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 <target name="help" depends="usage" />
24 <target name="usage" depends="init">
25 <echo message="~~~Jalview Ant build.xml Usage~~~~" />
26 <echo message="Targets include:" />
27 <echo message="usage - default target, displays this message" />
28 <echo message="buildindices - generates JavaHelpSearch from the help files" />
29 <echo message="build - compiles all necessary files for Application" />
30 <echo message="makedist - compiles and places all necessary jar files into directory dist" />
31 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
32 <echo message=" this needs a keystore and key."/>
33 <echo message=" Add -Dtimestamp to timestamp signed jars"/>
34 <echo message=" -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
35 <echo message=" See docs/building.html for more information." />
36 <echo message="compileApplet - compiles all necessary files for Applet" />
37 <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
38 <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
39 <echo message=" you can specify particular test groups as a list via -Dtestng-groups=" />
40 <echo message="See docs/building.html and the comments in build file for other targets." />
41 <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 " />
42 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
46 <!-- utils is a class path to additional utilities needed for
47 building docs, jars and webstart stuff -->
49 Userdefined build property defaults
51 wsdl.server list (plus namespace mapping info ???) - also want
52 ... to make this a dynamically generatable property
54 Build location - provide a temporary root for speed
55 jarsigner keystore and info
56 Jakarta and axis classpath ?
57 Default argument for starting Jalview (if it exists).
62 <path id="axis.classpath">
64 <fileset dir="/usr/local/axis/lib">
65 <include name="**/*.jar" />
67 <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
68 <include name="**/*.jar"/>
69 <include name="*.jar"/>
73 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
74 <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
76 <property name="INSTALLATION" value="Source" />
78 <!-- 2.4 (VAMSAS)" -->
79 <!-- Include debugging information in javac true or false -->
80 <property name="javac.debug" value="true" />
82 <!-- JarSigner Key Store for Webstart Distribution -->
83 <property name="jalview.keystore" value="./keys/.keystore" />
84 <!-- Keystore Password -->
85 <property name="jalview.keystore.pass" value="alignmentisfun" />
87 <property name="jalview.key" value="jalview" />
89 <property name="jalview.key.pass" value="alignmentisfun" />
90 <!-- time stamp server URL -->
91 <property name="jalview.tsaurl" value="" />
92 <!-- locally valid proxy for signing with external time server -->
93 <property name="proxyPort" value="80"/>
94 <property name="proxyHost" value="sqid"/>
95 <!-- key sign/digest algorithms -->
96 <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
97 <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
99 <!-- default TestNG groups to run -->
100 <property name="testng-groups" value="Functional" />
101 <!-- Java 9 JVM args -->
102 <condition property="java9">
103 <equals arg1="${ant.java.version}" arg2="9"/>
106 <!-- Don't change anything below here unless you know what you are doing! -->
107 <!-- Url path for WebStart in JNLP file -->
108 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
109 <!-- Webstart Image - looked for in resources/images -->
110 <property name="WebStartImage" value="JalviewLogo_big.png" />
111 <!-- J2SE version needed for webstart launch -->
112 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
113 <property name="j2sev" value="1.7+" />
114 <!-- Java Compilation settings - source and target javac version -->
115 <property name="javac.source" value="1.8" />
116 <property name="javac.target" value="1.8" />
118 <!-- Permissions for running Java applets and applications. -->
119 <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
120 <property name="application.codebase" value="*.jalview.org" />
121 <!-- and allowing the applet to be deployed from any URL -->
122 <!-- 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 -->
123 <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
124 <property name="applet.caller-codebase" value="${applet.codebase}" />
126 <!-- build directory configuration -->
127 <property name="libDir" value="lib" />
128 <property name="resourceDir" value="resources" />
129 <property name="helpDir" value="help" />
130 <property name="docDir" value="doc" />
131 <property name="sourceDir" value="src" />
132 <property name="schemaDir" value="schemas" />
133 <property name="outputDir" value="classes" />
134 <property name="packageDir" value="dist" />
135 <property name="outputJar" value="jalview.jar" />
136 <!-- Jalview Applet JMol Jar Dependency -->
137 <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
138 <property name="varnaJar" value="VARNAv3-93.jar" />
139 <property name="jsoup" value="jsoup-1.8.1.jar" />
140 <property name="jsonSimple" value="json_simple-1.1.jar" />
141 <property name="javaJson" value="java-json.jar" />
142 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
143 <property name="reportDir" value="test-reports" />
144 <property name="testDir" value="test" />
145 <property name="testOutputDir" value="tests" />
146 <!-- switch to indicate if we should obfuscate jalviewLite -->
147 <!-- <property name="donotobfuscate" value="true"/> -->
148 <!-- switch to exclude associations from generated jnlp files -->
149 <!-- <property name="nojnlpfileassocs" value="true"/> -->
151 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
152 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
