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="."
22 xmlns:unless="ant:unless">
23 <taskdef classpath="${clover.jar}" resource="cloverlib.xml" if:set="clover.jar"/>
24 <clover-env if:set="clover.jar"/>
26 <target name="help" depends="usage" />
27 <target name="usage" depends="init">
28 <echo message="~~~Jalview Ant build.xml Usage~~~~" />
29 <echo message="Targets include:" />
30 <echo message="usage - default target, displays this message" />
31 <echo message="buildindices - generates JavaHelpSearch from the help files" />
32 <echo message="build - compiles all necessary files for Application" />
33 <echo message="makedist - compiles and places all necessary jar files into directory dist" />
34 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
35 <echo message=" this needs a keystore and key."/>
36 <echo message=" Add -Dtimestamp to timestamp signed jars"/>
37 <echo message=" -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
38 <echo message=" See docs/building.html for more information." />
39 <echo message="compileApplet - compiles all necessary files for Applet" />
40 <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
41 <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
42 <echo message=" you can specify particular test groups as a list via -Dtestng-groups=" />
43 <echo message="See docs/building.html and the comments in build file for other targets." />
44 <echo message="note: compile and makeApplet optionally compile/obfuscate applet against a different Java version by specifying -Djava118.home=PathtoJDK/lib which is the lib directory in the JDK install that contains rt.jar " />
45 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
46 <echo message="Useful -D flags: -Dclover.jar to specify path to openclover for testng coverage report" />
50 <!-- utils is a class path to additional utilities needed for
51 building docs, jars and webstart stuff -->
53 Userdefined build property defaults
55 wsdl.server list (plus namespace mapping info ???) - also want
56 ... to make this a dynamically generatable property
58 Build location - provide a temporary root for speed
59 jarsigner keystore and info
60 Jakarta and axis classpath ?
61 Default argument for starting Jalview (if it exists).
66 <path id="axis.classpath">
68 <fileset dir="/usr/local/axis/lib">
69 <include name="**/*.jar" />
71 <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
72 <include name="**/*.jar"/>
73 <include name="*.jar"/>
77 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
78 <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
80 <property name="INSTALLATION" value="Source" />
82 <!-- 2.4 (VAMSAS)" -->
83 <!-- Include debugging information in javac true or false -->
84 <property name="javac.debug" value="true" />
86 <!-- JarSigner Key Store for Webstart Distribution -->
87 <property name="jalview.keystore" value="./keys/.keystore" />
88 <!-- Keystore Password -->
89 <property name="jalview.keystore.pass" value="alignmentisfun" />
91 <property name="jalview.key" value="jalview" />
93 <property name="jalview.key.pass" value="alignmentisfun" />
94 <!-- time stamp server URL -->
95 <property name="jalview.tsaurl" value="" />
96 <!-- locally valid proxy for signing with external time server -->
97 <property name="proxyPort" value="80"/>
98 <property name="proxyHost" value="sqid"/>
99 <!-- key sign/digest algorithms -->
100 <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
101 <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
103 <!-- default TestNG groups to run -->
104 <property name="testng-groups" value="Functional" />
105 <!-- Java 9 JVM args -->
106 <condition property="java9">
107 <equals arg1="${ant.java.version}" arg2="9"/>
110 <!-- Don't change anything below here unless you know what you are doing! -->
111 <!-- Url path for WebStart in JNLP file -->
112 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
113 <!-- Webstart Image - looked for in resources/images -->
114 <property name="WebStartImage" value="JalviewLogo_big.png" />
115 <!-- J2SE version needed for webstart launch -->
116 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
117 <property name="j2sev" value="1.7+" />
118 <!-- Java Compilation settings - source and target javac version -->
119 <property name="javac.source" value="1.8" />
