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="packageDir" value="dist" />
140 <property name="outputJar" value="jalview.jar" />
141 <!-- Jalview Applet JMol Jar Dependency -->
142 <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
143 <property name="varnaJar" value="VARNAv3-93.jar" />
144 <property name="jsoup" value="jsoup-1.8.1.jar" />
145 <property name="jsonSimple" value="json_simple-1.1.jar" />
146 <property name="javaJson" value="java-json.jar" />
147 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
148 <property name="reportDir" value="test-reports" />
149 <property name="testDir" value="test" />
150 <property name="testOutputDir" value="tests" />
151 <!-- switch to indicate if we should obfuscate jalviewLite -->
152 <!-- <property name="donotobfuscate" value="true"/> -->
153 <!-- switch to exclude associations from generated jnlp files -->
154 <!-- <property name="nojnlpfileassocs" value="true"/> -->
156 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
157 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
158 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
159 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
160 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
161 <property name="WSInterf" value="MsaWS" />
162 <property name="wsdl.Namespace" value="vamsas" />
163 <property name="wsdl.ClientNS" value="ext.vamsas" />
164 <!-- the class path for building the application -->
165 <path id="build.classpath">
166 <fileset dir="utils">
167 <include name="*.jar" />
168 <include name="**/*.jar" />
170 <fileset dir="${libDir}">
171 <include name="*.jar" />
172 <include name="**/*.jar" />
174 <fileset dir="${java.home}/lib">
175 <include name="plugin.jar" />
177 <fileset dir="appletlib">
178 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
180 <include name="${jmolJar}" />
181 <include name="${varnaJar}" />
184 <path id="test.classpath">
185 <pathelement path="${outputDir}" />
186 <path refid="build.classpath" />
188 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
189 <!-- The Location of the java 1.1.8 jdk -->
190 <property name="java118.home" value="${java.home}" />
191 <!-- jre for 1.4 version -->
192 <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
194 <!-- the classpath for building the 1.1 applet -->
195 <path id="jalviewlite.deps">
196 <fileset dir="${java118.home}">
197 <include name="lib/rt.jar" />
199 <fileset dir="${java.home}/lib">
200 <include name="plugin.jar" />
202 <pathelement location="appletlib/${jmolJar}" />
203 <pathelement location="lib/${varnaJar}" />
204 <pathelement location="appletlib/${jsoup}" />
205 <pathelement location="appletlib/${jsonSimple}" />
206 <pathelement location="appletlib/${javaJson}" />
209 <!-- default location for outputting javadoc -->
210 <property name="javadocDir" value="${packageDir}/javadoc" />
214 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
215 <target name="buildPropertiesFile" depends="init">
216 <tstamp prefix="build">
217 <format property="date" pattern="dd MMMM yyyy" />
219 <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
220 <arg value="rev-parse" />
221 <arg value="--short" />
224 <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
225 <arg value="rev-parse" />
226 <arg value="--abbrev-ref" />
229 <properties file="${outputDir}/.build_properties">
231 ---Jalview Build Details---
233 <property name="VERSION" value="${JALVIEW_VERSION}" />
234 <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
235 <property name="BUILD_DATE" value="${build.date}" />
240 <target name="clean" depends="init">
241 <!-- not efficient yet. -->
242 <delete dir="${outputDir}" includes="*,**/*" />
245 <target name="distclean" depends="init, clean">
247 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
250 <include name="${outputJar}" />
251 <include name="#*#" />
252 <include name="#*.*#" />
253 <include name="**/#*#" />
254 <include name="**/#*.*#" />
255 <include name="*~" />
256 <include name="*.*~" />
257 <include name="**/*~" />
258 <include name="**/*.*~" />
263 <target name="prepare" depends="init">
264 <mkdir dir="${outputDir}" />
265 <copy todir="${outputDir}">
267 <include name="${docDir}/**/*.*" />
268 <include name="${helpDir}/**/*.*" />
269 <include name="${libDir}/*.jar" />
271 <fileset dir="${resourceDir}">
272 <include name="**/*.*" />
277 <target name="build" depends="prepare">
278 <!-- not efficient yet. -->
279 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
280 <exclude name="jalview/*applet*" />
281 <exclude name="jalview/appletgui/**" />
282 <exclude name="com/stevesoft/**" />