153 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
154 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
155 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
156 <property name="WSInterf" value="MsaWS" />
157 <property name="wsdl.Namespace" value="vamsas" />
158 <property name="wsdl.ClientNS" value="ext.vamsas" />
159 <!-- the class path for building the application -->
160 <path id="build.classpath">
161 <fileset dir="utils">
162 <include name="*.jar" />
163 <include name="**/*.jar" />
165 <fileset dir="${libDir}">
166 <include name="*.jar" />
167 <include name="**/*.jar" />
169 <fileset dir="${java.home}/lib">
170 <include name="plugin.jar" />
172 <fileset dir="appletlib">
173 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
175 <include name="${jmolJar}" />
176 <include name="${varnaJar}" />
179 <path id="test.classpath">
180 <pathelement path="${outputDir}" />
181 <path refid="build.classpath" />
183 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
184 <!-- The Location of the java 1.1.8 jdk -->
185 <property name="java118.home" value="${java.home}" />
186 <!-- jre for 1.4 version -->
187 <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
189 <!-- the classpath for building the 1.1 applet -->
190 <path id="jalviewlite.deps">
191 <fileset dir="${java118.home}">
192 <include name="lib/rt.jar" />
194 <fileset dir="${java.home}/lib">
195 <include name="plugin.jar" />
197 <pathelement location="appletlib/${jmolJar}" />
198 <pathelement location="lib/${varnaJar}" />
199 <pathelement location="appletlib/${jsoup}" />
200 <pathelement location="appletlib/${jsonSimple}" />
201 <pathelement location="appletlib/${javaJson}" />
204 <!-- default location for outputting javadoc -->
205 <property name="javadocDir" value="${packageDir}/javadoc" />
209 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
210 <target name="buildPropertiesFile" depends="init">
211 <tstamp prefix="build">
212 <format property="date" pattern="dd MMMM yyyy" />
214 <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
215 <arg value="rev-parse" />
216 <arg value="--short" />
219 <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
220 <arg value="rev-parse" />
221 <arg value="--abbrev-ref" />
224 <properties file="${outputDir}/.build_properties">
226 ---Jalview Build Details---
228 <property name="VERSION" value="${JALVIEW_VERSION}" />
229 <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
230 <property name="BUILD_DATE" value="${build.date}" />
235 <target name="clean" depends="init">
236 <!-- not efficient yet. -->
237 <delete dir="${outputDir}" includes="*,**/*" />
240 <target name="distclean" depends="init, clean">
242 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
245 <include name="${outputJar}" />
246 <include name="#*#" />
247 <include name="#*.*#" />
248 <include name="**/#*#" />
249 <include name="**/#*.*#" />
250 <include name="*~" />
251 <include name="*.*~" />
252 <include name="**/*~" />
253 <include name="**/*.*~" />
258 <target name="prepare" depends="init">
259 <mkdir dir="${outputDir}" />
260 <copy todir="${outputDir}">
262 <include name="${docDir}/**/*.*" />
263 <include name="${helpDir}/**/*.*" />
264 <include name="${libDir}/*.jar" />
266 <fileset dir="${resourceDir}">
267 <include name="**/*.*" />
272 <target name="build" depends="prepare">
273 <!-- not efficient yet. -->
274 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
275 <exclude name="jalview/*applet*" />
276 <exclude name="jalview/appletgui/**" />
277 <exclude name="com/stevesoft/**" />
282 <target name="testclean" depends="init">
283 <delete dir="${testOutputDir}" includes="*,**/*" />
286 <target name="prepareTests" depends="init,testclean">
287 <mkdir dir="${testOutputDir}" />
290 <target name="buildTests" depends="build,buildindices,prepareTests">
291 <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
295 <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
297 <target name="testng" depends="buildTests">
298 <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
301 <pathelement location="${testOutputDir}" />
302 <path refid="test.classpath" />
304 <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
305 <jvmarg value="--illegal-access=warn" if:set="java9"/>
306 <classfileset dir="${testOutputDir}" includes="**/*.class" />
310 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
311 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
316 <target name="preparejnlp" depends="makedist">
317 <copy todir="${packageDir}">
318 <fileset dir="${resourceDir}/images">
319 <include name="${WebStartImage}" />
323 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
325 <!-- create a dummy jar which will eventually contain the jnlp template -->
326 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
327 <fileset dir="${packageDir}">
328 <include name="jalview.jar" />
332 <mkdir dir="${packageDir}/JNLP-INF" />
333 <antcall target="writejnlpf">
334 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
335 <param name="inih" value="*" />
336 <param name="maxh" value="*" />
339 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
340 <fileset dir="${packageDir}">
341 <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
345 <antcall target="writejnlpf">
346 <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
347 <param name="inih" value="10M" />
348 <param name="maxh" value="256M" />
351 <antcall target="writejnlpf">
352 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
353 <param name="inih" value="128M" />
354 <param name="maxh" value="512M" />
357 <antcall target="writejnlpf">
358 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
359 <param name="inih" value="256M" />
360 <param name="maxh" value="1024M" />
363 <!-- finally, need to postprocess to add in associations at end of 'information' element
