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="${ant.java.version}" arg2="9"/>
109 <!-- Java 10 JVM args -->
110 <condition property="java10">
111 <equals arg1="${ant.java.version}" arg2="10"/>
113 <!-- Java 11 JVM args -->
114 <condition property="java11">
115 <equals arg1="${ant.java.version}" arg2="11"/>
117 <echo message="java version is ${ant.java.version}"/>
118 <echo message="java9 is ${java9}"/>
119 <echo message="java10 is ${java10}"/>
120 <echo message="java11 is ${java11}"/>
122 <!-- Don't change anything below here unless you know what you are doing! -->
123 <!-- Url path for WebStart in JNLP file -->
124 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
125 <!-- Webstart Image - looked for in resources/images -->
126 <property name="WebStartImage" value="JalviewLogo_big.png" />
127 <!-- J2SE version needed for webstart launch -->
128 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
129 <property name="j2sev" value="1.7+" />
130 <!-- Java Compilation settings - source and target javac version -->
131 <property name="javac.source" value="1.8" />
132 <property name="javac.target" value="1.8" />
134 <!-- Permissions for running Java applets and applications. -->
135 <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
136 <property name="application.codebase" value="*.jalview.org" />
137 <!-- and allowing the applet to be deployed from any URL -->
138 <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
139 <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
140 <property name="applet.caller-codebase" value="${applet.codebase}" />
142 <!-- build directory configuration -->
143 <property name="libDir" value="lib" />
144 <property name="j11libDir" value="j11lib" />
145 <property name="resourceDir" value="resources" />
146 <property name="helpDir" value="help" />
147 <property name="docDir" value="doc" />
148 <property name="sourceDir" value="src" />
149 <property name="schemaDir" value="schemas" />
150 <property name="outputDir" value="classes" unless:set="clover.jar"/>
151 <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
152 <property name="packageDir" value="dist" />
153 <property name="outputJar" value="jalview.jar" />
154 <!-- Jalview Applet JMol Jar Dependency -->
155 <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
156 <property name="varnaJar" value="VARNAv3-93.jar" />
157 <property name="jsoup" value="jsoup-1.8.1.jar" />
158 <property name="jsonSimple" value="json_simple-1.1.jar" />
159 <property name="javaJson" value="java-json.jar" />
160 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
161 <property name="reportDir" value="test-reports" />
162 <property name="testDir" value="test" />
163 <property name="testOutputDir" value="tests" />
164 <!-- switch to indicate if we should obfuscate jalviewLite -->
165 <!-- <property name="donotobfuscate" value="true"/> -->
166 <!-- switch to exclude associations from generated jnlp files -->
167 <!-- <property name="nojnlpfileassocs" value="true"/> -->
169 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
170 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
171 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
172 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
173 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
174 <property name="WSInterf" value="MsaWS" />
175 <property name="wsdl.Namespace" value="vamsas" />
176 <property name="wsdl.ClientNS" value="ext.vamsas" />
177 <!-- the class path for building the application -->
178 <path id="build.classpath">
179 <fileset dir="utils">
180 <include name="*.jar" />
181 <include name="**/*.jar" />
183 <fileset dir="${j11libDir}">
184 <include name="*.jar" />
185 <include name="**/*.jar" />
187 <fileset dir="${libDir}">
188 <include name="*.jar" />
189 <include name="**/*.jar" />
191 <fileset dir="${java.home}/lib">
192 <include name="plugin.jar" />
194 <fileset dir="appletlib">
195 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
197 <include name="${jmolJar}" />
198 <include name="${varnaJar}" />
201 <path id="test.classpath">
202 <pathelement path="${outputDir}" />
203 <path refid="build.classpath" />
205 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
206 <!-- The Location of the java 1.1.8 jdk -->
207 <property name="java118.home" value="${java.home}" />
208 <!-- jre for 1.4 version -->
209 <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
211 <!-- the classpath for building the 1.1 applet -->
212 <path id="jalviewlite.deps">
213 <fileset dir="${java118.home}">
214 <include name="lib/rt.jar" />
216 <fileset dir="${java.home}/lib">
217 <include name="plugin.jar" />
219 <pathelement location="appletlib/${jmolJar}" />
