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="ant.java.version is ${ant.java.version}"/>
119 <!-- Don't change anything below here unless you know what you are doing! -->
120 <!-- Url path for WebStart in JNLP file -->
121 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
122 <!-- Webstart Image - looked for in resources/images -->
123 <property name="WebStartImage" value="JalviewLogo_big.png" />
124 <!-- J2SE version needed for webstart launch -->
125 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
126 <property name="j2sev" value="1.7+" />
127 <!-- Java Compilation settings - source and target javac version -->
128 <property name="javac.source" value="11" if:set="java11" />
129 <property name="javac.target" value="11" if:set="java11" />
130 <property name="javac.source" value="1.8" unless:set="java11" />
131 <property name="javac.target" value="1.8" unless:set="java11" />
132 <echo message="javac.source is ${javac.source}"/>
133 <echo message="javac.target is ${javac.target}"/>
135 <!-- Permissions for running Java applets and applications. -->
136 <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
137 <property name="application.codebase" value="*.jalview.org" />
138 <!-- and allowing the applet to be deployed from any URL -->
139 <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
140 <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
141 <property name="applet.caller-codebase" value="${applet.codebase}" />
143 <!-- build directory configuration -->
144 <property name="libDir" value="lib" />
145 <property name="j11libDir" value="j11lib" />
146 <property name="resourceDir" value="resources" />
147 <property name="helpDir" value="help" />
148 <property name="docDir" value="doc" />
149 <property name="sourceDir" value="src" />
150 <property name="schemaDir" value="schemas" />
151 <property name="outputDir" value="classes" unless:set="clover.jar"/>
152 <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
153 <property name="packageDir" value="dist" />
154 <property name="outputJar" value="jalview.jar" />
155 <!-- Jalview Applet JMol Jar Dependency -->
156 <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
157 <property name="varnaJar" value="VARNAv3-93.jar" />
158 <property name="jsoup" value="jsoup-1.8.1.jar" />
159 <property name="jsonSimple" value="json_simple-1.1.jar" />
160 <property name="javaJson" value="java-json.jar" />
161 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
162 <property name="reportDir" value="test-reports" />
163 <property name="testDir" value="test" />
164 <property name="testOutputDir" value="tests" />
165 <!-- switch to indicate if we should obfuscate jalviewLite -->
166 <!-- <property name="donotobfuscate" value="true"/> -->
167 <!-- switch to exclude associations from generated jnlp files -->
168 <!-- <property name="nojnlpfileassocs" value="true"/> -->
170 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
171 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
172 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
173 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
174 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
175 <property name="WSInterf" value="MsaWS" />
176 <property name="wsdl.Namespace" value="vamsas" />
177 <property name="wsdl.ClientNS" value="ext.vamsas" />
178 <!-- the class path for building the application -->
179 <path id="build.classpath">
180 <fileset dir="utils">
181 <include name="*.jar" />
182 <include name="**/*.jar" />
184 <fileset dir="${j11libDir}">
185 <include name="*.jar" />
186 <include name="**/*.jar" />
188 <fileset dir="${libDir}">
189 <include name="*.jar" />
190 <include name="**/*.jar" />
192 <fileset dir="${java.home}/lib">
193 <include name="plugin.jar" />
195 <fileset dir="appletlib">
196 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
198 <include name="${jmolJar}" />
199 <include name="${varnaJar}" />
201 <pathelement location="${clover.jar}" if:set="clover.jar"/>
203 <path id="test.classpath">
204 <pathelement path="${outputDir}" />
205 <path refid="build.classpath" />
207 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
208 <!-- The Location of the java 1.1.8 jdk -->
209 <property name="java118.home" value="${java.home}" />
210 <!-- jre for 1.4 version -->
211 <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
213 <!-- the classpath for building the 1.1 applet -->
214 <path id="jalviewlite.deps">
215 <fileset dir="${java118.home}">
216 <include name="lib/rt.jar" />
218 <fileset dir="${java.home}/lib">
219 <include name="plugin.jar" />
221 <pathelement location="appletlib/${jmolJar}" />
222 <pathelement location="lib/${varnaJar}" />
223 <pathelement location="appletlib/${jsoup}" />
224 <pathelement location="appletlib/${jsonSimple}" />
