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" />
22 <target name="usage" depends="init">
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="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
34 <echo message=" you can specify particular test groups as a list via -Dtestng-groups=" />
35 <echo message="See docs/building.html and the comments in build file for other targets." />
36 <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
37 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
41 <!-- utils is a class path to additional utilities needed for
42 building docs, jars and webstart stuff -->
44 Userdefined build property defaults
46 wsdl.server list (plus namespace mapping info ???) - also want
47 ... to make this a dynamically generatable property
49 Build location - provide a temporary root for speed
50 jarsigner keystore and info
51 Jakarta and axis classpath ?
52 Default argument for starting Jalview (if it exists).
57 <path id="axis.classpath">
59 <fileset dir="/usr/local/axis/lib">
60 <include name="**/*.jar" />
62 <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
63 <include name="**/*.jar"/>
64 <include name="*.jar"/>
68 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
69 <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
71 <property name="INSTALLATION" value="Source" />
73 <!-- 2.4 (VAMSAS)" -->
74 <!-- Include debugging information in javac true or false -->
75 <property name="javac.debug" value="true" />
77 <!-- JarSigner Key Store for Webstart Distribution -->
78 <property name="jalview.keystore" value="./keys/.keystore" />
79 <!-- Keystore Password -->
80 <property name="jalview.keystore.pass" value="alignmentisfun" />
82 <property name="jalview.key" value="jalview" />
84 <property name="jalview.key.pass" value="alignmentisfun" />
86 <property name="testng-groups" value="Functional" />
88 <!-- Don't change anything below here unless you know what you are doing! -->
89 <!-- Url path for WebStart in JNLP file -->
90 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
91 <!-- Webstart Image - looked for in resources/images -->
92 <property name="WebStartImage" value="JalviewLogo_big.png" />
93 <!-- J2SE version needed for webstart launch -->
94 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
95 <property name="j2sev" value="1.7+" />
96 <!-- Java Compilation settings - source and target javac version -->
97 <property name="javac.source" value="1.7" />
98 <property name="javac.target" value="1.7" />
100 <!-- Permissions for running Java applets and applications. -->
101 <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
102 <property name="application.codebase" value="*.jalview.org" />
103 <!-- and allowing the applet to be deployed from any URL -->
104 <!-- 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 -->
105 <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
106 <property name="applet.caller-codebase" value="${applet.codebase}" />
108 <!-- build directory configuration -->
109 <property name="libDir" value="lib" />
110 <property name="resourceDir" value="resources" />
111 <property name="helpDir" value="help" />
112 <property name="docDir" value="doc" />
113 <property name="sourceDir" value="src" />
114 <property name="schemaDir" value="schemas" />
115 <property name="outputDir" value="classes" />
116 <property name="packageDir" value="dist" />
117 <property name="outputJar" value="jalview.jar" />
118 <!-- Jalview Applet JMol Jar Dependency -->
119 <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
120 <property name="varnaJar" value="VARNAv3-93.jar" />
121 <property name="jsoup" value="jsoup-1.8.1.jar" />
122 <property name="jsonSimple" value="json_simple-1.1.jar" />
123 <property name="javaJson" value="java-json.jar" />
124 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
125 <property name="reportDir" value="test-reports" />
126 <property name="testDir" value="test" />
127 <property name="testOutputDir" value="tests" />
128 <!-- switch to indicate if we should obfuscate jalviewLite -->
129 <!-- <property name="donotobfuscate" value="true"/> -->
130 <!-- switch to exclude associations from generated jnlp files -->
131 <!-- <property name="nojnlpfileassocs" value="true"/> -->
133 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
134 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
135 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
136 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
137 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
138 <property name="WSInterf" value="MsaWS" />
139 <property name="wsdl.Namespace" value="vamsas" />
140 <property name="wsdl.ClientNS" value="ext.vamsas" />
141 <!-- the class path for building the application -->
142 <path id="build.classpath">
143 <fileset dir="utils">
