3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
4 * Copyright (C) 2014 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 <!-- we use jalopy to format our sources -->
22 <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
24 <fileset dir="utils/jalopy/lib">
25 <include name="*.jar" />
30 <target name="help" depends="usage" />
32 <echo message="~~~Jalview Ant build.xml Usage~~~~" />
33 <echo message="Targets include:" />
34 <echo message="usage - default target, displays this message" />
35 <echo message="buildindices - generates JavaHelpSearch from the help files" />
36 <echo message="build - compiles all necessary files for Application" />
37 <echo message="makedist - compiles and places all necessary jar files into directory dist" />
38 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
39 <echo message=" this needs a keystore and key. See docs/building.html for more information." />
40 <echo message="compileApplet - compiles all necessary files for Applet" />
41 <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
42 <echo message="See docs/building.html and the comments in build file for other targets." />
43 <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
44 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
48 <!-- utils is a class path to additional utilities needed for
49 building docs, jars and webstart stuff -->
51 Userdefined build property defaults
53 wsdl.server list (plus namespace mapping info ???) - also want
54 ... to make this a dynamically generatable property
56 Build location - provide a temporary root for speed
57 jarsigner keystore and info
58 Jakarta and axis classpath ?
59 Default argument for starting Jalview (if it exists).
64 <path id="axis.classpath">
66 <fileset dir="/usr/local/axis/lib">
67 <include name="**/*.jar" />
69 <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
70 <include name="**/*.jar"/>
71 <include name="*.jar"/>
74 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
75 <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
76 <!-- 2.4 (VAMSAS)" -->
77 <!-- Include debugging information in javac true or false -->
78 <property name="javac.debug" value="true" />
80 <!-- JarSigner Key Store for Webstart Distribution -->
81 <property name="jalview.keystore" value="./keys/.keystore" />
82 <!-- Keystore Password -->
83 <property name="jalview.keystore.pass" value="alignmentisfun" />
85 <property name="jalview.key" value="jalview" />
87 <property name="jalview.key.pass" value="alignmentisfun" />
89 <!-- Don't change anything below here unless you know what you are doing! -->
90 <!-- Url path for WebStart in JNLP file -->
91 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
92 <!-- Webstart Image - looked for in resources/images -->
93 <property name="WebStartImage" value="JalviewLogo_big.png"/>
94 <!-- J2SE version needed for webstart launch -->
95 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
96 <property name="j2sev" value="1.7+"/>
98 <!-- Permissions for running Java applets and applications. -->
99 <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
100 <property name="application.codebase" value="*.jalview.org" />
101 <!-- and allowing the applet to be deployed from any URL -->
102 <!-- 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 -->
103 <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
104 <property name="applet.caller-codebase" value="${applet.codebase}" />
106 <!-- build directory configuration -->
107 <property name="libDir" value="lib" />
108 <property name="resourceDir" value="resources" />
109 <property name="helpDir" value="help" />
110 <property name="docDir" value="doc" />
111 <property name="sourceDir" value="src" />
112 <property name="schemaDir" value="schemas" />
113 <property name="outputDir" value="classes" />
114 <property name="packageDir" value="dist" />
115 <property name="outputJar" value="jalview.jar" />
116 <!-- Jalview Applet JMol Jar Dependency -->
117 <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
118 <property name="varnaJar" value="VARNAv3-9.jar" />
119 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
120 <!-- switch to indicate if we should obfuscate jalviewLite -->
121 <!-- <property name="donotobfuscate" value="true"/> -->
122 <!-- switch to exclude associations from generated jnlp files -->
123 <!-- <property name="nojnlpfileassocs" value="true"/> -->