365 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
372 <association mime-type="application-x/ext-file" extensions="fa"/>
373 <association mime-type="application-x/ext-file" extensions="fasta"/>
374 <association mime-type="application-x/ext-file" extensions="mfa"/>
375 <association mime-type="application-x/ext-file" extensions="fastq"/>
376 <association mime-type="application-x/ext-file" extensions="blc"/>
377 <association mime-type="application-x/ext-file" extensions="msf"/>
378 <association mime-type="application-x/ext-file" extensions="pfam"/>
379 <association mime-type="application-x/ext-file" extensions="aln"/>
380 <association mime-type="application-x/ext-file" extensions="pir"/>
381 <association mime-type="application-x/ext-file" extensions="amsa"/>
382 <association mime-type="application-x/ext-file" extensions="stk"/>
383 <association mime-type="application-x/ext-file" extensions="jar"/>-->
386 <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
387 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
388 tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
389 <fileset dir="${packageDir}">
390 <include name="*.jar" />
394 <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
395 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
396 <fileset dir="${packageDir}">
397 <include name="*.jar" />
402 <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
403 <!-- and sign the jars -->
404 <!-- the default keystore details might need to be edited here -->
407 <target name="runenv" depends="init">
408 <path id="run.classpath">
409 <pathelement location="${outputDir}" />
410 <fileset dir="${outputDir}">
411 <include name="${libDir}/*.jar" />
414 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
416 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
420 <target name="-generatejnlpf">
421 <presetdef name="jnlpf">
422 <jnlp codebase="${WebStartLocation}">
424 <title>Jalview</title>
425 <vendor>The Barton Group</vendor>
426 <homepage href="http://www.jalview.org" />
427 <description>Jalview Multiple Alignment Editor</description>
428 <description kind="short">Jalview</description>
429 <icon href="${WebStartImage}" />
433 <j2se version="1.8+" />
434 <jar main="true" href="jalview.jar"/>
435 <fileset dir="${packageDir}">
436 <exclude name="jalview.jar" />
437 <include name="*.jar" />
438 <include name="*_*.jar" />
439 <exclude name="*quaqua*.jar" />
441 <property name="jalview.version" value="${JALVIEW_VERSION}" />
443 <resources os="Mac OS X">
444 <fileset dir="${packageDir}">
445 <include name="quaqua-filechooser-only-8.0.jar"/>
446 <include name="*quaqua64*.jnilib.jar" />
450 <application_desc main_class="jalview.bin.Jalview">
458 <jnlpf toFile="${jnlpFile}" />
459 <!-- add the add-modules j2se attribute for java 9 -->
460 <replace file="${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"">
461 <replacetoken>j2se version="1.8+"</replacetoken>
466 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
467 <echo message="Not adding JNLP File Associations" />
470 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
471 <replace file="${jnlpFile}">
473 <![CDATA[</information>]]></replacetoken>
476 <association mime-type="application-x/ext-file" extensions="fa" />
477 <association mime-type="application-x/ext-file" extensions="fasta" />
478 <association mime-type="application-x/ext-file" extensions="mfa" />
479 <association mime-type="application-x/ext-file" extensions="fastq" />
480 <association mime-type="application-x/ext-file" extensions="blc" />
481 <association mime-type="application-x/ext-file" extensions="msf" />
482 <association mime-type="application-x/ext-file" extensions="pfam" />
483 <association mime-type="application-x/ext-file" extensions="aln"/>
484 <association mime-type="application-x/ext-file" extensions="pir"/>
485 <association mime-type="application-x/ext-file" extensions="amsa"/>
486 <association mime-type="application-x/ext-file" extensions="stk"/>
487 <association mime-type="application-x/ext-file" extensions="jvp"/>
488 </information>]]></replacevalue>
490 <echo message="Added file associations to JNLP file" />
492 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
495 <target name="buildextclients" depends="init">
496 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
497 <condition property="dontextbuild">
498 <equals arg1="n" arg2="${doextbuild.response}" />
500 <condition property="dontextbuild">
501 <equals arg1="N" arg2="${doextbuild.response}" />
503 <fail if="dontextbuild">
504 Build External Client Code process aborted by user. Jalview source is unchanged.
506 <!-- Currently, this doesn't happen automatically.
507 1. Run WSDL2Java as below, which generates an ext.vamsas +
508 vamsas.<datapackages> fileset.
509 2. refactor ext.vamsas.SpecificserviceWS* to
510 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
511 3. Update the jalview.ws.*WServices classes to reflect the
512 interface type, and all locations of this wsdl type that Jalview
516 <path id="axisbuild">
