3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4 * Copyright (C) 2011 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" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
23 <fileset dir="utils/jalopy/lib">
24 <include name="*.jar" />
29 <target name="help" depends="usage" />
31 <echo message="~~~Jalview Ant build.xml Usage~~~~" />
32 <echo message="Targets include:" />
33 <echo message="usage - default target, displays this message" />
34 <echo message="buildindices - generates JavaHelpSearch from the help files" />
35 <echo message="build - compiles all necessary files for Application" />
36 <echo message="makedist - compiles and places all necessary jar files into directory dist" />
37 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
38 <echo message=" this needs a keystore and key. See docs/building.html for more information." />
39 <echo message="compileApplet - compiles all necessary files for Applet" />
40 <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
41 <echo message="See docs/building.html and the comments in build file for other targets." />
42 <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
43 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
47 <!-- utils is a class path to additional utilities needed for
48 building docs, jars and webstart stuff -->
50 Userdefined build property defaults
52 wsdl.server list (plus namespace mapping info ???) - also want
53 ... to make this a dynamically generatable property
55 Build location - provide a temporary root for speed
56 jarsigner keystore and info
57 Jakarta and axis classpath ?
58 Default argument for starting Jalview (if it exists).
63 <path id="axis.classpath">
65 <fileset dir="/usr/local/axis/lib">
66 <include name="**/*.jar" />
68 <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
69 <include name="**/*.jar"/>
70 <include name="*.jar"/>
73 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
74 <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
75 <!-- 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 <!-- J2SE version needed for webstart launch -->
92 <property name="j2sev" value="1.6+"/>
93 <!-- build directory configuration -->
94 <property name="libDir" value="lib" />
95 <property name="resourceDir" value="resources" />
96 <property name="helpDir" value="help" />
97 <property name="docDir" value="doc" />
98 <property name="sourceDir" value="src" />
99 <property name="schemaDir" value="schemas" />
100 <property name="outputDir" value="classes" />
101 <property name="packageDir" value="dist" />
102 <property name="outputJar" value="jalview.jar" />
103 <!-- Jalview Applet JMol Jar Dependency -->
104 <property name="jmolJar" value="JmolApplet-12.1.13.jar" />
105 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
106 <!-- switch to indicate if we should obfuscate jalviewLite -->
107 <!--<property name="donotobfuscate" value="true"/> -->
109 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
110 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
111 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
112 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
113 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
114 <property name="WSInterf" value="MsaWS" />
115 <property name="wsdl.Namespace" value="vamsas" />
116 <property name="wsdl.ClientNS" value="ext.vamsas" />
117 <!-- the class path for building the application -->
118 <path id="build.classpath">
119 <fileset dir="utils">
120 <include name="*.jar" />
121 <include name="**/*.jar" />
123 <fileset dir="${libDir}">
124 <include name="*.jar" />
125 <include name="**/*.jar" />
127 <fileset dir="${java.home}/lib">
128 <include name="plugin.jar"/>
130 <fileset dir="appletlib">
131 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
133 <include name="${jmolJar}" />
137 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
138 <!-- The Location of the java 1.1.8 jdk -->
139 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
141 <property name="java118.home" value="${java.home}" />
142 <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
143 --><!-- jre for 1.4 version -->
144 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
146 <!-- the classpath for building the 1.1 applet -->
147 <path id="jalviewlite.deps">
148 <fileset dir="${java118.home}">
149 <include name="lib/classes.zip" />
151 <fileset dir="${java.home}/lib">
152 <include name="plugin.jar"/>
154 <pathelement location="appletlib/${jmolJar}" />
156 <!-- default location for outputting javadoc -->
157 <property name="javadocDir" value="${packageDir}/javadoc"/>
161 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
162 <target name="buildPropertiesFile" depends="init">
163 <tstamp prefix="build">
164 <format property="date" pattern="dd MMMM yyyy" />
166 <properties file="${outputDir}/.build_properties">
168 ---Jalview Build Details---
170 <property name="VERSION" value="${JALVIEW_VERSION}" />
171 <property name="BUILD_DATE" value="${build.date}" />
