3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
4 * Copyright (C) 2015 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" />
85 <!-- time stamp server URL -->
86 <property name="jalview.tsaurl" value="" />
88 <property name="testng-groups" value="Functional" />
90 <!-- Don't change anything below here unless you know what you are doing! -->
91 <!-- Url path for WebStart in JNLP file -->
92 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
93 <!-- Webstart Image - looked for in resources/images -->
94 <property name="WebStartImage" value="JalviewLogo_big.png" />
95 <!-- J2SE version needed for webstart launch -->
96 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
97 <property name="j2sev" value="1.7+" />
98 <!-- Java Compilation settings - source and target javac version -->
99 <property name="javac.source" value="1.7" />
100 <property name="javac.target" value="1.7" />
102 <!-- Permissions for running Java applets and applications. -->
103 <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
104 <property name="application.codebase" value="*.jalview.org" />
105 <!-- and allowing the applet to be deployed from any URL -->
106 <!-- 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 -->
107 <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
108 <property name="applet.caller-codebase" value="${applet.codebase}" />
110 <!-- build directory configuration -->
111 <property name="libDir" value="lib" />
112 <property name="resourceDir" value="resources" />
113 <property name="helpDir" value="help" />
114 <property name="docDir" value="doc" />
115 <property name="sourceDir" value="src" />
116 <property name="schemaDir" value="schemas" />
117 <property name="outputDir" value="classes" />
118 <property name="packageDir" value="dist" />
119 <property name="outputJar" value="jalview.jar" />
120 <!-- Jalview Applet JMol Jar Dependency -->
121 <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
122 <property name="varnaJar" value="VARNAv3-93.jar" />
123 <property name="jsoup" value="jsoup-1.8.1.jar" />
124 <property name="jsonSimple" value="json_simple-1.1.jar" />
125 <property name="javaJson" value="java-json.jar" />
126 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
127 <property name="reportDir" value="test-reports" />
128 <property name="testDir" value="test" />
129 <property name="testOutputDir" value="tests" />
130 <!-- switch to indicate if we should obfuscate jalviewLite -->
131 <!-- <property name="donotobfuscate" value="true"/> -->
132 <!-- switch to exclude associations from generated jnlp files -->
133 <!-- <property name="nojnlpfileassocs" value="true"/> -->
135 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
136 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
137 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
138 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
139 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
140 <property name="WSInterf" value="MsaWS" />
141 <property name="wsdl.Namespace" value="vamsas" />
142 <property name="wsdl.ClientNS" value="ext.vamsas" />
143 <!-- the class path for building the application -->
144 <path id="build.classpath">
145 <fileset dir="utils">
146 <include name="*.jar" />
147 <include name="**/*.jar" />
149 <fileset dir="${libDir}">
150 <include name="*.jar" />
151 <include name="**/*.jar" />
153 <fileset dir="${java.home}/lib">
154 <include name="plugin.jar" />
156 <fileset dir="appletlib">
157 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
159 <include name="${jmolJar}" />
160 <include name="${varnaJar}" />
163 <path id="test.classpath">
164 <pathelement path="${outputDir}" />
165 <path refid="build.classpath" />
167 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
168 <!-- The Location of the java 1.1.8 jdk -->
169 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
170 <property name="java118.home" value="${java.home}" />
171 <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
173 <!-- jre for 1.4 version -->
174 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
176 <!-- the classpath for building the 1.1 applet -->
177 <path id="jalviewlite.deps">
178 <fileset dir="${java118.home}">
179 <include name="lib/classes.zip" />
181 <fileset dir="${java.home}/lib">
182 <include name="plugin.jar" />
184 <pathelement location="appletlib/${jmolJar}" />
185 <pathelement location="lib/${varnaJar}" />
186 <pathelement location="lib/${jsoup}" />
187 <pathelement location="lib/${jsonSimple}" />
188 <pathelement location="lib/${javaJson}" />
191 <!-- default location for outputting javadoc -->
192 <property name="javadocDir" value="${packageDir}/javadoc" />
196 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
197 <target name="buildPropertiesFile" depends="init">
198 <tstamp prefix="build">
199 <format property="date" pattern="dd MMMM yyyy" />
201 <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
202 <arg value="rev-parse" />
203 <arg value="--short" />
206 <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
207 <arg value="rev-parse" />
208 <arg value="--abbrev-ref" />
211 <properties file="${outputDir}/.build_properties">
213 ---Jalview Build Details---