144 <include name="*.jar" />
145 <include name="**/*.jar" />
147 <fileset dir="${libDir}">
148 <include name="*.jar" />
149 <include name="**/*.jar" />
151 <fileset dir="${java.home}/lib">
152 <include name="plugin.jar" />
154 <fileset dir="appletlib">
155 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
157 <include name="${jmolJar}" />
158 <include name="${varnaJar}" />
161 <path id="test.classpath">
162 <pathelement path="${outputDir}" />
163 <path refid="build.classpath" />
165 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
166 <!-- The Location of the java 1.1.8 jdk -->
167 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
168 <property name="java118.home" value="${java.home}" />
169 <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
171 <!-- jre for 1.4 version -->
172 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
174 <!-- the classpath for building the 1.1 applet -->
175 <path id="jalviewlite.deps">
176 <fileset dir="${java118.home}">
177 <include name="lib/classes.zip" />
179 <fileset dir="${java.home}/lib">
180 <include name="plugin.jar" />
182 <pathelement location="appletlib/${jmolJar}" />
183 <pathelement location="lib/${varnaJar}" />
184 <pathelement location="lib/${jsoup}" />
185 <pathelement location="lib/${jsonSimple}" />
186 <pathelement location="lib/${javaJson}" />
189 <!-- default location for outputting javadoc -->
190 <property name="javadocDir" value="${packageDir}/javadoc" />
194 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
195 <target name="buildPropertiesFile" depends="init">
196 <tstamp prefix="build">
197 <format property="date" pattern="dd MMMM yyyy" />
199 <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
200 <arg value="rev-parse" />
201 <arg value="--short" />
204 <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
205 <arg value="rev-parse" />
206 <arg value="--abbrev-ref" />
209 <properties file="${outputDir}/.build_properties">
211 ---Jalview Build Details---
213 <property name="VERSION" value="${JALVIEW_VERSION}" />
214 <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
215 <property name="BUILD_DATE" value="${build.date}" />
220 <target name="clean" depends="init">
221 <!-- not efficient yet. -->
222 <delete dir="${outputDir}" includes="*,**/*" />
225 <target name="distclean" depends="init, clean">
227 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
230 <include name="${outputJar}" />
231 <include name="#*#" />
232 <include name="#*.*#" />
233 <include name="**/#*#" />
234 <include name="**/#*.*#" />
235 <include name="*~" />
236 <include name="*.*~" />
237 <include name="**/*~" />
238 <include name="**/*.*~" />
243 <target name="prepare" depends="init">
244 <mkdir dir="${outputDir}" />
245 <copy todir="${outputDir}">
247 <include name="${docDir}/**/*.*" />
248 <include name="${helpDir}/**/*.*" />
249 <include name="${libDir}/*.jar" />
251 <fileset dir="${resourceDir}">
252 <include name="**/*.*" />
257 <target name="build" depends="prepare">
258 <!-- not efficient yet. -->
259 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
260 <exclude name="jalview/*applet*" />
261 <exclude name="jalview/appletgui/**" />
262 <exclude name="com/stevesoft/**" />
267 <target name="testclean" depends="init">
268 <delete dir="${testOutputDir}" includes="*,**/*" />
271 <target name="prepareTests" depends="init,testclean">
272 <mkdir dir="${testOutputDir}" />
275 <target name="buildTests" depends="build,buildindices,prepareTests">
276 <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
280 <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
282 <target name="testng" depends="buildTests">
283 <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
286 <pathelement location="${testOutputDir}" />
287 <path refid="test.classpath" />
289 <classfileset dir="${testOutputDir}" includes="**/*.class" />
293 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
294 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
299 <target name="makefulldist" depends="makedist">
300 <copy todir="${packageDir}">
301 <fileset dir="${resourceDir}/images">
302 <include name="${WebStartImage}" />
306 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
308 <!-- create a dummy jar which will eventually contain the jnlp template -->
309 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
310 <fileset dir="${packageDir}">
311 <include name="jalview.jar" />
315 <mkdir dir="${packageDir}/JNLP-INF" />
316 <antcall target="writejnlpf">
317 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
318 <param name="inih" value="*" />
319 <param name="maxh" value="*" />
322 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
323 <fileset dir="${packageDir}">
324 <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
328 <antcall target="writejnlpf">