176 <target name="clean" depends="init">
177 <!-- not efficient yet. -->
178 <delete dir="${outputDir}" includes="*,**/*"/>
181 <target name="distclean" depends="init, clean">
183 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
186 <include name="${outputJar}" />
187 <include name="#*#" />
188 <include name="#*.*#" />
189 <include name="**/#*#" />
190 <include name="**/#*.*#" />
191 <include name="*~" />
192 <include name="*.*~" />
193 <include name="**/*~" />
194 <include name="**/*.*~" />
199 <target name="prepare" depends="init">
200 <mkdir dir="${outputDir}" />
201 <copy todir="${outputDir}">
203 <include name="${docDir}/**/*.*" />
204 <include name="${helpDir}/**/*.*" />
205 <include name="${libDir}/*.jar" />
207 <fileset dir="${resourceDir}">
208 <include name="**/*.*" />
213 <target name="build" depends="prepare">
214 <!-- not efficient yet. -->
215 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
216 <exclude name="jalview/*applet*" />
217 <exclude name="jalview/appletgui/**" />
218 <exclude name="com/stevesoft/**" />
221 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
222 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
227 <target name="makefulldist" depends="makedist">
228 <!-- the default keystore details might need to be edited here -->
229 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
231 <fileset dir="${packageDir}">
232 <include name="*.jar" />
235 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
237 <!-- codebase="http://www.jalview.org/jalview/webstart" -->
238 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
239 <jnlp toFile="${packageDir}/jalview_noa.jnlp" codebase="${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"/>
258 <association mime-type="application-x/ext-file" extensions="stk"/>-->
261 <j2se version="${j2sev}" initial_heap_size="10M" />
262 <fileset dir="${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">
278 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
280 <title>Jalview</title>
281 <vendor>The Barton Group</vendor>
282 <homepage href="http://www.jalview.org" />
283 <description>Jalview Multiple Alignment Editor</description>
284 <description kind="short">Jalview</description>
285 <icon href="logo_big.gif" />
287 <association mime-type="application-x/ext-file" extensions="fa"/>
288 <association mime-type="application-x/ext-file" extensions="fasta"/>
289 <association mime-type="application-x/ext-file" extensions="fastq"/>
290 <association mime-type="application-x/ext-file" extensions="blc"/>
291 <association mime-type="application-x/ext-file" extensions="msf"/>
292 <association mime-type="application-x/ext-file" extensions="pfam"/>
293 <association mime-type="application-x/ext-file" extensions="aln"/>
294 <association mime-type="application-x/ext-file" extensions="pir"/>
295 <association mime-type="application-x/ext-file" extensions="amsa"/>
296 <association mime-type="application-x/ext-file" extensions="stk"/>
299 <j2se version="${j2sev}" initial_heap_size="10M"/>
300 <fileset dir="${packageDir}">
301 <include name="jalview.jar" />
303 <fileset dir="${packageDir}">
304 <include name="*.jar" />
305 <include name="*_*.jar" />
306 <exclude name="jalview.jar" />
308 <property name="jalview.version" value="${JALVIEW_VERSION}" />
310 <application_desc main_class="jalview.bin.Jalview">
317 <jnlp toFile="${packageDir}/jalview_noa_1G.jnlp" codebase="${WebStartLocation}">
319 <title>Jalview</title>
320 <vendor>The Barton Group</vendor>
321 <homepage href="http://www.jalview.org" />
322 <description>Jalview Multiple Alignment Editor</description>
323 <description kind="short">Jalview</description>
324 <icon href="logo_big.gif" />
327 <association mime-type="application-x/ext-file" extensions="fa"/>
328 <association mime-type="application-x/ext-file" extensions="fasta"/>
329 <association mime-type="application-x/ext-file" extensions="fastq"/>
330 <association mime-type="application-x/ext-file" extensions="blc"/>
331 <association mime-type="application-x/ext-file" extensions="msf"/>
332 <association mime-type="application-x/ext-file" extensions="pfam"/>
333 <association mime-type="application-x/ext-file" extensions="aln"/>
334 <association mime-type="application-x/ext-file" extensions="pir"/>
335 <association mime-type="application-x/ext-file" extensions="amsa"/>
336 <association mime-type="application-x/ext-file" extensions="stk"/>-->
339 <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
340 <fileset dir="${packageDir}">
341 <include name="jalview.jar" />
343 <fileset dir="${packageDir}">
344 <include name="*.jar" />
345 <include name="*_*.jar" />
346 <exclude name="jalview.jar" />
348 <property name="jalview.version" value="${JALVIEW_VERSION}" />
350 <application_desc main_class="jalview.bin.Jalview">
356 <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
358 <title>Jalview</title>
359 <vendor>The Barton Group</vendor>
360 <homepage href="http://www.jalview.org" />