215 <property name="VERSION" value="${JALVIEW_VERSION}" />
216 <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
217 <property name="BUILD_DATE" value="${build.date}" />
222 <target name="clean" depends="init">
223 <!-- not efficient yet. -->
224 <delete dir="${outputDir}" includes="*,**/*" />
227 <target name="distclean" depends="init, clean">
229 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
232 <include name="${outputJar}" />
233 <include name="#*#" />
234 <include name="#*.*#" />
235 <include name="**/#*#" />
236 <include name="**/#*.*#" />
237 <include name="*~" />
238 <include name="*.*~" />
239 <include name="**/*~" />
240 <include name="**/*.*~" />
245 <target name="prepare" depends="init">
246 <mkdir dir="${outputDir}" />
247 <copy todir="${outputDir}">
249 <include name="${docDir}/**/*.*" />
250 <include name="${helpDir}/**/*.*" />
251 <include name="${libDir}/*.jar" />
253 <fileset dir="${resourceDir}">
254 <include name="**/*.*" />
259 <target name="build" depends="prepare">
260 <!-- not efficient yet. -->
261 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
262 <exclude name="jalview/*applet*" />
263 <exclude name="jalview/appletgui/**" />
264 <exclude name="com/stevesoft/**" />
269 <target name="testclean" depends="init">
270 <delete dir="${testOutputDir}" includes="*,**/*" />
273 <target name="prepareTests" depends="init,testclean">
274 <mkdir dir="${testOutputDir}" />
277 <target name="buildTests" depends="build,buildindices,prepareTests">
278 <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
282 <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
284 <target name="testng" depends="buildTests">
285 <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
288 <pathelement location="${testOutputDir}" />
289 <path refid="test.classpath" />
291 <classfileset dir="${testOutputDir}" includes="**/*.class" />
295 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
296 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
301 <target name="makefulldist" depends="makedist">
302 <copy todir="${packageDir}">
303 <fileset dir="${resourceDir}/images">
304 <include name="${WebStartImage}" />
308 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
310 <!-- create a dummy jar which will eventually contain the jnlp template -->
311 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
312 <fileset dir="${packageDir}">
313 <include name="jalview.jar" />
317 <mkdir dir="${packageDir}/JNLP-INF" />
318 <antcall target="writejnlpf">
319 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
320 <param name="inih" value="*" />
321 <param name="maxh" value="*" />
324 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
325 <fileset dir="${packageDir}">
326 <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
330 <antcall target="writejnlpf">
331 <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
332 <param name="inih" value="10M" />
333 <param name="maxh" value="256M" />
336 <antcall target="writejnlpf">
337 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
338 <param name="inih" value="128M" />
339 <param name="maxh" value="512M" />
342 <antcall target="writejnlpf">
343 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
344 <param name="inih" value="256M" />
345 <param name="maxh" value="1024M" />
348 <!-- finally, need to postprocess to add in associations at end of 'information' element
350 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
357 <association mime-type="application-x/ext-file" extensions="fa"/>
358 <association mime-type="application-x/ext-file" extensions="fasta"/>
359 <association mime-type="application-x/ext-file" extensions="mfa"/>
360 <association mime-type="application-x/ext-file" extensions="fastq"/>
361 <association mime-type="application-x/ext-file" extensions="blc"/>
362 <association mime-type="application-x/ext-file" extensions="msf"/>
363 <association mime-type="application-x/ext-file" extensions="pfam"/>
364 <association mime-type="application-x/ext-file" extensions="aln"/>
365 <association mime-type="application-x/ext-file" extensions="pir"/>
366 <association mime-type="application-x/ext-file" extensions="amsa"/>
367 <association mime-type="application-x/ext-file" extensions="stk"/>
368 <association mime-type="application-x/ext-file" extensions="jar"/>-->
369 <!-- and sign the jars -->
370 <!-- the default keystore details might need to be edited here -->
371 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA"
372 tsaurl="${jalview.tsaurl}">
373 <fileset dir="${packageDir}">
374 <include name="*.jar" />
380 <target name="runenv" depends="init">
381 <path id="run.classpath">
382 <pathelement location="${outputDir}" />
383 <fileset dir="${outputDir}">
384 <include name="${libDir}/*.jar" />
387 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
389 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
393 <target name="-generatejnlpf">
394 <presetdef name="jnlpf">
395 <jnlp codebase="${WebStartLocation}">
397 <title>Jalview</title>
398 <vendor>The Barton Group</vendor>
399 <homepage href="http://www.jalview.org" />
400 <description>Jalview Multiple Alignment Editor</description>
