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="jsoup" value="jsoup-1.8.1.jar" />
115 <property name="jsonSimple" value="json_simple-1.1.jar" />
116 <property name="javaJson" value="java-json.jar" />
117 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
118 <!-- switch to indicate if we should obfuscate jalviewLite -->
119 <!-- <property name="donotobfuscate" value="true"/> -->
120 <!-- switch to exclude associations from generated jnlp files -->
121 <!-- <property name="nojnlpfileassocs" value="true"/> -->
123 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
124 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
125 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
126 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
127 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
128 <property name="WSInterf" value="MsaWS" />
129 <property name="wsdl.Namespace" value="vamsas" />
130 <property name="wsdl.ClientNS" value="ext.vamsas" />
131 <!-- the class path for building the application -->
132 <path id="build.classpath">
133 <fileset dir="utils">
134 <include name="*.jar" />
135 <include name="**/*.jar" />
137 <fileset dir="${libDir}">
138 <include name="*.jar" />
139 <include name="**/*.jar" />
141 <fileset dir="${java.home}/lib">
142 <include name="plugin.jar"/>
144 <fileset dir="appletlib">
145 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
147 <include name="${jmolJar}" />
148 <include name="${varnaJar}" />
152 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
153 <!-- The Location of the java 1.1.8 jdk -->
154 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
155 <property name="java118.home" value="${java.home}" />
156 <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
158 <!-- jre for 1.4 version -->
159 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
161 <!-- the classpath for building the 1.1 applet -->
162 <path id="jalviewlite.deps">
163 <fileset dir="${java118.home}">
164 <include name="lib/classes.zip" />
166 <fileset dir="${java.home}/lib">
167 <include name="plugin.jar"/>
169 <pathelement location="appletlib/${jmolJar}" />
170 <pathelement location="lib/${varnaJar}" />
171 <pathelement location="lib/${jsoup}" />
172 <pathelement location="lib/${jsonSimple}" />
173 <pathelement location="lib/${javaJson}" />
176 <!-- default location for outputting javadoc -->
177 <property name="javadocDir" value="${packageDir}/javadoc"/>
181 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
182 <target name="buildPropertiesFile" depends="init">
183 <tstamp prefix="build">
184 <format property="date" pattern="dd MMMM yyyy" />
186 <properties file="${outputDir}/.build_properties">
188 ---Jalview Build Details---
190 <property name="VERSION" value="${JALVIEW_VERSION}" />
191 <property name="INSTALLATION" value="${INSTALLATION}" />
192 <property name="BUILD_DATE" value="${build.date}" />
197 <target name="clean" depends="init">
198 <!-- not efficient yet. -->
199 <delete dir="${outputDir}" includes="*,**/*"/>
202 <target name="distclean" depends="init, clean">
204 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
207 <include name="${outputJar}" />
208 <include name="#*#" />
209 <include name="#*.*#" />
210 <include name="**/#*#" />
211 <include name="**/#*.*#" />
212 <include name="*~" />
213 <include name="*.*~" />
214 <include name="**/*~" />
215 <include name="**/*.*~" />
220 <target name="prepare" depends="init">
221 <mkdir dir="${outputDir}" />
222 <copy todir="${outputDir}">
224 <include name="${docDir}/**/*.*" />
225 <include name="${helpDir}/**/*.*" />
226 <include name="${libDir}/*.jar" />
228 <fileset dir="${resourceDir}">
229 <include name="**/*.*" />
234 <target name="build" depends="prepare">
235 <!-- not efficient yet. -->
236 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
237 <exclude name="jalview/*applet*" />
238 <exclude name="jalview/appletgui/**" />
239 <exclude name="com/stevesoft/**" />
242 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
243 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
248 <target name="makefulldist" depends="makedist">
249 <copy todir="${packageDir}">
250 <fileset dir="${resourceDir}/images">
251 <include name="${WebStartImage}"/>
255 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
257 <!-- create a dummy jar which will eventually contain the jnlp template -->
258 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
259 <fileset dir="${packageDir}">
260 <include name="jalview.jar" />
264 <mkdir dir="${packageDir}/JNLP-INF"/>
265 <antcall target="writejnlpf">
266 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
267 <param name="inih" value="*" />
268 <param name="maxh" value="*"/>
271 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
272 <fileset dir="${packageDir}">
273 <include name="JNLP-INF"/>
