3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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/>.
18 * The Jalview Authors are detailed in the 'AUTHORS' file.
20 <project name="jalviewX" default="usage" basedir=".">
21 <target name="help" depends="usage" />
23 <echo message="~~~Jalview Ant build.xml Usage~~~~" />
24 <echo message="Targets include:" />
25 <echo message="usage - default target, displays this message" />
26 <echo message="buildindices - generates JavaHelpSearch from the help files" />
27 <echo message="build - compiles all necessary files for Application" />
28 <echo message="makedist - compiles and places all necessary jar files into directory dist" />
29 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
30 <echo message=" this needs a keystore and key. See docs/building.html for more information." />
31 <echo message="compileApplet - compiles all necessary files for Applet" />
32 <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
33 <echo message="See docs/building.html and the comments in build file for other targets." />
34 <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
35 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
39 <!-- utils is a class path to additional utilities needed for
40 building docs, jars and webstart stuff -->
42 Userdefined build property defaults
44 wsdl.server list (plus namespace mapping info ???) - also want
45 ... to make this a dynamically generatable property
47 Build location - provide a temporary root for speed
48 jarsigner keystore and info
49 Jakarta and axis classpath ?
50 Default argument for starting Jalview (if it exists).
55 <path id="axis.classpath">
57 <fileset dir="/usr/local/axis/lib">
58 <include name="**/*.jar" />
60 <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
61 <include name="**/*.jar"/>
62 <include name="*.jar"/>
66 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
67 <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
69 <property name="INSTALLATION" value="Source" />
71 <!-- 2.4 (VAMSAS)" -->
72 <!-- Include debugging information in javac true or false -->
73 <property name="javac.debug" value="true" />
75 <!-- JarSigner Key Store for Webstart Distribution -->
76 <property name="jalview.keystore" value="./keys/.keystore" />
77 <!-- Keystore Password -->
78 <property name="jalview.keystore.pass" value="alignmentisfun" />
80 <property name="jalview.key" value="jalview" />
82 <property name="jalview.key.pass" value="alignmentisfun" />
84 <!-- Don't change anything below here unless you know what you are doing! -->
85 <!-- Url path for WebStart in JNLP file -->
86 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
87 <!-- Webstart Image - looked for in resources/images -->
88 <property name="WebStartImage" value="JalviewLogo_big.png"/>
89 <!-- J2SE version needed for webstart launch -->
90 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
91 <property name="j2sev" value="1.7+"/>
93 <!-- Permissions for running Java applets and applications. -->
94 <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
95 <property name="application.codebase" value="*.jalview.org" />
96 <!-- and allowing the applet to be deployed from any URL -->
97 <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
98 <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
99 <property name="applet.caller-codebase" value="${applet.codebase}" />
101 <!-- build directory configuration -->
102 <property name="libDir" value="lib" />
103 <property name="resourceDir" value="resources" />
104 <property name="helpDir" value="help" />
105 <property name="docDir" value="doc" />
106 <property name="sourceDir" value="src" />
107 <property name="schemaDir" value="schemas" />
108 <property name="outputDir" value="classes" />
109 <property name="packageDir" value="dist" />
110 <property name="outputJar" value="jalview.jar" />
111 <!-- Jalview Applet JMol Jar Dependency -->
112 <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
113 <property name="varnaJar" value="VARNAv3-91.jar" />
114 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
115 <!-- switch to indicate if we should obfuscate jalviewLite -->
116 <!-- <property name="donotobfuscate" value="true"/> -->
117 <!-- switch to exclude associations from generated jnlp files -->
118 <!-- <property name="nojnlpfileassocs" value="true"/> -->
120 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