361 <description>Jalview Multiple Alignment Editor</description>
362 <description kind="short">Jalview</description>
363 <icon href="logo_big.gif" />
365 <association mime-type="application-x/ext-file" extensions="fa"/>
366 <association mime-type="application-x/ext-file" extensions="fasta"/>
367 <association mime-type="application-x/ext-file" extensions="fastq"/>
368 <association mime-type="application-x/ext-file" extensions="blc"/>
369 <association mime-type="application-x/ext-file" extensions="msf"/>
370 <association mime-type="application-x/ext-file" extensions="pfam"/>
371 <association mime-type="application-x/ext-file" extensions="aln"/>
372 <association mime-type="application-x/ext-file" extensions="pir"/>
373 <association mime-type="application-x/ext-file" extensions="amsa"/>
374 <association mime-type="application-x/ext-file" extensions="stk"/>
377 <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
378 <fileset dir="${packageDir}">
379 <include name="jalview.jar" />
381 <fileset dir="${packageDir}">
382 <include name="*.jar" />
383 <include name="*_*.jar" />
384 <exclude name="jalview.jar" />
386 <property name="jalview.version" value="${JALVIEW_VERSION}" />
388 <application_desc main_class="jalview.bin.Jalview">
394 <jnlp toFile="${packageDir}/jalview_noac_2G.jnlp" codebase="${WebStartLocation}">
396 <title>Jalview</title>
397 <vendor>The Barton Group</vendor>
398 <homepage href="http://www.jalview.org" />
399 <description>Jalview Multiple Alignment Editor</description>
400 <description kind="short">Jalview</description>
401 <icon href="logo_big.gif" />
404 <association mime-type="application-x/ext-file" extensions="fa"/>
405 <association mime-type="application-x/ext-file" extensions="fasta"/>
406 <association mime-type="application-x/ext-file" extensions="fastq"/>
407 <association mime-type="application-x/ext-file" extensions="blc"/>
408 <association mime-type="application-x/ext-file" extensions="msf"/>
409 <association mime-type="application-x/ext-file" extensions="pfam"/>
410 <association mime-type="application-x/ext-file" extensions="aln"/>
411 <association mime-type="application-x/ext-file" extensions="pir"/>
412 <association mime-type="application-x/ext-file" extensions="amsa"/>
413 <association mime-type="application-x/ext-file" extensions="stk"/>
417 <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
418 <fileset dir="${packageDir}">
419 <include name="jalview.jar" />
421 <fileset dir="${packageDir}">
422 <include name="*.jar" />
423 <include name="*_*.jar" />
424 <exclude name="jalview.jar" />
426 <property name="jalview.version" value="${JALVIEW_VERSION}" />
428 <application_desc main_class="jalview.bin.Jalview">
434 <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
436 <title>Jalview</title>
437 <vendor>The Barton Group</vendor>
438 <homepage href="http://www.jalview.org" />
439 <description>Jalview Multiple Alignment Editor</description>
440 <description kind="short">Jalview</description>
441 <icon href="logo_big.gif" />
443 <association mime-type="application-x/ext-file" extensions="fa"/>
444 <association mime-type="application-x/ext-file" extensions="fasta"/>
445 <association mime-type="application-x/ext-file" extensions="fastq"/>
446 <association mime-type="application-x/ext-file" extensions="blc"/>
447 <association mime-type="application-x/ext-file" extensions="msf"/>
448 <association mime-type="application-x/ext-file" extensions="pfam"/>
449 <association mime-type="application-x/ext-file" extensions="aln"/>
450 <association mime-type="application-x/ext-file" extensions="pir"/>
451 <association mime-type="application-x/ext-file" extensions="amsa"/>
452 <association mime-type="application-x/ext-file" extensions="stk"/>
455 <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
456 <fileset dir="${packageDir}">
457 <include name="jalview.jar" />
459 <fileset dir="${packageDir}">
460 <include name="*.jar" />
461 <include name="*_*.jar" />
462 <exclude name="jalview.jar" />
464 <property name="jalview.version" value="${JALVIEW_VERSION}" />
466 <application_desc main_class="jalview.bin.Jalview">
475 <target name="runenv" depends="init">
476 <path id="run.classpath">
477 <pathelement location="${outputDir}" />
478 <fileset dir="${outputDir}">
479 <include name="${libDir}/*.jar" />
482 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
484 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
488 <target name="buildextclients" depends="init">
489 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
490 <condition property="dontextbuild">
491 <equals arg1="n" arg2="${doextbuild.response}" />
493 <condition property="dontextbuild">
494 <equals arg1="N" arg2="${doextbuild.response}" />
496 <fail if="dontextbuild">
497 Build External Client Code process aborted by user. Jalview source is unchanged.
499 <!-- Currently, this doesn't happen automatically.
500 1. Run WSDL2Java as below, which generates an ext.vamsas +
501 vamsas.<datapackages> fileset.