125 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
126 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
127 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
128 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
129 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
130 <property name="WSInterf" value="MsaWS" />
131 <property name="wsdl.Namespace" value="vamsas" />
132 <property name="wsdl.ClientNS" value="ext.vamsas" />
133 <!-- the class path for building the application -->
134 <path id="build.classpath">
135 <fileset dir="utils">
136 <include name="*.jar" />
137 <include name="**/*.jar" />
139 <fileset dir="${libDir}">
140 <include name="*.jar" />
141 <include name="**/*.jar" />
143 <fileset dir="${java.home}/lib">
144 <include name="plugin.jar"/>
146 <fileset dir="appletlib">
147 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
149 <include name="${jmolJar}" />
150 <include name="${varnaJar}" />
154 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
155 <!-- The Location of the java 1.1.8 jdk -->
156 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
157 <property name="java118.home" value="${java.home}" />
158 <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
160 <!-- jre for 1.4 version -->
161 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
163 <!-- the classpath for building the 1.1 applet -->
164 <path id="jalviewlite.deps">
165 <fileset dir="${java118.home}">
166 <include name="lib/classes.zip" />
168 <fileset dir="${java.home}/lib">
169 <include name="plugin.jar"/>
171 <pathelement location="appletlib/${jmolJar}" />
172 <pathelement location="lib/${varnaJar}" />
174 <!-- default location for outputting javadoc -->
175 <property name="javadocDir" value="${packageDir}/javadoc"/>
179 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
180 <target name="buildPropertiesFile" depends="init">
181 <tstamp prefix="build">
182 <format property="date" pattern="dd MMMM yyyy" />
184 <properties file="${outputDir}/.build_properties">
186 ---Jalview Build Details---
188 <property name="VERSION" value="${JALVIEW_VERSION}" />
189 <property name="BUILD_DATE" value="${build.date}" />
194 <target name="clean" depends="init">
195 <!-- not efficient yet. -->
196 <delete dir="${outputDir}" includes="*,**/*"/>
199 <target name="distclean" depends="init, clean">
201 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
204 <include name="${outputJar}" />
205 <include name="#*#" />
206 <include name="#*.*#" />
207 <include name="**/#*#" />
208 <include name="**/#*.*#" />
209 <include name="*~" />
210 <include name="*.*~" />
211 <include name="**/*~" />
212 <include name="**/*.*~" />
217 <target name="prepare" depends="init">
218 <mkdir dir="${outputDir}" />
219 <copy todir="${outputDir}">
221 <include name="${docDir}/**/*.*" />
222 <include name="${helpDir}/**/*.*" />
223 <include name="${libDir}/*.jar" />
225 <fileset dir="${resourceDir}">
226 <include name="**/*.*" />
231 <target name="build" depends="prepare">
232 <!-- not efficient yet. -->
233 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
234 <exclude name="jalview/*applet*" />
235 <exclude name="jalview/appletgui/**" />
236 <exclude name="com/stevesoft/**" />
239 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
240 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
245 <target name="makefulldist" depends="makedist">
246 <copy todir="${packageDir}">
247 <fileset dir="${resourceDir}/images">
248 <include name="${WebStartImage}"/>
252 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
254 <!-- create a dummy jar which will eventually contain the jnlp template -->
255 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
256 <fileset dir="${packageDir}">
257 <include name="jalview.jar" />
261 <mkdir dir="${packageDir}/JNLP-INF"/>
262 <antcall target="writejnlpf">
263 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
264 <param name="inih" value="*" />
265 <param name="maxh" value="*"/>
268 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
269 <fileset dir="${packageDir}">
270 <include name="JNLP-INF"/>
274 <antcall target="writejnlpf">
275 <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
276 <param name="inih" value="10M" />
277 <param name="maxh" value="256M"/>
280 <antcall target="writejnlpf">
281 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
282 <param name="inih" value="128M" />
