3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 <project name="jalviewX" default="usage" basedir=".">
20 <!-- we use jalopy to format our sources -->
21 <taskdef name="jalopy"
22 classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
24 <fileset dir="utils/jalopy/lib">
25 <include name="*.jar" />
30 <target name="help" depends="usage"/>
32 <echo message="~~~Jalview Ant build.xml Usage~~~~"/>
33 <echo message="Targets include:"/>
34 <echo message="usage - default target, displays this message"/>
35 <echo message="buildindices - generates JavaHelpSearch from the help files"/>
36 <echo message="build - compiles all necessary files for Application"/>
37 <echo message="makedist - compiles and places all necessary jar files into directory dist"/>
38 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution"/>
39 <echo message=" this needs a keystore and key. See docs/building.html for more information."/>
40 <echo message="compileApplet - compiles all necessary files for Applet"/>
41 <echo message="makeApplet - compiles, then packages and obfuscates the Applet"/>
42 <echo message="See docs/building.html and the comments in build file for other targets."/>
43 <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk."/>
44 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation"/>
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"/>
76 <!-- 2.4 (VAMSAS)" -->
77 <!-- Include debugging information in javac true or false -->
78 <property name="javac.debug" value="true"/>
80 <!-- JarSigner Key Store for Webstart Distribution -->
81 <property name="jalview.keystore" value="./keys/.keystore"/>
82 <!-- Keystore Password -->
83 <property name="jalview.keystore.pass" value="alignmentisfun"/>
85 <property name="jalview.key" value="jalview"/>
87 <property name="jalview.key.pass" value="alignmentisfun"/>
89 <!-- Don't change anything below here unless you know what you are doing! -->
90 <!-- Url path for WebStart in JNLP file -->
91 <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
92 <!-- build directory configuration -->
93 <property name="libDir" value="lib"/>
94 <property name="resourceDir" value="resources"/>
95 <property name="helpDir" value="help"/>
96 <property name="docDir" value="doc"/>
97 <property name="sourceDir" value="src" />
98 <property name="schemaDir" value="schemas" />
99 <property name="outputDir" value="classes" />
100 <property name="packageDir" value="dist" />
101 <property name="outputJar" value="jalview.jar" />
102 <!-- Jalview Applet JMol Jar Dependency -->
103 <property name="jmolJar" value="JmolApplet-12.1.11_dev.jar" />
104 <property name="jalviewLiteJar" value="jalviewApplet.jar"/>
105 <!-- switch to indicate if we should obfuscate jalviewLite -->
106 <!--<property name="donotobfuscate" value="true"/> -->
108 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
109 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
110 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
111 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
112 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
113 <property name="WSInterf" value="MsaWS" />
114 <property name="wsdl.Namespace" value="vamsas" />
115 <property name="wsdl.ClientNS" value="ext.vamsas" />
116 <!-- the class path for building the application -->
117 <path id="build.classpath">
118 <fileset dir="utils">
119 <include name="*.jar"/>
120 <include name="**/*.jar"/>
122 <fileset dir="${libDir}">
123 <include name="*.jar"/>
124 <include name="**/*.jar"/>
128 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz"/>
129 <!-- The Location of the java 1.1.8 jdk -->
130 <property name="java118.home" value="C:\Sun\jdk1.1.8" />
131 <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip"/>
132 <!-- jre for 1.4 version
133 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
135 <!-- the classpath for building the 1.1 applet -->
136 <path id="jalviewlite.deps">
137 <fileset dir="${java118.home}">
138 <include name="lib/classes.zip"/>
140 <pathelement location="appletlib/${jmolJar}"/>
145 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties"/>
146 <target name="buildPropertiesFile" depends="init">
147 <tstamp prefix="build">
148 <format property="date" pattern="dd MMMM yyyy"/>
150 <properties file="${outputDir}/.build_properties">
152 ---Jalview Build Details---