225 <pathelement location="appletlib/${javaJson}" />
228 <!-- default location for outputting javadoc -->
229 <property name="javadocDir" value="${packageDir}/javadoc" />
233 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
234 <target name="buildPropertiesFile" depends="init">
235 <tstamp prefix="build">
236 <format property="date" pattern="dd MMMM yyyy" />
238 <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
239 <arg value="rev-parse" />
240 <arg value="--short" />
243 <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
244 <arg value="rev-parse" />
245 <arg value="--abbrev-ref" />
248 <properties file="${outputDir}/.build_properties">
250 ---Jalview Build Details---
252 <property name="VERSION" value="${JALVIEW_VERSION}" />
253 <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
254 <property name="BUILD_DATE" value="${build.date}" />
259 <target name="clean" depends="init">
260 <!-- not efficient yet. -->
261 <delete dir="${outputDir}" includes="*,**/*" />
264 <target name="distclean" depends="init, clean">
266 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
269 <include name="${outputJar}" />
270 <include name="#*#" />
271 <include name="#*.*#" />
272 <include name="**/#*#" />
273 <include name="**/#*.*#" />
274 <include name="*~" />
275 <include name="*.*~" />
276 <include name="**/*~" />
277 <include name="**/*.*~" />
282 <target name="prepare" depends="init">
283 <mkdir dir="${outputDir}" />
284 <copy todir="${outputDir}">
286 <include name="${docDir}/**/*.*" />
287 <include name="${helpDir}/**/*.*" />
288 <include name="${libDir}/*.jar" />
290 <fileset dir="${resourceDir}">
291 <include name="**/*.*" />
296 <target name="build" depends="prepare">
297 <!-- not efficient yet. -->
298 <!-- Echo the build.classpath
299 <pathconvert property="echoClasspath" refid="build.classpath" />
300 <echo message="build.classpath is '${echoClasspath}'" />
302 <echo message="javac.target is '${javac.target}'" />
303 <javac includeantruntime="false" source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
304 <exclude name="jalview/*applet*" />
305 <exclude name="jalview/appletgui/**" />
306 <exclude name="com/stevesoft/**" />
311 <target name="testclean" depends="init">
312 <delete dir="${testOutputDir}" includes="*,**/*" />
315 <target name="prepareTests" depends="init,testclean">
316 <mkdir dir="${testOutputDir}" />
319 <target name="buildTests" depends="build,buildindices,prepareTests">
320 <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
324 <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
326 <target name="testng" depends="buildTests">
327 <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
330 <pathelement location="${testOutputDir}" />
331 <pathelement location="${clover.jar}" if:set="clover.jar"/>
332 <path refid="test.classpath" />
334 <jvmarg value="--module-path=${j11libDir}:${java.home}/jmods" if:set="java11"/>
335 <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
336 <jvmarg value="--illegal-access=warn" if:set="java9"/>
337 <classfileset dir="${testOutputDir}" includes="**/*.class" />
341 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
342 <replace value="${JALVIEW_VERSION}">
343 <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
344 <fileset dir="${outputDir}/${helpDir}">
345 <include name="help.jhm" />
349 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
354 <target name="preparejnlp" depends="makedist">
355 <copy todir="${packageDir}">
356 <fileset dir="${resourceDir}/images">
357 <include name="${WebStartImage}" />
361 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
363 <!-- create a dummy jar which will eventually contain the jnlp template -->
364 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
365 <fileset dir="${packageDir}">
366 <include name="jalview.jar" />
370 <mkdir dir="${packageDir}/JNLP-INF" />
371 <antcall target="writejnlpf">
372 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
373 <param name="inih" value="*" />
374 <param name="maxh" value="*" />
377 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
378 <fileset dir="${packageDir}">
379 <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
383 <antcall target="writejnlpf">
384 <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
385 <param name="inih" value="10M" />
386 <param name="maxh" value="256M" />
388 <antcall target="writejnlpf">
389 <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
390 <param name="inih" value="800M" />
391 <param name="maxh" value="1024M" />
394 <antcall target="writejnlpf">
395 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
396 <param name="inih" value="128M" />
397 <param name="maxh" value="512M" />
400 <antcall target="writejnlpf">
401 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
402 <param name="inih" value="800M" />
