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=".">
21 <target name="help" depends="usage" />
22 <target name="usage" depends="init">
23 <echo message="~~~Jalview Ant build.xml Usage~~~~" />
24 <echo message="Targets include:" />
25 <echo message="usage - default target, displays this message" />
26 <echo message="buildindices - generates JavaHelpSearch from the help files" />
27 <echo message="build - compiles all necessary files for Application" />
28 <echo message="makedist - compiles and places all necessary jar files into directory dist" />
29 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
30 <echo message=" this needs a keystore and key."/>
31 <echo message=" Add -Dtimestamp to timestamp signed jars"/>
32 <echo message=" -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
33 <echo message=" See docs/building.html for more information." />
34 <echo message="compileApplet - compiles all necessary files for Applet" />
35 <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
36 <echo message="testng - run jalview's tests via testNG. Default group is '${testng-groups}'" />
37 <echo message=" you can specify particular test groups as a list via -Dtestng-groups=" />
38 <echo message="See docs/building.html and the comments in build file for other targets." />
39 <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
40 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
44 <!-- utils is a class path to additional utilities needed for
45 building docs, jars and webstart stuff -->
47 Userdefined build property defaults
49 wsdl.server list (plus namespace mapping info ???) - also want
50 ... to make this a dynamically generatable property
52 Build location - provide a temporary root for speed
53 jarsigner keystore and info
54 Jakarta and axis classpath ?
55 Default argument for starting Jalview (if it exists).
60 <path id="axis.classpath">
62 <fileset dir="/usr/local/axis/lib">
63 <include name="**/*.jar" />
65 <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
66 <include name="**/*.jar"/>
67 <include name="*.jar"/>
71 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
72 <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
74 <property name="INSTALLATION" value="Source" />
76 <!-- 2.4 (VAMSAS)" -->
77 <!-- Include debugging information in javac true or false -->
78 <property name="javac.debug" value="true" />
80 <!-- JarSigner Key Store for Webstart Distribution -->
81 <property name="jalview.keystore" value="./keys/.keystore" />
82 <!-- Keystore Password -->
83 <property name="jalview.keystore.pass" value="alignmentisfun" />
85 <property name="jalview.key" value="jalview" />
87 <property name="jalview.key.pass" value="alignmentisfun" />
88 <!-- time stamp server URL -->
89 <property name="jalview.tsaurl" value="" />
90 <!-- locally valid proxy for signing with external time server -->
91 <property name="proxyPort" value="80"/>
92 <property name="proxyHost" value="sqid"/>
93 <!-- key sign/digest algorithms -->
94 <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
95 <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
97 <!-- default TestNG groups to run -->
98 <property name="testng-groups" value="Functional" />
100 <!-- Don't change anything below here unless you know what you are doing! -->
101 <!-- Url path for WebStart in JNLP file -->
102 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
103 <!-- Webstart Image - looked for in resources/images -->
104 <property name="WebStartImage" value="JalviewLogo_big.png" />
105 <!-- J2SE version needed for webstart launch -->
106 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
107 <property name="j2sev" value="1.7+" />
108 <!-- Java Compilation settings - source and target javac version -->
109 <property name="javac.source" value="1.7" />
110 <property name="javac.target" value="1.7" />
112 <!-- Permissions for running Java applets and applications. -->
113 <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
114 <property name="application.codebase" value="*.jalview.org" />
115 <!-- and allowing the applet to be deployed from any URL -->
116 <!-- 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 -->
117 <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
118 <property name="applet.caller-codebase" value="${applet.codebase}" />
120 <!-- build directory configuration -->
121 <property name="libDir" value="lib" />
122 <property name="resourceDir" value="resources" />
123 <property name="helpDir" value="help" />
124 <property name="docDir" value="doc" />
125 <property name="sourceDir" value="src" />
126 <property name="schemaDir" value="schemas" />
127 <property name="outputDir" value="classes" />
128 <property name="packageDir" value="dist" />
129 <property name="outputJar" value="jalview.jar" />
130 <!-- Jalview Applet JMol Jar Dependency -->
131 <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
132 <property name="varnaJar" value="VARNAv3-93.jar" />
133 <property name="jsoup" value="jsoup-1.8.1.jar" />
134 <property name="jsonSimple" value="json_simple-1.1.jar" />
135 <property name="javaJson" value="java-json.jar" />
136 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
137 <property name="reportDir" value="test-reports" />
138 <property name="testDir" value="test" />
139 <property name="testOutputDir" value="tests" />
140 <!-- switch to indicate if we should obfuscate jalviewLite -->
141 <!-- <property name="donotobfuscate" value="true"/> -->