277 <antcall target="writejnlpf">
278 <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
279 <param name="inih" value="10M" />
280 <param name="maxh" value="256M"/>
283 <antcall target="writejnlpf">
284 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
285 <param name="inih" value="128M" />
286 <param name="maxh" value="512M"/>
289 <antcall target="writejnlpf">
290 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
291 <param name="inih" value="256M" />
292 <param name="maxh" value="1024M"/>
295 <!-- finally, need to postprocess to add in associations at end of 'information' element
297 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
304 <association mime-type="application-x/ext-file" extensions="fa"/>
305 <association mime-type="application-x/ext-file" extensions="fasta"/>
306 <association mime-type="application-x/ext-file" extensions="mfa"/>
307 <association mime-type="application-x/ext-file" extensions="fastq"/>
308 <association mime-type="application-x/ext-file" extensions="blc"/>
309 <association mime-type="application-x/ext-file" extensions="msf"/>
310 <association mime-type="application-x/ext-file" extensions="pfam"/>
311 <association mime-type="application-x/ext-file" extensions="aln"/>
312 <association mime-type="application-x/ext-file" extensions="pir"/>
313 <association mime-type="application-x/ext-file" extensions="amsa"/>
314 <association mime-type="application-x/ext-file" extensions="stk"/>
315 <association mime-type="application-x/ext-file" extensions="jar"/>-->
316 <!-- and sign the jars -->
317 <!-- the default keystore details might need to be edited here -->
318 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
319 <fileset dir="${packageDir}">
320 <include name="*.jar" />
325 <target name="runenv" depends="init">
326 <path id="run.classpath">
327 <pathelement location="${outputDir}" />
328 <fileset dir="${outputDir}">
329 <include name="${libDir}/*.jar" />
332 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
334 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
338 <target name="-generatejnlpf">
339 <presetdef name="jnlpf">
340 <jnlp codebase="${WebStartLocation}">
342 <title>Jalview</title>
343 <vendor>The Barton Group</vendor>
344 <homepage href="http://www.jalview.org" />
345 <description>Jalview Multiple Alignment Editor</description>
346 <description kind="short">Jalview</description>
347 <icon href="${WebStartImage}" />
351 <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
352 <fileset dir="${packageDir}">
353 <include name="jalview.jar" />
355 <fileset dir="${packageDir}">
356 <include name="*.jar" />
357 <include name="*_*.jar" />
358 <exclude name="jalview.jar" />
359 <exclude name="*jnilib.jar"/>
362 <resources os="Mac OS X">
363 <property name="jalview.version" value="${JALVIEW_VERSION}" />
364 <fileset dir="${packageDir}">
365 <include name="*quaqua*.jnilib.jar"/>
369 <application_desc main_class="jalview.bin.Jalview">
377 <jnlpf toFile="${jnlpFile}"/>
381 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
382 <echo message="Not adding JNLP File Associations"/>
385 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
386 <replace file="${jnlpFile}">
388 <![CDATA[</information>]]></replacetoken>
391 <association mime-type="application-x/ext-file" extensions="fa" />
392 <association mime-type="application-x/ext-file" extensions="fasta" />
393 <association mime-type="application-x/ext-file" extensions="mfa" />
394 <association mime-type="application-x/ext-file" extensions="fastq" />
395 <association mime-type="application-x/ext-file" extensions="blc" />
396 <association mime-type="application-x/ext-file" extensions="msf" />
397 <association mime-type="application-x/ext-file" extensions="pfam" />
398 <association mime-type="application-x/ext-file" extensions="aln"/>
399 <association mime-type="application-x/ext-file" extensions="pir"/>
400 <association mime-type="application-x/ext-file" extensions="amsa"/>
401 <association mime-type="application-x/ext-file" extensions="stk"/>
402 <association mime-type="application-x/ext-file" extensions="jvp"/>
403 </information>]]></replacevalue>
405 <echo message="Added file associations to JNLP file"/>
407 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
410 <target name="buildextclients" depends="init">
411 <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" />
412 <condition property="dontextbuild">
413 <equals arg1="n" arg2="${doextbuild.response}" />
415 <condition property="dontextbuild">
416 <equals arg1="N" arg2="${doextbuild.response}" />
418 <fail if="dontextbuild">
419 Build External Client Code process aborted by user. Jalview source is unchanged.
421 <!-- Currently, this doesn't happen automatically.
422 1. Run WSDL2Java as below, which generates an ext.vamsas +
423 vamsas.<datapackages> fileset.