220 <pathelement location="lib/${varnaJar}" />
221 <pathelement location="appletlib/${jsoup}" />
222 <pathelement location="appletlib/${jsonSimple}" />
223 <pathelement location="appletlib/${javaJson}" />
226 <!-- default location for outputting javadoc -->
227 <property name="javadocDir" value="${packageDir}/javadoc" />
231 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
232 <target name="buildPropertiesFile" depends="init">
233 <tstamp prefix="build">
234 <format property="date" pattern="dd MMMM yyyy" />
236 <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
237 <arg value="rev-parse" />
238 <arg value="--short" />
241 <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
242 <arg value="rev-parse" />
243 <arg value="--abbrev-ref" />
246 <properties file="${outputDir}/.build_properties">
248 ---Jalview Build Details---
250 <property name="VERSION" value="${JALVIEW_VERSION}" />
251 <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
252 <property name="BUILD_DATE" value="${build.date}" />
257 <target name="clean" depends="init">
258 <!-- not efficient yet. -->
259 <delete dir="${outputDir}" includes="*,**/*" />
262 <target name="distclean" depends="init, clean">
264 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
267 <include name="${outputJar}" />
268 <include name="#*#" />
269 <include name="#*.*#" />
270 <include name="**/#*#" />
271 <include name="**/#*.*#" />
272 <include name="*~" />
273 <include name="*.*~" />
274 <include name="**/*~" />
275 <include name="**/*.*~" />
280 <target name="prepare" depends="init">
281 <mkdir dir="${outputDir}" />
282 <copy todir="${outputDir}">
284 <include name="${docDir}/**/*.*" />
285 <include name="${helpDir}/**/*.*" />
286 <include name="${libDir}/*.jar" />
288 <fileset dir="${resourceDir}">
289 <include name="**/*.*" />
294 <target name="build" depends="prepare">
295 <!-- not efficient yet. -->
296 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
297 <exclude name="jalview/*applet*" />
298 <exclude name="jalview/appletgui/**" />
299 <exclude name="com/stevesoft/**" />
304 <target name="testclean" depends="init">
305 <delete dir="${testOutputDir}" includes="*,**/*" />
308 <target name="prepareTests" depends="init,testclean">
309 <mkdir dir="${testOutputDir}" />
312 <target name="buildTests" depends="build,buildindices,prepareTests">
313 <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
317 <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
319 <target name="testng" depends="buildTests">
320 <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
323 <pathelement location="${testOutputDir}" />
324 <pathelement location="${clover.jar}" if:set="clover.jar"/>
325 <path refid="test.classpath" />
327 <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
328 <jvmarg value="--illegal-access=warn" if:set="java9"/>
329 <classfileset dir="${testOutputDir}" includes="**/*.class" />
333 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
334 <replace value="${JALVIEW_VERSION}">
335 <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
336 <fileset dir="${outputDir}/${helpDir}">
337 <include name="help.jhm" />
341 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
346 <target name="preparejnlp" depends="makedist">
347 <copy todir="${packageDir}">
348 <fileset dir="${resourceDir}/images">
349 <include name="${WebStartImage}" />
353 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
355 <!-- create a dummy jar which will eventually contain the jnlp template -->
356 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
357 <fileset dir="${packageDir}">
358 <include name="jalview.jar" />
362 <mkdir dir="${packageDir}/JNLP-INF" />
363 <antcall target="writejnlpf">
364 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
365 <param name="inih" value="*" />
366 <param name="maxh" value="*" />
369 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
370 <fileset dir="${packageDir}">
371 <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
375 <antcall target="writejnlpf">
376 <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
377 <param name="inih" value="10M" />
378 <param name="maxh" value="256M" />
380 <antcall target="writejnlpf">
381 <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
382 <param name="inih" value="800M" />
383 <param name="maxh" value="1024M" />
386 <antcall target="writejnlpf">
387 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
388 <param name="inih" value="128M" />
389 <param name="maxh" value="512M" />
392 <antcall target="writejnlpf">
393 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
394 <param name="inih" value="800M" />
395 <param name="maxh" value="1024M" />
398 <!-- finally, need to postprocess to add in associations at end of 'information' element
