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="${testOutputDir}" includes="**/*.class" />
341 <target name="testngclass" depends="buildTests">
342 <condition property="propsSpecified">
343 <isset property="class.name" />
345 <fail unless="propsSpecified" message="class.name property not specified."/>
346 <echo message="testng-groups is '${testng-groups}'" />
347 <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng" verbose="2">
349 <pathelement location="${testOutputDir}" />
350 <pathelement location="${clover.jar}" if:set="clover.jar"/>
351 <path refid="test.classpath" />
353 <jvmarg value="--module-path=${j11libDir}:${java.home}/jmods" if:set="java11"/>
354 <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
355 <jvmarg value="--illegal-access=warn" if:set="java9"/>
356 <classfileset dir="${testOutputDir}" includes="${class.name}" />
360 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
361 <replace value="${JALVIEW_VERSION}">
362 <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
363 <fileset dir="${outputDir}/${helpDir}">
364 <include name="help.jhm" />
368 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
373 <target name="preparejnlp" depends="makedist">
374 <copy todir="${packageDir}">
375 <fileset dir="${resourceDir}/images">
376 <include name="${WebStartImage}" />
380 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
382 <!-- create a dummy jar which will eventually contain the jnlp template -->
383 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
384 <fileset dir="${packageDir}">
385 <include name="jalview.jar" />
389 <mkdir dir="${packageDir}/JNLP-INF" />
390 <antcall target="writejnlpf">
391 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
392 <param name="inih" value="*" />
393 <param name="maxh" value="*" />
396 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
397 <fileset dir="${packageDir}">
398 <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
402 <antcall target="writejnlpf">
403 <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
404 <param name="inih" value="10M" />
405 <param name="maxh" value="256M" />
407 <antcall target="writejnlpf">
408 <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
409 <param name="inih" value="800M" />
410 <param name="maxh" value="1024M" />
413 <antcall target="writejnlpf">
414 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
415 <param name="inih" value="128M" />
416 <param name="maxh" value="512M" />
419 <antcall target="writejnlpf">
420 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
421 <param name="inih" value="800M" />
422 <param name="maxh" value="1024M" />
425 <!-- finally, need to postprocess to add in associations at end of 'information' element
427 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
434 <association mime-type="application-x/ext-file" extensions="fa"/>
435 <association mime-type="application-x/ext-file" extensions="fasta"/>
436 <association mime-type="application-x/ext-file" extensions="mfa"/>
437 <association mime-type="application-x/ext-file" extensions="fastq"/>
438 <association mime-type="application-x/ext-file" extensions="blc"/>
439 <association mime-type="application-x/ext-file" extensions="msf"/>
440 <association mime-type="application-x/ext-file" extensions="pfam"/>
441 <association mime-type="application-x/ext-file" extensions="aln"/>
442 <association mime-type="application-x/ext-file" extensions="pir"/>
443 <association mime-type="application-x/ext-file" extensions="amsa"/>
444 <association mime-type="application-x/ext-file" extensions="stk"/>
445 <association mime-type="application-x/ext-file" extensions="jar"/>-->
448 <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
449 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
450 tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
451 <fileset dir="${packageDir}">
452 <include name="*.jar" />
456 <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
457 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
458 <fileset dir="${packageDir}">
459 <include name="*.jar" />
464 <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
465 <!-- and sign the jars -->
466 <!-- the default keystore details might need to be edited here -->
469 <target name="runenv" depends="init">
470 <path id="run.classpath">
471 <pathelement location="${outputDir}" />
472 <fileset dir="${outputDir}">
473 <include name="${libDir}/*.jar" />
476 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
478 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
482 <target name="-generatejnlpf">
483 <presetdef name="jnlpf">
484 <jnlp codebase="${WebStartLocation}">
486 <title>Jalview</title>
487 <vendor>The Barton Group</vendor>
488 <homepage href="http://www.jalview.org" />
489 <description>Jalview Multiple Alignment Editor</description>
490 <description kind="short">Jalview</description>
491 <icon href="${WebStartImage}" />
495 <j2se version="1.8+" />
496 <jar main="true" href="jalview.jar"/>
497 <fileset dir="${packageDir}">
498 <exclude name="jalview.jar" />
499 <include name="*.jar" />
500 <include name="*_*.jar" />
501 <exclude name="*quaqua*.jar" />
503 <property name="jalview.version" value="${JALVIEW_VERSION}" />
505 <resources os="Mac OS X">
506 <fileset dir="${packageDir}">
507 <include name="quaqua-filechooser-only-8.0.jar"/>
508 <include name="*quaqua64*.jnilib.jar" />
512 <application_desc main_class="jalview.bin.Jalview">
520 <jnlpf toFile="${jnlpFile}" />
521 <!-- add the add-modules j2se attribute for java 9 -->