121 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
122 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
123 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
124 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
125 <property name="WSInterf" value="MsaWS" />
126 <property name="wsdl.Namespace" value="vamsas" />
127 <property name="wsdl.ClientNS" value="ext.vamsas" />
128 <!-- the class path for building the application -->
129 <path id="build.classpath">
130 <fileset dir="utils">
131 <include name="*.jar" />
132 <include name="**/*.jar" />
134 <fileset dir="${libDir}">
135 <include name="*.jar" />
136 <include name="**/*.jar" />
138 <fileset dir="${java.home}/lib">
139 <include name="plugin.jar"/>
141 <fileset dir="appletlib">
142 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
144 <include name="${jmolJar}" />
145 <include name="${varnaJar}" />
149 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
150 <!-- The Location of the java 1.1.8 jdk -->
151 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
152 <property name="java118.home" value="${java.home}" />
153 <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
155 <!-- jre for 1.4 version -->
156 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
158 <!-- the classpath for building the 1.1 applet -->
159 <path id="jalviewlite.deps">
160 <fileset dir="${java118.home}">
161 <include name="lib/classes.zip" />
163 <fileset dir="${java.home}/lib">
164 <include name="plugin.jar"/>
166 <pathelement location="appletlib/${jmolJar}" />
167 <pathelement location="lib/${varnaJar}" />
169 <!-- default location for outputting javadoc -->
170 <property name="javadocDir" value="${packageDir}/javadoc"/>
174 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
175 <target name="buildPropertiesFile" depends="init">
176 <tstamp prefix="build">
177 <format property="date" pattern="dd MMMM yyyy" />
179 <properties file="${outputDir}/.build_properties">
181 ---Jalview Build Details---
183 <property name="VERSION" value="${JALVIEW_VERSION}" />
184 <property name="INSTALLATION" value="${INSTALLATION}" />
185 <property name="BUILD_DATE" value="${build.date}" />
190 <target name="clean" depends="init">
191 <!-- not efficient yet. -->
192 <delete dir="${outputDir}" includes="*,**/*"/>
195 <target name="distclean" depends="init, clean">
197 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
200 <include name="${outputJar}" />
201 <include name="#*#" />
202 <include name="#*.*#" />
203 <include name="**/#*#" />
204 <include name="**/#*.*#" />
205 <include name="*~" />
206 <include name="*.*~" />
207 <include name="**/*~" />
208 <include name="**/*.*~" />
213 <target name="prepare" depends="init">
214 <mkdir dir="${outputDir}" />
215 <copy todir="${outputDir}">
217 <include name="${docDir}/**/*.*" />
218 <include name="${helpDir}/**/*.*" />
219 <include name="${libDir}/*.jar" />
221 <fileset dir="${resourceDir}">
222 <include name="**/*.*" />
227 <target name="build" depends="prepare">
228 <!-- not efficient yet. -->
229 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
230 <exclude name="jalview/*applet*" />
231 <exclude name="jalview/appletgui/**" />
232 <exclude name="com/stevesoft/**" />
235 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
236 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
241 <target name="makefulldist" depends="makedist">
242 <copy todir="${packageDir}">
243 <fileset dir="${resourceDir}/images">
244 <include name="${WebStartImage}"/>
248 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
250 <!-- create a dummy jar which will eventually contain the jnlp template -->
251 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
252 <fileset dir="${packageDir}">
253 <include name="jalview.jar" />
257 <mkdir dir="${packageDir}/JNLP-INF"/>
258 <antcall target="writejnlpf">
259 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
260 <param name="inih" value="*" />
261 <param name="maxh" value="*"/>
264 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
265 <fileset dir="${packageDir}">
266 <include name="JNLP-INF"/>
270 <antcall target="writejnlpf">
271 <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
272 <param name="inih" value="10M" />
273 <param name="maxh" value="256M"/>
276 <antcall target="writejnlpf">
277 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
278 <param name="inih" value="128M" />
279 <param name="maxh" value="512M"/>
282 <antcall target="writejnlpf">
