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 <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"/>
65 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
66 <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
67 <!-- 2.4 (VAMSAS)" -->
68 <!-- Include debugging information in javac true or false -->
69 <property name="javac.debug" value="true" />
71 <!-- JarSigner Key Store for Webstart Distribution -->
72 <property name="jalview.keystore" value="./keys/.keystore" />
73 <!-- Keystore Password -->
74 <property name="jalview.keystore.pass" value="alignmentisfun" />
76 <property name="jalview.key" value="jalview" />
78 <property name="jalview.key.pass" value="alignmentisfun" />
80 <!-- Don't change anything below here unless you know what you are doing! -->
81 <!-- Url path for WebStart in JNLP file -->
82 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
83 <!-- Webstart Image - looked for in resources/images -->
84 <property name="WebStartImage" value="JalviewLogo_big.png"/>
85 <!-- J2SE version needed for webstart launch -->
86 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
87 <property name="j2sev" value="1.7+"/>
89 <!-- Permissions for running Java applets and applications. -->
90 <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
91 <property name="application.codebase" value="*.jalview.org" />
92 <!-- and allowing the applet to be deployed from any URL -->
93 <!-- 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 -->
94 <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
95 <property name="applet.caller-codebase" value="${applet.codebase}" />
97 <!-- build directory configuration -->
98 <property name="libDir" value="lib" />
99 <property name="resourceDir" value="resources" />
100 <property name="helpDir" value="help" />
101 <property name="docDir" value="doc" />
102 <property name="sourceDir" value="src" />
103 <property name="schemaDir" value="schemas" />
104 <property name="outputDir" value="classes" />
105 <property name="packageDir" value="dist" />
106 <property name="outputJar" value="jalview.jar" />
107 <!-- Jalview Applet JMol Jar Dependency -->
108 <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
109 <property name="varnaJar" value="VARNAv3-91.jar" />
110 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
111 <!-- switch to indicate if we should obfuscate jalviewLite -->
112 <!-- <property name="donotobfuscate" value="true"/> -->
113 <!-- switch to exclude associations from generated jnlp files -->
114 <!-- <property name="nojnlpfileassocs" value="true"/> -->
116 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
117 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
118 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
119 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
120 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
121 <property name="WSInterf" value="MsaWS" />
122 <property name="wsdl.Namespace" value="vamsas" />
123 <property name="wsdl.ClientNS" value="ext.vamsas" />
124 <!-- the class path for building the application -->
125 <path id="build.classpath">
126 <fileset dir="utils">
127 <include name="*.jar" />
128 <include name="**/*.jar" />
130 <fileset dir="${libDir}">
131 <include name="*.jar" />
132 <include name="**/*.jar" />
134 <fileset dir="${java.home}/lib">
135 <include name="plugin.jar"/>
137 <fileset dir="appletlib">
138 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
140 <include name="${jmolJar}" />
141 <include name="${varnaJar}" />
145 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
146 <!-- The Location of the java 1.1.8 jdk -->
147 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
148 <property name="java118.home" value="${java.home}" />
149 <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
151 <!-- jre for 1.4 version -->
152 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
154 <!-- the classpath for building the 1.1 applet -->
155 <path id="jalviewlite.deps">
156 <fileset dir="${java118.home}">
157 <include name="lib/classes.zip" />
159 <fileset dir="${java.home}/lib">
160 <include name="plugin.jar"/>
162 <pathelement location="appletlib/${jmolJar}" />
163 <pathelement location="lib/${varnaJar}" />
165 <!-- default location for outputting javadoc -->
166 <property name="javadocDir" value="${packageDir}/javadoc"/>
170 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
171 <target name="buildPropertiesFile" depends="init">
172 <tstamp prefix="build">
173 <format property="date" pattern="dd MMMM yyyy" />
175 <properties file="${outputDir}/.build_properties">
177 ---Jalview Build Details---
179 <property name="VERSION" value="${JALVIEW_VERSION}" />
180 <property name="BUILD_DATE" value="${build.date}" />
185 <target name="clean" depends="init">
186 <!-- not efficient yet. -->
187 <delete dir="${outputDir}" includes="*,**/*"/>
190 <target name="distclean" depends="init, clean">
192 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
195 <include name="${outputJar}" />
196 <include name="#*#" />
197 <include name="#*.*#" />
198 <include name="**/#*#" />
199 <include name="**/#*.*#" />
200 <include name="*~" />
201 <include name="*.*~" />
202 <include name="**/*~" />
203 <include name="**/*.*~" />
208 <target name="prepare" depends="init">
209 <mkdir dir="${outputDir}" />
210 <copy todir="${outputDir}">
212 <include name="${docDir}/**/*.*" />
213 <include name="${helpDir}/**/*.*" />
214 <include name="${libDir}/*.jar" />
216 <fileset dir="${resourceDir}">
217 <include name="**/*.*" />
222 <target name="build" depends="prepare">
223 <!-- not efficient yet. -->