287 <target name="testclean" depends="init">
288 <delete dir="${testOutputDir}" includes="*,**/*" />
291 <target name="prepareTests" depends="init,testclean">
292 <mkdir dir="${testOutputDir}" />
295 <target name="buildTests" depends="build,buildindices,prepareTests">
296 <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
300 <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
302 <target name="testng" depends="buildTests">
303 <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
306 <pathelement location="${testOutputDir}" />
307 <pathelement location="${clover.jar}" if:set="clover.jar"/>
308 <path refid="test.classpath" />
310 <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
311 <jvmarg value="--illegal-access=warn" if:set="java9"/>
312 <classfileset dir="${testOutputDir}" includes="**/*.class" />
316 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
317 <replace value="${JALVIEW_VERSION}">
319 <![CDATA[$$Version-Rel$$]]>
321 <fileset dir="${outputDir}/${helpDir}">
322 <include name="help.jhm" />
326 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
331 <target name="preparejnlp" depends="makedist">
332 <copy todir="${packageDir}">
333 <fileset dir="${resourceDir}/images">
334 <include name="${WebStartImage}" />
338 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
340 <!-- create a dummy jar which will eventually contain the jnlp template -->
341 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
342 <fileset dir="${packageDir}">
343 <include name="jalview.jar" />
347 <mkdir dir="${packageDir}/JNLP-INF" />
348 <antcall target="writejnlpf">
349 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
350 <param name="inih" value="*" />
351 <param name="maxh" value="*" />
354 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
355 <fileset dir="${packageDir}">
356 <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
360 <antcall target="writejnlpf">
361 <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
362 <param name="inih" value="10M" />
363 <param name="maxh" value="256M" />
365 <antcall target="writejnlpf">
366 <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
367 <param name="inih" value="800M" />
368 <param name="maxh" value="1024M" />
371 <antcall target="writejnlpf">
372 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
373 <param name="inih" value="128M" />
374 <param name="maxh" value="512M" />
377 <antcall target="writejnlpf">
378 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
379 <param name="inih" value="800M" />
380 <param name="maxh" value="1024M" />
383 <!-- finally, need to postprocess to add in associations at end of 'information' element
385 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
392 <association mime-type="application-x/ext-file" extensions="fa"/>
393 <association mime-type="application-x/ext-file" extensions="fasta"/>
394 <association mime-type="application-x/ext-file" extensions="mfa"/>
395 <association mime-type="application-x/ext-file" extensions="fastq"/>
396 <association mime-type="application-x/ext-file" extensions="blc"/>
397 <association mime-type="application-x/ext-file" extensions="msf"/>
398 <association mime-type="application-x/ext-file" extensions="pfam"/>
399 <association mime-type="application-x/ext-file" extensions="aln"/>
400 <association mime-type="application-x/ext-file" extensions="pir"/>
401 <association mime-type="application-x/ext-file" extensions="amsa"/>
402 <association mime-type="application-x/ext-file" extensions="stk"/>
403 <association mime-type="application-x/ext-file" extensions="jar"/>-->
406 <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
407 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
408 tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
409 <fileset dir="${packageDir}">
410 <include name="*.jar" />
414 <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
415 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
416 <fileset dir="${packageDir}">
417 <include name="*.jar" />
422 <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
423 <!-- and sign the jars -->
424 <!-- the default keystore details might need to be edited here -->
427 <target name="runenv" depends="init">
428 <path id="run.classpath">
429 <pathelement location="${outputDir}" />
430 <fileset dir="${outputDir}">
431 <include name="${libDir}/*.jar" />
434 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
436 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
440 <target name="-generatejnlpf">
441 <presetdef name="jnlpf">
442 <jnlp codebase="${WebStartLocation}">
444 <title>Jalview</title>