329 <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
330 <param name="inih" value="10M" />
331 <param name="maxh" value="256M" />
334 <antcall target="writejnlpf">
335 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
336 <param name="inih" value="128M" />
337 <param name="maxh" value="512M" />
340 <antcall target="writejnlpf">
341 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
342 <param name="inih" value="256M" />
343 <param name="maxh" value="1024M" />
346 <!-- finally, need to postprocess to add in associations at end of 'information' element
348 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
355 <association mime-type="application-x/ext-file" extensions="fa"/>
356 <association mime-type="application-x/ext-file" extensions="fasta"/>
357 <association mime-type="application-x/ext-file" extensions="mfa"/>
358 <association mime-type="application-x/ext-file" extensions="fastq"/>
359 <association mime-type="application-x/ext-file" extensions="blc"/>
360 <association mime-type="application-x/ext-file" extensions="msf"/>
361 <association mime-type="application-x/ext-file" extensions="pfam"/>
362 <association mime-type="application-x/ext-file" extensions="aln"/>
363 <association mime-type="application-x/ext-file" extensions="pir"/>
364 <association mime-type="application-x/ext-file" extensions="amsa"/>
365 <association mime-type="application-x/ext-file" extensions="stk"/>
366 <association mime-type="application-x/ext-file" extensions="jar"/>-->
367 <!-- and sign the jars -->
368 <!-- the default keystore details might need to be edited here -->
369 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
370 <fileset dir="${packageDir}">
371 <include name="*.jar" />
376 <target name="runenv" depends="init">
377 <path id="run.classpath">
378 <pathelement location="${outputDir}" />
379 <fileset dir="${outputDir}">
380 <include name="${libDir}/*.jar" />
383 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
385 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
389 <target name="-generatejnlpf">
390 <presetdef name="jnlpf">
391 <jnlp codebase="${WebStartLocation}">
393 <title>Jalview</title>
394 <vendor>The Barton Group</vendor>
395 <homepage href="http://www.jalview.org" />
396 <description>Jalview Multiple Alignment Editor</description>
397 <description kind="short">Jalview</description>
398 <icon href="${WebStartImage}" />
402 <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
403 <fileset dir="${packageDir}">
404 <include name="jalview.jar" />
406 <fileset dir="${packageDir}">
407 <include name="*.jar" />
408 <include name="*_*.jar" />
409 <exclude name="jalview.jar" />
410 <exclude name="*jnilib.jar" />
413 <resources os="Mac OS X">
414 <property name="jalview.version" value="${JALVIEW_VERSION}" />
415 <fileset dir="${packageDir}">
416 <include name="*quaqua*.jnilib.jar" />
420 <application_desc main_class="jalview.bin.Jalview">
428 <jnlpf toFile="${jnlpFile}" />
432 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
433 <echo message="Not adding JNLP File Associations" />
436 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
437 <replace file="${jnlpFile}">
439 <![CDATA[</information>]]></replacetoken>
442 <association mime-type="application-x/ext-file" extensions="fa" />
443 <association mime-type="application-x/ext-file" extensions="fasta" />
444 <association mime-type="application-x/ext-file" extensions="mfa" />
445 <association mime-type="application-x/ext-file" extensions="fastq" />
446 <association mime-type="application-x/ext-file" extensions="blc" />
447 <association mime-type="application-x/ext-file" extensions="msf" />
448 <association mime-type="application-x/ext-file" extensions="pfam" />
449 <association mime-type="application-x/ext-file" extensions="aln"/>
450 <association mime-type="application-x/ext-file" extensions="pir"/>
451 <association mime-type="application-x/ext-file" extensions="amsa"/>
452 <association mime-type="application-x/ext-file" extensions="stk"/>
453 <association mime-type="application-x/ext-file" extensions="jvp"/>
454 </information>]]></replacevalue>
456 <echo message="Added file associations to JNLP file" />
458 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
461 <target name="buildextclients" depends="init">
462 <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" />
463 <condition property="dontextbuild">
464 <equals arg1="n" arg2="${doextbuild.response}" />
466 <condition property="dontextbuild">
467 <equals arg1="N" arg2="${doextbuild.response}" />
469 <fail if="dontextbuild">
470 Build External Client Code process aborted by user. Jalview source is unchanged.
472 <!-- Currently, this doesn't happen automatically.
473 1. Run WSDL2Java as below, which generates an ext.vamsas +
474 vamsas.<datapackages> fileset.