224 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
225 <exclude name="jalview/*applet*" />
226 <exclude name="jalview/appletgui/**" />
227 <exclude name="com/stevesoft/**" />
230 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
231 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
236 <target name="makefulldist" depends="makedist">
237 <copy todir="${packageDir}">
238 <fileset dir="${resourceDir}/images">
239 <include name="${WebStartImage}"/>
243 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
245 <!-- create a dummy jar which will eventually contain the jnlp template -->
246 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
247 <fileset dir="${packageDir}">
248 <include name="jalview.jar" />
252 <mkdir dir="${packageDir}/JNLP-INF"/>
253 <antcall target="writejnlpf">
254 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
255 <param name="inih" value="*" />
256 <param name="maxh" value="*"/>
259 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
260 <fileset dir="${packageDir}">
261 <include name="JNLP-INF"/>
265 <antcall target="writejnlpf">
266 <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
267 <param name="inih" value="10M" />
268 <param name="maxh" value="256M"/>
271 <antcall target="writejnlpf">
272 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
273 <param name="inih" value="128M" />
274 <param name="maxh" value="512M"/>
277 <antcall target="writejnlpf">
278 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
279 <param name="inih" value="256M" />
280 <param name="maxh" value="1024M"/>
283 <!-- finally, need to postprocess to add in associations at end of 'information' element
285 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
292 <association mime-type="application-x/ext-file" extensions="fa"/>
293 <association mime-type="application-x/ext-file" extensions="fasta"/>
294 <association mime-type="application-x/ext-file" extensions="mfa"/>
295 <association mime-type="application-x/ext-file" extensions="fastq"/>
296 <association mime-type="application-x/ext-file" extensions="blc"/>
297 <association mime-type="application-x/ext-file" extensions="msf"/>
298 <association mime-type="application-x/ext-file" extensions="pfam"/>
299 <association mime-type="application-x/ext-file" extensions="aln"/>
300 <association mime-type="application-x/ext-file" extensions="pir"/>
301 <association mime-type="application-x/ext-file" extensions="amsa"/>
302 <association mime-type="application-x/ext-file" extensions="stk"/>
303 <association mime-type="application-x/ext-file" extensions="jar"/>-->
304 <!-- and sign the jars -->
305 <!-- the default keystore details might need to be edited here -->
306 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
307 <fileset dir="${packageDir}">
308 <include name="*.jar" />
313 <target name="runenv" depends="init">
314 <path id="run.classpath">
315 <pathelement location="${outputDir}" />
316 <fileset dir="${outputDir}">
317 <include name="${libDir}/*.jar" />
320 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
322 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
326 <target name="-generatejnlpf">
327 <presetdef name="jnlpf">
328 <jnlp codebase="${WebStartLocation}">
330 <title>Jalview</title>
331 <vendor>The Barton Group</vendor>
332 <homepage href="http://www.jalview.org" />
333 <description>Jalview Multiple Alignment Editor</description>
334 <description kind="short">Jalview</description>
335 <icon href="${WebStartImage}" />
339 <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
340 <fileset dir="${packageDir}">
341 <include name="jalview.jar" />
343 <fileset dir="${packageDir}">
344 <include name="*.jar" />
345 <include name="*_*.jar" />
346 <exclude name="jalview.jar" />
348 <property name="jalview.version" value="${JALVIEW_VERSION}" />
350 <application_desc main_class="jalview.bin.Jalview">
358 <jnlpf toFile="${jnlpFile}"/>
362 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
363 <echo message="Not adding JNLP File Associations"/>
366 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
367 <replace file="${jnlpFile}">
369 <![CDATA[</information>]]></replacetoken>
372 <association mime-type="application-x/ext-file" extensions="fa" />
373 <association mime-type="application-x/ext-file" extensions="fasta" />
374 <association mime-type="application-x/ext-file" extensions="mfa" />
375 <association mime-type="application-x/ext-file" extensions="fastq" />
376 <association mime-type="application-x/ext-file" extensions="blc" />
377 <association mime-type="application-x/ext-file" extensions="msf" />
378 <association mime-type="application-x/ext-file" extensions="pfam" />
379 <association mime-type="application-x/ext-file" extensions="aln"/>
380 <association mime-type="application-x/ext-file" extensions="pir"/>
381 <association mime-type="application-x/ext-file" extensions="amsa"/>
382 <association mime-type="application-x/ext-file" extensions="stk"/>
383 <association mime-type="application-x/ext-file" extensions="jvp"/>
384 </information>]]></replacevalue>
386 <echo message="Added file associations to JNLP file"/>
388 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
391 <target name="buildextclients" depends="init">
392 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
393 <condition property="dontextbuild">
394 <equals arg1="n" arg2="${doextbuild.response}" />
396 <condition property="dontextbuild">
397 <equals arg1="N" arg2="${doextbuild.response}" />
399 <fail if="dontextbuild">
400 Build External Client Code process aborted by user. Jalview source is unchanged.
402 <!-- Currently, this doesn't happen automatically.