522 <replace file="${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"">
523 <replacetoken>j2se version="1.8+"</replacetoken>
527 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
528 <echo message="Not adding JNLP File Associations" />
531 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
532 <replace file="${jnlpFile}">
534 <![CDATA[</information>]]></replacetoken>
537 <association mime-type="application-x/ext-file" extensions="fa" />
538 <association mime-type="application-x/ext-file" extensions="fasta" />
539 <association mime-type="application-x/ext-file" extensions="mfa" />
540 <association mime-type="application-x/ext-file" extensions="fastq" />
541 <association mime-type="application-x/ext-file" extensions="blc" />
542 <association mime-type="application-x/ext-file" extensions="msf" />
543 <association mime-type="application-x/ext-file" extensions="pfam" />
544 <association mime-type="application-x/ext-file" extensions="aln"/>
545 <association mime-type="application-x/ext-file" extensions="pir"/>
546 <association mime-type="application-x/ext-file" extensions="amsa"/>
547 <association mime-type="application-x/ext-file" extensions="stk"/>
548 <association mime-type="application-x/ext-file" extensions="jvp"/>
549 </information>]]></replacevalue>
551 <echo message="Added file associations to JNLP file" />
553 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
556 <target name="buildextclients" depends="init">
557 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
558 <condition property="dontextbuild">
559 <equals arg1="n" arg2="${doextbuild.response}" />
561 <condition property="dontextbuild">
562 <equals arg1="N" arg2="${doextbuild.response}" />
564 <fail if="dontextbuild">
565 Build External Client Code process aborted by user. Jalview source is unchanged.
567 <!-- Currently, this doesn't happen automatically.
568 1. Run WSDL2Java as below, which generates an ext.vamsas +
569 vamsas.<datapackages> fileset.
570 2. refactor ext.vamsas.SpecificserviceWS* to
571 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
572 3. Update the jalview.ws.*WServices classes to reflect the
573 interface type, and all locations of this wsdl type that Jalview
577 <path id="axisbuild">
578 <path refid="build.classpath" />
580 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
582 <fileset dir="${sourceDir}" id="client">
583 <include name="${wsdl.ClientNS}/*.*" />
587 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
589 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
590 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
595 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
596 <fail if="clover.jar">
597 Ignoring request to build jalview distribution with clover-instrumented classes
599 <!-- make the package jar if not already existing -->
600 <mkdir dir="${packageDir}" />
601 <!-- clean dir if it already existed -->
603 <fileset dir="${packageDir}">
604 <include name="*.jar" />
607 <jar destfile="${packageDir}/${outputJar}" index="true">
609 <attribute name="Main-Class" value="jalview.bin.Jalview" />
610 <attribute name="Permissions" value="all-permissions" />
611 <attribute name="Application-Name" value="Jalview Desktop" />
612 <attribute name="Codebase" value="${application.codebase}" />
614 <fileset dir="${outputDir}/">
615 <exclude name="cache*/**" />
616 <exclude name="*.jar" />
617 <exclude name="*.jar.*" />
618 <exclude name="**/*.jar" />
619 <exclude name="**/*.jar.*" />
623 <copy toDir="${packageDir}" flatten="true">
624 <fileset dir="${outputDir}">
625 <include name="*.jar" />
626 <include name="**/*.jar" />
632 <!-- jalopy code reformatter -->
633 <target name="sourcescrub" depends="init,build">
634 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
635 <fileset dir="${sourceDir}">
636 <include name="*.java" />
637 <include name="**/*.java" />
638 <include name="**/**/*.java" />
645 <!-- Compile, package and obfuscate Jalview Applet -->
646 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
648 <target name="compileApplet" depends="init,clean">
649 <mkdir dir="${outputDir}" />
650 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
653 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
654 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
655 <copy todir="${outputDir}/lang">
656 <fileset dir="${resourceDir}/lang">
657 <include name="**.*" />
660 <jar destfile="in.jar" index="true">
662 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
663 <attribute name="Application-Name" value="JalviewLite" />
664 <attribute name="Codebase" value="${applet.codebase}" />
666 <fileset dir="${outputDir}">
667 <include name="com/**" />
668 <include name="MCview/**" />
669 <include name="jalview/**" />
670 <include name=".build_properties" />
671 <include name="images/link.gif" />
672 <include name="lang/**" />
676 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
678 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
679 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
680 <delete file="in.jar" />
682 <target name="-obfuscatereally" unless="donotobfuscate">
684 <path id="obfuscateDeps.path">
685 <pathelement location="${applet.jre.tools}" />
686 <pathelement location="appletlib/${jmolJar}" />
687 <pathelement location="lib/${varnaJar}" />
688 <pathelement location="appletlib/${jsoup}" />
689 <pathelement location="appletlib/${jsonSimple}" />
690 <pathelement location="appletlib/${javaJson}" />
691 <fileset dir="${java.home}/lib">
692 <include name="plugin.jar" />
695 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