401 <description kind="short">Jalview</description>
402 <icon href="${WebStartImage}" />
406 <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
407 <fileset dir="${packageDir}">
408 <include name="jalview.jar" />
410 <fileset dir="${packageDir}">
411 <include name="*.jar" />
412 <include name="*_*.jar" />
413 <exclude name="jalview.jar" />
414 <exclude name="*jnilib.jar" />
417 <resources os="Mac OS X">
418 <property name="jalview.version" value="${JALVIEW_VERSION}" />
419 <fileset dir="${packageDir}">
420 <include name="*quaqua*.jnilib.jar" />
424 <application_desc main_class="jalview.bin.Jalview">
432 <jnlpf toFile="${jnlpFile}" />
436 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
437 <echo message="Not adding JNLP File Associations" />
440 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
441 <replace file="${jnlpFile}">
443 <![CDATA[</information>]]></replacetoken>
446 <association mime-type="application-x/ext-file" extensions="fa" />
447 <association mime-type="application-x/ext-file" extensions="fasta" />
448 <association mime-type="application-x/ext-file" extensions="mfa" />
449 <association mime-type="application-x/ext-file" extensions="fastq" />
450 <association mime-type="application-x/ext-file" extensions="blc" />
451 <association mime-type="application-x/ext-file" extensions="msf" />
452 <association mime-type="application-x/ext-file" extensions="pfam" />
453 <association mime-type="application-x/ext-file" extensions="aln"/>
454 <association mime-type="application-x/ext-file" extensions="pir"/>
455 <association mime-type="application-x/ext-file" extensions="amsa"/>
456 <association mime-type="application-x/ext-file" extensions="stk"/>
457 <association mime-type="application-x/ext-file" extensions="jvp"/>
458 </information>]]></replacevalue>
460 <echo message="Added file associations to JNLP file" />
462 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
465 <target name="buildextclients" depends="init">
466 <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" />
467 <condition property="dontextbuild">
468 <equals arg1="n" arg2="${doextbuild.response}" />
470 <condition property="dontextbuild">
471 <equals arg1="N" arg2="${doextbuild.response}" />
473 <fail if="dontextbuild">
474 Build External Client Code process aborted by user. Jalview source is unchanged.
476 <!-- Currently, this doesn't happen automatically.
477 1. Run WSDL2Java as below, which generates an ext.vamsas +
478 vamsas.<datapackages> fileset.
479 2. refactor ext.vamsas.SpecificserviceWS* to
480 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
481 3. Update the jalview.ws.*WServices classes to reflect the
482 interface type, and all locations of this wsdl type that Jalview
486 <path id="axisbuild">
487 <path refid="build.classpath" />
489 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
491 <fileset dir="${sourceDir}" id="client">
492 <include name="${wsdl.ClientNS}/*.*" />
496 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
498 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
499 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
504 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
505 <!-- make the package jar if not already existing -->
506 <mkdir dir="${packageDir}" />
507 <!-- clean dir if it already existed -->
509 <fileset dir="${packageDir}">
510 <include name="*.jar" />
513 <jar destfile="${packageDir}/${outputJar}" index="true">
515 <attribute name="Main-Class" value="jalview.bin.Jalview" />
516 <attribute name="Permissions" value="all-permissions" />
517 <attribute name="Application-Name" value="Jalview Desktop" />
518 <attribute name="Codebase" value="${application.codebase}" />
520 <fileset dir="${outputDir}/">
521 <exclude name="cache*/**" />
522 <exclude name="*.jar" />
523 <exclude name="*.jar.*" />
524 <exclude name="**/*.jar" />
525 <exclude name="**/*.jar.*" />
529 <copy toDir="${packageDir}" flatten="true">
530 <fileset dir="${outputDir}">
531 <include name="*.jar" />
532 <include name="**/*.jar" />
538 <!-- jalopy code reformatter -->
539 <target name="sourcescrub" depends="init,build">
540 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
541 <fileset dir="${sourceDir}">
542 <include name="*.java" />
543 <include name="**/*.java" />
544 <include name="**/**/*.java" />
551 <!-- Compile, package and obfuscate Jalview Applet -->
552 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
554 <target name="compileApplet" depends="init,clean">
555 <mkdir dir="${outputDir}" />
556 <javac source="${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/**" />
559 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
560 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
561 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
562 <copy todir="${outputDir}/lang">
563 <fileset dir="${resourceDir}/lang">
564 <include name="**.*" />
567 <jar destfile="in.jar" index="true">
569 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
570 <attribute name="Application-Name" value="JalviewLite" />
571 <attribute name="Codebase" value="${applet.codebase}" />
573 <fileset dir="${outputDir}">
574 <include name="com/**" />
575 <include name="MCview/**" />