283 <param name="maxh" value="512M"/>
286 <antcall target="writejnlpf">
287 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
288 <param name="inih" value="256M" />
289 <param name="maxh" value="1024M"/>
292 <!-- finally, need to postprocess to add in associations at end of 'information' element
294 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
301 <association mime-type="application-x/ext-file" extensions="fa"/>
302 <association mime-type="application-x/ext-file" extensions="fasta"/>
303 <association mime-type="application-x/ext-file" extensions="mfa"/>
304 <association mime-type="application-x/ext-file" extensions="fastq"/>
305 <association mime-type="application-x/ext-file" extensions="blc"/>
306 <association mime-type="application-x/ext-file" extensions="msf"/>
307 <association mime-type="application-x/ext-file" extensions="pfam"/>
308 <association mime-type="application-x/ext-file" extensions="aln"/>
309 <association mime-type="application-x/ext-file" extensions="pir"/>
310 <association mime-type="application-x/ext-file" extensions="amsa"/>
311 <association mime-type="application-x/ext-file" extensions="stk"/>
312 <association mime-type="application-x/ext-file" extensions="jar"/>-->
313 <!-- and sign the jars -->
314 <!-- the default keystore details might need to be edited here -->
315 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
316 <fileset dir="${packageDir}">
317 <include name="*.jar" />
322 <target name="runenv" depends="init">
323 <path id="run.classpath">
324 <pathelement location="${outputDir}" />
325 <fileset dir="${outputDir}">
326 <include name="${libDir}/*.jar" />
329 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
331 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
335 <target name="-generatejnlpf">
336 <presetdef name="jnlpf">
337 <jnlp codebase="${WebStartLocation}">
339 <title>Jalview</title>
340 <vendor>The Barton Group</vendor>
341 <homepage href="http://www.jalview.org" />
342 <description>Jalview Multiple Alignment Editor</description>
343 <description kind="short">Jalview</description>
344 <icon href="${WebStartImage}" />
348 <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
349 <fileset dir="${packageDir}">
350 <include name="jalview.jar" />
352 <fileset dir="${packageDir}">
353 <include name="*.jar" />
354 <include name="*_*.jar" />
355 <exclude name="jalview.jar" />
357 <property name="jalview.version" value="${JALVIEW_VERSION}" />
359 <application_desc main_class="jalview.bin.Jalview">
367 <jnlpf toFile="${jnlpFile}"/>
371 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
372 <echo message="Not adding JNLP File Associations"/>
375 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
376 <replace file="${jnlpFile}">
378 <![CDATA[</information>]]></replacetoken>
381 <association mime-type="application-x/ext-file" extensions="fa" />
382 <association mime-type="application-x/ext-file" extensions="fasta" />
383 <association mime-type="application-x/ext-file" extensions="mfa" />
384 <association mime-type="application-x/ext-file" extensions="fastq" />
385 <association mime-type="application-x/ext-file" extensions="blc" />
386 <association mime-type="application-x/ext-file" extensions="msf" />
387 <association mime-type="application-x/ext-file" extensions="pfam" />
388 <association mime-type="application-x/ext-file" extensions="aln"/>
389 <association mime-type="application-x/ext-file" extensions="pir"/>
390 <association mime-type="application-x/ext-file" extensions="amsa"/>
391 <association mime-type="application-x/ext-file" extensions="stk"/>
392 <association mime-type="application-x/ext-file" extensions="jvp"/>
393 </information>]]></replacevalue>
395 <echo message="Added file associations to JNLP file"/>
397 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
400 <target name="buildextclients" depends="init">
401 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
402 <condition property="dontextbuild">
403 <equals arg1="n" arg2="${doextbuild.response}" />
405 <condition property="dontextbuild">
406 <equals arg1="N" arg2="${doextbuild.response}" />
408 <fail if="dontextbuild">
409 Build External Client Code process aborted by user. Jalview source is unchanged.
411 <!-- Currently, this doesn't happen automatically.
412 1. Run WSDL2Java as below, which generates an ext.vamsas +
413 vamsas.<datapackages> fileset.