154 <property name="VERSION" value="${JALVIEW_VERSION}"/>
155 <property name="BUILD_DATE" value="${build.date}"/>
160 <target name="clean" depends="init">
161 <!-- not efficient yet. -->
162 <delete dir="${outputDir}"/>
165 <target name="distclean" depends="init, clean">
167 <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
170 <include name="${outputJar}"/>
171 <include name="#*#"/>
172 <include name="#*.*#"/>
173 <include name="**/#*#"/>
174 <include name="**/#*.*#"/>
176 <include name="*.*~"/>
177 <include name="**/*~"/>
178 <include name="**/*.*~"/>
183 <target name="prepare" depends="init">
184 <mkdir dir="${outputDir}"/>
185 <copy todir="${outputDir}">
187 <include name="${docDir}/**/*.*"/>
188 <include name="${helpDir}/**/*.*"/>
189 <include name="${libDir}/*.jar"/>
191 <fileset dir="${resourceDir}">
192 <include name="**/*.*"/>
197 <target name="build" depends="prepare">
198 <!-- not efficient yet. -->
199 <javac source="1.5" target="1.5"
200 srcdir ="${sourceDir}"
201 destdir="${outputDir}"
202 debug="${javac.debug}"
203 classpathref="build.classpath">
204 <exclude name="jalview/*applet*"/>
205 <exclude name="jalview/appletgui/**"/>
206 <exclude name="com/stevesoft/**"/>
209 <target name="buildindices" depends="init, prepare"
210 unless="help.uptodate">
212 classname="com.sun.java.help.search.Indexer"
213 classpathref="build.classpath"
215 dir="${outputDir}/${helpDir}"
221 <target name="makefulldist" depends="makedist">
222 <!-- the default keystore details might need to be edited here -->
223 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
225 <fileset dir="${packageDir}">
226 <include name="*.jar" />
229 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
231 <!-- codebase="http://www.jalview.org/jalview/webstart" -->
232 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
233 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
235 <title>Jalview</title>
236 <vendor>The Barton Group</vendor>
237 <homepage href="http://www.jalview.org" />
238 <description>Jalview Multiple Alignment Editor</description>
239 <description kind="short">Jalview</description>
240 <icon href="logo_big.gif" />
243 <association mime-type="application-x/ext-file" extensions="fa"/>
244 <association mime-type="application-x/ext-file" extensions="fasta"/>
245 <association mime-type="application-x/ext-file" extensions="fastq"/>
246 <association mime-type="application-x/ext-file" extensions="blc"/>
247 <association mime-type="application-x/ext-file" extensions="msf"/>
248 <association mime-type="application-x/ext-file" extensions="pfam"/>
249 <association mime-type="application-x/ext-file" extensions="aln"/>
250 <association mime-type="application-x/ext-file" extensions="pir"/>
251 <association mime-type="application-x/ext-file" extensions="amsa"/>
255 <j2se version="1.5+" initial_heap_size="10M"/>
256 <fileset dir="${packageDir}">
257 <include name="jalview.jar" />
259 <fileset dir="${packageDir}">
260 <include name="*.jar" />
261 <include name="*_*.jar" />
262 <exclude name="jalview.jar" />
264 <property name="jalview.version" value="${JALVIEW_VERSION}" />
266 <application_desc main_class="jalview.bin.Jalview">
272 <!-- the rest of these jnlp tasks are copy and pastes of the above but with different Vm args -->
273 <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
275 <title>Jalview</title>
276 <vendor>The Barton Group</vendor>
277 <homepage href="http://www.jalview.org" />
278 <description>Jalview Multiple Alignment Editor</description>
279 <description kind="short">Jalview</description>
280 <icon href="logo_big.gif" />
283 <association mime-type="application-x/ext-file" extensions="fa"/>
284 <association mime-type="application-x/ext-file" extensions="fasta"/>
285 <association mime-type="application-x/ext-file" extensions="fastq"/>
286 <association mime-type="application-x/ext-file" extensions="blc"/>
287 <association mime-type="application-x/ext-file" extensions="msf"/>
288 <association mime-type="application-x/ext-file" extensions="pfam"/>
289 <association mime-type="application-x/ext-file" extensions="aln"/>
290 <association mime-type="application-x/ext-file" extensions="pir"/>
291 <association mime-type="application-x/ext-file" extensions="amsa"/>
295 <j2se version="1.5+" initial_heap_size="64M" max_heap_size="512M"/>