445 <vendor>The Barton Group</vendor>
446 <homepage href="http://www.jalview.org" />
447 <description>Jalview Multiple Alignment Editor</description>
448 <description kind="short">Jalview</description>
449 <icon href="${WebStartImage}" />
453 <j2se version="1.8+" />
454 <jar main="true" href="jalview.jar"/>
455 <fileset dir="${packageDir}">
456 <exclude name="jalview.jar" />
457 <include name="*.jar" />
458 <include name="*_*.jar" />
459 <exclude name="*quaqua*.jar" />
461 <property name="jalview.version" value="${JALVIEW_VERSION}" />
463 <resources os="Mac OS X">
464 <fileset dir="${packageDir}">
465 <include name="quaqua-filechooser-only-8.0.jar"/>
466 <include name="*quaqua64*.jnilib.jar" />
470 <application_desc main_class="jalview.bin.Jalview">
478 <jnlpf toFile="${jnlpFile}" />
479 <!-- add the add-modules j2se attribute for java 9 -->
480 <replace file="${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"">
481 <replacetoken>j2se version="1.8+"</replacetoken>
485 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
486 <echo message="Not adding JNLP File Associations" />
489 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
490 <replace file="${jnlpFile}">
492 <![CDATA[</information>]]></replacetoken>
495 <association mime-type="application-x/ext-file" extensions="fa" />
496 <association mime-type="application-x/ext-file" extensions="fasta" />
497 <association mime-type="application-x/ext-file" extensions="mfa" />
498 <association mime-type="application-x/ext-file" extensions="fastq" />
499 <association mime-type="application-x/ext-file" extensions="blc" />
500 <association mime-type="application-x/ext-file" extensions="msf" />
501 <association mime-type="application-x/ext-file" extensions="pfam" />
502 <association mime-type="application-x/ext-file" extensions="aln"/>
503 <association mime-type="application-x/ext-file" extensions="pir"/>
504 <association mime-type="application-x/ext-file" extensions="amsa"/>
505 <association mime-type="application-x/ext-file" extensions="stk"/>
506 <association mime-type="application-x/ext-file" extensions="jvp"/>
507 </information>]]></replacevalue>
509 <echo message="Added file associations to JNLP file" />
511 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
514 <target name="buildextclients" depends="init">
515 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
516 <condition property="dontextbuild">
517 <equals arg1="n" arg2="${doextbuild.response}" />
519 <condition property="dontextbuild">
520 <equals arg1="N" arg2="${doextbuild.response}" />
522 <fail if="dontextbuild">
523 Build External Client Code process aborted by user. Jalview source is unchanged.
525 <!-- Currently, this doesn't happen automatically.
526 1. Run WSDL2Java as below, which generates an ext.vamsas +
527 vamsas.<datapackages> fileset.
528 2. refactor ext.vamsas.SpecificserviceWS* to
529 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
530 3. Update the jalview.ws.*WServices classes to reflect the
531 interface type, and all locations of this wsdl type that Jalview
535 <path id="axisbuild">
536 <path refid="build.classpath" />
538 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
540 <fileset dir="${sourceDir}" id="client">
541 <include name="${wsdl.ClientNS}/*.*" />
545 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
547 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
548 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
553 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
554 <fail if="clover.jar">
555 Ignoring request to build jalview distribution with clover-instrumented classes
557 <!-- make the package jar if not already existing -->
558 <mkdir dir="${packageDir}" />
559 <!-- clean dir if it already existed -->
561 <fileset dir="${packageDir}">
562 <include name="*.jar" />
565 <jar destfile="${packageDir}/${outputJar}" index="true">
567 <attribute name="Main-Class" value="jalview.bin.Jalview" />
568 <attribute name="Permissions" value="all-permissions" />
569 <attribute name="Application-Name" value="Jalview Desktop" />
570 <attribute name="Codebase" value="${application.codebase}" />
572 <fileset dir="${outputDir}/">
573 <exclude name="cache*/**" />
574 <exclude name="*.jar" />
575 <exclude name="*.jar.*" />
576 <exclude name="**/*.jar" />
577 <exclude name="**/*.jar.*" />
581 <copy toDir="${packageDir}" flatten="true">
582 <fileset dir="${outputDir}">
583 <include name="*.jar" />
584 <include name="**/*.jar" />
590 <!-- jalopy code reformatter -->
591 <target name="sourcescrub" depends="init,build">
592 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