403 1. Run WSDL2Java as below, which generates an ext.vamsas +
404 vamsas.<datapackages> fileset.
405 2. refactor ext.vamsas.SpecificserviceWS* to
406 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
407 3. Update the jalview.ws.*WServices classes to reflect the
408 interface type, and all locations of this wsdl type that Jalview
412 <path id="axisbuild">
413 <path refid="build.classpath" />
415 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
417 <fileset dir="${sourceDir}" id="client">
418 <include name="${wsdl.ClientNS}/*.*" />
422 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
424 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
425 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
430 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
431 <!-- make the package jar if not already existing -->
432 <mkdir dir="${packageDir}" />
433 <!-- clean dir if it already existed -->
435 <fileset dir="${packageDir}">
436 <include name="*.jar"/>
439 <jar destfile="${packageDir}/${outputJar}" index="true">
441 <attribute name="Main-Class" value="jalview.bin.Jalview" />
442 <attribute name="Permissions" value="all-permissions" />
443 <attribute name="Application-Name" value="Jalview Desktop" />
444 <attribute name="Codebase" value="${application.codebase}" />
446 <fileset dir="${outputDir}/">
447 <exclude name="cache*/**" />
448 <exclude name="*.jar" />
449 <exclude name="*.jar.*" />
450 <exclude name="**/*.jar" />
451 <exclude name="**/*.jar.*" />
455 <copy toDir="${packageDir}" flatten="true">
456 <fileset dir="${outputDir}">
457 <include name="*.jar" />
458 <include name="**/*.jar" />
464 <!-- jalopy code reformatter -->
465 <target name="sourcescrub" depends="init,build">
466 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
467 <fileset dir="${sourceDir}">
468 <include name="*.java" />
469 <include name="**/*.java" />
470 <include name="**/**/*.java" />
477 <!-- Compile, package and obfuscate Jalview Applet -->
478 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
480 <target name="compileApplet" depends="init,clean">
481 <mkdir dir="${outputDir}" />
482 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
483 classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
484 excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
487 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
488 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
489 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
490 <copy todir="${outputDir}/lang">
491 <fileset dir="${resourceDir}/lang">
492 <include name="**.*"/>
495 <jar destfile="in.jar" index="true">
497 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
498 <attribute name="Application-Name" value="JalviewLite" />
499 <attribute name="Codebase" value="${applet.codebase}" />
501 <fileset dir="${outputDir}">
502 <include name="com/**" />
503 <include name="MCview/**" />
504 <include name="jalview/**" />
505 <include name=".build_properties" />
506 <include name="images/idwidth.gif" />
507 <include name="images/link.gif" />
508 <include name="lang/**" />
512 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
514 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
515 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
516 <delete file="in.jar" />
518 <target name="-obfuscatereally" unless="donotobfuscate">
520 <path id="obfuscateDeps.path">
521 <pathelement location="${applet.jre.tools}" />
522 <pathelement location="appletlib/${jmolJar}" />
524 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
527 <injar file="in.jar" />
528 <outjar file="${jalviewLiteJar}" />
529 <libraryjar refid="obfuscateDeps.path" />
531 <keep access="public" type="class" name="jalview.bin.JalviewLite">
532 <field access="public" />
533 <method access="public" />
534 <constructor access="public" />
536 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
537 <field access="public" />
538 <method access="public" />
539 <constructor access="public" />
541 <!-- -libraryjars "${obfuscateDeps}"
543 -outjars jalviewApplet.jar
544 -keep public class jalview.bin.JalviewLite
547 <delete file="in.jar" />
550 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
551 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
553 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
554 <include name="*.java" />
555 <include name="descriptors/*.java" />
558 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
559 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
560 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
561 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
563 now build the jalview.binding package with the old schema set
566 <fileset dir="${sourceDir}/jalview/binding/">
567 <include name="**" />
570 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
571 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
572 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
574 <target name="sourcedist" description="create jalview source distribution" depends="init">
575 <delete file="${source.dist.name}" />
576 <tar destfile="${source.dist.name}" compression="gzip">
577 <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
578 <include name="LICENSE" />
579 <include name="README" />
580 <include name="build.xml" />
581 <include name="jalview-jalopy.xml" />
582 <include name="JalviewApplet.jpx" />
583 <include name="JalviewX.jpx" />
584 <include name="nbbuild.xml"/>
585 <include name="nbproject/genfiles.properties"/>
586 <include name="nbproject/project.properties"/>
587 <include name="nbproject/project.xml"/>
588 <include name="${sourceDir}/*.java" />
