="create jalview source distribution" depends="init">
479 <delete file="${source.dist.name}"/>
480 <tar destfile="${source.dist.name}" compression="gzip">
481 <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
482 <include name="LICENSE"/>
483 <include name="README"/>
484 <include name="build.xml"/>
485 <include name="jalview-jalopy.xml"/>
486 <include name="JalviewApplet.jpx"/>
487 <include name="JalviewX.jpx"/>
488 <include name="${sourceDir}/*.java"/>
489 <include name="${sourceDir}/**/*.java"/>
490 <include name="${sourceDir}/**/*.cdr"/>
491 <include name="${libDir}/**/*"/>
492 <include name="${resourceDir}/**/*"/>
493 <include name="${helpDir}/**/*"/>
494 <include name="utils/**/*"/>
495 <include name="${schemaDir}/**/*"/>
496 <include name="${docDir}/**/*"/>