400 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
407 <association mime-type="application-x/ext-file" extensions="fa"/>
408 <association mime-type="application-x/ext-file" extensions="fasta"/>
409 <association mime-type="application-x/ext-file" extensions="mfa"/>
410 <association mime-type="application-x/ext-file" extensions="fastq"/>
411 <association mime-type="application-x/ext-file" extensions="blc"/>
412 <association mime-type="application-x/ext-file" extensions="msf"/>
413 <association mime-type="application-x/ext-file" extensions="pfam"/>
414 <association mime-type="application-x/ext-file" extensions="aln"/>
415 <association mime-type="application-x/ext-file" extensions="pir"/>
416 <association mime-type="application-x/ext-file" extensions="amsa"/>
417 <association mime-type="application-x/ext-file" extensions="stk"/>
418 <association mime-type="application-x/ext-file" extensions="jar"/>-->
421 <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
422 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
423 tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
424 <fileset dir="${packageDir}">
425 <include name="*.jar" />
429 <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
430 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
431 <fileset dir="${packageDir}">
432 <include name="*.jar" />
437 <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
438 <!-- and sign the jars -->
439 <!-- the default keystore details might need to be edited here -->
442 <target name="runenv" depends="init">
443 <path id="run.classpath">
444 <pathelement location="${outputDir}" />
445 <fileset dir="${outputDir}">
446 <include name="${libDir}/*.jar" />
449 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
451 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
455 <target name="-generatejnlpf">
456 <presetdef name="jnlpf">
457 <jnlp codebase="${WebStartLocation}">
459 <title>Jalview</title>
460 <vendor>The Barton Group</vendor>
461 <homepage href="http://www.jalview.org" />
462 <description>Jalview Multiple Alignment Editor</description>
463 <description kind="short">Jalview</description>
464 <icon href="${WebStartImage}" />
468 <j2se version="1.8+" />
469 <jar main="true" href="jalview.jar"/>
470 <fileset dir="${packageDir}">
471 <exclude name="jalview.jar" />
472 <include name="*.jar" />
473 <include name="*_*.jar" />
474 <exclude name="*quaqua*.jar" />
476 <property name="jalview.version" value="${JALVIEW_VERSION}" />
478 <resources os="Mac OS X">
479 <fileset dir="${packageDir}">
480 <include name="quaqua-filechooser-only-8.0.jar"/>
481 <include name="*quaqua64*.jnilib.jar" />
485 <application_desc main_class="jalview.bin.Jalview">
493 <jnlpf toFile="${jnlpFile}" />
494 <!-- add the add-modules j2se attribute for java 9 -->
495 <replace file="${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"">
496 <replacetoken>j2se version="1.8+"</replacetoken>
500 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
501 <echo message="Not adding JNLP File Associations" />
504 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
505 <replace file="${jnlpFile}">
507 <![CDATA[</information>]]></replacetoken>
510 <association mime-type="application-x/ext-file" extensions="fa" />
511 <association mime-type="application-x/ext-file" extensions="fasta" />
512 <association mime-type="application-x/ext-file" extensions="mfa" />
513 <association mime-type="application-x/ext-file" extensions="fastq" />
514 <association mime-type="application-x/ext-file" extensions="blc" />
515 <association mime-type="application-x/ext-file" extensions="msf" />
516 <association mime-type="application-x/ext-file" extensions="pfam" />
517 <association mime-type="application-x/ext-file" extensions="aln"/>
518 <association mime-type="application-x/ext-file" extensions="pir"/>
519 <association mime-type="application-x/ext-file" extensions="amsa"/>
520 <association mime-type="application-x/ext-file" extensions="stk"/>
521 <association mime-type="application-x/ext-file" extensions="jvp"/>
522 </information>]]></replacevalue>
524 <echo message="Added file associations to JNLP file" />
526 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
529 <target name="buildextclients" depends="init">
530 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
531 <condition property="dontextbuild">
532 <equals arg1="n" arg2="${doextbuild.response}" />
534 <condition property="dontextbuild">
535 <equals arg1="N" arg2="${doextbuild.response}" />
537 <fail if="dontextbuild">
538 Build External Client Code process aborted by user. Jalview source is unchanged.
540 <!-- Currently, this doesn't happen automatically.