283 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
284 <param name="inih" value="256M" />
285 <param name="maxh" value="1024M"/>
288 <!-- finally, need to postprocess to add in associations at end of 'information' element
290 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
297 <association mime-type="application-x/ext-file" extensions="fa"/>
298 <association mime-type="application-x/ext-file" extensions="fasta"/>
299 <association mime-type="application-x/ext-file" extensions="mfa"/>
300 <association mime-type="application-x/ext-file" extensions="fastq"/>
301 <association mime-type="application-x/ext-file" extensions="blc"/>
302 <association mime-type="application-x/ext-file" extensions="msf"/>
303 <association mime-type="application-x/ext-file" extensions="pfam"/>
304 <association mime-type="application-x/ext-file" extensions="aln"/>
305 <association mime-type="application-x/ext-file" extensions="pir"/>
306 <association mime-type="application-x/ext-file" extensions="amsa"/>
307 <association mime-type="application-x/ext-file" extensions="stk"/>
308 <association mime-type="application-x/ext-file" extensions="jar"/>-->
309 <!-- and sign the jars -->
310 <!-- the default keystore details might need to be edited here -->
311 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
312 <fileset dir="${packageDir}">
313 <include name="*.jar" />
318 <target name="runenv" depends="init">
319 <path id="run.classpath">
320 <pathelement location="${outputDir}" />
321 <fileset dir="${outputDir}">
322 <include name="${libDir}/*.jar" />
325 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
327 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
331 <target name="-generatejnlpf">
332 <presetdef name="jnlpf">
333 <jnlp codebase="${WebStartLocation}">
335 <title>Jalview</title>
336 <vendor>The Barton Group</vendor>
337 <homepage href="http://www.jalview.org" />
338 <description>Jalview Multiple Alignment Editor</description>
339 <description kind="short">Jalview</description>
340 <icon href="${WebStartImage}" />
344 <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
345 <fileset dir="${packageDir}">
346 <include name="jalview.jar" />
348 <fileset dir="${packageDir}">
349 <include name="*.jar" />
350 <include name="*_*.jar" />
351 <exclude name="jalview.jar" />
352 <exclude name="*jnilib.jar"/>
355 <resources os="Mac OS X">
356 <property name="jalview.version" value="${JALVIEW_VERSION}" />
357 <fileset dir="${packageDir}">
358 <include name="*quaqua*.jnilib.jar"/>
362 <application_desc main_class="jalview.bin.Jalview">
370 <jnlpf toFile="${jnlpFile}"/>
374 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
375 <echo message="Not adding JNLP File Associations"/>
378 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
379 <replace file="${jnlpFile}">
381 <![CDATA[</information>]]></replacetoken>
384 <association mime-type="application-x/ext-file" extensions="fa" />
385 <association mime-type="application-x/ext-file" extensions="fasta" />
386 <association mime-type="application-x/ext-file" extensions="mfa" />
387 <association mime-type="application-x/ext-file" extensions="fastq" />
388 <association mime-type="application-x/ext-file" extensions="blc" />
389 <association mime-type="application-x/ext-file" extensions="msf" />
390 <association mime-type="application-x/ext-file" extensions="pfam" />
391 <association mime-type="application-x/ext-file" extensions="aln"/>
392 <association mime-type="application-x/ext-file" extensions="pir"/>
393 <association mime-type="application-x/ext-file" extensions="amsa"/>
394 <association mime-type="application-x/ext-file" extensions="stk"/>
395 <association mime-type="application-x/ext-file" extensions="jvp"/>
396 </information>]]></replacevalue>
398 <echo message="Added file associations to JNLP file"/>
400 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
403 <target name="buildextclients" depends="init">
404 <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" />
405 <condition property="dontextbuild">
406 <equals arg1="n" arg2="${doextbuild.response}" />
408 <condition property="dontextbuild">
409 <equals arg1="N" arg2="${doextbuild.response}" />
411 <fail if="dontextbuild">
412 Build External Client Code process aborted by user. Jalview source is unchanged.
414 <!-- Currently, this doesn't happen automatically.
415 1. Run WSDL2Java as below, which generates an ext.vamsas +
416 vamsas.<datapackages> fileset.