475 2. refactor ext.vamsas.SpecificserviceWS* to
476 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
477 3. Update the jalview.ws.*WServices classes to reflect the
478 interface type, and all locations of this wsdl type that Jalview
482 <path id="axisbuild">
483 <path refid="build.classpath" />
485 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
487 <fileset dir="${sourceDir}" id="client">
488 <include name="${wsdl.ClientNS}/*.*" />
492 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
494 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
495 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
500 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
501 <!-- make the package jar if not already existing -->
502 <mkdir dir="${packageDir}" />
503 <!-- clean dir if it already existed -->
505 <fileset dir="${packageDir}">
506 <include name="*.jar" />
509 <jar destfile="${packageDir}/${outputJar}" index="true">
511 <attribute name="Main-Class" value="jalview.bin.Jalview" />
512 <attribute name="Permissions" value="all-permissions" />
513 <attribute name="Application-Name" value="Jalview Desktop" />
514 <attribute name="Codebase" value="${application.codebase}" />
516 <fileset dir="${outputDir}/">
517 <exclude name="cache*/**" />
518 <exclude name="*.jar" />
519 <exclude name="*.jar.*" />
520 <exclude name="**/*.jar" />
521 <exclude name="**/*.jar.*" />
525 <copy toDir="${packageDir}" flatten="true">
526 <fileset dir="${outputDir}">
527 <include name="*.jar" />
528 <include name="**/*.jar" />
534 <!-- jalopy code reformatter -->
535 <target name="sourcescrub" depends="init,build">
536 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
537 <fileset dir="${sourceDir}">
538 <include name="*.java" />
539 <include name="**/*.java" />
540 <include name="**/**/*.java" />
547 <!-- Compile, package and obfuscate Jalview Applet -->
548 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
550 <target name="compileApplet" depends="init,clean">
551 <mkdir dir="${outputDir}" />
552 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
555 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
556 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
557 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
558 <copy todir="${outputDir}/lang">
559 <fileset dir="${resourceDir}/lang">
560 <include name="**.*" />
563 <jar destfile="in.jar" index="true">
565 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
566 <attribute name="Application-Name" value="JalviewLite" />
567 <attribute name="Codebase" value="${applet.codebase}" />
569 <fileset dir="${outputDir}">
570 <include name="com/**" />
571 <include name="MCview/**" />
572 <include name="jalview/**" />
573 <include name=".build_properties" />
574 <include name="images/idwidth.gif" />
575 <include name="images/link.gif" />
576 <include name="lang/**" />
580 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
582 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
583 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
584 <delete file="in.jar" />
586 <target name="-obfuscatereally" unless="donotobfuscate">
588 <path id="obfuscateDeps.path">
589 <pathelement location="${applet.jre.tools}" />
590 <pathelement location="appletlib/${jmolJar}" />
591 <pathelement location="appletlib/${jsonSimple}" />
592 <pathelement location="appletlib/${javaJson}" />
594 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
597 <injar file="in.jar" />
598 <outjar file="${jalviewLiteJar}" />
599 <libraryjar refid="obfuscateDeps.path" />
601 <keep access="public" type="class" name="jalview.bin.JalviewLite">
602 <field access="public" />
603 <method access="public" />
604 <constructor access="public" />
606 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
607 <field access="public" />
608 <method access="public" />
609 <constructor access="public" />
611 <!-- -libraryjars "${obfuscateDeps}"
613 -outjars jalviewApplet.jar
614 -keep public class jalview.bin.JalviewLite
617 <delete file="in.jar" />
620 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
621 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
623 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
624 <include name="*.java" />
625 <include name="descriptors/*.java" />
628 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
629 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
630 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
631 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
633 now build the jalview.binding package with the old schema set
636 <fileset dir="${sourceDir}/jalview/binding/">
637 <include name="**" />
640 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
641 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
642 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
644 <target name="sourcedist" description="create jalview source distribution" depends="init">
645 <delete file="${source.dist.name}" />
646 <tar destfile="${source.dist.name}" compression="gzip">
647 <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
648 <include name="LICENSE" />
649 <include name="README" />
650 <include name="build.xml" />
651 <include name="jalview-jalopy.xml" />
652 <include name="JalviewApplet.jpx" />
653 <include name="JalviewX.jpx" />
654 <include name="nbbuild.xml" />
655 <include name="nbproject/genfiles.properties" />
656 <include name="nbproject/project.properties" />
657 <include name="nbproject/project.xml" />
658 <include name="${sourceDir}/*.java" />
659 <include name="${sourceDir}/**/*.java" />
660 <include name="${sourceDir}/**/*.cdr" />
661 <include name="${libDir}/**/*" />
662 <include name="${resourceDir}/**/*" />
663 <include name="${helpDir}/**/*" />
664 <include name="appletlib/${jmolJar}" />
665 <exclude name="**/*locales" />
666 <exclude name="*locales/**" />
667 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
668 <exclude name="utils/InstallAnywhere/**Build*/**" />
669 <exclude name="utils/InstallAnywhere/**Build*/**" />
670 <exclude name="utils/InstallAnywhere/**locale*" />
671 <exclude name="utils/InstallAnywhere/**locale*/**" />
672 <include name="${schemaDir}/**/*" />
673 <include name="utils/**/*" />
674 <include name="${docDir}/**/*" />
675 <include name="examples/**/*" />
679 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
680 <copy todir="${packageDir}/examples">
681 <fileset dir="examples">
682 <include name="**/*" />
683 <include name="javascript/*" />
684 <include name="jmol/*" />