120 <property name="javac.target" value="1.8" />
122 <!-- Permissions for running Java applets and applications. -->
123 <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
124 <property name="application.codebase" value="*.jalview.org" />
125 <!-- and allowing the applet to be deployed from any URL -->
126 <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
127 <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
128 <property name="applet.caller-codebase" value="${applet.codebase}" />
130 <!-- build directory configuration -->
131 <property name="libDir" value="lib" />
132 <property name="resourceDir" value="resources" />
133 <property name="helpDir" value="help" />
134 <property name="docDir" value="doc" />
135 <property name="sourceDir" value="src" />
136 <property name="schemaDir" value="schemas" />
137 <property name="outputDir" value="classes" unless:set="clover.jar"/>
138 <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
139 <property name="outputDir" value="classes" />
140 <property name="packageDir" value="dist" />
141 <property name="outputJar" value="jalview.jar" />
142 <!-- Jalview Applet JMol Jar Dependency -->
143 <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
144 <property name="varnaJar" value="VARNAv3-93.jar" />
145 <property name="jsoup" value="jsoup-1.8.1.jar" />
146 <property name="jsonSimple" value="json_simple-1.1.jar" />
147 <property name="javaJson" value="java-json.jar" />
148 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
149 <property name="reportDir" value="test-reports" />
150 <property name="testDir" value="test" />
151 <property name="testOutputDir" value="tests" />
152 <!-- switch to indicate if we should obfuscate jalviewLite -->
153 <!-- <property name="donotobfuscate" value="true"/> -->
154 <!-- switch to exclude associations from generated jnlp files -->
155 <!-- <property name="nojnlpfileassocs" value="true"/> -->
157 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
158 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
159 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
160 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
161 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
162 <property name="WSInterf" value="MsaWS" />
163 <property name="wsdl.Namespace" value="vamsas" />
164 <property name="wsdl.ClientNS" value="ext.vamsas" />
165 <!-- the class path for building the application -->
166 <path id="build.classpath">
167 <fileset dir="utils">
168 <include name="*.jar" />
169 <include name="**/*.jar" />
171 <fileset dir="${libDir}">
172 <include name="*.jar" />
173 <include name="**/*.jar" />
175 <fileset dir="${java.home}/lib">
176 <include name="plugin.jar" />
178 <fileset dir="appletlib">
179 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
181 <include name="${jmolJar}" />
182 <include name="${varnaJar}" />
185 <path id="test.classpath">
186 <pathelement path="${outputDir}" />
187 <path refid="build.classpath" />
189 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
190 <!-- The Location of the java 1.1.8 jdk -->
191 <property name="java118.home" value="${java.home}" />
192 <!-- jre for 1.4 version -->
193 <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
195 <!-- the classpath for building the 1.1 applet -->
196 <path id="jalviewlite.deps">
197 <fileset dir="${java118.home}">
198 <include name="lib/rt.jar" />
200 <fileset dir="${java.home}/lib">
201 <include name="plugin.jar" />
203 <pathelement location="appletlib/${jmolJar}" />
204 <pathelement location="lib/${varnaJar}" />
205 <pathelement location="appletlib/${jsoup}" />
206 <pathelement location="appletlib/${jsonSimple}" />
207 <pathelement location="appletlib/${javaJson}" />
210 <!-- default location for outputting javadoc -->
211 <property name="javadocDir" value="${packageDir}/javadoc" />
215 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
216 <target name="buildPropertiesFile" depends="init">
217 <tstamp prefix="build">
218 <format property="date" pattern="dd MMMM yyyy" />
220 <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
221 <arg value="rev-parse" />
222 <arg value="--short" />
225 <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
226 <arg value="rev-parse" />
227 <arg value="--abbrev-ref" />
230 <properties file="${outputDir}/.build_properties">