593 <fileset dir="${sourceDir}">
594 <include name="*.java" />
595 <include name="**/*.java" />
596 <include name="**/**/*.java" />
603 <!-- Compile, package and obfuscate Jalview Applet -->
604 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
606 <target name="compileApplet" depends="init,clean">
607 <mkdir dir="${outputDir}" />
608 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
611 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
612 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
613 <copy todir="${outputDir}/lang">
614 <fileset dir="${resourceDir}/lang">
615 <include name="**.*" />
618 <jar destfile="in.jar" index="true">
620 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
621 <attribute name="Application-Name" value="JalviewLite" />
622 <attribute name="Codebase" value="${applet.codebase}" />
624 <fileset dir="${outputDir}">
625 <include name="com/**" />
626 <include name="MCview/**" />
627 <include name="jalview/**" />
628 <include name=".build_properties" />
629 <include name="images/link.gif" />
630 <include name="lang/**" />
634 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
636 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
637 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
638 <delete file="in.jar" />
640 <target name="-obfuscatereally" unless="donotobfuscate">
642 <path id="obfuscateDeps.path">
643 <pathelement location="${applet.jre.tools}" />
644 <pathelement location="appletlib/${jmolJar}" />
645 <pathelement location="lib/${varnaJar}" />
646 <pathelement location="appletlib/${jsoup}" />
647 <pathelement location="appletlib/${jsonSimple}" />
648 <pathelement location="appletlib/${javaJson}" />
649 <fileset dir="${java.home}/lib">
650 <include name="plugin.jar" />
653 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
655 <proguard verbose="true" >
656 <injar file="in.jar" />
657 <outjar file="${jalviewLiteJar}" />
658 <libraryjar refid="obfuscateDeps.path" />
660 <keep access="public" type="class" name="jalview.bin.JalviewLite">
661 <field access="public" />
662 <method access="public" />
663 <constructor access="public" />
665 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
666 <field access="public" />
667 <method access="public" />
668 <constructor access="public" />
671 <keep name="jalview.json.binding**">
676 <keep access="public" type="class" name="MCview.PDBfile">
677 <field access="public" />
678 <method access="public" />
679 <constructor access="public" />
682 <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
683 <field access="public" />
684 <method access="public" />
685 <constructor access="public" />
688 <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
689 <field access="public" />
690 <method access="public" />
691 <constructor access="public" />
695 <!-- -libraryjars "${obfuscateDeps}"
697 -outjars jalviewApplet.jar
698 -keep public class jalview.bin.JalviewLite
701 <delete file="in.jar" />
704 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
705 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
707 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
708 <include name="*.java" />
709 <include name="descriptors/*.java" />
712 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
713 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
714 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
715 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
717 now build the jalview.binding package with the old schema set
720 <fileset dir="${sourceDir}/jalview/binding/">
721 <include name="**" />
724 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
725 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
726 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
728 <target name="sourcedist" description="create jalview source distribution" depends="init">
729 <delete file="${source.dist.name}" />
730 <!-- temporary copy of source to update timestamps -->
731 <copy todir="_sourcedist">
733 <exclude name=".*" />
734 <exclude name="**/.*" />
735 <exclude name="*.class" />
736 <exclude name="**/*.class" />
737 <include name="LICENSE" />
738 <include name="README" />
739 <include name="build.xml" />
740 <include name="jalview-jalopy.xml" />
741 <include name="JalviewApplet.jpx" />
742 <include name="JalviewX.jpx" />
743 <include name="nbbuild.xml" />
744 <include name="nbproject/genfiles.properties" />
745 <include name="nbproject/project.properties" />
746 <include name="nbproject/project.xml" />
747 <include name="${sourceDir}/*.java" />
748 <include name="${sourceDir}/**/*.java" />
749 <include name="${sourceDir}/**/*.cdr" />