541 1. Run WSDL2Java as below, which generates an ext.vamsas +
542 vamsas.<datapackages> fileset.
543 2. refactor ext.vamsas.SpecificserviceWS* to
544 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
545 3. Update the jalview.ws.*WServices classes to reflect the
546 interface type, and all locations of this wsdl type that Jalview
550 <path id="axisbuild">
551 <path refid="build.classpath" />
553 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
555 <fileset dir="${sourceDir}" id="client">
556 <include name="${wsdl.ClientNS}/*.*" />
560 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
562 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
563 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
568 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
569 <fail if="clover.jar">
570 Ignoring request to build jalview distribution with clover-instrumented classes
572 <!-- make the package jar if not already existing -->
573 <mkdir dir="${packageDir}" />
574 <!-- clean dir if it already existed -->
576 <fileset dir="${packageDir}">
577 <include name="*.jar" />
580 <jar destfile="${packageDir}/${outputJar}" index="true">
582 <attribute name="Main-Class" value="jalview.bin.Jalview" />
583 <attribute name="Permissions" value="all-permissions" />
584 <attribute name="Application-Name" value="Jalview Desktop" />
585 <attribute name="Codebase" value="${application.codebase}" />
587 <fileset dir="${outputDir}/">
588 <exclude name="cache*/**" />
589 <exclude name="*.jar" />
590 <exclude name="*.jar.*" />
591 <exclude name="**/*.jar" />
592 <exclude name="**/*.jar.*" />
596 <copy toDir="${packageDir}" flatten="true">
597 <fileset dir="${outputDir}">
598 <include name="*.jar" />
599 <include name="**/*.jar" />
605 <!-- jalopy code reformatter -->
606 <target name="sourcescrub" depends="init,build">
607 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
608 <fileset dir="${sourceDir}">
609 <include name="*.java" />
610 <include name="**/*.java" />
611 <include name="**/**/*.java" />
618 <!-- Compile, package and obfuscate Jalview Applet -->
619 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
621 <target name="compileApplet" depends="init,clean">
622 <mkdir dir="${outputDir}" />
623 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
626 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
627 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
628 <copy todir="${outputDir}/lang">
629 <fileset dir="${resourceDir}/lang">
630 <include name="**.*" />
633 <jar destfile="in.jar" index="true">
635 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
636 <attribute name="Application-Name" value="JalviewLite" />
637 <attribute name="Codebase" value="${applet.codebase}" />
639 <fileset dir="${outputDir}">
640 <include name="com/**" />
641 <include name="MCview/**" />
642 <include name="jalview/**" />
643 <include name=".build_properties" />
644 <include name="images/link.gif" />
645 <include name="lang/**" />
649 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
651 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
652 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
653 <delete file="in.jar" />
655 <target name="-obfuscatereally" unless="donotobfuscate">
657 <path id="obfuscateDeps.path">
658 <pathelement location="${applet.jre.tools}" />
659 <pathelement location="appletlib/${jmolJar}" />
660 <pathelement location="lib/${varnaJar}" />
661 <pathelement location="appletlib/${jsoup}" />
662 <pathelement location="appletlib/${jsonSimple}" />
663 <pathelement location="appletlib/${javaJson}" />
664 <fileset dir="${java.home}/lib">
665 <include name="plugin.jar" />
668 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
670 <proguard verbose="true" >
671 <injar file="in.jar" />
672 <outjar file="${jalviewLiteJar}" />
673 <libraryjar refid="obfuscateDeps.path" />
675 <keep access="public" type="class" name="jalview.bin.JalviewLite">
676 <field access="public" />
677 <method access="public" />
678 <constructor access="public" />
680 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
681 <field access="public" />
682 <method access="public" />
683 <constructor access="public" />
686 <keep name="jalview.json.binding**">
691 <keep access="public" type="class" name="MCview.PDBfile">
692 <field access="public" />
693 <method access="public" />
694 <constructor access="public" />
697 <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
698 <field access="public" />
699 <method access="public" />
700 <constructor access="public" />
703 <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
704 <field access="public" />
705 <method access="public" />
706 <constructor access="public" />
710 <!-- -libraryjars "${obfuscateDeps}"
712 -outjars jalviewApplet.jar
713 -keep public class jalview.bin.JalviewLite
716 <delete file="in.jar" />
719 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
720 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
722 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
723 <include name="*.java" />
724 <include name="descriptors/*.java" />
727 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
728 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