697 <proguard verbose="true" >
698 <injar file="in.jar" />
699 <outjar file="${jalviewLiteJar}" />
700 <libraryjar refid="obfuscateDeps.path" />
702 <keep access="public" type="class" name="jalview.bin.JalviewLite">
703 <field access="public" />
704 <method access="public" />
705 <constructor access="public" />
707 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
708 <field access="public" />
709 <method access="public" />
710 <constructor access="public" />
713 <keep name="jalview.json.binding**">
718 <keep access="public" type="class" name="MCview.PDBfile">
719 <field access="public" />
720 <method access="public" />
721 <constructor access="public" />
724 <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
725 <field access="public" />
726 <method access="public" />
727 <constructor access="public" />
730 <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
731 <field access="public" />
732 <method access="public" />
733 <constructor access="public" />
737 <!-- -libraryjars "${obfuscateDeps}"
739 -outjars jalviewApplet.jar
740 -keep public class jalview.bin.JalviewLite
743 <delete file="in.jar" />
746 <target name="sourcedist" description="create jalview source distribution" depends="init">
747 <delete file="${source.dist.name}" />
748 <!-- temporary copy of source to update timestamps -->
749 <copy todir="_sourcedist">
751 <exclude name=".*" />
752 <exclude name="**/.*" />
753 <exclude name="*.class" />
754 <exclude name="**/*.class" />
755 <include name="LICENSE" />
756 <include name="README" />
757 <include name="build.xml" />
758 <include name="jalview-jalopy.xml" />
759 <include name="JalviewApplet.jpx" />
760 <include name="JalviewX.jpx" />
761 <include name="nbbuild.xml" />
762 <include name="nbproject/genfiles.properties" />
763 <include name="nbproject/project.properties" />
764 <include name="nbproject/project.xml" />
765 <include name="${sourceDir}/*.java" />
766 <include name="${sourceDir}/**/*.java" />
767 <include name="${sourceDir}/**/*.cdr" />
768 <include name="${libDir}/**/*" />
769 <include name="${resourceDir}/**/*" />
770 <include name="${helpDir}/**/*" />
771 <include name="appletlib/${jmolJar}" />
772 <include name="appletlib/${jsonSimple}" />
773 <include name="appletlib/${javaJson}" />
774 <exclude name="**/*locales" />
775 <exclude name="*locales/**" />
776 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
777 <exclude name="utils/InstallAnywhere/**Build*/**" />
778 <exclude name="utils/InstallAnywhere/**Build*/**" />
779 <exclude name="utils/InstallAnywhere/.build*.*/**" />
780 <exclude name="utils/InstallAnywhere/**locale*" />
781 <exclude name="utils/InstallAnywhere/**locale*/**" />
782 <exclude name="utils/InstallAnywhere/**locale*/**" />
783 <include name="${schemaDir}/**/*" />
784 <include name="utils/**/*" />
785 <include name="${docDir}/**/*" />
786 <include name="examples/**/*" />
790 <tstamp prefix="build">
791 <format property="year" pattern="yyyy" />
793 <!-- each replacetoken CDATA body must be on one line -
794 otherwise the pattern doesn't match -->
795 <replace value="${JALVIEW_VERSION}">
796 <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
797 <fileset dir="_sourcedist">
798 <include name="**/*" />
801 <replace dir="_sourcedist" value="${build.year}">
802 <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
803 <fileset dir="_sourcedist">
804 <include name="**/*" />
808 <tar destfile="${source.dist.name}" compression="gzip">
809 <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
813 <delete dir="_sourcedist" />
815 <target name="prepubapplet_1" depends="makeApplet">
816 <copy todir="${packageDir}/examples">
817 <fileset dir="examples">
818 <include name="**/*" />
819 <include name="javascript/*" />
820 <include name="jmol/*" />
823 <include name="${jalviewLiteJar}" />
825 <fileset dir="appletlib">
826 <include name="**/*" />
829 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
830 <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
831 <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
832 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
834 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
835 <!-- <attribute name="Permissions" value="sandbox" /> -->
836 <!--<attribute name="Trusted-Lib" value="true" /> -->
837 <attribute name="Codebase" value="${applet.codebase}" />
838 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
842 <presetdef name="ap_applet.jar">
843 <!-- build a signed applet with 'all-permissions' -
844 Needs 'param name="permissions' value="all-permissions"' in applet tag
845 JalviewLite+JmolApplet linked sequence/structure fails
846 Mixed code warnings are raised
848 <jar update="true" index="true">
850 <attribute name="Application-Name" value="JalviewLite" />
851 <attribute name="Permissions" value="all-permissions" />
852 <attribute name="Codebase" value="${applet.codebase}" />
853 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
854 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
858 <presetdef name="applet.jar">
859 <!-- build signed applet with sandbox permissions -
860 Needs 'param name="permissions' value="sandbox"' in applet tag
861 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
864 <jar update="true" index="true">
866 <attribute name="Application-Name" value="JalviewLite" />
867 <attribute name="Permissions" value="sandbox" />
868 <attribute name="Codebase" value="${applet.codebase}" />
869 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
870 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