417 2. refactor ext.vamsas.SpecificserviceWS* to
418 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
419 3. Update the jalview.ws.*WServices classes to reflect the
420 interface type, and all locations of this wsdl type that Jalview
424 <path id="axisbuild">
425 <path refid="build.classpath" />
427 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
429 <fileset dir="${sourceDir}" id="client">
430 <include name="${wsdl.ClientNS}/*.*" />
434 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
436 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
437 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
442 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
443 <!-- make the package jar if not already existing -->
444 <mkdir dir="${packageDir}" />
445 <!-- clean dir if it already existed -->
447 <fileset dir="${packageDir}">
448 <include name="*.jar"/>
451 <jar destfile="${packageDir}/${outputJar}" index="true">
453 <attribute name="Main-Class" value="jalview.bin.Jalview" />
454 <attribute name="Permissions" value="all-permissions" />
455 <attribute name="Application-Name" value="Jalview Desktop" />
456 <attribute name="Codebase" value="${application.codebase}" />
458 <fileset dir="${outputDir}/">
459 <exclude name="cache*/**" />
460 <exclude name="*.jar" />
461 <exclude name="*.jar.*" />
462 <exclude name="**/*.jar" />
463 <exclude name="**/*.jar.*" />
467 <copy toDir="${packageDir}" flatten="true">
468 <fileset dir="${outputDir}">
469 <include name="*.jar" />
470 <include name="**/*.jar" />
476 <!-- jalopy code reformatter -->
477 <target name="sourcescrub" depends="init,build">
478 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
479 <fileset dir="${sourceDir}">
480 <include name="*.java" />
481 <include name="**/*.java" />
482 <include name="**/**/*.java" />
489 <!-- Compile, package and obfuscate Jalview Applet -->
490 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
492 <target name="compileApplet" depends="init,clean">
493 <mkdir dir="${outputDir}" />
494 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
495 classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
496 excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
499 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
500 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
501 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
502 <copy todir="${outputDir}/lang">
503 <fileset dir="${resourceDir}/lang">
504 <include name="**.*"/>
507 <jar destfile="in.jar" index="true">
509 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
510 <attribute name="Application-Name" value="JalviewLite" />
511 <attribute name="Codebase" value="${applet.codebase}" />
513 <fileset dir="${outputDir}">
514 <include name="com/**" />
515 <include name="MCview/**" />
516 <include name="jalview/**" />
517 <include name=".build_properties" />
518 <include name="images/idwidth.gif" />
519 <include name="images/link.gif" />
520 <include name="lang/**" />
524 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
526 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
527 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
528 <delete file="in.jar" />
530 <target name="-obfuscatereally" unless="donotobfuscate">
532 <path id="obfuscateDeps.path">
533 <pathelement location="${applet.jre.tools}" />
534 <pathelement location="appletlib/${jmolJar}" />
536 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
539 <injar file="in.jar" />
540 <outjar file="${jalviewLiteJar}" />
541 <libraryjar refid="obfuscateDeps.path" />
543 <keep access="public" type="class" name="jalview.bin.JalviewLite">
544 <field access="public" />
545 <method access="public" />
546 <constructor access="public" />
548 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
549 <field access="public" />
550 <method access="public" />
551 <constructor access="public" />
553 <!-- -libraryjars "${obfuscateDeps}"
555 -outjars jalviewApplet.jar
556 -keep public class jalview.bin.JalviewLite
559 <delete file="in.jar" />
562 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
563 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
565 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
566 <include name="*.java" />
567 <include name="descriptors/*.java" />
570 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
571 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
572 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
573 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
575 now build the jalview.binding package with the old schema set
578 <fileset dir="${sourceDir}/jalview/binding/">
579 <include name="**" />
582 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
583 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
584 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
586 <target name="sourcedist" description="create jalview source distribution" depends="init">
587 <delete file="${source.dist.name}" />
588 <tar destfile="${source.dist.name}" compression="gzip">
589 <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
590 <include name="LICENSE" />
591 <include name="README" />
592 <include name="build.xml" />
593 <include name="jalview-jalopy.xml" />
594 <include name="JalviewApplet.jpx" />
595 <include name="JalviewX.jpx" />
596 <include name="nbbuild.xml"/>
597 <include name="nbproject/genfiles.properties"/>
598 <include name="nbproject/project.properties"/>
599 <include name="nbproject/project.xml"/>
600 <include name="${sourceDir}/*.java" />
601 <include name="${sourceDir}/**/*.java" />
602 <include name="${sourceDir}/**/*.cdr" />
603 <include name="${libDir}/**/*" />
604 <include name="${resourceDir}/**/*" />
605 <include name="${helpDir}/**/*" />
606 <include name="appletlib/${jmolJar}" />
607 <exclude name="**/*locales" />