729 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
730 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
732 now build the jalview.binding package with the old schema set
735 <fileset dir="${sourceDir}/jalview/binding/">
736 <include name="**" />
739 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
740 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
741 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
743 <target name="sourcedist" description="create jalview source distribution" depends="init">
744 <delete file="${source.dist.name}" />
745 <!-- temporary copy of source to update timestamps -->
746 <copy todir="_sourcedist">
748 <exclude name=".*" />
749 <exclude name="**/.*" />
750 <exclude name="*.class" />
751 <exclude name="**/*.class" />
752 <include name="LICENSE" />
753 <include name="README" />
754 <include name="build.xml" />
755 <include name="jalview-jalopy.xml" />
756 <include name="JalviewApplet.jpx" />
757 <include name="JalviewX.jpx" />
758 <include name="nbbuild.xml" />
759 <include name="nbproject/genfiles.properties" />
760 <include name="nbproject/project.properties" />
761 <include name="nbproject/project.xml" />
762 <include name="${sourceDir}/*.java" />
763 <include name="${sourceDir}/**/*.java" />
764 <include name="${sourceDir}/**/*.cdr" />
765 <include name="${libDir}/**/*" />
766 <include name="${resourceDir}/**/*" />
767 <include name="${helpDir}/**/*" />
768 <include name="appletlib/${jmolJar}" />
769 <include name="appletlib/${jsonSimple}" />
770 <include name="appletlib/${javaJson}" />
771 <exclude name="**/*locales" />
772 <exclude name="*locales/**" />
773 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
774 <exclude name="utils/InstallAnywhere/**Build*/**" />
775 <exclude name="utils/InstallAnywhere/**Build*/**" />
776 <exclude name="utils/InstallAnywhere/.build*.*/**" />
777 <exclude name="utils/InstallAnywhere/**locale*" />
778 <exclude name="utils/InstallAnywhere/**locale*/**" />
779 <exclude name="utils/InstallAnywhere/**locale*/**" />
780 <include name="${schemaDir}/**/*" />
781 <include name="utils/**/*" />
782 <include name="${docDir}/**/*" />
783 <include name="examples/**/*" />
787 <tstamp prefix="build">
788 <format property="year" pattern="yyyy" />
790 <!-- each replacetoken CDATA body must be on one line -
791 otherwise the pattern doesn't match -->
792 <replace value="${JALVIEW_VERSION}">
793 <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
794 <fileset dir="_sourcedist">
795 <include name="**/*" />
798 <replace dir="_sourcedist" value="${build.year}">
799 <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
800 <fileset dir="_sourcedist">
801 <include name="**/*" />
805 <tar destfile="${source.dist.name}" compression="gzip">
806 <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
810 <delete dir="_sourcedist" />
812 <target name="prepubapplet_1" depends="makeApplet">
813 <copy todir="${packageDir}/examples">
814 <fileset dir="examples">
815 <include name="**/*" />
816 <include name="javascript/*" />
817 <include name="jmol/*" />
820 <include name="${jalviewLiteJar}" />
822 <fileset dir="appletlib">
823 <include name="**/*" />
826 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
827 <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
828 <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
829 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
831 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
832 <!-- <attribute name="Permissions" value="sandbox" /> -->
833 <!--<attribute name="Trusted-Lib" value="true" /> -->
834 <attribute name="Codebase" value="${applet.codebase}" />
835 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
839 <presetdef name="ap_applet.jar">
840 <!-- build a signed applet with 'all-permissions' -
841 Needs 'param name="permissions' value="all-permissions"' in applet tag
842 JalviewLite+JmolApplet linked sequence/structure fails
843 Mixed code warnings are raised
845 <jar update="true" index="true">
847 <attribute name="Application-Name" value="JalviewLite" />
848 <attribute name="Permissions" value="all-permissions" />
849 <attribute name="Codebase" value="${applet.codebase}" />
850 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
851 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
855 <presetdef name="applet.jar">
856 <!-- build signed applet with sandbox permissions -
857 Needs 'param name="permissions' value="sandbox"' in applet tag
858 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
861 <jar update="true" index="true">
863 <attribute name="Application-Name" value="JalviewLite" />
864 <attribute name="Permissions" value="sandbox" />
865 <attribute name="Codebase" value="${applet.codebase}" />
866 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
867 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
871 <presetdef name="tl_applet.jar">
872 <!-- build signed applet with trusted library/trusted permissions -
873 Needs 'param name="permissions' value="all-permissions"' in applet tag
875 No mixed code warnings raised
876 Jmol/JalviewLite sequence/structure example doesn't link structures
