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
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.
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.
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
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">
25 <fileset dir="utils/jalopy/lib">
26 <include name="*.jar" />
31 <target name="help" depends="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."/>
48 <!-- utils is a class path to additional utilities needed for
49 building docs, jars and webstart stuff -->
51 Userdefined build property defaults
53 wsdl.server list (plus namespace mapping info ???) - also want
54 ... to make this a dynamically generatable property
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).
64 <path id="axis.classpath">
66 <fileset dir="/usr/local/axis/lib">
67 <include name="**/*.jar" />
69 <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
70 <include name="**/*.jar"/>
71 <include name="*.jar"/>
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"/>
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"/>
84 <property name="jalview.key" value="jalview"/>
86 <property name="jalview.key.pass" value="alignmentisfun"/>
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"/> -->
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"/>
121 <fileset dir="${libDir}">
122 <include name="*.jar"/>
123 <include name="**/*.jar"/>
127 <property name="source.dist.name" value="${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"/>
134 <!-- the classpath for building the 1.1 applet -->
135 <path id="jalviewlite.deps">
136 <fileset dir="${java118.home}">
137 <include name="lib/classes.zip"/>
139 <pathelement location="lib/${jmolJar}"/>
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"/>
149 <properties file="${outputDir}/.build_properties">
151 ---Jalview Build Details---
153 <property name="VERSION" value="${JALVIEW_VERSION}"/>
154 <property name="BUILD_DATE" value="${build.date}"/>
159 <target name="clean" depends="init">
160 <!-- not efficient yet. -->
161 <delete dir="${outputDir}"/>
164 <target name="distclean" depends="init, clean">
166 <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
169 <include name="${outputJar}"/>
170 <include name="#*#"/>
171 <include name="#*.*#"/>
172 <include name="**/#*#"/>
173 <include name="**/#*.*#"/>
175 <include name="*.*~"/>
176 <include name="**/*~"/>
177 <include name="**/*.*~"/>
182 <target name="prepare" depends="init">
183 <mkdir dir="${outputDir}"/>
184 <copy todir="${outputDir}">
186 <include name="${docDir}/**/*.*"/>
187 <include name="${helpDir}/**/*.*"/>
188 <include name="${libDir}/*.jar"/>
190 <fileset dir="${resourceDir}">
191 <include name="**/*.*"/>
196 <target name="build" depends="prepare">
197 <!-- not efficient yet. -->
198 <javac source="1.4" target="1.4"
199 srcdir ="${sourceDir}"
200 destdir="${outputDir}"
201 debug="${javac.debug}"
202 classpathref="build.classpath">
203 <exclude name="jalview/*applet*"/>
204 <exclude name="com/stevesoft/**"/>
207 <target name="buildindices" depends="init, prepare"
208 unless="help.uptodate">
210 classname="com.sun.java.help.search.Indexer"
211 classpathref="build.classpath"
213 dir="${outputDir}/${helpDir}"
219 <target name="makefulldist" depends="makedist">
220 <!-- the default keystore details might need to be edited here -->
222 storepass="${jalview.keystore.pass}"
223 keypass="${jalview.key.pass}"
224 keystore="${jalview.keystore}"
225 alias="${jalview.key}"
230 <fileset dir="${packageDir}">
231 <include name="*.jar"/>
234 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
236 <!-- codebase="http://www.jalview.org/jalview/webstart" -->
237 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
238 <jnlp toFile="${packageDir}/jalview.jnlp"
239 codebase="${WebStartLocation}">
241 <title>Jalview</title>
242 <vendor>The Barton Group</vendor>
243 <homepage href="http://www.jalview.org"/>