750 <include name="${libDir}/**/*" />
751 <include name="${resourceDir}/**/*" />
752 <include name="${helpDir}/**/*" />
753 <include name="appletlib/${jmolJar}" />
754 <include name="appletlib/${jsonSimple}" />
755 <include name="appletlib/${javaJson}" />
756 <exclude name="**/*locales" />
757 <exclude name="*locales/**" />
758 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
759 <exclude name="utils/InstallAnywhere/**Build*/**" />
760 <exclude name="utils/InstallAnywhere/**Build*/**" />
761 <exclude name="utils/InstallAnywhere/.build*.*/**" />
762 <exclude name="utils/InstallAnywhere/**locale*" />
763 <exclude name="utils/InstallAnywhere/**locale*/**" />
764 <exclude name="utils/InstallAnywhere/**locale*/**" />
765 <include name="${schemaDir}/**/*" />
766 <include name="utils/**/*" />
767 <include name="${docDir}/**/*" />
768 <include name="examples/**/*" />
772 <tstamp prefix="build">
773 <format property="year" pattern="yyyy" />
775 <!-- each replacetoken CDATA body must be on one line -
776 otherwise the pattern doesn't match -->
777 <replace value="${JALVIEW_VERSION}">
779 <![CDATA[$$Version-Rel$$]]>
781 <fileset dir="_sourcedist">
782 <include name="**/*" />
785 <replace dir="_sourcedist" value="${build.year}">
787 <![CDATA[$$Year-Rel$$]]>
789 <fileset dir="_sourcedist">
790 <include name="**/*" />
794 <tar destfile="${source.dist.name}" compression="gzip">
795 <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
799 <delete dir="_sourcedist" />
801 <target name="prepubapplet_1" depends="makeApplet">
802 <copy todir="${packageDir}/examples">
803 <fileset dir="examples">
804 <include name="**/*" />
805 <include name="javascript/*" />
806 <include name="jmol/*" />
809 <include name="${jalviewLiteJar}" />
811 <fileset dir="appletlib">
812 <include name="**/*" />
815 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
816 <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
817 <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
818 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
820 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
821 <!-- <attribute name="Permissions" value="sandbox" /> -->
822 <!--<attribute name="Trusted-Lib" value="true" /> -->
823 <attribute name="Codebase" value="${applet.codebase}" />
824 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
828 <presetdef name="ap_applet.jar">
829 <!-- build a signed applet with 'all-permissions' -
830 Needs 'param name="permissions' value="all-permissions"' in applet tag
831 JalviewLite+JmolApplet linked sequence/structure fails
832 Mixed code warnings are raised
834 <jar update="true" index="true">
836 <attribute name="Application-Name" value="JalviewLite" />
837 <attribute name="Permissions" value="all-permissions" />
838 <attribute name="Codebase" value="${applet.codebase}" />
839 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
840 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
844 <presetdef name="applet.jar">
845 <!-- build signed applet with sandbox permissions -
846 Needs 'param name="permissions' value="sandbox"' in applet tag
847 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
850 <jar update="true" index="true">
852 <attribute name="Application-Name" value="JalviewLite" />
853 <attribute name="Permissions" value="sandbox" />
854 <attribute name="Codebase" value="${applet.codebase}" />
855 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
856 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
860 <presetdef name="tl_applet.jar">
861 <!-- build signed applet with trusted library/trusted permissions -
862 Needs 'param name="permissions' value="all-permissions"' in applet tag
864 No mixed code warnings raised
865 Jmol/JalviewLite sequence/structure example doesn't link structures
866 Raises dialog asking user to allow page to control applet via LiveConnect javascript
870 <jar update="true" index="true">
872 <attribute name="Application-Name" value="JalviewLite" />
873 <attribute name="Permissions" value="all-permissions" />
874 <attribute name="Codebase" value="${applet.codebase}" />
875 <attribute name="Trusted-Only" value="true" />
876 <attribute name="Trusted-Library" value="true" />
880 <presetdef name="to_applet.jar">
881 <!-- not fully test variant (yet) -->
882 <jar update="true" index="true">
884 <attribute name="Application-Name" value="JalviewLite" />
885 <attribute name="Permissions" value="all-permissions" />
886 <attribute name="Codebase" value="${applet.codebase}" />
887 <attribute name="Trusted-Only" value="true" />
891 <!-- create differently privileged artefacts -->