232 ---Jalview Build Details---
234 <property name="VERSION" value="${JALVIEW_VERSION}" />
235 <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
236 <property name="BUILD_DATE" value="${build.date}" />
241 <target name="clean" depends="init">
242 <!-- not efficient yet. -->
243 <delete dir="${outputDir}" includes="*,**/*" />
246 <target name="distclean" depends="init, clean">
248 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
251 <include name="${outputJar}" />
252 <include name="#*#" />
253 <include name="#*.*#" />
254 <include name="**/#*#" />
255 <include name="**/#*.*#" />
256 <include name="*~" />
257 <include name="*.*~" />
258 <include name="**/*~" />
259 <include name="**/*.*~" />
264 <target name="prepare" depends="init">
265 <mkdir dir="${outputDir}" />
266 <copy todir="${outputDir}">
268 <include name="${docDir}/**/*.*" />
269 <include name="${helpDir}/**/*.*" />
270 <include name="${libDir}/*.jar" />
272 <fileset dir="${resourceDir}">
273 <include name="**/*.*" />
278 <target name="build" depends="prepare">
279 <!-- not efficient yet. -->
280 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
281 <exclude name="jalview/*applet*" />
282 <exclude name="jalview/appletgui/**" />
283 <exclude name="com/stevesoft/**" />
288 <target name="testclean" depends="init">
289 <delete dir="${testOutputDir}" includes="*,**/*" />
292 <target name="prepareTests" depends="init,testclean">
293 <mkdir dir="${testOutputDir}" />
296 <target name="buildTests" depends="build,buildindices,prepareTests">
297 <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
301 <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
303 <target name="testng" depends="buildTests">
304 <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
307 <pathelement location="${testOutputDir}" />
308 <pathelement location="${clover.jar}" if:set="clover.jar"/>
309 <path refid="test.classpath" />
311 <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
312 <jvmarg value="--illegal-access=warn" if:set="java9"/>
313 <classfileset dir="${testOutputDir}" includes="**/*.class" />
317 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
318 <replace value="${JALVIEW_VERSION}">
319 <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
320 <fileset dir="${outputDir}/${helpDir}">
321 <include name="help.jhm" />
325 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
330 <target name="preparejnlp" depends="makedist">
331 <copy todir="${packageDir}">
332 <fileset dir="${resourceDir}/images">
333 <include name="${WebStartImage}" />
337 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
339 <!-- create a dummy jar which will eventually contain the jnlp template -->
340 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
341 <fileset dir="${packageDir}">
342 <include name="jalview.jar" />
346 <mkdir dir="${packageDir}/JNLP-INF" />
347 <antcall target="writejnlpf">
348 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
349 <param name="inih" value="*" />
350 <param name="maxh" value="*" />
353 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
354 <fileset dir="${packageDir}">
355 <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
359 <antcall target="writejnlpf">
360 <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
361 <param name="inih" value="10M" />
362 <param name="maxh" value="256M" />
365 <antcall target="writejnlpf">
366 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
367 <param name="inih" value="128M" />
368 <param name="maxh" value="512M" />
371 <antcall target="writejnlpf">
372 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
373 <param name="inih" value="256M" />
374 <param name="maxh" value="1024M" />
377 <!-- finally, need to postprocess to add in associations at end of 'information' element
379 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
386 <association mime-type="application-x/ext-file" extensions="fa"/>
387 <association mime-type="application-x/ext-file" extensions="fasta"/>
388 <association mime-type="application-x/ext-file" extensions="mfa"/>
389 <association mime-type="application-x/ext-file" extensions="fastq"/>
390 <association mime-type="application-x/ext-file" extensions="blc"/>
391 <association mime-type="application-x/ext-file" extensions="msf"/>
392 <association mime-type="application-x/ext-file" extensions="pfam"/>