877 Raises dialog asking user to allow page to control applet via LiveConnect javascript
881 <jar update="true" index="true">
883 <attribute name="Application-Name" value="JalviewLite" />
884 <attribute name="Permissions" value="all-permissions" />
885 <attribute name="Codebase" value="${applet.codebase}" />
886 <attribute name="Trusted-Only" value="true" />
887 <attribute name="Trusted-Library" value="true" />
891 <presetdef name="to_applet.jar">
892 <!-- not fully test variant (yet) -->
893 <jar update="true" index="true">
895 <attribute name="Application-Name" value="JalviewLite" />
896 <attribute name="Permissions" value="all-permissions" />
897 <attribute name="Codebase" value="${applet.codebase}" />
898 <attribute name="Trusted-Only" value="true" />
902 <!-- create differently privileged artefacts -->
903 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
904 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
905 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
906 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
907 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
908 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
909 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
910 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
911 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
912 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
913 <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
914 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
915 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
916 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
917 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
918 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
919 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
920 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
921 <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
922 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
923 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
924 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
925 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
926 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
927 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
928 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
929 <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
930 <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
931 <!-- finally, create manifest for original jars -->
932 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
933 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
934 <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
935 <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
937 <!-- todo - write examples/downloads for alternate versions of the applet
938 probably don't need to do this now since we don't have alternate versions anymore !-->
940 <target name="-signapplet" depends="prepubapplet_1">
941 <fileset id="signappletjarset" dir="${packageDir}/examples">
942 <exclude name="u_*.jar" />
943 <include name="${jalviewLiteJar}" />
944 <include name="${jmolJar}" />
945 <include name="${javaJson}" />
946 <include name="${jsonSimple}" />
947 <include name="to_${jalviewLiteJar}" />
948 <include name="to_${jmolJar}" />
949 <include name="to_${javaJson}" />
950 <include name="to_${jsonSimple}" />
951 <include name="tl_${jalviewLiteJar}" />
952 <include name="tl_${jmolJar}" />
953 <include name="tl_${javaJson}" />
954 <include name="tl_${jsonSimple}" />
955 <include name="ap_${jalviewLiteJar}" />
956 <include name="ap_${jmolJar}" />
957 <include name="ap_${javaJson}" />
958 <include name="ap_${jsonSimple}" />
961 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
962 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
963 <fileset refid="signappletjarset" />
967 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
968 <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}">
969 <fileset refid="signappletjarset" />
973 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
975 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
977 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
978 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
979 <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
980 <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
981 <!-- finally, replace any launchApp servlet tags with a version specification -->
982 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
984 <![CDATA[http://www.jalview.org/services/launchApp"]]>
986 <fileset dir="${packageDir}/examples">
987 <include name="**/*.html" />
990 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
992 <![CDATA[http://www.jalview.org/services/launchApp']]>
994 <fileset dir="${packageDir}/examples">
995 <include name="**/*.html" />
1000 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
1001 <javadoc destdir="${javadocDir}">
1002 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
1006 <target name="linkcheck" depends="init,prepare">
1007 <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
1008 <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
1009 <arg file="${helpDir}"/>
1010 <arg value="-nointernet"/>