517 <path refid="build.classpath" />
519 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
521 <fileset dir="${sourceDir}" id="client">
522 <include name="${wsdl.ClientNS}/*.*" />
526 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
528 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
529 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
534 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
535 <!-- make the package jar if not already existing -->
536 <mkdir dir="${packageDir}" />
537 <!-- clean dir if it already existed -->
539 <fileset dir="${packageDir}">
540 <include name="*.jar" />
543 <jar destfile="${packageDir}/${outputJar}" index="true">
545 <attribute name="Main-Class" value="jalview.bin.Jalview" />
546 <attribute name="Permissions" value="all-permissions" />
547 <attribute name="Application-Name" value="Jalview Desktop" />
548 <attribute name="Codebase" value="${application.codebase}" />
550 <fileset dir="${outputDir}/">
551 <exclude name="cache*/**" />
552 <exclude name="*.jar" />
553 <exclude name="*.jar.*" />
554 <exclude name="**/*.jar" />
555 <exclude name="**/*.jar.*" />
559 <copy toDir="${packageDir}" flatten="true">
560 <fileset dir="${outputDir}">
561 <include name="*.jar" />
562 <include name="**/*.jar" />
568 <!-- jalopy code reformatter -->
569 <target name="sourcescrub" depends="init,build">
570 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
571 <fileset dir="${sourceDir}">
572 <include name="*.java" />
573 <include name="**/*.java" />
574 <include name="**/**/*.java" />
581 <!-- Compile, package and obfuscate Jalview Applet -->
582 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
584 <target name="compileApplet" depends="init,clean">
585 <mkdir dir="${outputDir}" />
586 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
589 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
590 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
591 <copy todir="${outputDir}/lang">
592 <fileset dir="${resourceDir}/lang">
593 <include name="**.*" />
596 <jar destfile="in.jar" index="true">
598 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
599 <attribute name="Application-Name" value="JalviewLite" />
600 <attribute name="Codebase" value="${applet.codebase}" />
602 <fileset dir="${outputDir}">
603 <include name="com/**" />
604 <include name="MCview/**" />
605 <include name="jalview/**" />
606 <include name=".build_properties" />
607 <include name="images/link.gif" />
608 <include name="lang/**" />
612 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
614 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
615 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
616 <delete file="in.jar" />
618 <target name="-obfuscatereally" unless="donotobfuscate">
620 <path id="obfuscateDeps.path">
621 <pathelement location="${applet.jre.tools}" />
622 <pathelement location="appletlib/${jmolJar}" />
623 <pathelement location="lib/${varnaJar}" />
624 <pathelement location="appletlib/${jsoup}" />
625 <pathelement location="appletlib/${jsonSimple}" />
626 <pathelement location="appletlib/${javaJson}" />
627 <fileset dir="${java.home}/lib">
628 <include name="plugin.jar" />
631 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
633 <proguard verbose="true" >
634 <injar file="in.jar" />
635 <outjar file="${jalviewLiteJar}" />
636 <libraryjar refid="obfuscateDeps.path" />
638 <keep access="public" type="class" name="jalview.bin.JalviewLite">
639 <field access="public" />
640 <method access="public" />
641 <constructor access="public" />
643 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
644 <field access="public" />
645 <method access="public" />
646 <constructor access="public" />
649 <keep name="jalview.json.binding**">
654 <keep access="public" type="class" name="MCview.PDBfile">
655 <field access="public" />
656 <method access="public" />
657 <constructor access="public" />
660 <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
661 <field access="public" />
662 <method access="public" />
663 <constructor access="public" />
666 <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
667 <field access="public" />
668 <method access="public" />
669 <constructor access="public" />
673 <!-- -libraryjars "${obfuscateDeps}"
675 -outjars jalviewApplet.jar
676 -keep public class jalview.bin.JalviewLite
679 <delete file="in.jar" />
682 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
683 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
685 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
686 <include name="*.java" />
687 <include name="descriptors/*.java" />
690 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
691 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
692 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
693 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
695 now build the jalview.binding package with the old schema set
698 <fileset dir="${sourceDir}/jalview/binding/">
699 <include name="**" />
702 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