874 <presetdef name="tl_applet.jar">
875 <!-- build signed applet with trusted library/trusted permissions -
876 Needs 'param name="permissions' value="all-permissions"' in applet tag
878 No mixed code warnings raised
879 Jmol/JalviewLite sequence/structure example doesn't link structures
880 Raises dialog asking user to allow page to control applet via LiveConnect javascript
884 <jar update="true" index="true">
886 <attribute name="Application-Name" value="JalviewLite" />
887 <attribute name="Permissions" value="all-permissions" />
888 <attribute name="Codebase" value="${applet.codebase}" />
889 <attribute name="Trusted-Only" value="true" />
890 <attribute name="Trusted-Library" value="true" />
894 <presetdef name="to_applet.jar">
895 <!-- not fully test variant (yet) -->
896 <jar update="true" index="true">
898 <attribute name="Application-Name" value="JalviewLite" />
899 <attribute name="Permissions" value="all-permissions" />
900 <attribute name="Codebase" value="${applet.codebase}" />
901 <attribute name="Trusted-Only" value="true" />
905 <!-- create differently privileged artefacts -->
906 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
907 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
908 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
909 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
910 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
911 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
912 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
913 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
914 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
915 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
916 <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
917 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
918 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
919 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
920 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
921 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
922 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
923 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
924 <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
925 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
926 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
927 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
928 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
929 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
930 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
931 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
932 <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
933 <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
934 <!-- finally, create manifest for original jars -->
935 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
936 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
937 <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
938 <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
940 <!-- todo - write examples/downloads for alternate versions of the applet
941 probably don't need to do this now since we don't have alternate versions anymore !-->
943 <target name="-signapplet" depends="prepubapplet_1">
944 <fileset id="signappletjarset" dir="${packageDir}/examples">
945 <exclude name="u_*.jar" />
946 <include name="${jalviewLiteJar}" />
947 <include name="${jmolJar}" />
948 <include name="${javaJson}" />
949 <include name="${jsonSimple}" />
950 <include name="to_${jalviewLiteJar}" />
951 <include name="to_${jmolJar}" />
952 <include name="to_${javaJson}" />
953 <include name="to_${jsonSimple}" />
954 <include name="tl_${jalviewLiteJar}" />
955 <include name="tl_${jmolJar}" />
956 <include name="tl_${javaJson}" />
957 <include name="tl_${jsonSimple}" />
958 <include name="ap_${jalviewLiteJar}" />
959 <include name="ap_${jmolJar}" />
960 <include name="ap_${javaJson}" />
961 <include name="ap_${jsonSimple}" />
964 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
965 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
966 <fileset refid="signappletjarset" />
970 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
971 <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}">
972 <fileset refid="signappletjarset" />
976 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
978 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
980 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
981 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
982 <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
983 <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
984 <!-- finally, replace any launchApp servlet tags with a version specification -->
985 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
987 <![CDATA[http://www.jalview.org/services/launchApp"]]>
989 <fileset dir="${packageDir}/examples">
990 <include name="**/*.html" />
993 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
995 <![CDATA[http://www.jalview.org/services/launchApp']]>
997 <fileset dir="${packageDir}/examples">
998 <include name="**/*.html" />
1003 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
1004 <javadoc destdir="${javadocDir}">
1005 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
1009 <target name="linkcheck" depends="init,prepare">
1010 <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
1011 <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
1012 <arg file="${helpDir}"/>
1013 <arg value="-nointernet"/>