3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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" />
90 <!-- Don't change anything below here unless you know what you are doing! -->
91 <!-- Url path for WebStart in JNLP file -->
92 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
93 <!-- Webstart Image - looked for in resources/images -->
94 <property name="WebStartImage" value="JalviewLogo_big.png"/>
95 <!-- J2SE version needed for webstart launch -->
96 <property name="j2sev" value="1.6+"/>
98 <!-- Permissions for running Java applets and applications. Defaults are those suitable for deploying jalview webstart/jalviewLite at www.jalview.org -->
99 <property name="application.codebase" value="*.jalview.org"/>
100 <property name="applet.codebase" value="*.jalview.org"/>
101 <property name="applet.caller-codebase" value="${applet.codebase}"/>
103 <!-- build directory configuration -->
104 <property name="libDir" value="lib" />
105 <property name="resourceDir" value="resources" />
106 <property name="helpDir" value="help" />
107 <property name="docDir" value="doc" />
108 <property name="sourceDir" value="src" />
109 <property name="schemaDir" value="schemas" />
110 <property name="outputDir" value="classes" />
111 <property name="packageDir" value="dist" />
112 <property name="outputJar" value="jalview.jar" />
113 <!-- Jalview Applet JMol Jar Dependency -->
114 <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
115 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
116 <!-- switch to indicate if we should obfuscate jalviewLite -->
117 <!--<property name="donotobfuscate" value="true"/> -->
119 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
120 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
121 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
122 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
123 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
124 <property name="WSInterf" value="MsaWS" />
125 <property name="wsdl.Namespace" value="vamsas" />
126 <property name="wsdl.ClientNS" value="ext.vamsas" />
127 <!-- the class path for building the application -->
128 <path id="build.classpath">
129 <fileset dir="utils">
130 <include name="*.jar" />
131 <include name="**/*.jar" />
133 <fileset dir="${libDir}">
134 <include name="*.jar" />
135 <include name="**/*.jar" />
137 <fileset dir="${java.home}/lib">
138 <include name="plugin.jar"/>
140 <fileset dir="appletlib">
141 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
143 <include name="${jmolJar}" />
147 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
148 <!-- The Location of the java 1.1.8 jdk -->
149 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
151 <property name="java118.home" value="${java.home}" />
152 <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
153 --><!-- jre for 1.4 version -->
154 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
156 <!-- the classpath for building the 1.1 applet -->
157 <path id="jalviewlite.deps">
158 <fileset dir="${java118.home}">
159 <include name="lib/classes.zip" />
161 <fileset dir="${java.home}/lib">
162 <include name="plugin.jar"/>
164 <pathelement location="appletlib/${jmolJar}" />
166 <!-- default location for outputting javadoc -->
167 <property name="javadocDir" value="${packageDir}/javadoc"/>
171 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
172 <target name="buildPropertiesFile" depends="init">
173 <tstamp prefix="build">
174 <format property="date" pattern="dd MMMM yyyy" />
176 <properties file="${outputDir}/.build_properties">
178 ---Jalview Build Details---
180 <property name="VERSION" value="${JALVIEW_VERSION}" />
181 <property name="BUILD_DATE" value="${build.date}" />
186 <target name="clean" depends="init">
187 <!-- not efficient yet. -->
188 <delete dir="${outputDir}" includes="*,**/*"/>
191 <target name="distclean" depends="init, clean">
193 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
196 <include name="${outputJar}" />
197 <include name="#*#" />
198 <include name="#*.*#" />
199 <include name="**/#*#" />
200 <include name="**/#*.*#" />
201 <include name="*~" />
202 <include name="*.*~" />
203 <include name="**/*~" />
204 <include name="**/*.*~" />
209 <target name="prepare" depends="init">
210 <mkdir dir="${outputDir}" />
211 <copy todir="${outputDir}">
213 <include name="${docDir}/**/*.*" />
214 <include name="${helpDir}/**/*.*" />
215 <include name="${libDir}/*.jar" />
217 <fileset dir="${resourceDir}">
218 <include name="**/*.*" />
223 <target name="build" depends="prepare">
224 <!-- not efficient yet. -->
225 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
226 <exclude name="jalview/*applet*" />