142 <!-- switch to exclude associations from generated jnlp files -->
143 <!-- <property name="nojnlpfileassocs" value="true"/> -->
145 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
146 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
147 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
148 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
149 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
150 <property name="WSInterf" value="MsaWS" />
151 <property name="wsdl.Namespace" value="vamsas" />
152 <property name="wsdl.ClientNS" value="ext.vamsas" />
153 <!-- the class path for building the application -->
154 <path id="build.classpath">
155 <fileset dir="utils">
156 <include name="*.jar" />
157 <include name="**/*.jar" />
159 <fileset dir="${libDir}">
160 <include name="*.jar" />
161 <include name="**/*.jar" />
163 <fileset dir="${java.home}/lib">
164 <include name="plugin.jar" />
166 <fileset dir="appletlib">
167 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
169 <include name="${jmolJar}" />
170 <include name="${varnaJar}" />
173 <path id="test.classpath">
174 <pathelement path="${outputDir}" />
175 <path refid="build.classpath" />
177 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
178 <!-- The Location of the java 1.1.8 jdk -->
179 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
180 <property name="java118.home" value="${java.home}" />
181 <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
183 <!-- jre for 1.4 version -->
184 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
186 <!-- the classpath for building the 1.1 applet -->
187 <path id="jalviewlite.deps">
188 <fileset dir="${java118.home}">
189 <include name="lib/classes.zip" />
191 <fileset dir="${java.home}/lib">
192 <include name="plugin.jar" />
194 <pathelement location="appletlib/${jmolJar}" />
195 <pathelement location="lib/${varnaJar}" />
196 <pathelement location="appletlib/${jsoup}" />
197 <pathelement location="appletlib/${jsonSimple}" />
198 <pathelement location="appletlib/${javaJson}" />
201 <!-- default location for outputting javadoc -->
202 <property name="javadocDir" value="${packageDir}/javadoc" />
206 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
207 <target name="buildPropertiesFile" depends="init">
208 <tstamp prefix="build">
209 <format property="date" pattern="dd MMMM yyyy" />
211 <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
212 <arg value="rev-parse" />
213 <arg value="--short" />
216 <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
217 <arg value="rev-parse" />
218 <arg value="--abbrev-ref" />
221 <properties file="${outputDir}/.build_properties">
223 ---Jalview Build Details---
225 <property name="VERSION" value="${JALVIEW_VERSION}" />
226 <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
227 <property name="BUILD_DATE" value="${build.date}" />
232 <target name="clean" depends="init">
233 <!-- not efficient yet. -->
234 <delete dir="${outputDir}" includes="*,**/*" />
237 <target name="distclean" depends="init, clean">
239 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
242 <include name="${outputJar}" />
243 <include name="#*#" />
244 <include name="#*.*#" />
245 <include name="**/#*#" />
246 <include name="**/#*.*#" />
247 <include name="*~" />
248 <include name="*.*~" />
249 <include name="**/*~" />
250 <include name="**/*.*~" />
255 <target name="prepare" depends="init">
256 <mkdir dir="${outputDir}" />
257 <copy todir="${outputDir}">
259 <include name="${docDir}/**/*.*" />
260 <include name="${helpDir}/**/*.*" />
261 <include name="${libDir}/*.jar" />
263 <fileset dir="${resourceDir}">
264 <include name="**/*.*" />
269 <target name="build" depends="prepare">
270 <!-- not efficient yet. -->
271 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
272 <exclude name="jalview/*applet*" />
273 <exclude name="jalview/appletgui/**" />
274 <exclude name="com/stevesoft/**" />
279 <target name="testclean" depends="init">
280 <delete dir="${testOutputDir}" includes="*,**/*" />
283 <target name="prepareTests" depends="init,testclean">
284 <mkdir dir="${testOutputDir}" />
287 <target name="buildTests" depends="build,buildindices,prepareTests">
288 <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
292 <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
294 <target name="testng" depends="buildTests">
295 <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
298 <pathelement location="${testOutputDir}" />
299 <path refid="test.classpath" />
301 <classfileset dir="${testOutputDir}" includes="**/*.class" />
305 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
306 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
311 <target name="preparejnlp" depends="makedist">
312 <copy todir="${packageDir}">
313 <fileset dir="${resourceDir}/images">
314 <include name="${WebStartImage}" />
318 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
320 <!-- create a dummy jar which will eventually contain the jnlp template -->
321 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
322 <fileset dir="${packageDir}">
323 <include name="jalview.jar" />
327 <mkdir dir="${packageDir}/JNLP-INF" />
328 <antcall target="writejnlpf">
329 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
330 <param name="inih" value="*" />
331 <param name="maxh" value="*" />
334 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
335 <fileset dir="${packageDir}">
336 <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
340 <antcall target="writejnlpf">