296 <fileset dir="${packageDir}">
297 <include name="jalview.jar" />
299 <fileset dir="${packageDir}">
300 <include name="*.jar" />
301 <include name="*_*.jar" />
302 <exclude name="jalview.jar" />
304 <property name="jalview.version" value="${JALVIEW_VERSION}" />
306 <application_desc main_class="jalview.bin.Jalview">
312 <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
314 <title>Jalview</title>
315 <vendor>The Barton Group</vendor>
316 <homepage href="http://www.jalview.org" />
317 <description>Jalview Multiple Alignment Editor</description>
318 <description kind="short">Jalview</description>
319 <icon href="logo_big.gif" />
322 <association mime-type="application-x/ext-file" extensions="fa"/>
323 <association mime-type="application-x/ext-file" extensions="fasta"/>
324 <association mime-type="application-x/ext-file" extensions="fastq"/>
325 <association mime-type="application-x/ext-file" extensions="blc"/>
326 <association mime-type="application-x/ext-file" extensions="msf"/>
327 <association mime-type="application-x/ext-file" extensions="pfam"/>
328 <association mime-type="application-x/ext-file" extensions="aln"/>
329 <association mime-type="application-x/ext-file" extensions="pir"/>
330 <association mime-type="application-x/ext-file" extensions="amsa"/>
334 <j2se version="1.5+" initial_heap_size="256M" max_heap_size="1024M"/>
335 <fileset dir="${packageDir}">
336 <include name="jalview.jar" />
338 <fileset dir="${packageDir}">
339 <include name="*.jar" />
340 <include name="*_*.jar" />
341 <exclude name="jalview.jar" />
343 <property name="jalview.version" value="${JALVIEW_VERSION}" />
345 <application_desc main_class="jalview.bin.Jalview">
354 <target name="runenv" depends="init">
355 <path id="run.classpath">
356 <pathelement location="${outputDir}"/>
357 <fileset dir="${outputDir}">
358 <include name="${libDir}/*.jar"/>
361 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
363 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
367 <target name="buildextclients" depends="init">
368 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
369 validargs="Y,y,n,N" defaultvalue="N"
370 addproperty="doextbuild.response"/>
371 <condition property="dontextbuild">
372 <equals arg1="n" arg2="${doextbuild.response}"/>
374 <condition property="dontextbuild">
375 <equals arg1="N" arg2="${doextbuild.response}"/>
377 <fail if="dontextbuild">
378 Build External Client Code process aborted by user. Jalview source is unchanged.
380 <!-- Currently, this doesn't happen automatically.
381 1. Run WSDL2Java as below, which generates an ext.vamsas +
382 vamsas.<datapackages> fileset.
383 2. refactor ext.vamsas.SpecificserviceWS* to
384 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
385 3. Update the jalview.ws.*WServices classes to reflect the
386 interface type, and all locations of this wsdl type that Jalview
390 <path id="axisbuild">
391 <path refid="build.classpath"/>
393 <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
395 <fileset dir="${sourceDir}" id="client">
396 <include name="${wsdl.ClientNS}/*.*"/>
401 output="${sourceDir}"
405 deployscope="Request"
412 namespace="${wsdl.Namespace}"
413 package="${wsdl.ClientNS}"
415 <mapping namespace="http://dataTypes.vamsas"
416 package="${wsdl.ClientNS}"/>
421 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
422 <!-- make the package jar -->
423 <mkdir dir="${packageDir}"/>
425 <jar destfile="${packageDir}/${outputJar}">
427 <attribute name="Main-Class" value="jalview.bin.Jalview"/>
429 <fileset dir="${outputDir}/">
430 <exclude name="cache*/**"/>
431 <exclude name="*.jar" />
432 <exclude name="*.jar.*" />
433 <exclude name="**/*.jar" />
434 <exclude name="**/*.jar.*" />
438 <copy toDir="${packageDir}" flatten="true">
439 <fileset dir="${outputDir}">
440 <include name="*.jar"/>
441 <include name="**/*.jar"/>
447 <!-- jalopy code reformatter -->
448 <target name="sourcescrub" depends="init,build">
449 <jalopy destdir="jsrc" classpathref="run.classpath"
450 convention="jalview-jalopy.xml">
451 <fileset dir="${sourceDir}">
452 <include name="*.java"/>
453 <include name="**/*.java"/>
454 <include name="**/**/*.java"/>
461 <!-- Compile, package and obfuscate Jalview Applet -->
462 <target name="makeApplet" depends="obfuscate"/>
464 <target name="compileApplet" depends="init,clean">
