File: build.xml

package info (click to toggle)
jalview 2.7.dfsg-2
  • links: PTS, VCS
  • area: main
  • in suites: wheezy
  • size: 10,152 kB
  • sloc: java: 162,883; xml: 1,131; haskell: 43; makefile: 20; sh: 18
file content (584 lines) | stat: -rw-r--r-- 24,119 bytes parent folder | download | duplicates (3)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
<?xml version="1.0"?>
<!--
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 * 
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
-->
<project name="jalviewX" default="usage" basedir=".">
	<!-- we use jalopy to format our sources -->

	<target name="help" depends="usage" />
	<target name="usage">
		<echo message="~~~Jalview Ant build.xml Usage~~~~" />
		<echo message="Targets include:" />
		<echo message="usage - default target, displays this message" />
		<echo message="buildindices - generates JavaHelpSearch from the help files" />
		<echo message="build - compiles all necessary files for Application" />
		<echo message="makedist - compiles and places all necessary jar files into directory dist" />
		<echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
		<echo message="              this needs a keystore and key. See docs/building.html for more information." />
		<echo message="compileApplet - compiles all necessary files for Applet" />
		<echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
		<echo message="See docs/building.html and the comments in build file for other targets." />
		<echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
		<echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
	</target>


	<!-- utils is a class path to additional utilities needed for
    building docs, jars and webstart stuff -->
	<!--
        Userdefined build property defaults

        wsdl.server list (plus namespace mapping info ???)  - also want
                ... to make this a dynamically generatable property
        WebStart Location
        Build location - provide a temporary root for speed
        jarsigner keystore and info
        Jakarta and axis classpath ?
        Default argument for starting Jalview (if it exists).

-->

	<target name="init">
		<path id="axis.classpath">
			<!-->
			<fileset dir="/usr/local/axis/lib">
				<include name="**/*.jar" />
			</fileset>
			<fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
				<include name="**/*.jar"/>
				<include name="*.jar"/>
			</fileset> -->
      </path>
		<!-- Jalview Version String displayed by application on startup and used to check for updates -->
		<property name="JALVIEW_VERSION" value="DEVELOPMENT" />
		<!-- 2.4 (VAMSAS)" -->
		<!-- Include debugging information in javac true or false -->
		<property name="javac.debug" value="true" />

		<!-- JarSigner Key Store for Webstart Distribution -->
		<property name="jalview.keystore" value="./keys/.keystore" />
		<!-- Keystore Password -->
		<property name="jalview.keystore.pass" value="alignmentisfun" />
		<!-- Key Name -->
		<property name="jalview.key" value="jalview" />
		<!-- Key Password -->
		<property name="jalview.key.pass" value="alignmentisfun" />

		<!-- Don't change anything below here unless you know what you are doing! -->
		<!-- Url path for WebStart in JNLP file -->
		<property name="WebStartLocation" value="http://www.jalview.org/webstart" />
		<!-- build directory configuration -->
		<property name="libDir" value="lib" />
		<property name="resourceDir" value="resources" />
		<property name="helpDir" value="help" />
		<property name="docDir" value="doc" />
		<property name="sourceDir" value="src" />
		<property name="schemaDir" value="schemas" />
		<property name="outputDir" value="classes" />
		<property name="packageDir" value="dist" />
		<property name="outputJar" value="jalview.jar" />
		<!-- Jalview Applet JMol Jar Dependency -->
		<property name="jmolJar" value="JmolApplet-12.2.4.jar" />
		<property name="jalviewLiteJar" value="jalviewApplet.jar" />
		<!-- switch to indicate if we should obfuscate jalviewLite -->
		<!--<property name="donotobfuscate" value="true"/> -->

		<!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
		<property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
		<property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
		<property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
		<property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
		<property name="WSInterf" value="MsaWS" />
		<property name="wsdl.Namespace" value="vamsas" />
		<property name="wsdl.ClientNS" value="ext.vamsas" />
		<!-- the class path for building the application -->
		<path id="build.classpath">
			<fileset dir="${libDir}">
				<include name="*.jar" />
				<include name="**/*.jar" />
			</fileset>
			<fileset dir="${java.home}/lib">
				<include name="plugin.jar"/>
			</fileset>
			<fileset dir="appletlib">
				<!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
				-->
				<include name="${jmolJar}" />
			</fileset>

		</path>
		<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
		<!-- The Location of the java 1.1.8 jdk -->
		<!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
		-->
		<property name="java118.home" value="${java.home}" />
		    <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
		--><!-- jre for 1.4 version -->
		<property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
		
		<!-- the classpath for building the 1.1 applet -->
		<path id="jalviewlite.deps">
			<fileset dir="${java118.home}">
				<include name="lib/classes.zip" />
			</fileset>
			<fileset dir="${java.home}/lib">
				<include name="plugin.jar"/>
			</fileset>
			<pathelement location="appletlib/${jmolJar}" />
		</path>
    <!-- default location for outputting javadoc -->
    <property name="javadocDir" value="${packageDir}/javadoc"/>
	</target>