393 <association mime-type="application-x/ext-file" extensions="aln"/>
394 <association mime-type="application-x/ext-file" extensions="pir"/>
395 <association mime-type="application-x/ext-file" extensions="amsa"/>
396 <association mime-type="application-x/ext-file" extensions="stk"/>
397 <association mime-type="application-x/ext-file" extensions="jar"/>-->
400 <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
401 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
402 tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
403 <fileset dir="${packageDir}">
404 <include name="*.jar" />
408 <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
409 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
410 <fileset dir="${packageDir}">
411 <include name="*.jar" />
416 <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
417 <!-- and sign the jars -->
418 <!-- the default keystore details might need to be edited here -->
421 <target name="runenv" depends="init">
422 <path id="run.classpath">
423 <pathelement location="${outputDir}" />
424 <fileset dir="${outputDir}">
425 <include name="${libDir}/*.jar" />
428 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
430 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
434 <target name="-generatejnlpf">
435 <presetdef name="jnlpf">
436 <jnlp codebase="${WebStartLocation}">
438 <title>Jalview</title>
439 <vendor>The Barton Group</vendor>
440 <homepage href="http://www.jalview.org" />
441 <description>Jalview Multiple Alignment Editor</description>
442 <description kind="short">Jalview</description>
443 <icon href="${WebStartImage}" />
447 <j2se version="1.8+" />
448 <jar main="true" href="jalview.jar"/>
449 <fileset dir="${packageDir}">
450 <exclude name="jalview.jar" />
451 <include name="*.jar" />
452 <include name="*_*.jar" />
453 <exclude name="*quaqua*.jar" />
455 <property name="jalview.version" value="${JALVIEW_VERSION}" />
457 <resources os="Mac OS X">
458 <fileset dir="${packageDir}">
459 <include name="quaqua-filechooser-only-8.0.jar"/>
460 <include name="*quaqua64*.jnilib.jar" />
464 <application_desc main_class="jalview.bin.Jalview">
472 <jnlpf toFile="${jnlpFile}" />
473 <!-- add the add-modules j2se attribute for java 9 -->
474 <replace file="${jnlpFile}" value="j2se version="1.8+" initial-heap-size="${inih}" max-heap-size="${maxh}" java-vm-args="--add-modules=java.se.ee --illegal-access=warn"">
475 <replacetoken>j2se version="1.8+"</replacetoken>
479 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
480 <echo message="Not adding JNLP File Associations" />
483 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
484 <replace file="${jnlpFile}">
486 <![CDATA[</information>]]></replacetoken>
489 <association mime-type="application-x/ext-file" extensions="fa" />
490 <association mime-type="application-x/ext-file" extensions="fasta" />
491 <association mime-type="application-x/ext-file" extensions="mfa" />
492 <association mime-type="application-x/ext-file" extensions="fastq" />
493 <association mime-type="application-x/ext-file" extensions="blc" />
494 <association mime-type="application-x/ext-file" extensions="msf" />
495 <association mime-type="application-x/ext-file" extensions="pfam" />
496 <association mime-type="application-x/ext-file" extensions="aln"/>
497 <association mime-type="application-x/ext-file" extensions="pir"/>
498 <association mime-type="application-x/ext-file" extensions="amsa"/>
499 <association mime-type="application-x/ext-file" extensions="stk"/>
500 <association mime-type="application-x/ext-file" extensions="jvp"/>
501 </information>]]></replacevalue>
503 <echo message="Added file associations to JNLP file" />
505 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
508 <target name="buildextclients" depends="init">
509 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
510 <condition property="dontextbuild">
511 <equals arg1="n" arg2="${doextbuild.response}" />
513 <condition property="dontextbuild">
514 <equals arg1="N" arg2="${doextbuild.response}" />
516 <fail if="dontextbuild">
517 Build External Client Code process aborted by user. Jalview source is unchanged.
519 <!-- Currently, this doesn't happen automatically.
520 1. Run WSDL2Java as below, which generates an ext.vamsas +
521 vamsas.<datapackages> fileset.