414 2. refactor ext.vamsas.SpecificserviceWS* to
415 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
416 3. Update the jalview.ws.*WServices classes to reflect the
417 interface type, and all locations of this wsdl type that Jalview
421 <path id="axisbuild">
422 <path refid="build.classpath" />
424 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
426 <fileset dir="${sourceDir}" id="client">
427 <include name="${wsdl.ClientNS}/*.*" />
431 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
433 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
434 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
439 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
440 <!-- make the package jar if not already existing -->
441 <mkdir dir="${packageDir}" />
442 <!-- clean dir if it already existed -->
444 <fileset dir="${packageDir}">
445 <include name="*.jar"/>
448 <jar destfile="${packageDir}/${outputJar}" index="true">
450 <attribute name="Main-Class" value="jalview.bin.Jalview" />
451 <attribute name="Permissions" value="all-permissions" />
452 <attribute name="Application-Name" value="Jalview Desktop" />
453 <attribute name="Codebase" value="${application.codebase}" />
455 <fileset dir="${outputDir}/">
456 <exclude name="cache*/**" />
457 <exclude name="*.jar" />
458 <exclude name="*.jar.*" />
459 <exclude name="**/*.jar" />
460 <exclude name="**/*.jar.*" />
464 <copy toDir="${packageDir}" flatten="true">
465 <fileset dir="${outputDir}">
466 <include name="*.jar" />
467 <include name="**/*.jar" />
473 <!-- jalopy code reformatter -->
474 <target name="sourcescrub" depends="init,build">
475 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
476 <fileset dir="${sourceDir}">
477 <include name="*.java" />
478 <include name="**/*.java" />
479 <include name="**/**/*.java" />
486 <!-- Compile, package and obfuscate Jalview Applet -->
487 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
489 <target name="compileApplet" depends="init,clean">
490 <mkdir dir="${outputDir}" />
491 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
492 classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
493 excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
496 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
497 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
498 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
499 <copy todir="${outputDir}/lang">
500 <fileset dir="${resourceDir}/lang">
501 <include name="**.*"/>
504 <jar destfile="in.jar" index="true">
506 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
507 <attribute name="Application-Name" value="JalviewLite" />
508 <attribute name="Codebase" value="${applet.codebase}" />
510 <fileset dir="${outputDir}">
511 <include name="com/**" />
512 <include name="MCview/**" />
513 <include name="jalview/**" />
514 <include name=".build_properties" />
515 <include name="images/idwidth.gif" />
516 <include name="images/link.gif" />
517 <include name="lang/**" />
521 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
523 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
524 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
525 <delete file="in.jar" />
527 <target name="-obfuscatereally" unless="donotobfuscate">
529 <path id="obfuscateDeps.path">
530 <pathelement location="${applet.jre.tools}" />
531 <pathelement location="appletlib/${jmolJar}" />
533 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
536 <injar file="in.jar" />
537 <outjar file="${jalviewLiteJar}" />
538 <libraryjar refid="obfuscateDeps.path" />
540 <keep access="public" type="class" name="jalview.bin.JalviewLite">
541 <field access="public" />
542 <method access="public" />
543 <constructor access="public" />
545 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
546 <field access="public" />
547 <method access="public" />
548 <constructor access="public" />
550 <!-- -libraryjars "${obfuscateDeps}"
552 -outjars jalviewApplet.jar
553 -keep public class jalview.bin.JalviewLite
556 <delete file="in.jar" />
559 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
560 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
562 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
563 <include name="*.java" />
564 <include name="descriptors/*.java" />
567 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
568 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
569 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
570 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
572 now build the jalview.binding package with the old schema set
575 <fileset dir="${sourceDir}/jalview/binding/">
576 <include name="**" />
579 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
580 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
581 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
583 <target name="sourcedist" description="create jalview source distribution" depends="init">
584 <delete file="${source.dist.name}" />
585 <tar destfile="${source.dist.name}" compression="gzip">
586 <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
587 <include name="LICENSE" />
588 <include name="README" />
589 <include name="build.xml" />
590 <include name="jalview-jalopy.xml" />
591 <include name="JalviewApplet.jpx" />
592 <include name="JalviewX.jpx" />
593 <include name="nbbuild.xml"/>
594 <include name="nbproject/genfiles.properties"/>
595 <include name="nbproject/project.properties"/>
596 <include name="nbproject/project.xml"/>
597 <include name="${sourceDir}/*.java" />
598 <include name="${sourceDir}/**/*.java" />
599 <include name="${sourceDir}/**/*.cdr" />