465 <mkdir dir="${outputDir}"/>
468 srcdir="${sourceDir}"
469 destdir="${outputDir}"
470 debug="${javac.debug}"
471 classpath="appletlib/${jmolJar}"
472 includes="jalview/appletgui/**"
473 excludes="ext/**,MCview/**,org/**,vamsas/**"
477 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
478 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif"/>
479 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif"/>
480 <jar destfile="in.jar">
482 <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
484 <fileset dir="${outputDir}">
485 <include name="com/**"/>
486 <include name="MCview/**"/>
487 <include name="jalview/**"/>
488 <include name=".build_properties"/>
489 <include name="images/idwidth.gif"/>
490 <include name="images/link.gif"/>
494 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
496 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
497 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true"/>
498 <delete file="in.jar"/>
500 <target name="-obfuscatereally" unless="donotobfuscate">
502 <path id="obfuscateDeps.path">
503 <pathelement location="${applet.jre.tools}"/>
504 <pathelement location="appletlib/${jmolJar}"/>
506 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
509 <injar file="in.jar"/>
510 <outjar file="${jalviewLiteJar}"/>
511 <libraryjar refid="obfuscateDeps.path"/>
512 <keep access="public" type="class"
513 name="jalview.bin.JalviewLite">
514 <field access="public"/>
515 <method access="public"/>
516 <constructor access="public"/>
518 <!-- -libraryjars "${obfuscateDeps}"
520 -outjars jalviewApplet.jar
521 -keep public class jalview.bin.JalviewLite
524 <delete file="in.jar"/>
527 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
528 <taskdef name="castor-srcgen"
529 classname="org.castor.anttask.CastorCodeGenTask"
530 classpathref="build.classpath" />
532 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
533 <include name="*.java"/>
534 <include name="descriptors/*.java"/>
537 <castor-srcgen file="${schemaDir}/vamsas.xsd"
539 package="jalview.schemabinding.version2"
543 properties="${schemaDir}/jalview.properties"
545 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
547 package="jalview.schemabinding.version2"
551 properties="${schemaDir}/jalview.properties"
553 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd"
555 package="jalview.schemabinding.version2"
559 properties="${schemaDir}/jalview.properties"
561 <castor-srcgen file="${schemaDir}/jalview.xsd"
563 package="jalview.schemabinding.version2"
567 properties="${schemaDir}/jalview.properties"
571 now build the jalview.binding package with the old schema set
574 <fileset dir="${sourceDir}/jalview/binding/">
578 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd"
580 package="jalview.binding"
584 properties="${schemaDir}/jalview.nodesc.properties"
586 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
588 package="jalview.binding"
592 properties="${schemaDir}/jalview.nodesc.properties"
594 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
596 package="jalview.binding"
600 properties="${schemaDir}/jalview.nodesc.properties"
603 <target name="sourcedist" description="create jalview source distribution" depends="init">
604 <delete file="${source.dist.name}"/>
605 <tar destfile="${source.dist.name}" compression="gzip">
606 <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
607 <include name="LICENSE"/>
608 <include name="README"/>
609 <include name="build.xml"/>
610 <include name="jalview-jalopy.xml"/>
611 <include name="JalviewApplet.jpx"/>
612 <include name="JalviewX.jpx"/>
613 <include name="${sourceDir}/*.java"/>
614 <include name="${sourceDir}/**/*.java"/>
615 <include name="${sourceDir}/**/*.cdr"/>
616 <include name="${libDir}/**/*"/>
617 <include name="${resourceDir}/**/*"/>
618 <include name="${helpDir}/**/*"/>
619 <include name="appletlib/${jmolJar}"/>
620 <exclude name="**/*locales"/>
621 <exclude name="*locales/**"/>
622 <exclude name="utils/InstallAnywhere/**Build.iap_xml"/>
623 <exclude name="utils/InstallAnywhere/**Build*/**"/>
624 <exclude name="utils/InstallAnywhere/**Build*/**"/>
625 <exclude name="utils/InstallAnywhere/**locale*"/>
626 <exclude name="utils/InstallAnywhere/**locale*/**"/>
627 <include name="${schemaDir}/**/*"/>
628 <include name="utils/**/*"/>
629 <include name="${docDir}/**/*"/>