522 2. refactor ext.vamsas.SpecificserviceWS* to
523 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
524 3. Update the jalview.ws.*WServices classes to reflect the
525 interface type, and all locations of this wsdl type that Jalview
529 <path id="axisbuild">
530 <path refid="build.classpath" />
532 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
534 <fileset dir="${sourceDir}" id="client">
535 <include name="${wsdl.ClientNS}/*.*" />
539 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
541 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
542 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
547 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
548 <!-- make the package jar if not already existing -->
549 <mkdir dir="${packageDir}" />
550 <!-- clean dir if it already existed -->
552 <fileset dir="${packageDir}">
553 <include name="*.jar" />
556 <jar destfile="${packageDir}/${outputJar}" index="true">
558 <attribute name="Main-Class" value="jalview.bin.Jalview" />
559 <attribute name="Permissions" value="all-permissions" />
560 <attribute name="Application-Name" value="Jalview Desktop" />
561 <attribute name="Codebase" value="${application.codebase}" />
563 <fileset dir="${outputDir}/">
564 <exclude name="cache*/**" />
565 <exclude name="*.jar" />
566 <exclude name="*.jar.*" />
567 <exclude name="**/*.jar" />
568 <exclude name="**/*.jar.*" />
572 <copy toDir="${packageDir}" flatten="true">
573 <fileset dir="${outputDir}">
574 <include name="*.jar" />
575 <include name="**/*.jar" />
581 <!-- jalopy code reformatter -->
582 <target name="sourcescrub" depends="init,build">
583 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
584 <fileset dir="${sourceDir}">
585 <include name="*.java" />
586 <include name="**/*.java" />
587 <include name="**/**/*.java" />
594 <!-- Compile, package and obfuscate Jalview Applet -->
595 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
597 <target name="compileApplet" depends="init,clean">
598 <mkdir dir="${outputDir}" />
599 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
602 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
603 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
604 <copy todir="${outputDir}/lang">
605 <fileset dir="${resourceDir}/lang">
606 <include name="**.*" />
609 <jar destfile="in.jar" index="true">
611 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
612 <attribute name="Application-Name" value="JalviewLite" />
613 <attribute name="Codebase" value="${applet.codebase}" />
615 <fileset dir="${outputDir}">
616 <include name="com/**" />
617 <include name="MCview/**" />
618 <include name="jalview/**" />
619 <include name=".build_properties" />
620 <include name="images/link.gif" />
621 <include name="lang/**" />
625 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
627 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
628 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
629 <delete file="in.jar" />
631 <target name="-obfuscatereally" unless="donotobfuscate">
633 <path id="obfuscateDeps.path">
634 <pathelement location="${applet.jre.tools}" />
635 <pathelement location="appletlib/${jmolJar}" />
636 <pathelement location="lib/${varnaJar}" />
637 <pathelement location="appletlib/${jsoup}" />
638 <pathelement location="appletlib/${jsonSimple}" />
639 <pathelement location="appletlib/${javaJson}" />
640 <fileset dir="${java.home}/lib">
641 <include name="plugin.jar" />
644 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
646 <proguard verbose="true" >
647 <injar file="in.jar" />
648 <outjar file="${jalviewLiteJar}" />
649 <libraryjar refid="obfuscateDeps.path" />
651 <keep access="public" type="class" name="jalview.bin.JalviewLite">
652 <field access="public" />
653 <method access="public" />
654 <constructor access="public" />
656 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
657 <field access="public" />
658 <method access="public" />
659 <constructor access="public" />
662 <keep name="jalview.json.binding**">
667 <keep access="public" type="class" name="MCview.PDBfile">
668 <field access="public" />
669 <method access="public" />
670 <constructor access="public" />
673 <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
674 <field access="public" />
675 <method access="public" />
676 <constructor access="public" />
679 <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
680 <field access="public" />
681 <method access="public" />
682 <constructor access="public" />
686 <!-- -libraryjars "${obfuscateDeps}"
688 -outjars jalviewApplet.jar
689 -keep public class jalview.bin.JalviewLite
692 <delete file="in.jar" />
695 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
696 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
698 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
699 <include name="*.java" />
700 <include name="descriptors/*.java" />
703 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
704 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
705 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
706 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