244 <description>Jalview Multiple Alignment Editor</description>
245 <description kind="short">Jalview</description>
246 <icon href="logo_big.gif"/>
249 <association mime-type="application-x/ext-file" extensions="fa"/>
250 <association mime-type="application-x/ext-file" extensions="fasta"/>
251 <association mime-type="application-x/ext-file" extensions="fastq"/>
252 <association mime-type="application-x/ext-file" extensions="blc"/>
253 <association mime-type="application-x/ext-file" extensions="msf"/>
254 <association mime-type="application-x/ext-file" extensions="pfam"/>
255 <association mime-type="application-x/ext-file" extensions="aln"/>
256 <association mime-type="application-x/ext-file" extensions="pir"/>
257 <association mime-type="application-x/ext-file" extensions="amsa"/>
261 <j2se version="1.4+"/>
262 <fileset dir="${packageDir}">
263 <include name="jalview.jar"/>
265 <fileset dir="${packageDir}">
266 <include name="*.jar"/>
267 <include name="*_*.jar"/>
268 <exclude name="jalview.jar"/>
270 <property name="jalview.version" value="${JALVIEW_VERSION}"/>
272 <application_desc main_class="jalview.bin.Jalview">
279 <target name="runenv" depends="init">
280 <path id="run.classpath">
281 <pathelement location="${outputDir}"/>
282 <fileset dir="${outputDir}">
283 <include name="${libDir}/*.jar"/>
286 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
288 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
292 <target name="buildextclients" depends="init">
293 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
294 validargs="Y,y,n,N" defaultvalue="N"
295 addproperty="doextbuild.response"/>
296 <condition property="dontextbuild">
297 <equals arg1="n" arg2="${doextbuild.response}"/>
299 <condition property="dontextbuild">
300 <equals arg1="N" arg2="${doextbuild.response}"/>
302 <fail if="dontextbuild">
303 Build External Client Code process aborted by user. Jalview source is unchanged.
305 <!-- Currently, this doesn't happen automatically.
306 1. Run WSDL2Java as below, which generates an ext.vamsas +
307 vamsas.<datapackages> fileset.
308 2. refactor ext.vamsas.SpecificserviceWS* to
309 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
310 3. Update the jalview.ws.*WServices classes to reflect the
311 interface type, and all locations of this wsdl type that Jalview
315 <path id="axisbuild">
316 <path refid="build.classpath"/>
318 <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
320 <fileset dir="${sourceDir}" id="client">
321 <include name="${wsdl.ClientNS}/*.*"/>
326 output="${sourceDir}"
330 deployscope="Request"
337 namespace="${wsdl.Namespace}"
338 package="${wsdl.ClientNS}"
340 <mapping namespace="http://dataTypes.vamsas"
341 package="${wsdl.ClientNS}"/>
346 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
347 <!-- make the package jar -->
348 <mkdir dir="${packageDir}"/>
350 <jar destfile="${packageDir}/${outputJar}">
352 <attribute name="Main-Class" value="jalview.bin.Jalview"/>
354 <fileset dir="${outputDir}/">
355 <exclude name="cache*/**"/>
356 <exclude name="*.jar" />
357 <exclude name="*.jar.*" />
358 <exclude name="**/*.jar" />
359 <exclude name="**/*.jar.*" />
363 <copy toDir="${packageDir}" flatten="true">
364 <fileset dir="${outputDir}">
365 <include name="*.jar"/>
366 <include name="**/*.jar"/>
372 <!-- jalopy code reformatter -->
373 <target name="sourcescrub" depends="init,build">
374 <jalopy destdir="jsrc" classpathref="run.classpath"
375 convention="jalview-jalopy.xml">
376 <fileset dir="${sourceDir}">
377 <include name="*.java"/>
378 <include name="**/*.java"/>
379 <include name="**/**/*.java"/>
386 <!-- Compile, package and obfuscate Jalview Applet -->
387 <target name="makeApplet" depends="obfuscate"/>
389 <target name="compileApplet" depends="init,clean">
390 <mkdir dir="${outputDir}"/>
393 srcdir="${sourceDir}"
394 destdir="${outputDir}"
395 debug="${javac.debug}"
396 classpath="lib/${jmolJar}"