703 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
704 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
706 <target name="sourcedist" description="create jalview source distribution" depends="init">
707 <delete file="${source.dist.name}" />
708 <!-- temporary copy of source to update timestamps -->
709 <copy todir="_sourcedist">
711 <exclude name=".*" />
712 <exclude name="**/.*" />
713 <exclude name="*.class" />
714 <exclude name="**/*.class" />
715 <include name="LICENSE" />
716 <include name="README" />
717 <include name="build.xml" />
718 <include name="jalview-jalopy.xml" />
719 <include name="JalviewApplet.jpx" />
720 <include name="JalviewX.jpx" />
721 <include name="nbbuild.xml" />
722 <include name="nbproject/genfiles.properties" />
723 <include name="nbproject/project.properties" />
724 <include name="nbproject/project.xml" />
725 <include name="${sourceDir}/*.java" />
726 <include name="${sourceDir}/**/*.java" />
727 <include name="${sourceDir}/**/*.cdr" />
728 <include name="${libDir}/**/*" />
729 <include name="${resourceDir}/**/*" />
730 <include name="${helpDir}/**/*" />
731 <include name="appletlib/${jmolJar}" />
732 <include name="appletlib/${jsonSimple}" />
733 <include name="appletlib/${javaJson}" />
734 <exclude name="**/*locales" />
735 <exclude name="*locales/**" />
736 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
737 <exclude name="utils/InstallAnywhere/**Build*/**" />
738 <exclude name="utils/InstallAnywhere/**Build*/**" />
739 <exclude name="utils/InstallAnywhere/.build*.*/**" />
740 <exclude name="utils/InstallAnywhere/**locale*" />
741 <exclude name="utils/InstallAnywhere/**locale*/**" />
742 <exclude name="utils/InstallAnywhere/**locale*/**" />
743 <include name="${schemaDir}/**/*" />
744 <include name="utils/**/*" />
745 <include name="${docDir}/**/*" />
746 <include name="examples/**/*" />
750 <tstamp prefix="build">
751 <format property="year" pattern="yyyy" />
753 <!-- each replacetoken CDATA body must be on one line -
754 otherwise the pattern doesn't match -->
755 <replace value="${JALVIEW_VERSION}">
756 <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
757 <fileset dir="_sourcedist">
758 <include name="**/*" />
761 <replace dir="_sourcedist" value="${build.year}">
762 <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
763 <fileset dir="_sourcedist">
764 <include name="**/*" />
768 <tar destfile="${source.dist.name}" compression="gzip">
769 <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
773 <delete dir="_sourcedist" />
775 <target name="prepubapplet_1" depends="makeApplet">
776 <copy todir="${packageDir}/examples">
777 <fileset dir="examples">
778 <include name="**/*" />
779 <include name="javascript/*" />
780 <include name="jmol/*" />
783 <include name="${jalviewLiteJar}" />
785 <fileset dir="appletlib">
786 <include name="**/*" />
789 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
790 <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
791 <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
792 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
794 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
795 <!-- <attribute name="Permissions" value="sandbox" /> -->
796 <!--<attribute name="Trusted-Lib" value="true" /> -->
797 <attribute name="Codebase" value="${applet.codebase}" />
798 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
802 <presetdef name="ap_applet.jar">
803 <!-- build a signed applet with 'all-permissions' -
804 Needs 'param name="permissions' value="all-permissions"' in applet tag
805 JalviewLite+JmolApplet linked sequence/structure fails
806 Mixed code warnings are raised
808 <jar update="true" index="true">
810 <attribute name="Application-Name" value="JalviewLite" />
811 <attribute name="Permissions" value="all-permissions" />
812 <attribute name="Codebase" value="${applet.codebase}" />
813 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
814 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
818 <presetdef name="applet.jar">
819 <!-- build signed applet with sandbox permissions -
820 Needs 'param name="permissions' value="sandbox"' in applet tag
821 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
824 <jar update="true" index="true">
826 <attribute name="Application-Name" value="JalviewLite" />
827 <attribute name="Permissions" value="sandbox" />
828 <attribute name="Codebase" value="${applet.codebase}" />
829 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
830 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
834 <presetdef name="tl_applet.jar">
835 <!-- build signed applet with trusted library/trusted permissions -
836 Needs 'param name="permissions' value="all-permissions"' in applet tag
838 No mixed code warnings raised
839 Jmol/JalviewLite sequence/structure example doesn't link structures
840 Raises dialog asking user to allow page to control applet via LiveConnect javascript
844 <jar update="true" index="true">
846 <attribute name="Application-Name" value="JalviewLite" />