	<taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
	<target name="buildPropertiesFile" depends="init">
		<tstamp prefix="build">
			<format property="date" pattern="dd MMMM yyyy" />
		</tstamp>
		<properties file="${outputDir}/.build_properties">
			<header>
          ---Jalview Build Details---
        </header>
			<property name="VERSION" value="${JALVIEW_VERSION}" />
			<property name="BUILD_DATE" value="${build.date}" />
		</properties>
	</target>


	<target name="clean" depends="init">
		<!-- not efficient yet. -->
		<delete dir="${outputDir}" includes="*,**/*"/>
	</target>

	<target name="distclean" depends="init, clean">

		<echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
		<delete>
			<fileset dir=".">
				<include name="${outputJar}" />
				<include name="#*#" />
				<include name="#*.*#" />
				<include name="**/#*#" />
				<include name="**/#*.*#" />
				<include name="*~" />
				<include name="*.*~" />
				<include name="**/*~" />
				<include name="**/*.*~" />
			</fileset>
		</delete>
	</target>

	<target name="prepare" depends="init">
		<mkdir dir="${outputDir}" />
		<copy todir="${outputDir}">
			<fileset dir=".">
				<include name="${docDir}/**/*.*" />
				<include name="${helpDir}/**/*.*" />
				<include name="${libDir}/*.jar" />
			</fileset>
			<fileset dir="${resourceDir}">
				<include name="**/*.*" />
			</fileset>
		</copy>
	</target>

	<target name="build" depends="prepare">
		<!-- not efficient yet. -->
		<javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
			<exclude name="jalview/*applet*" />
			<exclude name="jalview/appletgui/**" />
			<exclude name="com/stevesoft/**" />
		</javac>
	</target>
	<target name="buildindices" depends="init, prepare" unless="help.uptodate">
		<java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
			<arg line="html" />
		</java>
	</target>

	<target name="makefulldist" depends="makedist">
		<!-- the default keystore details might need to be edited here -->
		<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">

			<fileset dir="${packageDir}">
				<include name="*.jar" />
			</fileset>
		</signjar>
		<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />

		<!--    codebase="http://www.jalview.org/jalview/webstart" -->
		<!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
		<jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
			<information>
				<title>Jalview</title>
				<vendor>The Barton Group</vendor>
				<homepage href="http://www.jalview.org" />
				<description>Jalview Multiple Alignment Editor</description>
				<description kind="short">Jalview</description>
				<icon href="logo_big.gif" />
				<offline_allowed />
				<!--
	<association mime-type="application-x/ext-file" extensions="fa"/>
        <association mime-type="application-x/ext-file" extensions="fasta"/>
        <association mime-type="application-x/ext-file" extensions="fastq"/>
        <association mime-type="application-x/ext-file" extensions="blc"/>
        <association mime-type="application-x/ext-file" extensions="msf"/>
        <association mime-type="application-x/ext-file" extensions="pfam"/>
        <association mime-type="application-x/ext-file" extensions="aln"/>
        <association mime-type="application-x/ext-file" extensions="pir"/>
        <association mime-type="application-x/ext-file" extensions="amsa"/>
	-->
			</information>
			<resources>
				<j2se version="1.5+" initial_heap_size="10M" />
				<fileset dir="${packageDir}">
					<include name="jalview.jar" />
				</fileset>
				<fileset dir="${packageDir}">
					<include name="*.jar" />
					<include name="*_*.jar" />
					<exclude name="jalview.jar" />
				</fileset>
				<property name="jalview.version" value="${JALVIEW_VERSION}" />
			</resources>
			<application_desc main_class="jalview.bin.Jalview">
			</application_desc>
			<security>
				<all_permissions />
			</security>
		</jnlp>
		<!-- the rest of these jnlp tasks are copy and pastes of the above but with different Vm args -->
		<jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
			<information>
				<title>Jalview</title>
				<vendor>The Barton Group</vendor>
				<homepage href="http://www.jalview.org" />
				<description>Jalview Multiple Alignment Editor</description>
				<description kind="short">Jalview</description>
				<icon href="logo_big.gif" />
				<offline_allowed />
				<!--
		<association mime-type="application-x/ext-file" extensions="fa"/>
	        <association mime-type="application-x/ext-file" extensions="fasta"/>
	        <association mime-type="application-x/ext-file" extensions="fastq"/>
	        <association mime-type="application-x/ext-file" extensions="blc"/>
	        <association mime-type="application-x/ext-file" extensions="msf"/>
	        <association mime-type="application-x/ext-file" extensions="pfam"/>
	        <association mime-type="application-x/ext-file" extensions="aln"/>
	        <association mime-type="application-x/ext-file" extensions="pir"/>
	        <association mime-type="application-x/ext-file" extensions="amsa"/>
		-->
			</information>
			<resources>
				<j2se version="1.5+" initial_heap_size="64M" max_heap_size="512M" />
				<fileset dir="${packageDir}">
					<include name="jalview.jar" />
				</fileset>
				<fileset dir="${packageDir}">
					<include name="*.jar" />
					<include name="*_*.jar" />
					<exclude name="jalview.jar" />
				</fileset>
				<property name="jalview.version" value="${JALVIEW_VERSION}" />
			</resources>
			<application_desc main_class="jalview.bin.Jalview">
			</application_desc>
			<security>
				<all_permissions />
			</security>
		</jnlp>
		<jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
			<information>
				<title>Jalview</title>
				<vendor>The Barton Group</vendor>
				<homepage href="http://www.jalview.org" />
				<description>Jalview Multiple Alignment Editor</description>
				<description kind="short">Jalview</description>
				<icon href="logo_big.gif" />
				<offline_allowed />
				<!--
			<association mime-type="application-x/ext-file" extensions="fa"/>
		        <association mime-type="application-x/ext-file" extensions="fasta"/>
		        <association mime-type="application-x/ext-file" extensions="fastq"/>
		        <association mime-type="application-x/ext-file" extensions="blc"/>
		        <association mime-type="application-x/ext-file" extensions="msf"/>
		        <association mime-type="application-x/ext-file" extensions="pfam"/>
		        <association mime-type="application-x/ext-file" extensions="aln"/>
		        <association mime-type="application-x/ext-file" extensions="pir"/>
		        <association mime-type="application-x/ext-file" extensions="amsa"/>
			-->
			</information>
			<resources>
				<j2se version="1.5+" initial_heap_size="256M" max_heap_size="1024M" />
				<fileset dir="${packageDir}">
					<include name="jalview.jar" />
				</fileset>
				<fileset dir="${packageDir}">
					<include name="*.jar" />
					<include name="*_*.jar" />
					<exclude name="jalview.jar" />
				</fileset>
				<property name="jalview.version" value="${JALVIEW_VERSION}" />
			</resources>
			<application_desc main_class="jalview.bin.Jalview">
			</application_desc>
			<security>
				<all_permissions />
			</security>
		</jnlp>