708 now build the jalview.binding package with the old schema set
711 <fileset dir="${sourceDir}/jalview/binding/">
712 <include name="**" />
715 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
716 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
717 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
719 <target name="sourcedist" description="create jalview source distribution" depends="init">
720 <delete file="${source.dist.name}" />
721 <!-- temporary copy of source to update timestamps -->
722 <copy todir="_sourcedist">
724 <exclude name=".*" />
725 <exclude name="**/.*" />
726 <exclude name="*.class" />
727 <exclude name="**/*.class" />
728 <include name="LICENSE" />
729 <include name="README" />
730 <include name="build.xml" />
731 <include name="jalview-jalopy.xml" />
732 <include name="JalviewApplet.jpx" />
733 <include name="JalviewX.jpx" />
734 <include name="nbbuild.xml" />
735 <include name="nbproject/genfiles.properties" />
736 <include name="nbproject/project.properties" />
737 <include name="nbproject/project.xml" />
738 <include name="${sourceDir}/*.java" />
739 <include name="${sourceDir}/**/*.java" />
740 <include name="${sourceDir}/**/*.cdr" />
741 <include name="${libDir}/**/*" />
742 <include name="${resourceDir}/**/*" />
743 <include name="${helpDir}/**/*" />
744 <include name="appletlib/${jmolJar}" />
745 <include name="appletlib/${jsonSimple}" />
746 <include name="appletlib/${javaJson}" />
747 <exclude name="**/*locales" />
748 <exclude name="*locales/**" />
749 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
750 <exclude name="utils/InstallAnywhere/**Build*/**" />
751 <exclude name="utils/InstallAnywhere/**Build*/**" />
752 <exclude name="utils/InstallAnywhere/.build*.*/**" />
753 <exclude name="utils/InstallAnywhere/**locale*" />
754 <exclude name="utils/InstallAnywhere/**locale*/**" />
755 <exclude name="utils/InstallAnywhere/**locale*/**" />
756 <include name="${schemaDir}/**/*" />
757 <include name="utils/**/*" />
758 <include name="${docDir}/**/*" />
759 <include name="examples/**/*" />
763 <tstamp prefix="build">
764 <format property="year" pattern="yyyy" />
766 <!-- each replacetoken CDATA body must be on one line -
767 otherwise the pattern doesn't match -->
768 <replace value="${JALVIEW_VERSION}">
769 <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
770 <fileset dir="_sourcedist">
771 <include name="**/*" />
774 <replace dir="_sourcedist" value="${build.year}">
775 <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
776 <fileset dir="_sourcedist">
777 <include name="**/*" />
781 <tar destfile="${source.dist.name}" compression="gzip">
782 <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
786 <delete dir="_sourcedist" />
788 <target name="prepubapplet_1" depends="makeApplet">
789 <copy todir="${packageDir}/examples">
790 <fileset dir="examples">
791 <include name="**/*" />
792 <include name="javascript/*" />
793 <include name="jmol/*" />
796 <include name="${jalviewLiteJar}" />
798 <fileset dir="appletlib">
799 <include name="**/*" />
802 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
803 <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
804 <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
805 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
807 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
808 <!-- <attribute name="Permissions" value="sandbox" /> -->
809 <!--<attribute name="Trusted-Lib" value="true" /> -->
810 <attribute name="Codebase" value="${applet.codebase}" />
811 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
815 <presetdef name="ap_applet.jar">
816 <!-- build a signed applet with 'all-permissions' -
817 Needs 'param name="permissions' value="all-permissions"' in applet tag
818 JalviewLite+JmolApplet linked sequence/structure fails
819 Mixed code warnings are raised
821 <jar update="true" index="true">
823 <attribute name="Application-Name" value="JalviewLite" />
824 <attribute name="Permissions" value="all-permissions" />
825 <attribute name="Codebase" value="${applet.codebase}" />
826 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
827 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
831 <presetdef name="applet.jar">
832 <!-- build signed applet with sandbox permissions -
833 Needs 'param name="permissions' value="sandbox"' in applet tag
834 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
837 <jar update="true" index="true">
839 <attribute name="Application-Name" value="JalviewLite" />
840 <attribute name="Permissions" value="sandbox" />
841 <attribute name="Codebase" value="${applet.codebase}" />
842 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
843 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
847 <presetdef name="tl_applet.jar">
848 <!-- build signed applet with trusted library/trusted permissions -
849 Needs 'param name="permissions' value="all-permissions"' in applet tag
851 No mixed code warnings raised
852 Jmol/JalviewLite sequence/structure example doesn't link structures
853 Raises dialog asking user to allow page to control applet via LiveConnect javascript
857 <jar update="true" index="true">