403 <param name="maxh" value="1024M" />
406 <!-- finally, need to postprocess to add in associations at end of 'information' element
408 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
415 <association mime-type="application-x/ext-file" extensions="fa"/>
416 <association mime-type="application-x/ext-file" extensions="fasta"/>
417 <association mime-type="application-x/ext-file" extensions="mfa"/>
418 <association mime-type="application-x/ext-file" extensions="fastq"/>
419 <association mime-type="application-x/ext-file" extensions="blc"/>
420 <association mime-type="application-x/ext-file" extensions="msf"/>
421 <association mime-type="application-x/ext-file" extensions="pfam"/>
422 <association mime-type="application-x/ext-file" extensions="aln"/>
423 <association mime-type="application-x/ext-file" extensions="pir"/>
424 <association mime-type="application-x/ext-file" extensions="amsa"/>
425 <association mime-type="application-x/ext-file" extensions="stk"/>
426 <association mime-type="application-x/ext-file" extensions="jar"/>-->
429 <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
430 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
431 tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
432 <fileset dir="${packageDir}">
433 <include name="*.jar" />
437 <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
438 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
439 <fileset dir="${packageDir}">
440 <include name="*.jar" />
445 <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
446 <!-- and sign the jars -->
447 <!-- the default keystore details might need to be edited here -->
450 <target name="runenv" depends="init">
451 <path id="run.classpath">
452 <pathelement location="${outputDir}" />
453 <fileset dir="${outputDir}">
454 <include name="${libDir}/*.jar" />
457 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
459 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
463 <target name="-generatejnlpf">
464 <presetdef name="jnlpf">
465 <jnlp codebase="${WebStartLocation}">
467 <title>Jalview</title>
468 <vendor>The Barton Group</vendor>
469 <homepage href="http://www.jalview.org" />
470 <description>Jalview Multiple Alignment Editor</description>
471 <description kind="short">Jalview</description>
472 <icon href="${WebStartImage}" />
476 <j2se version="1.8+" />
477 <jar main="true" href="jalview.jar"/>
478 <fileset dir="${packageDir}">
479 <exclude name="jalview.jar" />
480 <include name="*.jar" />
481 <include name="*_*.jar" />
482 <exclude name="*quaqua*.jar" />
484 <property name="jalview.version" value="${JALVIEW_VERSION}" />
486 <resources os="Mac OS X">
487 <fileset dir="${packageDir}">
488 <include name="quaqua-filechooser-only-8.0.jar"/>
489 <include name="*quaqua64*.jnilib.jar" />
493 <application_desc main_class="jalview.bin.Jalview">
501 <jnlpf toFile="${jnlpFile}" />
502 <!-- add the add-modules j2se attribute for java 9 -->
503 <replace file="${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"">
504 <replacetoken>j2se version="1.8+"</replacetoken>
508 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
509 <echo message="Not adding JNLP File Associations" />
512 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
513 <replace file="${jnlpFile}">
515 <![CDATA[</information>]]></replacetoken>
518 <association mime-type="application-x/ext-file" extensions="fa" />
519 <association mime-type="application-x/ext-file" extensions="fasta" />
520 <association mime-type="application-x/ext-file" extensions="mfa" />
521 <association mime-type="application-x/ext-file" extensions="fastq" />
522 <association mime-type="application-x/ext-file" extensions="blc" />
523 <association mime-type="application-x/ext-file" extensions="msf" />
524 <association mime-type="application-x/ext-file" extensions="pfam" />
525 <association mime-type="application-x/ext-file" extensions="aln"/>
526 <association mime-type="application-x/ext-file" extensions="pir"/>
527 <association mime-type="application-x/ext-file" extensions="amsa"/>
528 <association mime-type="application-x/ext-file" extensions="stk"/>
529 <association mime-type="application-x/ext-file" extensions="jvp"/>
530 </information>]]></replacevalue>
532 <echo message="Added file associations to JNLP file" />
534 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
537 <target name="buildextclients" depends="init">
538 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
539 <condition property="dontextbuild">
540 <equals arg1="n" arg2="${doextbuild.response}" />
542 <condition property="dontextbuild">
543 <equals arg1="N" arg2="${doextbuild.response}" />
545 <fail if="dontextbuild">
546 Build External Client Code process aborted by user. Jalview source is unchanged.
548 <!-- Currently, this doesn't happen automatically.