397 includes="jalview/appletgui/**"
398 excludes="ext/**,MCview/**,org/**,vamsas/**"
402 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
403 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
404 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
405 <jar destfile="in.jar">
407 <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
409 <fileset dir="${outputDir}">
410 <include name="com/**"/>
411 <include name="MCview/**"/>
412 <include name="jalview/**"/>
413 <include name=".build_properties"/>
414 <include name="images/idwidth.gif"/>
415 <include name="images/link.gif"/>
419 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
421 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
422 <copy file="in.jar" tofile="${jalviewLiteJar}" />
423 <delete file="in.jar"/>
425 <target name="-obfuscatereally" unless="donotobfuscate">
427 <path id="obfuscateDeps.path">
428 <pathelement location="${applet.jre.tools}"/>
429 <pathelement location="lib/${jmolJar}"/>
431 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
434 <injar file="in.jar"/>
435 <outjar file="${jalviewLiteJar}"/>
436 <libraryjar refid="obfuscateDeps.path"/>
437 <keep access="public" type="class"
438 name="jalview.bin.JalviewLite">
439 <field access="public"/>
440 <method access="public"/>
441 <constructor access="public"/>
443 <!-- -libraryjars "${obfuscateDeps}"
445 -outjars jalviewApplet.jar
446 -keep public class jalview.bin.JalviewLite
449 <delete file="in.jar"/>
452 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
453 <taskdef name="castor-srcgen"
454 classname="org.castor.anttask.CastorCodeGenTask"
455 classpathref="build.classpath" />
457 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
458 <include name="*.java"/>
459 <include name="descriptors/*.java"/>
462 <castor-srcgen file="${schemaDir}/vamsas.xsd"
464 package="jalview.schemabinding.version2"
468 properties="${schemaDir}/jalview.properties"
470 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
472 package="jalview.schemabinding.version2"
476 properties="${schemaDir}/jalview.properties"
478 <castor-srcgen file="${schemaDir}/jalview.xsd"
480 package="jalview.schemabinding.version2"
484 properties="${schemaDir}/jalview.properties"
488 now build the jalview.binding package with the old schema set
491 <fileset dir="${sourceDir}/jalview/binding/">
495 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd"
497 package="jalview.binding"
501 properties="${schemaDir}/jalview.nodesc.properties"
503 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
505 package="jalview.binding"
509 properties="${schemaDir}/jalview.nodesc.properties"
511 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
513 package="jalview.binding"
517 properties="${schemaDir}/jalview.nodesc.properties"
520 <target name="sourcedist" description="create jalview source distribution" depends="init">
521 <delete file="${source.dist.name}"/>
522 <tar destfile="${source.dist.name}" compression="gzip">
523 <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
524 <include name="LICENSE"/>
525 <include name="README"/>
526 <include name="build.xml"/>
527 <include name="jalview-jalopy.xml"/>
528 <include name="JalviewApplet.jpx"/>
529 <include name="JalviewX.jpx"/>
530 <include name="${sourceDir}/*.java"/>
531 <include name="${sourceDir}/**/*.java"/>
532 <include name="${sourceDir}/**/*.cdr"/>
533 <include name="${libDir}/**/*"/>
534 <include name="${resourceDir}/**/*"/>
535 <include name="${helpDir}/**/*"/>
536 <exclude name="**/*locales"/>
537 <exclude name="*locales/**"/>
538 <exclude name="utils/InstallAnywhere/**Build.iap_xml"/>
539 <exclude name="utils/InstallAnywhere/**Build*/**"/>
540 <exclude name="utils/InstallAnywhere/**Build*/**"/>
541 <exclude name="utils/InstallAnywhere/**locale*"/>
542 <exclude name="utils/InstallAnywhere/**locale*/**"/>
543 <include name="${schemaDir}/**/*"/>
544 <include name="utils/**/*"/>
545 <include name="${docDir}/**/*"/>