847 <attribute name="Permissions" value="all-permissions" />
848 <attribute name="Codebase" value="${applet.codebase}" />
849 <attribute name="Trusted-Only" value="true" />
850 <attribute name="Trusted-Library" value="true" />
854 <presetdef name="to_applet.jar">
855 <!-- not fully test variant (yet) -->
856 <jar update="true" index="true">
858 <attribute name="Application-Name" value="JalviewLite" />
859 <attribute name="Permissions" value="all-permissions" />
860 <attribute name="Codebase" value="${applet.codebase}" />
861 <attribute name="Trusted-Only" value="true" />
865 <!-- create differently privileged artefacts -->
866 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
867 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
868 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
869 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
870 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
871 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
872 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
873 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
874 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
875 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
876 <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
877 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
878 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
879 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
880 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
881 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
882 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
883 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
884 <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
885 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
886 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
887 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
888 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
889 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
890 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
891 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
892 <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
893 <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
894 <!-- finally, create manifest for original jars -->
895 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
896 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
897 <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
898 <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
900 <!-- todo - write examples/downloads for alternate versions of the applet
901 probably don't need to do this now since we don't have alternate versions anymore !-->
903 <target name="-signapplet" depends="prepubapplet_1">
904 <fileset id="signappletjarset" dir="${packageDir}/examples">
905 <exclude name="u_*.jar" />
906 <include name="${jalviewLiteJar}" />
907 <include name="${jmolJar}" />
908 <include name="${javaJson}" />
909 <include name="${jsonSimple}" />
910 <include name="to_${jalviewLiteJar}" />
911 <include name="to_${jmolJar}" />
912 <include name="to_${javaJson}" />
913 <include name="to_${jsonSimple}" />
914 <include name="tl_${jalviewLiteJar}" />
915 <include name="tl_${jmolJar}" />
916 <include name="tl_${javaJson}" />
917 <include name="tl_${jsonSimple}" />
918 <include name="ap_${jalviewLiteJar}" />
919 <include name="ap_${jmolJar}" />
920 <include name="ap_${javaJson}" />
921 <include name="ap_${jsonSimple}" />
924 <target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
925 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
926 <fileset refid="signappletjarset" />
930 <target name="-signapplettsa" if="timestamp" depends="-signapplet">
931 <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}">
932 <fileset refid="signappletjarset" />
936 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
938 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
940 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
941 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
942 <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
943 <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
944 <!-- finally, replace any launchApp servlet tags with a version specification -->
945 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
947 <![CDATA[http://www.jalview.org/services/launchApp"]]>
949 <fileset dir="${packageDir}/examples">
950 <include name="**/*.html" />
953 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
955 <![CDATA[http://www.jalview.org/services/launchApp']]>
957 <fileset dir="${packageDir}/examples">
958 <include name="**/*.html" />
963 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
964 <javadoc destdir="${javadocDir}">
965 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
969 <target name="linkcheck" depends="init,prepare">
970 <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
971 <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
972 <arg file="${helpDir}"/>
973 <arg value="-nointernet"/>