687 <include name="${jalviewLiteJar}" />
689 <fileset dir="appletlib">
690 <include name="**/*" />
693 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
694 <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
695 <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
696 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
698 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
699 <!-- <attribute name="Permissions" value="sandbox" /> -->
700 <!--<attribute name="Trusted-Lib" value="true" /> -->
701 <attribute name="Codebase" value="${applet.codebase}" />
702 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
705 <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
706 <fileset dir="${packageDir}/examples">
707 <include name="*.jar" />
710 <presetdef name="ap_applet.jar">
711 <!-- build a signed applet with 'all-permissions' -
712 Needs 'param name="permissions' value="all-permissions"' in applet tag
713 JalviewLite+JmolApplet linked sequence/structure fails
714 Mixed code warnings are raised
716 <jar update="true" index="true">
718 <attribute name="Application-Name" value="JalviewLite" />
719 <attribute name="Permissions" value="all-permissions" />
720 <attribute name="Codebase" value="${applet.codebase}" />
721 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
722 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
726 <presetdef name="applet.jar">
727 <!-- build signed applet with sandbox permissions -
728 Needs 'param name="permissions' value="sandbox"' in applet tag
729 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
732 <jar update="true" index="true">
734 <attribute name="Application-Name" value="JalviewLite" />
735 <attribute name="Permissions" value="sandbox" />
736 <attribute name="Codebase" value="${applet.codebase}" />
737 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
738 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
742 <presetdef name="tl_applet.jar">
743 <!-- build signed applet with trusted library/trusted permissions -
744 Needs 'param name="permissions' value="all-permissions"' in applet tag
746 No mixed code warnings raised
747 Jmol/JalviewLite sequence/structure example doesn't link structures
748 Raises dialog asking user to allow page to control applet via LiveConnect javascript
752 <jar update="true" index="true">
754 <attribute name="Application-Name" value="JalviewLite" />
755 <attribute name="Permissions" value="all-permissions" />
756 <attribute name="Codebase" value="${applet.codebase}" />
757 <attribute name="Trusted-Only" value="true" />
758 <attribute name="Trusted-Library" value="true" />
762 <presetdef name="to_applet.jar">
763 <!-- not fully test variant (yet) -->
764 <jar update="true" index="true">
766 <attribute name="Application-Name" value="JalviewLite" />
767 <attribute name="Permissions" value="all-permissions" />
768 <attribute name="Codebase" value="${applet.codebase}" />
769 <attribute name="Trusted-Only" value="true" />
773 <!-- create differently privileged artefacts -->
774 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
775 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
776 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
777 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
778 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
779 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
780 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
781 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
782 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
783 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
784 <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
785 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
786 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
787 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
788 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
789 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
790 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
791 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
792 <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
793 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
794 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
795 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
796 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
797 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
798 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
799 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
800 <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
801 <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
802 <!-- finally, create manifest for original jars -->
803 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
804 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
805 <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
806 <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
808 <!-- todo - write examples/downloads for alternate versions of the applet -->
809 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
811 <fileset dir="${packageDir}/examples">
812 <exclude name="u_*.jar" />
813 <include name="${jalviewLiteJar}" />
814 <include name="${jmolJar}" />
815 <include name="${javaJson}" />
816 <include name="${jsonSimple}" />
817 <include name="to_${jalviewLiteJar}" />
818 <include name="to_${jmolJar}" />
819 <include name="to_${javaJson}" />
820 <include name="to_${jsonSimple}" />
821 <include name="tl_${jalviewLiteJar}" />
822 <include name="tl_${jmolJar}" />
823 <include name="tl_${javaJson}" />
824 <include name="tl_${jsonSimple}" />
825 <include name="ap_${jalviewLiteJar}" />
826 <include name="ap_${jmolJar}" />
827 <include name="ap_${javaJson}" />
828 <include name="ap_${jsonSimple}" />
831 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
832 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
833 <!-- finally, replace any launchApp servlet tags with a version specification -->
834 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
836 <![CDATA[http://www.jalview.org/services/launchApp"]]>
838 <fileset dir="${packageDir}/examples">
839 <include name="**/*.html" />
842 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
844 <![CDATA[http://www.jalview.org/services/launchApp']]>
846 <fileset dir="${packageDir}/examples">
847 <include name="**/*.html" />
852 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
853 <javadoc destdir="${javadocDir}">
854 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">