589 <include name="${sourceDir}/**/*.java" />
590 <include name="${sourceDir}/**/*.cdr" />
591 <include name="${libDir}/**/*" />
592 <include name="${resourceDir}/**/*" />
593 <include name="${helpDir}/**/*" />
594 <include name="appletlib/${jmolJar}" />
595 <exclude name="**/*locales" />
596 <exclude name="*locales/**" />
597 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
598 <exclude name="utils/InstallAnywhere/**Build*/**" />
599 <exclude name="utils/InstallAnywhere/**Build*/**" />
600 <exclude name="utils/InstallAnywhere/**locale*" />
601 <exclude name="utils/InstallAnywhere/**locale*/**" />
602 <include name="${schemaDir}/**/*" />
603 <include name="utils/**/*" />
604 <include name="${docDir}/**/*" />
605 <include name="examples/**/*" />
609 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
610 <copy todir="${packageDir}/examples">
611 <fileset dir="examples">
612 <include name="**/*"/>
613 <include name="javascript/*"/>
614 <include name="jmol/*"/>
617 <include name="${jalviewLiteJar}" />
619 <fileset dir="appletlib">
620 <include name="**/*"/>
623 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
624 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
626 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
627 <!-- <attribute name="Permissions" value="sandbox" /> -->
628 <!--<attribute name="Trusted-Lib" value="true" /> -->
629 <attribute name="Codebase" value="${applet.codebase}"/>
630 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
633 <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
634 <fileset dir="${packageDir}/examples">
635 <include name="*.jar" />
638 <presetdef name="ap_applet.jar">
639 <!-- build a signed applet with 'all-permissions' -
640 Needs 'param name="permissions' value="all-permissions"' in applet tag
641 JalviewLite+JmolApplet linked sequence/structure fails
642 Mixed code warnings are raised
644 <jar update="true" index="true">
646 <attribute name="Application-Name" value="JalviewLite" />
647 <attribute name="Permissions" value="all-permissions" />
648 <attribute name="Codebase" value="${applet.codebase}" />
649 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
650 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
654 <presetdef name="applet.jar">
655 <!-- build signed applet with sandbox permissions -
656 Needs 'param name="permissions' value="sandbox"' in applet tag
657 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
660 <jar update="true" index="true">
662 <attribute name="Application-Name" value="JalviewLite" />
663 <attribute name="Permissions" value="sandbox" />
664 <attribute name="Codebase" value="${applet.codebase}" />
665 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
666 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
670 <presetdef name="tl_applet.jar">
671 <!-- build signed applet with trusted library/trusted permissions -
672 Needs 'param name="permissions' value="all-permissions"' in applet tag
674 No mixed code warnings raised
675 Jmol/JalviewLite sequence/structure example doesn't link structures
676 Raises dialog asking user to allow page to control applet via LiveConnect javascript
680 <jar update="true" index="true">
682 <attribute name="Application-Name" value="JalviewLite" />
683 <attribute name="Permissions" value="all-permissions" />
684 <attribute name="Codebase" value="${applet.codebase}" />
685 <attribute name="Trusted-Only" value="true" />
686 <attribute name="Trusted-Library" value="true" />
690 <presetdef name="to_applet.jar">
691 <!-- not fully test variant (yet) -->
692 <jar update="true" index="true">
694 <attribute name="Application-Name" value="JalviewLite" />
695 <attribute name="Permissions" value="all-permissions" />
696 <attribute name="Codebase" value="${applet.codebase}" />
697 <attribute name="Trusted-Only" value="true" />
701 <!-- create differently privileged artefacts -->
702 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
703 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
704 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
705 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
706 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
707 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
708 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
709 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
710 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
711 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
712 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
713 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
714 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
715 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
716 <!-- finally, create manifest for original jars -->
717 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
718 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
720 <!-- todo - write examples/downloads for alternate versions of the applet -->
721 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
723 <fileset dir="${packageDir}/examples">
724 <exclude name="u_*.jar"/>
725 <include name="${jalviewLiteJar}" />
726 <include name="${jmolJar}" />
727 <include name="to_${jalviewLiteJar}" />
728 <include name="to_${jmolJar}" />
729 <include name="tl_${jalviewLiteJar}" />
730 <include name="tl_${jmolJar}" />
731 <include name="ap_${jalviewLiteJar}" />
732 <include name="ap_${jmolJar}" />
735 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
736 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
738 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
739 <javadoc destdir="${javadocDir}">
740 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">