	</target>

	<target name="runenv" depends="init">
		<path id="run.classpath">
			<pathelement location="${outputDir}" />
			<fileset dir="${outputDir}">
				<include name="${libDir}/*.jar" />
			</fileset>
		</path>
		<pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />

		<echo>java -classpath ${run.classpath} jalview.bin.Jalview
      </echo>
	</target>

	<target name="buildextclients" depends="init">
		<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" />
		<condition property="dontextbuild">
			<equals arg1="n" arg2="${doextbuild.response}" />
		</condition>
		<condition property="dontextbuild">
			<equals arg1="N" arg2="${doextbuild.response}" />
		</condition>
		<fail if="dontextbuild">
        Build External Client Code process aborted by user. Jalview source is unchanged.
      </fail>
		<!-- Currently, this doesn't happen automatically.
     1. Run WSDL2Java as below, which generates an ext.vamsas +
     vamsas.<datapackages> fileset.
     2. refactor ext.vamsas.SpecificserviceWS* to
     ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
     3. Update the jalview.ws.*WServices classes to reflect the
     interface type, and all locations of this wsdl type that Jalview
     might be using.

-->
		<path id="axisbuild">
			<path refid="build.classpath" />
		</path>
		<taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
		<move todir="./bak">
			<fileset dir="${sourceDir}" id="client">
				<include name="${wsdl.ClientNS}/*.*" />
			</fileset>
		</move>

		<axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
			<mappingSet>
				<mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
				<mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
			</mappingSet>
		</axis-wsdl2java>
	</target>

	<target name="makedist" depends="build, buildindices">
		<!-- make the package jar if not already existing -->
		<mkdir dir="${packageDir}" />
		<!-- clean dir if it already existed -->
		<delete>
			<fileset dir="${packageDir}">
				<include name="*.jar"/>
			</fileset>
		</delete>
		<jar destfile="${packageDir}/${outputJar}">
			<manifest>
				<attribute name="Main-Class" value="jalview.bin.Jalview" />
			</manifest>
			<fileset dir="${outputDir}/">
				<exclude name="cache*/**" />
				<exclude name="*.jar" />
				<exclude name="*.jar.*" />
				<exclude name="**/*.jar" />
				<exclude name="**/*.jar.*" />
			</fileset>
		</jar>

		<copy toDir="${packageDir}" flatten="true">
			<fileset dir="${outputDir}">
				<include name="*.jar" />
				<include name="**/*.jar" />
			</fileset>
		</copy>
	</target>