549 1. Run WSDL2Java as below, which generates an ext.vamsas +
550 vamsas.<datapackages> fileset.
551 2. refactor ext.vamsas.SpecificserviceWS* to
552 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
553 3. Update the jalview.ws.*WServices classes to reflect the
554 interface type, and all locations of this wsdl type that Jalview
558 <path id="axisbuild">
559 <path refid="build.classpath" />
561 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
563 <fileset dir="${sourceDir}" id="client">
564 <include name="${wsdl.ClientNS}/*.*" />
568 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
570 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
571 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
576 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
577 <fail if="clover.jar">
578 Ignoring request to build jalview distribution with clover-instrumented classes
580 <!-- make the package jar if not already existing -->
581 <mkdir dir="${packageDir}" />
582 <!-- clean dir if it already existed -->
584 <fileset dir="${packageDir}">
585 <include name="*.jar" />
588 <jar destfile="${packageDir}/${outputJar}" index="true">
590 <attribute name="Main-Class" value="jalview.bin.Jalview" />
591 <attribute name="Permissions" value="all-permissions" />
592 <attribute name="Application-Name" value="Jalview Desktop" />
593 <attribute name="Codebase" value="${application.codebase}" />
595 <fileset dir="${outputDir}/">
596 <exclude name="cache*/**" />
597 <exclude name="*.jar" />
598 <exclude name="*.jar.*" />
599 <exclude name="**/*.jar" />
600 <exclude name="**/*.jar.*" />
604 <copy toDir="${packageDir}" flatten="true">
605 <fileset dir="${outputDir}">
606 <include name="*.jar" />
607 <include name="**/*.jar" />
613 <!-- jalopy code reformatter -->
614 <target name="sourcescrub" depends="init,build">
615 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
616 <fileset dir="${sourceDir}">
617 <include name="*.java" />
618 <include name="**/*.java" />
619 <include name="**/**/*.java" />
626 <!-- Compile, package and obfuscate Jalview Applet -->
627 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
629 <target name="compileApplet" depends="init,clean">
630 <mkdir dir="${outputDir}" />
631 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
634 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
635 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
636 <copy todir="${outputDir}/lang">
637 <fileset dir="${resourceDir}/lang">
638 <include name="**.*" />
641 <jar destfile="in.jar" index="true">
643 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
644 <attribute name="Application-Name" value="JalviewLite" />
645 <attribute name="Codebase" value="${applet.codebase}" />
647 <fileset dir="${outputDir}">
648 <include name="com/**" />
649 <include name="MCview/**" />
650 <include name="jalview/**" />
651 <include name=".build_properties" />
652 <include name="images/link.gif" />
653 <include name="lang/**" />
657 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
659 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
660 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
661 <delete file="in.jar" />
663 <target name="-obfuscatereally" unless="donotobfuscate">
665 <path id="obfuscateDeps.path">
666 <pathelement location="${applet.jre.tools}" />
667 <pathelement location="appletlib/${jmolJar}" />
668 <pathelement location="lib/${varnaJar}" />
669 <pathelement location="appletlib/${jsoup}" />
670 <pathelement location="appletlib/${jsonSimple}" />
671 <pathelement location="appletlib/${javaJson}" />
672 <fileset dir="${java.home}/lib">
673 <include name="plugin.jar" />
676 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
678 <proguard verbose="true" >
679 <injar file="in.jar" />
680 <outjar file="${jalviewLiteJar}" />
681 <libraryjar refid="obfuscateDeps.path" />
683 <keep access="public" type="class" name="jalview.bin.JalviewLite">
684 <field access="public" />
685 <method access="public" />
686 <constructor access="public" />
688 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
689 <field access="public" />
690 <method access="public" />
691 <constructor access="public" />
694 <keep name="jalview.json.binding**">
699 <keep access="public" type="class" name="MCview.PDBfile">
700 <field access="public" />
701 <method access="public" />
702 <constructor access="public" />
705 <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
706 <field access="public" />
707 <method access="public" />
708 <constructor access="public" />
711 <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
712 <field access="public" />
713 <method access="public" />
714 <constructor access="public" />
718 <!-- -libraryjars "${obfuscateDeps}"
720 -outjars jalviewApplet.jar
721 -keep public class jalview.bin.JalviewLite
724 <delete file="in.jar" />
727 <target name="sourcedist" description="create jalview source distribution" depends="init">