227 <exclude name="jalview/appletgui/**" />
228 <exclude name="com/stevesoft/**" />
231 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
232 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
237 <target name="makefulldist" depends="makedist">
238 <!-- the default keystore details might need to be edited here -->
239 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
241 <fileset dir="${packageDir}">
242 <include name="*.jar" />
245 <copy todir="${packageDir}">
246 <fileset dir="${resourceDir}/images">
247 <include name="${WebStartImage}"/>
251 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
253 <!-- codebase="http://www.jalview.org/jalview/webstart" -->
254 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
255 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
257 <title>Jalview</title>
258 <vendor>The Barton Group</vendor>
259 <homepage href="http://www.jalview.org" />
260 <description>Jalview Multiple Alignment Editor</description>
261 <description kind="short">Jalview</description>
262 <icon href="${WebStartImage}" />
266 <j2se version="${j2sev}" initial_heap_size="10M" />
267 <fileset dir="${packageDir}">
268 <include name="jalview.jar" />
270 <fileset dir="${packageDir}">
271 <include name="*.jar" />
272 <include name="*_*.jar" />
273 <exclude name="jalview.jar" />
275 <property name="jalview.version" value="${JALVIEW_VERSION}" />
277 <application_desc main_class="jalview.bin.Jalview">
283 <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
285 <title>Jalview</title>
286 <vendor>The Barton Group</vendor>
287 <homepage href="http://www.jalview.org" />
288 <description>Jalview Multiple Alignment Editor</description>
289 <description kind="short">Jalview</description>
290 <icon href="${WebStartImage}" />
294 <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
295 <fileset dir="${packageDir}">
296 <include name="jalview.jar" />
298 <fileset dir="${packageDir}">
299 <include name="*.jar" />
300 <include name="*_*.jar" />
301 <exclude name="jalview.jar" />
303 <property name="jalview.version" value="${JALVIEW_VERSION}" />
305 <application_desc main_class="jalview.bin.Jalview">
311 <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
313 <title>Jalview</title>
314 <vendor>The Barton Group</vendor>
315 <homepage href="http://www.jalview.org" />
316 <description>Jalview Multiple Alignment Editor</description>
317 <description kind="short">Jalview</description>
318 <icon href="${WebStartImage}" />
322 <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
323 <fileset dir="${packageDir}">
324 <include name="jalview.jar" />
326 <fileset dir="${packageDir}">
327 <include name="*.jar" />
328 <include name="*_*.jar" />
329 <exclude name="jalview.jar" />
331 <property name="jalview.version" value="${JALVIEW_VERSION}" />
333 <application_desc main_class="jalview.bin.Jalview">
339 <!-- finally, need to postprocess to add in associations at end of 'information' element
341 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
348 <association mime-type="application-x/ext-file" extensions="fa"/>
349 <association mime-type="application-x/ext-file" extensions="fasta"/>
350 <association mime-type="application-x/ext-file" extensions="fastq"/>
351 <association mime-type="application-x/ext-file" extensions="blc"/>
352 <association mime-type="application-x/ext-file" extensions="msf"/>
353 <association mime-type="application-x/ext-file" extensions="pfam"/>
354 <association mime-type="application-x/ext-file" extensions="aln"/>
355 <association mime-type="application-x/ext-file" extensions="pir"/>
356 <association mime-type="application-x/ext-file" extensions="amsa"/>
357 <association mime-type="application-x/ext-file" extensions="stk"/>
358 <association mime-type="application-x/ext-file" extensions="jar"/>-->
362 <target name="runenv" depends="init">
363 <path id="run.classpath">
364 <pathelement location="${outputDir}" />
365 <fileset dir="${outputDir}">
366 <include name="${libDir}/*.jar" />
369 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
371 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
375 <target name="buildextclients" depends="init">
376 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
377 <condition property="dontextbuild">
378 <equals arg1="n" arg2="${doextbuild.response}" />
380 <condition property="dontextbuild">
381 <equals arg1="N" arg2="${doextbuild.response}" />
383 <fail if="dontextbuild">
384 Build External Client Code process aborted by user. Jalview source is unchanged.
386 <!-- Currently, this doesn't happen automatically.
387 1. Run WSDL2Java as below, which generates an ext.vamsas +
388 vamsas.<datapackages> fileset.