	<!-- jalopy code reformatter -->
	<target name="sourcescrub" depends="init,build">
		<jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
			<fileset dir="${sourceDir}">
				<include name="*.java" />
				<include name="**/*.java" />
				<include name="**/**/*.java" />
			</fileset>
		</jalopy>
	</target>



	<!-- Compile, package and obfuscate Jalview Applet -->
	<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>

	<target name="compileApplet" depends="init,clean">
		<mkdir dir="${outputDir}" />
		<javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
			classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
			excludes="ext/**,MCview/**,org/**,vamsas/**" />
	</target>

	<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
		<copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
		<copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
		<jar destfile="in.jar">
			<manifest>
				<attribute name="Main-Class" value="jalview.bin.JalviewLite" />
			</manifest>
			<fileset dir="${outputDir}">
				<include name="com/**" />
				<include name="MCview/**" />
				<include name="jalview/**" />
				<include name=".build_properties" />
				<include name="images/idwidth.gif" />
				<include name="images/link.gif" />
			</fileset>
		</jar>
	</target>
	<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
	</target>
	<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
		<copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
		<delete file="in.jar" />
	</target>
	<target name="-obfuscatereally" unless="donotobfuscate">

		<path id="obfuscateDeps.path">
			<pathelement location="${applet.jre.tools}" />
			<pathelement location="appletlib/${jmolJar}" />
		</path>
		<taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />

		<proguard>
			<injar file="in.jar" />
			<outjar file="${jalviewLiteJar}" />
			<libraryjar refid="obfuscateDeps.path" />
			<keep access="public" type="class" name="jalview.bin.JalviewLite">
				<field access="public" />
				<method access="public" />
				<constructor access="public" />
			</keep>
			<!--      -libraryjars "${obfuscateDeps}"
      -injars      in.jar
      -outjars     jalviewApplet.jar
      -keep public class jalview.bin.JalviewLite
       { public * ; } -->
		</proguard>
		<delete file="in.jar" />
	</target>

	<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
		<taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
		<delete>
			<fileset dir="${sourceDir}/jalview/schemabinding/version2">
				<include name="*.java" />
				<include name="descriptors/*.java" />
			</fileset>
		</delete>
		<castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
		<castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
		<castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
		<castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
		<!-- 
		now build the jalview.binding package with the old schema set
		-->
		<delete>
			<fileset dir="${sourceDir}/jalview/binding/">
				<include name="**" />
			</fileset>
		</delete>
		<castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
		<castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
		<castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
	</target>
	<target name="sourcedist" description="create jalview source distribution" depends="init">
		<delete file="${source.dist.name}" />
		<tar destfile="${source.dist.name}" compression="gzip">
			<tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
				<include name="LICENSE" />
				<include name="README" />
				<include name="build.xml" />
				<include name="jalview-jalopy.xml" />
				<include name="JalviewApplet.jpx" />
				<include name="JalviewX.jpx" />
				<include name="nbbuild.xml"/>
				<include name="nbproject/genfiles.properties"/>
        <include name="nbproject/project.properties"/>
        <include name="nbproject/project.xml"/>
				<include name="${sourceDir}/*.java" />
				<include name="${sourceDir}/**/*.java" />
				<include name="${sourceDir}/**/*.cdr" />
				<include name="${libDir}/**/*" />
				<include name="${resourceDir}/**/*" />
				<include name="${helpDir}/**/*" />
				<include name="appletlib/${jmolJar}" />
				<exclude name="**/*locales" />
				<exclude name="*locales/**" />
				<exclude name="utils/InstallAnywhere/**Build.iap_xml" />
				<exclude name="utils/InstallAnywhere/**Build*/**" />
				<exclude name="utils/InstallAnywhere/**Build*/**" />
				<exclude name="utils/InstallAnywhere/**locale*" />
				<exclude name="utils/InstallAnywhere/**locale*/**" />
				<include name="${schemaDir}/**/*" />
				<include name="utils/**/*" />
				<include name="${docDir}/**/*" />
				<include name="examples/**/*" />
			</tarfileset>
		</tar>
	</target>
	<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
	  <copy todir="${packageDir}/examples">
	  <fileset dir="examples">
	  	<include name="**/*"/>
	  	<include name="javascript/*"/>
      <include name="jmol/*"/>
	  </fileset>
	  	<fileset dir=".">
	  	<include name="jalviewApplet.jar"/>
	  		</fileset>
	  	<fileset dir="appletlib">
	  	      <include name="**/*"/>
	  	        </fileset>
	  </copy>
	  		
	</target>
	<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
	 <javadoc destdir="${javadocDir}">
	 	<packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
	 	</packageset>
	 	</javadoc>
	</target>
	
</project>