424 2. refactor ext.vamsas.SpecificserviceWS* to
425 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
426 3. Update the jalview.ws.*WServices classes to reflect the
427 interface type, and all locations of this wsdl type that Jalview
431 <path id="axisbuild">
432 <path refid="build.classpath" />
434 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
436 <fileset dir="${sourceDir}" id="client">
437 <include name="${wsdl.ClientNS}/*.*" />
441 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
443 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
444 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
449 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
450 <!-- make the package jar if not already existing -->
451 <mkdir dir="${packageDir}" />
452 <!-- clean dir if it already existed -->
454 <fileset dir="${packageDir}">
455 <include name="*.jar"/>
458 <jar destfile="${packageDir}/${outputJar}" index="true">
460 <attribute name="Main-Class" value="jalview.bin.Jalview" />
461 <attribute name="Permissions" value="all-permissions" />
462 <attribute name="Application-Name" value="Jalview Desktop" />
463 <attribute name="Codebase" value="${application.codebase}" />
465 <fileset dir="${outputDir}/">
466 <exclude name="cache*/**" />
467 <exclude name="*.jar" />
468 <exclude name="*.jar.*" />
469 <exclude name="**/*.jar" />
470 <exclude name="**/*.jar.*" />
474 <copy toDir="${packageDir}" flatten="true">
475 <fileset dir="${outputDir}">
476 <include name="*.jar" />
477 <include name="**/*.jar" />
483 <!-- jalopy code reformatter -->
484 <target name="sourcescrub" depends="init,build">
485 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
486 <fileset dir="${sourceDir}">
487 <include name="*.java" />
488 <include name="**/*.java" />
489 <include name="**/**/*.java" />
496 <!-- Compile, package and obfuscate Jalview Applet -->
497 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
499 <target name="compileApplet" depends="init,clean">
500 <mkdir dir="${outputDir}" />
501 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
502 classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
503 excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
506 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
507 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
508 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
509 <copy todir="${outputDir}/lang">
510 <fileset dir="${resourceDir}/lang">
511 <include name="**.*"/>
514 <jar destfile="in.jar" index="true">
516 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
517 <attribute name="Application-Name" value="JalviewLite" />
518 <attribute name="Codebase" value="${applet.codebase}" />
520 <fileset dir="${outputDir}">
521 <include name="com/**" />
522 <include name="MCview/**" />
523 <include name="jalview/**" />
524 <include name=".build_properties" />
525 <include name="images/idwidth.gif" />
526 <include name="images/link.gif" />
527 <include name="lang/**" />
531 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
533 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
534 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
535 <delete file="in.jar" />
537 <target name="-obfuscatereally" unless="donotobfuscate">
539 <path id="obfuscateDeps.path">
540 <pathelement location="${applet.jre.tools}" />
541 <pathelement location="appletlib/${jmolJar}" />
542 <pathelement location="appletlib/${jsonSimple}" />
543 <pathelement location="appletlib/${javaJson}" />
545 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
548 <injar file="in.jar" />
549 <outjar file="${jalviewLiteJar}" />
550 <libraryjar refid="obfuscateDeps.path" />
552 <keep access="public" type="class" name="jalview.bin.JalviewLite">
553 <field access="public" />
554 <method access="public" />
555 <constructor access="public" />
557 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
558 <field access="public" />
559 <method access="public" />
560 <constructor access="public" />
562 <!-- -libraryjars "${obfuscateDeps}"
564 -outjars jalviewApplet.jar
565 -keep public class jalview.bin.JalviewLite
568 <delete file="in.jar" />
571 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
572 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
574 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
575 <include name="*.java" />
576 <include name="descriptors/*.java" />
579 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
580 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
581 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
582 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
584 now build the jalview.binding package with the old schema set
587 <fileset dir="${sourceDir}/jalview/binding/">
588 <include name="**" />
591 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
592 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
593 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
595 <target name="sourcedist" description="create jalview source distribution" depends="init">
596 <delete file="${source.dist.name}" />
597 <tar destfile="${source.dist.name}" compression="gzip">
598 <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
599 <include name="LICENSE" />
600 <include name="README" />
601 <include name="build.xml" />
602 <include name="jalview-jalopy.xml" />
603 <include name="JalviewApplet.jpx" />
604 <include name="JalviewX.jpx" />
605 <include name="nbbuild.xml"/>
606 <include name="nbproject/genfiles.properties"/>
607 <include name="nbproject/project.properties"/>
608 <include name="nbproject/project.xml"/>
609 <include name="${sourceDir}/*.java" />
610 <include name="${sourceDir}/**/*.java" />
611 <include name="${sourceDir}/**/*.cdr" />
612 <include name="${libDir}/**/*" />
613 <include name="${resourceDir}/**/*" />
614 <include name="${helpDir}/**/*" />
615 <include name="appletlib/${jmolJar}" />
616 <exclude name="**/*locales" />
617 <exclude name="*locales/**" />
618 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
619 <exclude name="utils/InstallAnywhere/**Build*/**" />
620 <exclude name="utils/InstallAnywhere/**Build*/**" />
621 <exclude name="utils/InstallAnywhere/**locale*" />
622 <exclude name="utils/InstallAnywhere/**locale*/**" />
623 <include name="${schemaDir}/**/*" />
624 <include name="utils/**/*" />
625 <include name="${docDir}/**/*" />
626 <include name="examples/**/*" />
630 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
631 <copy todir="${packageDir}/examples">
632 <fileset dir="examples">
633 <include name="**/*"/>