389 2. refactor ext.vamsas.SpecificserviceWS* to
390 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
391 3. Update the jalview.ws.*WServices classes to reflect the
392 interface type, and all locations of this wsdl type that Jalview
396 <path id="axisbuild">
397 <path refid="build.classpath" />
399 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
401 <fileset dir="${sourceDir}" id="client">
402 <include name="${wsdl.ClientNS}/*.*" />
406 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
408 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
409 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
414 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
415 <!-- make the package jar if not already existing -->
416 <mkdir dir="${packageDir}" />
417 <!-- clean dir if it already existed -->
419 <fileset dir="${packageDir}">
420 <include name="*.jar"/>
423 <jar destfile="${packageDir}/${outputJar}" index="true">
425 <attribute name="Main-Class" value="jalview.bin.Jalview" />
426 <attribute name="Permissions" value="all-permissions" />
427 <!--<attribute name="Trusted-Lib" value="true" /> -->
428 <attribute name="Application-Name" value="Jalview Desktop"/>
429 <attribute name="Codebase" value="${application.codebase}"/>
431 <fileset dir="${outputDir}/">
432 <exclude name="cache*/**" />
433 <exclude name="*.jar" />
434 <exclude name="*.jar.*" />
435 <exclude name="**/*.jar" />
436 <exclude name="**/*.jar.*" />
440 <copy toDir="${packageDir}" flatten="true">
441 <fileset dir="${outputDir}">
442 <include name="*.jar" />
443 <include name="**/*.jar" />
449 <!-- jalopy code reformatter -->
450 <target name="sourcescrub" depends="init,build">
451 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
452 <fileset dir="${sourceDir}">
453 <include name="*.java" />
454 <include name="**/*.java" />
455 <include name="**/**/*.java" />
462 <!-- Compile, package and obfuscate Jalview Applet -->
463 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
465 <target name="compileApplet" depends="init,clean">
466 <mkdir dir="${outputDir}" />
467 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
468 classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
469 excludes="ext/**,MCview/**,org/**,vamsas/**" />
472 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
473 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
474 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
475 <copy todir="${outputDir}/lang">
476 <fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
477 <jar destfile="in.jar" index="true">
479 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
480 <attribute name="Application-Name" value="JalviewLite Applet"/>
481 <!-- <attribute name="Permissions" value="sandbox" /> -->
482 <!--<attribute name="Trusted-Lib" value="true" /> -->
483 <attribute name="Codebase" value="${applet.codebase}"/>
484 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
486 <fileset dir="${outputDir}">
487 <include name="com/**" />
488 <include name="MCview/**" />
489 <include name="jalview/**" />
490 <include name=".build_properties" />
491 <include name="images/idwidth.gif" />
492 <include name="images/link.gif" />
493 <include name="lang/**" />
497 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
499 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
500 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
501 <delete file="in.jar" />
503 <target name="-obfuscatereally" unless="donotobfuscate">
505 <path id="obfuscateDeps.path">
506 <pathelement location="${applet.jre.tools}" />
507 <pathelement location="appletlib/${jmolJar}" />
509 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
512 <injar file="in.jar" />
513 <outjar file="${jalviewLiteJar}" />
514 <libraryjar refid="obfuscateDeps.path" />
516 <keep access="public" type="class" name="jalview.bin.JalviewLite">
517 <field access="public" />
518 <method access="public" />
519 <constructor access="public" />
521 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
522 <field access="public" />
523 <method access="public" />
524 <constructor access="public" />
526 <!-- -libraryjars "${obfuscateDeps}"
528 -outjars jalviewApplet.jar
529 -keep public class jalview.bin.JalviewLite
532 <delete file="in.jar" />
535 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
536 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
538 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
539 <include name="*.java" />
540 <include name="descriptors/*.java" />
543 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
544 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
545 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
546 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
548 now build the jalview.binding package with the old schema set
551 <fileset dir="${sourceDir}/jalview/binding/">
552 <include name="**" />
555 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
556 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
557 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
559 <target name="sourcedist" description="create jalview source distribution" depends="init">
560 <delete file="${source.dist.name}" />
561 <tar destfile="${source.dist.name}" compression="gzip">
562 <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
563 <include name="LICENSE" />
564 <include name="README" />
565 <include name="build.xml" />
566 <include name="jalview-jalopy.xml" />
567 <include name="JalviewApplet.jpx" />
568 <include name="JalviewX.jpx" />
569 <include name="nbbuild.xml"/>
570 <include name="nbproject/genfiles.properties"/>
571 <include name="nbproject/project.properties"/>
572 <include name="nbproject/project.xml"/>
573 <include name="${sourceDir}/*.java" />
574 <include name="${sourceDir}/**/*.java" />
575 <include name="${sourceDir}/**/*.cdr" />
576 <include name="${libDir}/**/*" />
577 <include name="${resourceDir}/**/*" />
578 <include name="${helpDir}/**/*" />
579 <include name="appletlib/${jmolJar}" />
580 <exclude name="**/*locales" />
581 <exclude name="*locales/**" />
582 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
583 <exclude name="utils/InstallAnywhere/**Build*/**" />
584 <exclude name="utils/InstallAnywhere/**Build*/**" />
585 <exclude name="utils/InstallAnywhere/**locale*" />
586 <exclude name="utils/InstallAnywhere/**locale*/**" />
587 <include name="${schemaDir}/**/*" />
588 <include name="utils/**/*" />
589 <include name="${docDir}/**/*" />
590 <include name="examples/**/*" />
594 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
595 <copy todir="${packageDir}/examples">
596 <fileset dir="examples">
597 <include name="**/*"/>
598 <include name="javascript/*"/>
599 <include name="jmol/*"/>
602 <include name="jalviewApplet.jar"/>
604 <fileset dir="appletlib">
605 <include name="**/*"/>
608 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
609 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
611 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
612 <!-- <attribute name="Permissions" value="sandbox" /> -->
613 <!--<attribute name="Trusted-Lib" value="true" /> -->
614 <attribute name="Codebase" value="${applet.codebase}"/>
615 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
618 <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
619 <fileset dir="${packageDir}/examples">
620 <include name="*.jar" />
624 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
625 <javadoc destdir="${javadocDir}">
626 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">