728 <delete file="${source.dist.name}" />
729 <!-- temporary copy of source to update timestamps -->
730 <copy todir="_sourcedist">
732 <exclude name=".*" />
733 <exclude name="**/.*" />
734 <exclude name="*.class" />
735 <exclude name="**/*.class" />
736 <include name="LICENSE" />
737 <include name="README" />
738 <include name="build.xml" />
739 <include name="jalview-jalopy.xml" />
740 <include name="JalviewApplet.jpx" />
741 <include name="JalviewX.jpx" />
742 <include name="nbbuild.xml" />
743 <include name="nbproject/genfiles.properties" />
744 <include name="nbproject/project.properties" />
745 <include name="nbproject/project.xml" />
746 <include name="${sourceDir}/*.java" />
747 <include name="${sourceDir}/**/*.java" />
748 <include name="${sourceDir}/**/*.cdr" />
749 <include name="${libDir}/**/*" />
750 <include name="${resourceDir}/**/*" />
751 <include name="${helpDir}/**/*" />
752 <include name="appletlib/${jmolJar}" />
753 <include name="appletlib/${jsonSimple}" />
754 <include name="appletlib/${javaJson}" />
755 <exclude name="**/*locales" />
756 <exclude name="*locales/**" />
757 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
758 <exclude name="utils/InstallAnywhere/**Build*/**" />
759 <exclude name="utils/InstallAnywhere/**Build*/**" />
760 <exclude name="utils/InstallAnywhere/.build*.*/**" />
761 <exclude name="utils/InstallAnywhere/**locale*" />
762 <exclude name="utils/InstallAnywhere/**locale*/**" />
763 <exclude name="utils/InstallAnywhere/**locale*/**" />
764 <include name="${schemaDir}/**/*" />
765 <include name="utils/**/*" />
766 <include name="${docDir}/**/*" />
767 <include name="examples/**/*" />
771 <tstamp prefix="build">
772 <format property="year" pattern="yyyy" />
774 <!-- each replacetoken CDATA body must be on one line -
775 otherwise the pattern doesn't match -->
776 <replace value="${JALVIEW_VERSION}">
777 <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
778 <fileset dir="_sourcedist">
779 <include name="**/*" />
782 <replace dir="_sourcedist" value="${build.year}">
783 <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
784 <fileset dir="_sourcedist">
785 <include name="**/*" />
789 <tar destfile="${source.dist.name}" compression="gzip">
790 <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
794 <delete dir="_sourcedist" />
796 <target name="prepubapplet_1" depends="makeApplet">
797 <copy todir="${packageDir}/examples">
798 <fileset dir="examples">
799 <include name="**/*" />
800 <include name="javascript/*" />
801 <include name="jmol/*" />
804 <include name="${jalviewLiteJar}" />
806 <fileset dir="appletlib">
807 <include name="**/*" />
810 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
811 <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
812 <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
813 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
815 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
816 <!-- <attribute name="Permissions" value="sandbox" /> -->
817 <!--<attribute name="Trusted-Lib" value="true" /> -->
818 <attribute name="Codebase" value="${applet.codebase}" />
819 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
823 <presetdef name="ap_applet.jar">
824 <!-- build a signed applet with 'all-permissions' -
825 Needs 'param name="permissions' value="all-permissions"' in applet tag
826 JalviewLite+JmolApplet linked sequence/structure fails
827 Mixed code warnings are raised
829 <jar update="true" index="true">
831 <attribute name="Application-Name" value="JalviewLite" />
832 <attribute name="Permissions" value="all-permissions" />
833 <attribute name="Codebase" value="${applet.codebase}" />
834 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
835 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
839 <presetdef name="applet.jar">
840 <!-- build signed applet with sandbox permissions -
841 Needs 'param name="permissions' value="sandbox"' in applet tag
842 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
845 <jar update="true" index="true">
847 <attribute name="Application-Name" value="JalviewLite" />
848 <attribute name="Permissions" value="sandbox" />
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="${applet.codebase}" />
855 <presetdef name="tl_applet.jar">
856 <!-- build signed applet with trusted library/trusted permissions -
857 Needs 'param name="permissions' value="all-permissions"' in applet tag
859 No mixed code warnings raised
860 Jmol/JalviewLite sequence/structure example doesn't link structures
861 Raises dialog asking user to allow page to control applet via LiveConnect javascript
865 <jar update="true" index="true">
867 <attribute name="Application-Name" value="JalviewLite" />
868 <attribute name="Permissions" value="all-permissions" />
869 <attribute name="Codebase" value="${applet.codebase}" />