600 <include name="${libDir}/**/*" />
601 <include name="${resourceDir}/**/*" />
602 <include name="${helpDir}/**/*" />
603 <include name="appletlib/${jmolJar}" />
604 <exclude name="**/*locales" />
605 <exclude name="*locales/**" />
606 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
607 <exclude name="utils/InstallAnywhere/**Build*/**" />
608 <exclude name="utils/InstallAnywhere/**Build*/**" />
609 <exclude name="utils/InstallAnywhere/**locale*" />
610 <exclude name="utils/InstallAnywhere/**locale*/**" />
611 <include name="${schemaDir}/**/*" />
612 <include name="utils/**/*" />
613 <include name="${docDir}/**/*" />
614 <include name="examples/**/*" />
618 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
619 <copy todir="${packageDir}/examples">
620 <fileset dir="examples">
621 <include name="**/*"/>
622 <include name="javascript/*"/>
623 <include name="jmol/*"/>
626 <include name="${jalviewLiteJar}" />
628 <fileset dir="appletlib">
629 <include name="**/*"/>
632 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
633 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
635 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
636 <!-- <attribute name="Permissions" value="sandbox" /> -->
637 <!--<attribute name="Trusted-Lib" value="true" /> -->
638 <attribute name="Codebase" value="${applet.codebase}"/>
639 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
642 <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
643 <fileset dir="${packageDir}/examples">
644 <include name="*.jar" />
647 <presetdef name="ap_applet.jar">
648 <!-- build a signed applet with 'all-permissions' -
649 Needs 'param name="permissions' value="all-permissions"' in applet tag
650 JalviewLite+JmolApplet linked sequence/structure fails
651 Mixed code warnings are raised
653 <jar update="true" index="true">
655 <attribute name="Application-Name" value="JalviewLite" />
656 <attribute name="Permissions" value="all-permissions" />
657 <attribute name="Codebase" value="${applet.codebase}" />
658 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
659 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
663 <presetdef name="applet.jar">
664 <!-- build signed applet with sandbox permissions -
665 Needs 'param name="permissions' value="sandbox"' in applet tag
666 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
669 <jar update="true" index="true">
671 <attribute name="Application-Name" value="JalviewLite" />
672 <attribute name="Permissions" value="sandbox" />
673 <attribute name="Codebase" value="${applet.codebase}" />
674 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
675 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
679 <presetdef name="tl_applet.jar">
680 <!-- build signed applet with trusted library/trusted permissions -
681 Needs 'param name="permissions' value="all-permissions"' in applet tag
683 No mixed code warnings raised
684 Jmol/JalviewLite sequence/structure example doesn't link structures
685 Raises dialog asking user to allow page to control applet via LiveConnect javascript
689 <jar update="true" index="true">
691 <attribute name="Application-Name" value="JalviewLite" />
692 <attribute name="Permissions" value="all-permissions" />
693 <attribute name="Codebase" value="${applet.codebase}" />
694 <attribute name="Trusted-Only" value="true" />
695 <attribute name="Trusted-Library" value="true" />
699 <presetdef name="to_applet.jar">
700 <!-- not fully test variant (yet) -->
701 <jar update="true" index="true">
703 <attribute name="Application-Name" value="JalviewLite" />
704 <attribute name="Permissions" value="all-permissions" />
705 <attribute name="Codebase" value="${applet.codebase}" />
706 <attribute name="Trusted-Only" value="true" />
710 <!-- create differently privileged artefacts -->
711 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
712 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
713 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
714 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
715 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
716 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
717 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
718 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
719 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
720 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
721 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
722 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
723 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
724 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
725 <!-- finally, create manifest for original jars -->
726 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
727 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
729 <!-- todo - write examples/downloads for alternate versions of the applet -->
730 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
732 <fileset dir="${packageDir}/examples">
733 <exclude name="u_*.jar"/>
734 <include name="${jalviewLiteJar}" />
735 <include name="${jmolJar}" />
736 <include name="to_${jalviewLiteJar}" />
737 <include name="to_${jmolJar}" />
738 <include name="tl_${jalviewLiteJar}" />
739 <include name="tl_${jmolJar}" />
740 <include name="ap_${jalviewLiteJar}" />
741 <include name="ap_${jmolJar}" />
744 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
745 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
747 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
748 <javadoc destdir="${javadocDir}">
749 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">