502 2. refactor ext.vamsas.SpecificserviceWS* to
503 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
504 3. Update the jalview.ws.*WServices classes to reflect the
505 interface type, and all locations of this wsdl type that Jalview
509 <path id="axisbuild">
510 <path refid="build.classpath" />
512 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
514 <fileset dir="${sourceDir}" id="client">
515 <include name="${wsdl.ClientNS}/*.*" />
519 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
521 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
522 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
527 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
528 <!-- make the package jar if not already existing -->
529 <mkdir dir="${packageDir}" />
530 <!-- clean dir if it already existed -->
532 <fileset dir="${packageDir}">
533 <include name="*.jar"/>
536 <jar destfile="${packageDir}/${outputJar}">
538 <attribute name="Main-Class" value="jalview.bin.Jalview" />
540 <fileset dir="${outputDir}/">
541 <exclude name="cache*/**" />
542 <exclude name="*.jar" />
543 <exclude name="*.jar.*" />
544 <exclude name="**/*.jar" />
545 <exclude name="**/*.jar.*" />
549 <copy toDir="${packageDir}" flatten="true">
550 <fileset dir="${outputDir}">
551 <include name="*.jar" />
552 <include name="**/*.jar" />
558 <!-- jalopy code reformatter -->
559 <target name="sourcescrub" depends="init,build">
560 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
561 <fileset dir="${sourceDir}">
562 <include name="*.java" />
563 <include name="**/*.java" />
564 <include name="**/**/*.java" />
571 <!-- Compile, package and obfuscate Jalview Applet -->
572 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
574 <target name="compileApplet" depends="init,clean">
575 <mkdir dir="${outputDir}" />
576 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
577 classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
578 excludes="ext/**,MCview/**,org/**,vamsas/**" />
581 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
582 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
583 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
584 <jar destfile="in.jar">
586 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
588 <fileset dir="${outputDir}">
589 <include name="com/**" />
590 <include name="MCview/**" />
591 <include name="jalview/**" />
592 <include name=".build_properties" />
593 <include name="images/idwidth.gif" />
594 <include name="images/link.gif" />
598 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
600 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
601 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
602 <delete file="in.jar" />
604 <target name="-obfuscatereally" unless="donotobfuscate">
606 <path id="obfuscateDeps.path">
607 <pathelement location="${applet.jre.tools}" />
608 <pathelement location="appletlib/${jmolJar}" />
610 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
613 <injar file="in.jar" />
614 <outjar file="${jalviewLiteJar}" />
615 <libraryjar refid="obfuscateDeps.path" />
616 <keep access="public" type="class" name="jalview.bin.JalviewLite">
617 <field access="public" />
618 <method access="public" />
619 <constructor access="public" />
621 <!-- -libraryjars "${obfuscateDeps}"
623 -outjars jalviewApplet.jar
624 -keep public class jalview.bin.JalviewLite
627 <delete file="in.jar" />
630 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
631 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
633 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
634 <include name="*.java" />
635 <include name="descriptors/*.java" />
638 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
639 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
640 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
641 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
643 now build the jalview.binding package with the old schema set
646 <fileset dir="${sourceDir}/jalview/binding/">
647 <include name="**" />
650 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
651 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
652 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
654 <target name="sourcedist" description="create jalview source distribution" depends="init">
655 <delete file="${source.dist.name}" />
656 <tar destfile="${source.dist.name}" compression="gzip">
657 <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
658 <include name="LICENSE" />
659 <include name="README" />
660 <include name="build.xml" />
661 <include name="jalview-jalopy.xml" />
662 <include name="JalviewApplet.jpx" />
663 <include name="JalviewX.jpx" />
664 <include name="nbbuild.xml"/>
665 <include name="nbproject/genfiles.properties"/>
666 <include name="nbproject/project.properties"/>
667 <include name="nbproject/project.xml"/>
668 <include name="${sourceDir}/*.java" />
669 <include name="${sourceDir}/**/*.java" />
670 <include name="${sourceDir}/**/*.cdr" />
671 <include name="${libDir}/**/*" />
672 <include name="${resourceDir}/**/*" />
673 <include name="${helpDir}/**/*" />
674 <include name="appletlib/${jmolJar}" />
675 <exclude name="**/*locales" />
676 <exclude name="*locales/**" />
677 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
678 <exclude name="utils/InstallAnywhere/**Build*/**" />
679 <exclude name="utils/InstallAnywhere/**Build*/**" />
680 <exclude name="utils/InstallAnywhere/**locale*" />
681 <exclude name="utils/InstallAnywhere/**locale*/**" />
682 <include name="${schemaDir}/**/*" />
683 <include name="utils/**/*" />
684 <include name="${docDir}/**/*" />
685 <include name="examples/**/*" />
689 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
690 <copy todir="${packageDir}/examples">
691 <fileset dir="examples">
692 <include name="**/*"/>
693 <include name="javascript/*"/>
694 <include name="jmol/*"/>
697 <include name="jalviewApplet.jar"/>
699 <fileset dir="appletlib">
700 <include name="**/*"/>
705 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
706 <javadoc destdir="${javadocDir}">
707 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">