892 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
893 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
894 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
895 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
896 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
897 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
898 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
899 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
900 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
901 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
902 <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
903 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
904 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
905 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
906 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
907 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
908 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
909 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
910 <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
911 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
912 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
913 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
914 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
915 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
916 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
917 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
918 <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
919 <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
920 <!-- finally, create manifest for original jars -->
921 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
922 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
923 <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
924 <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
926 <!-- todo - write examples/downloads for alternate versions of the applet
927 probably don't need to do this now since we don't have alternate versions anymore !-->
929 <target name="-signapplet" depends="prepubapplet_1">
930 <fileset id="signappletjarset" dir="${packageDir}/examples">
931 <exclude name="u_*.jar" />
932 <include name="${jalviewLiteJar}" />
933 <include name="${jmolJar}" />
934 <include name="${javaJson}" />
935 <include name="${jsonSimple}" />
936 <include name="to_${jalviewLiteJar}" />
937 <include name="to_${jmolJar}" />
938 <include name="to_${javaJson}" />
939 <include name="to_${jsonSimple}" />
940 <include name="tl_${jalviewLiteJar}" />
941 <include name="tl_${jmolJar}" />
942 <include name="tl_${javaJson}" />
943 <include name="tl_${jsonSimple}" />
944 <include name="ap_${jalviewLiteJar}" />
945 <include name="ap_${jmolJar}" />
946 <include name="ap_${javaJson}" />
947 <include name="ap_${jsonSimple}" />
950 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
951 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
952 <fileset refid="signappletjarset" />
956 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
957 <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}">
958 <fileset refid="signappletjarset" />
962 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
964 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
966 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
967 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
968 <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
969 <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
970 <!-- finally, replace any launchApp servlet tags with a version specification -->
971 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
973 <![CDATA[http://www.jalview.org/services/launchApp"]]>
975 <fileset dir="${packageDir}/examples">
976 <include name="**/*.html" />
979 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
981 <![CDATA[http://www.jalview.org/services/launchApp']]>
983 <fileset dir="${packageDir}/examples">
984 <include name="**/*.html" />
989 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
990 <javadoc destdir="${javadocDir}">
991 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
995 <target name="linkcheck" depends="init,prepare">
996 <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
997 <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
998 <arg file="${helpDir}"/>
999 <arg value="-nointernet" />
1003 <target name="eclipse-install" depends="init,prepare">
1005 <property name="eclipseTempFile" value="eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