859 <attribute name="Application-Name" value="JalviewLite" />
860 <attribute name="Permissions" value="all-permissions" />
861 <attribute name="Codebase" value="${applet.codebase}" />
862 <attribute name="Trusted-Only" value="true" />
863 <attribute name="Trusted-Library" value="true" />
867 <presetdef name="to_applet.jar">
868 <!-- not fully test variant (yet) -->
869 <jar update="true" index="true">
871 <attribute name="Application-Name" value="JalviewLite" />
872 <attribute name="Permissions" value="all-permissions" />
873 <attribute name="Codebase" value="${applet.codebase}" />
874 <attribute name="Trusted-Only" value="true" />
878 <!-- create differently privileged artefacts -->
879 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
880 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
881 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
882 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
883 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
884 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
885 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
886 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
887 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
888 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
889 <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
890 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
891 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
892 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
893 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
894 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
895 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
896 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
897 <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
898 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
899 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
900 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
901 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
902 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
903 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
904 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
905 <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
906 <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
907 <!-- finally, create manifest for original jars -->
908 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
909 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
910 <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
911 <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
913 <!-- todo - write examples/downloads for alternate versions of the applet
914 probably don't need to do this now since we don't have alternate versions anymore !-->
916 <target name="-signapplet" depends="prepubapplet_1">
917 <fileset id="signappletjarset" dir="${packageDir}/examples">
918 <exclude name="u_*.jar" />
919 <include name="${jalviewLiteJar}" />
920 <include name="${jmolJar}" />
921 <include name="${javaJson}" />
922 <include name="${jsonSimple}" />
923 <include name="to_${jalviewLiteJar}" />
924 <include name="to_${jmolJar}" />
925 <include name="to_${javaJson}" />
926 <include name="to_${jsonSimple}" />
927 <include name="tl_${jalviewLiteJar}" />
928 <include name="tl_${jmolJar}" />
929 <include name="tl_${javaJson}" />
930 <include name="tl_${jsonSimple}" />
931 <include name="ap_${jalviewLiteJar}" />
932 <include name="ap_${jmolJar}" />
933 <include name="ap_${javaJson}" />
934 <include name="ap_${jsonSimple}" />
937 <target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
938 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
939 <fileset refid="signappletjarset" />
943 <target name="-signapplettsa" if="timestamp" depends="-signapplet">
944 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
945 <fileset refid="signappletjarset" />
949 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
951 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
953 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
954 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
955 <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
956 <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
957 <!-- finally, replace any launchApp servlet tags with a version specification -->
958 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
960 <![CDATA[http://www.jalview.org/services/launchApp"]]>
962 <fileset dir="${packageDir}/examples">
963 <include name="**/*.html" />
966 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
968 <![CDATA[http://www.jalview.org/services/launchApp']]>
970 <fileset dir="${packageDir}/examples">
971 <include name="**/*.html" />
976 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
977 <javadoc destdir="${javadocDir}">
978 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
982 <target name="linkcheck" depends="init,prepare">
983 <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
984 <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
985 <arg file="${helpDir}"/>
986 <arg value="-nointernet"/>