608 <exclude name="*locales/**" />
609 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
610 <exclude name="utils/InstallAnywhere/**Build*/**" />
611 <exclude name="utils/InstallAnywhere/**Build*/**" />
612 <exclude name="utils/InstallAnywhere/**locale*" />
613 <exclude name="utils/InstallAnywhere/**locale*/**" />
614 <include name="${schemaDir}/**/*" />
615 <include name="utils/**/*" />
616 <include name="${docDir}/**/*" />
617 <include name="examples/**/*" />
621 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
622 <copy todir="${packageDir}/examples">
623 <fileset dir="examples">
624 <include name="**/*"/>
625 <include name="javascript/*"/>
626 <include name="jmol/*"/>
629 <include name="${jalviewLiteJar}" />
631 <fileset dir="appletlib">
632 <include name="**/*"/>
635 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
636 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
638 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
639 <!-- <attribute name="Permissions" value="sandbox" /> -->
640 <!--<attribute name="Trusted-Lib" value="true" /> -->
641 <attribute name="Codebase" value="${applet.codebase}"/>
642 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
645 <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
646 <fileset dir="${packageDir}/examples">
647 <include name="*.jar" />
650 <presetdef name="ap_applet.jar">
651 <!-- build a signed applet with 'all-permissions' -
652 Needs 'param name="permissions' value="all-permissions"' in applet tag
653 JalviewLite+JmolApplet linked sequence/structure fails
654 Mixed code warnings are raised
656 <jar update="true" index="true">
658 <attribute name="Application-Name" value="JalviewLite" />
659 <attribute name="Permissions" value="all-permissions" />
660 <attribute name="Codebase" value="${applet.codebase}" />
661 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
662 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
666 <presetdef name="applet.jar">
667 <!-- build signed applet with sandbox permissions -
668 Needs 'param name="permissions' value="sandbox"' in applet tag
669 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
672 <jar update="true" index="true">
674 <attribute name="Application-Name" value="JalviewLite" />
675 <attribute name="Permissions" value="sandbox" />
676 <attribute name="Codebase" value="${applet.codebase}" />
677 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
678 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
682 <presetdef name="tl_applet.jar">
683 <!-- build signed applet with trusted library/trusted permissions -
684 Needs 'param name="permissions' value="all-permissions"' in applet tag
686 No mixed code warnings raised
687 Jmol/JalviewLite sequence/structure example doesn't link structures
688 Raises dialog asking user to allow page to control applet via LiveConnect javascript
692 <jar update="true" index="true">
694 <attribute name="Application-Name" value="JalviewLite" />
695 <attribute name="Permissions" value="all-permissions" />
696 <attribute name="Codebase" value="${applet.codebase}" />
697 <attribute name="Trusted-Only" value="true" />
698 <attribute name="Trusted-Library" value="true" />
702 <presetdef name="to_applet.jar">
703 <!-- not fully test variant (yet) -->
704 <jar update="true" index="true">
706 <attribute name="Application-Name" value="JalviewLite" />
707 <attribute name="Permissions" value="all-permissions" />
708 <attribute name="Codebase" value="${applet.codebase}" />
709 <attribute name="Trusted-Only" value="true" />
713 <!-- create differently privileged artefacts -->
714 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
715 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
716 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
717 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
718 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
719 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
720 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
721 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
722 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
723 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
724 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
725 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
726 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
727 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
728 <!-- finally, create manifest for original jars -->
729 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
730 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
732 <!-- todo - write examples/downloads for alternate versions of the applet -->
733 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
735 <fileset dir="${packageDir}/examples">
736 <exclude name="u_*.jar"/>
737 <include name="${jalviewLiteJar}" />
738 <include name="${jmolJar}" />
739 <include name="to_${jalviewLiteJar}" />
740 <include name="to_${jmolJar}" />
741 <include name="tl_${jalviewLiteJar}" />
742 <include name="tl_${jmolJar}" />
743 <include name="ap_${jalviewLiteJar}" />
744 <include name="ap_${jmolJar}" />
747 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
748 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
749 <!-- finally, replace any launchApp servlet tags with a version specification -->
750 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
751 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
752 <fileset dir="${packageDir}/examples">
753 <include name="**/*.html"/>
756 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
757 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
758 <fileset dir="${packageDir}/examples">
759 <include name="**/*.html"/>
764 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
765 <javadoc destdir="${javadocDir}">
766 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">