1006 <property name="eclipseInstallURL" value="http://mirror.csclub.uwaterloo.ca/eclipse/technology/epp/downloads/release/oxygen/R/eclipse-jee-oxygen-R-linux-gtk-x86_64.tar.gz"/>
1007 <property name="java2scriptURL" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.core/dist/dropins/net.sf.j2s.core.jar?raw=true"/>
1009 <get url="${eclipseInstallURL}" dest="${eclipseTempFile}"/>
1010 <untar compression="gzip" src="${eclipseTempFile}" dest="${eclipse-inst}"/>
1012 <!-- not needed since we ship transpiler with source
1013 <get url="${java2scriptURL}" dest="eclipse-inst/dropins/net.sf.j2s.core.jar" /> -->
1017 <target name="build-site" depends="init,prepare,compile-site,unzip-to-site">
1018 <!-- closure compile -->
1020 <tar compression="gzip" destfile="site.tar.gz">
1021 <tarfileset dir="site" />
1024 <target name="prepare-site" depends="init,prepare">
1025 <property name="swingjsdir" value="swingjs"/>
1026 <property name="eclipse-inst" value="/home/bamboo/buildtools/eclipse/eclipse-js"/>
1027 <property name="eclipse-exec" value="${eclipse-inst}/eclipse"/>
1028 <property name="site" value="site"/>
1029 <!-- where the eclipse js workspace has been initialised -->
1030 <property name="eclipse-work" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace"/>
1031 <!-- git repository linked to project in workspace -->
1032 <property name="eclipse-workrepo" value="/home/bamboo/buildtools/eclipse/eclipse-js-workspace/jalview-js"/>
1034 <target name="clean-site" depends="prepare-site">
1035 <delete dir="${eclipse-workrepo}/${site}"/>
1036 <mkdir dir="${eclipse-workrepo}/${site}"/>
1038 <target name="compile-site" depends="prepare-site,clean-site">
1039 <!-- update transpiler -->
1040 <copy file="${swingjsdir}/net.sf.j2s.core.jar" todir="${eclipse-inst}/dropins" overwrite="true" failonerror="true"/>
1041 <!-- update the git repo linked to the eclipse workspace -->
1042 <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="true">
1043 <arg value="rev-parse" />
1044 <arg value="--short" />
1045 <arg value="HEAD" />
1047 <!-- update and checkout the same commit in the workspace project -->
1048 <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1049 <arg value="reset" />
1050 <arg value="--hard" />
1052 <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1053 <arg value="pull" />
1055 <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1056 <arg value="checkout" />
1057 <arg value="${git.commit}" />
1059 <!-- custom classpath for .js builds -->
1060 <copy file=".classpath.js" tofile="${eclipse-workrepo}/.classpath" overwrite="true"/>
1061 <!-- clean eclipse log -->
1062 <delete file="${eclipse-work}/.metadata/.log"/>
1064 <!-- execute the eclipse build - the build may fail but valid javascript may still be produced, so we ignore return codes -->
1065 <exec executable="${eclipse-exec}" failonerror="no">
1066 <arg value="-nosplash"/>
1067 <arg value="--launcher.suppressErrors"/>
1068 <arg value="-application"/>
1069 <arg value="org.eclipse.jdt.apt.core.aptBuild"/>
1070 <arg value="-data"/>
1071 <arg value="${eclipse-work}"/>
1074 <exec executable="/bin/cat">
1075 <arg value="${eclipse-work}/.metadata/.log"/>
1077 <!-- TODO: run jslint and something else here to check we have a complete set of .js files for java -->
1078 <!-- possibly compare timestamps between .js files and their mate in source - any newer or not present triggers a new build -->
1079 <!-- <mkdir dir="${packageDir}/${site}" /> -->
1080 <!-- <property name="swingjs.zipurl" value="https://github.com/BobHanson/java2script/blob/master/sources/net.sf.j2s.java.core/dist/SwingJS-site.zip?raw=true" /> -->
1082 <!-- and reset the .classpath -->
1083 <exec executable="/usr/bin/git" failifexecutionfails="true" dir="${eclipse-workrepo}">
1084 <arg value="checkout" />
1085 <arg value="${git.commit}"/>
1087 <arg value=".classpath" />
1090 <!-- finally copy artefacts from eclipse project checkout to the build site -->
1091 <copy todir="${site}">
1092 <fileset dir="${eclipse-workrepo}/site"/>
1095 <target name="unzip-to-site" depends="prepare-site">
1096 <property name="swingjs.zip" value="${swingjsdir}/SwingJS-site.zip" />
1097 <unzip dest="${site}/" overwrite="true">
1098 <fileset dir="libjs">
1099 <include name="*.zip" />
1102 <copy overwrite="true" todir="${site}/swingjs/j2s/">
1103 <fileset dir="${resourceDir}">
1104 <include name="**"/>
1108 <!-- copy test files into place in site -->
1109 <copy todir="${site}/examples">
1110 <fileset dir="examples">
1111 <include name="*.*"/>
1114 <!-- lastly, update SwingJS -->
1115 <unzip dest="${site}/" overwrite="true">
1116 <fileset dir="${swingjsdir}">
1117 <include name="SwingJS-site.zip"/>