634 <include name="javascript/*"/>
635 <include name="jmol/*"/>
638 <include name="${jalviewLiteJar}" />
640 <fileset dir="appletlib">
641 <include name="**/*"/>
644 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
645 <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
646 <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
647 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
649 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
650 <!-- <attribute name="Permissions" value="sandbox" /> -->
651 <!--<attribute name="Trusted-Lib" value="true" /> -->
652 <attribute name="Codebase" value="${applet.codebase}"/>
653 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
656 <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
657 <fileset dir="${packageDir}/examples">
658 <include name="*.jar" />
661 <presetdef name="ap_applet.jar">
662 <!-- build a signed applet with 'all-permissions' -
663 Needs 'param name="permissions' value="all-permissions"' in applet tag
664 JalviewLite+JmolApplet linked sequence/structure fails
665 Mixed code warnings are raised
667 <jar update="true" index="true">
669 <attribute name="Application-Name" value="JalviewLite" />
670 <attribute name="Permissions" value="all-permissions" />
671 <attribute name="Codebase" value="${applet.codebase}" />
672 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
673 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
677 <presetdef name="applet.jar">
678 <!-- build signed applet with sandbox permissions -
679 Needs 'param name="permissions' value="sandbox"' in applet tag
680 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
683 <jar update="true" index="true">
685 <attribute name="Application-Name" value="JalviewLite" />
686 <attribute name="Permissions" value="sandbox" />
687 <attribute name="Codebase" value="${applet.codebase}" />
688 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
689 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
693 <presetdef name="tl_applet.jar">
694 <!-- build signed applet with trusted library/trusted permissions -
695 Needs 'param name="permissions' value="all-permissions"' in applet tag
697 No mixed code warnings raised
698 Jmol/JalviewLite sequence/structure example doesn't link structures
699 Raises dialog asking user to allow page to control applet via LiveConnect javascript
703 <jar update="true" index="true">
705 <attribute name="Application-Name" value="JalviewLite" />
706 <attribute name="Permissions" value="all-permissions" />
707 <attribute name="Codebase" value="${applet.codebase}" />
708 <attribute name="Trusted-Only" value="true" />
709 <attribute name="Trusted-Library" value="true" />
713 <presetdef name="to_applet.jar">
714 <!-- not fully test variant (yet) -->
715 <jar update="true" index="true">
717 <attribute name="Application-Name" value="JalviewLite" />
718 <attribute name="Permissions" value="all-permissions" />
719 <attribute name="Codebase" value="${applet.codebase}" />
720 <attribute name="Trusted-Only" value="true" />
724 <!-- create differently privileged artefacts -->
725 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
726 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
727 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
728 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
729 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
730 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
731 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
732 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
733 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
734 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
735 <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
736 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
737 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
738 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
739 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
740 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
741 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
742 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
743 <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
744 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
745 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
746 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
747 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
748 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
749 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
750 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
751 <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
752 <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
753 <!-- finally, create manifest for original jars -->
754 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
755 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
756 <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
757 <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
759 <!-- todo - write examples/downloads for alternate versions of the applet -->
760 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
762 <fileset dir="${packageDir}/examples">
763 <exclude name="u_*.jar"/>
764 <include name="${jalviewLiteJar}" />
765 <include name="${jmolJar}" />
766 <include name="${javaJson}" />
767 <include name="${jsonSimple}" />
768 <include name="to_${jalviewLiteJar}" />
769 <include name="to_${jmolJar}" />
770 <include name="to_${javaJson}" />
771 <include name="to_${jsonSimple}" />
772 <include name="tl_${jalviewLiteJar}" />
773 <include name="tl_${jmolJar}" />
774 <include name="tl_${javaJson}" />
775 <include name="tl_${jsonSimple}" />
776 <include name="ap_${jalviewLiteJar}" />
777 <include name="ap_${jmolJar}" />
778 <include name="ap_${javaJson}" />
779 <include name="ap_${jsonSimple}" />
782 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
783 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
784 <!-- finally, replace any launchApp servlet tags with a version specification -->
785 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
786 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
787 <fileset dir="${packageDir}/examples">
788 <include name="**/*.html"/>
791 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
792 <replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
793 <fileset dir="${packageDir}/examples">
794 <include name="**/*.html"/>
799 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
800 <javadoc destdir="${javadocDir}">
801 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">