576 <include name="jalview/**" />
577 <include name=".build_properties" />
578 <include name="images/idwidth.gif" />
579 <include name="images/link.gif" />
580 <include name="lang/**" />
584 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
586 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
587 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
588 <delete file="in.jar" />
590 <target name="-obfuscatereally" unless="donotobfuscate">
592 <path id="obfuscateDeps.path">
593 <pathelement location="${applet.jre.tools}" />
594 <pathelement location="appletlib/${jmolJar}" />
595 <pathelement location="appletlib/${jsonSimple}" />
596 <pathelement location="appletlib/${javaJson}" />
598 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
601 <injar file="in.jar" />
602 <outjar file="${jalviewLiteJar}" />
603 <libraryjar refid="obfuscateDeps.path" />
605 <keep access="public" type="class" name="jalview.bin.JalviewLite">
606 <field access="public" />
607 <method access="public" />
608 <constructor access="public" />
610 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
611 <field access="public" />
612 <method access="public" />
613 <constructor access="public" />
615 <!-- -libraryjars "${obfuscateDeps}"
617 -outjars jalviewApplet.jar
618 -keep public class jalview.bin.JalviewLite
621 <delete file="in.jar" />
624 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
625 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
627 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
628 <include name="*.java" />
629 <include name="descriptors/*.java" />
632 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
633 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
634 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
635 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
637 now build the jalview.binding package with the old schema set
640 <fileset dir="${sourceDir}/jalview/binding/">
641 <include name="**" />
644 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
645 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
646 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
648 <target name="sourcedist" description="create jalview source distribution" depends="init">
649 <delete file="${source.dist.name}" />
650 <tar destfile="${source.dist.name}" compression="gzip">
651 <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
652 <include name="LICENSE" />
653 <include name="README" />
654 <include name="build.xml" />
655 <include name="jalview-jalopy.xml" />
656 <include name="JalviewApplet.jpx" />
657 <include name="JalviewX.jpx" />
658 <include name="nbbuild.xml" />
659 <include name="nbproject/genfiles.properties" />
660 <include name="nbproject/project.properties" />
661 <include name="nbproject/project.xml" />
662 <include name="${sourceDir}/*.java" />
663 <include name="${sourceDir}/**/*.java" />
664 <include name="${sourceDir}/**/*.cdr" />
665 <include name="${libDir}/**/*" />
666 <include name="${resourceDir}/**/*" />
667 <include name="${helpDir}/**/*" />
668 <include name="appletlib/${jmolJar}" />
669 <exclude name="**/*locales" />
670 <exclude name="*locales/**" />
671 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
672 <exclude name="utils/InstallAnywhere/**Build*/**" />
673 <exclude name="utils/InstallAnywhere/**Build*/**" />
674 <exclude name="utils/InstallAnywhere/**locale*" />
675 <exclude name="utils/InstallAnywhere/**locale*/**" />
676 <include name="${schemaDir}/**/*" />
677 <include name="utils/**/*" />
678 <include name="${docDir}/**/*" />
679 <include name="examples/**/*" />
683 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
684 <copy todir="${packageDir}/examples">
685 <fileset dir="examples">
686 <include name="**/*" />
687 <include name="javascript/*" />
688 <include name="jmol/*" />
691 <include name="${jalviewLiteJar}" />
693 <fileset dir="appletlib">
694 <include name="**/*" />
697 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
698 <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
699 <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
700 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
702 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
703 <!-- <attribute name="Permissions" value="sandbox" /> -->
704 <!--<attribute name="Trusted-Lib" value="true" /> -->
705 <attribute name="Codebase" value="${applet.codebase}" />
706 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
709 <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
710 <fileset dir="${packageDir}/examples">
711 <include name="*.jar" />
714 <presetdef name="ap_applet.jar">
715 <!-- build a signed applet with 'all-permissions' -
716 Needs 'param name="permissions' value="all-permissions"' in applet tag
717 JalviewLite+JmolApplet linked sequence/structure fails
718 Mixed code warnings are raised
720 <jar update="true" index="true">
722 <attribute name="Application-Name" value="JalviewLite" />
723 <attribute name="Permissions" value="all-permissions" />
724 <attribute name="Codebase" value="${applet.codebase}" />
725 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
726 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