870 <attribute name="Trusted-Only" value="true" />
871 <attribute name="Trusted-Library" value="true" />
875 <presetdef name="to_applet.jar">
876 <!-- not fully test variant (yet) -->
877 <jar update="true" index="true">
879 <attribute name="Application-Name" value="JalviewLite" />
880 <attribute name="Permissions" value="all-permissions" />
881 <attribute name="Codebase" value="${applet.codebase}" />
882 <attribute name="Trusted-Only" value="true" />
886 <!-- create differently privileged artefacts -->
887 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
888 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
889 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
890 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
891 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
892 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
893 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
894 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
895 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
896 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
897 <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
898 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
899 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
900 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
901 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
902 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
903 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
904 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
905 <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
906 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
907 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
908 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
909 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
910 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
911 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
912 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
913 <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
914 <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
915 <!-- finally, create manifest for original jars -->
916 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
917 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
918 <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
919 <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
921 <!-- todo - write examples/downloads for alternate versions of the applet
922 probably don't need to do this now since we don't have alternate versions anymore !-->
924 <target name="-signapplet" depends="prepubapplet_1">
925 <fileset id="signappletjarset" dir="${packageDir}/examples">
926 <exclude name="u_*.jar" />
927 <include name="${jalviewLiteJar}" />
928 <include name="${jmolJar}" />
929 <include name="${javaJson}" />
930 <include name="${jsonSimple}" />
931 <include name="to_${jalviewLiteJar}" />
932 <include name="to_${jmolJar}" />
933 <include name="to_${javaJson}" />
934 <include name="to_${jsonSimple}" />
935 <include name="tl_${jalviewLiteJar}" />
936 <include name="tl_${jmolJar}" />
937 <include name="tl_${javaJson}" />
938 <include name="tl_${jsonSimple}" />
939 <include name="ap_${jalviewLiteJar}" />
940 <include name="ap_${jmolJar}" />
941 <include name="ap_${javaJson}" />
942 <include name="ap_${jsonSimple}" />
945 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
946 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
947 <fileset refid="signappletjarset" />
951 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
952 <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}">
953 <fileset refid="signappletjarset" />
957 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
959 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
961 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
962 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
963 <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
964 <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
965 <!-- finally, replace any launchApp servlet tags with a version specification -->
966 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
968 <![CDATA[http://www.jalview.org/services/launchApp"]]>
970 <fileset dir="${packageDir}/examples">
971 <include name="**/*.html" />
974 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
976 <![CDATA[http://www.jalview.org/services/launchApp']]>
978 <fileset dir="${packageDir}/examples">
979 <include name="**/*.html" />
984 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
985 <javadoc destdir="${javadocDir}">
986 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
990 <target name="linkcheck" depends="init,prepare">
991 <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
992 <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
993 <arg file="${helpDir}"/>
994 <arg value="-nointernet"/>