730 <presetdef name="applet.jar">
731 <!-- build signed applet with sandbox permissions -
732 Needs 'param name="permissions' value="sandbox"' in applet tag
733 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
736 <jar update="true" index="true">
738 <attribute name="Application-Name" value="JalviewLite" />
739 <attribute name="Permissions" value="sandbox" />
740 <attribute name="Codebase" value="${applet.codebase}" />
741 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
742 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
746 <presetdef name="tl_applet.jar">
747 <!-- build signed applet with trusted library/trusted permissions -
748 Needs 'param name="permissions' value="all-permissions"' in applet tag
750 No mixed code warnings raised
751 Jmol/JalviewLite sequence/structure example doesn't link structures
752 Raises dialog asking user to allow page to control applet via LiveConnect javascript
756 <jar update="true" index="true">
758 <attribute name="Application-Name" value="JalviewLite" />
759 <attribute name="Permissions" value="all-permissions" />
760 <attribute name="Codebase" value="${applet.codebase}" />
761 <attribute name="Trusted-Only" value="true" />
762 <attribute name="Trusted-Library" value="true" />
766 <presetdef name="to_applet.jar">
767 <!-- not fully test variant (yet) -->
768 <jar update="true" index="true">
770 <attribute name="Application-Name" value="JalviewLite" />
771 <attribute name="Permissions" value="all-permissions" />
772 <attribute name="Codebase" value="${applet.codebase}" />
773 <attribute name="Trusted-Only" value="true" />
777 <!-- create differently privileged artefacts -->
778 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
779 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
780 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
781 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
782 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
783 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
784 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
785 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
786 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
787 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
788 <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
789 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
790 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
791 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
792 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
793 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
794 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
795 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
796 <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
797 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
798 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
799 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
800 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
801 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
802 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
803 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
804 <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
805 <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
806 <!-- finally, create manifest for original jars -->
807 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
808 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
809 <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
810 <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
812 <!-- todo - write examples/downloads for alternate versions of the applet -->
813 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
815 <fileset dir="${packageDir}/examples">
816 <exclude name="u_*.jar" />
817 <include name="${jalviewLiteJar}" />
818 <include name="${jmolJar}" />
819 <include name="${javaJson}" />
820 <include name="${jsonSimple}" />
821 <include name="to_${jalviewLiteJar}" />
822 <include name="to_${jmolJar}" />
823 <include name="to_${javaJson}" />
824 <include name="to_${jsonSimple}" />
825 <include name="tl_${jalviewLiteJar}" />
826 <include name="tl_${jmolJar}" />
827 <include name="tl_${javaJson}" />
828 <include name="tl_${jsonSimple}" />
829 <include name="ap_${jalviewLiteJar}" />
830 <include name="ap_${jmolJar}" />
831 <include name="ap_${javaJson}" />
832 <include name="ap_${jsonSimple}" />
835 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
836 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
837 <!-- finally, replace any launchApp servlet tags with a version specification -->
838 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
840 <![CDATA[http://www.jalview.org/services/launchApp"]]>
842 <fileset dir="${packageDir}/examples">
843 <include name="**/*.html" />
846 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
848 <![CDATA[http://www.jalview.org/services/launchApp']]>
850 <fileset dir="${packageDir}/examples">
851 <include name="**/*.html" />
856 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
857 <javadoc destdir="${javadocDir}">
858 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">