341 <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
342 <param name="inih" value="10M" />
343 <param name="maxh" value="256M" />
346 <antcall target="writejnlpf">
347 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
348 <param name="inih" value="128M" />
349 <param name="maxh" value="512M" />
352 <antcall target="writejnlpf">
353 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
354 <param name="inih" value="256M" />
355 <param name="maxh" value="1024M" />
358 <!-- finally, need to postprocess to add in associations at end of 'information' element
360 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
367 <association mime-type="application-x/ext-file" extensions="fa"/>
368 <association mime-type="application-x/ext-file" extensions="fasta"/>
369 <association mime-type="application-x/ext-file" extensions="mfa"/>
370 <association mime-type="application-x/ext-file" extensions="fastq"/>
371 <association mime-type="application-x/ext-file" extensions="blc"/>
372 <association mime-type="application-x/ext-file" extensions="msf"/>
373 <association mime-type="application-x/ext-file" extensions="pfam"/>
374 <association mime-type="application-x/ext-file" extensions="aln"/>
375 <association mime-type="application-x/ext-file" extensions="pir"/>
376 <association mime-type="application-x/ext-file" extensions="amsa"/>
377 <association mime-type="application-x/ext-file" extensions="stk"/>
378 <association mime-type="application-x/ext-file" extensions="jar"/>-->
381 <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
382 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
383 tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
384 <fileset dir="${packageDir}">
385 <include name="*.jar" />
389 <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
390 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
391 <fileset dir="${packageDir}">
392 <include name="*.jar" />
397 <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
398 <!-- and sign the jars -->
399 <!-- the default keystore details might need to be edited here -->
402 <target name="runenv" depends="init">
403 <path id="run.classpath">
404 <pathelement location="${outputDir}" />
405 <fileset dir="${outputDir}">
406 <include name="${libDir}/*.jar" />
409 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
411 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
415 <target name="-generatejnlpf">
416 <presetdef name="jnlpf">
417 <jnlp codebase="${WebStartLocation}">
419 <title>Jalview</title>
420 <vendor>The Barton Group</vendor>
421 <homepage href="http://www.jalview.org" />
422 <description>Jalview Multiple Alignment Editor</description>
423 <description kind="short">Jalview</description>
424 <icon href="${WebStartImage}" />
428 <j2se version="1.7+" />
429 <jar main="true" href="jalview.jar"/>
430 <fileset dir="${packageDir}">
431 <exclude name="jalview.jar" />
432 <include name="*.jar" />
433 <include name="*_*.jar" />
434 <exclude name="*quaqua*.jar" />
436 <property name="jalview.version" value="${JALVIEW_VERSION}" />
438 <resources os="Mac OS X">
439 <fileset dir="${packageDir}">
440 <include name="quaqua-filechooser-only-8.0.jar"/>
441 <include name="*quaqua64*.jnilib.jar" />
445 <application_desc main_class="jalview.bin.Jalview">
453 <jnlpf toFile="${jnlpFile}" />
454 <!-- add the add-modules j2se attribute for java 9 -->
455 <replace file="${jnlpFile}" value="j2se version="1.7+" initial-heap-size="${inih}" max-heap-size="${maxh}" java-vm-args="--add-modules=java.se.ee --illegal-access=warn"">
456 <replacetoken>j2se version="1.7+"</replacetoken>
461 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
462 <echo message="Not adding JNLP File Associations" />
465 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
466 <replace file="${jnlpFile}">
468 <![CDATA[</information>]]></replacetoken>
471 <association mime-type="application-x/ext-file" extensions="fa" />
472 <association mime-type="application-x/ext-file" extensions="fasta" />
473 <association mime-type="application-x/ext-file" extensions="mfa" />
474 <association mime-type="application-x/ext-file" extensions="fastq" />
475 <association mime-type="application-x/ext-file" extensions="blc" />
476 <association mime-type="application-x/ext-file" extensions="msf" />
477 <association mime-type="application-x/ext-file" extensions="pfam" />
478 <association mime-type="application-x/ext-file" extensions="aln"/>
479 <association mime-type="application-x/ext-file" extensions="pir"/>
480 <association mime-type="application-x/ext-file" extensions="amsa"/>
481 <association mime-type="application-x/ext-file" extensions="stk"/>
482 <association mime-type="application-x/ext-file" extensions="jvp"/>
483 </information>]]></replacevalue>
485 <echo message="Added file associations to JNLP file" />
487 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
490 <target name="buildextclients" depends="init">
491 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
492 <condition property="dontextbuild">
493 <equals arg1="n" arg2="${doextbuild.response}" />
495 <condition property="dontextbuild">
496 <equals arg1="N" arg2="${doextbuild.response}" />
498 <fail if="dontextbuild">
499 Build External Client Code process aborted by user. Jalview source is unchanged.
501 <!-- Currently, this doesn't happen automatically.
502 1. Run WSDL2Java as below, which generates an ext.vamsas +
503 vamsas.<datapackages> fileset.
504 2. refactor ext.vamsas.SpecificserviceWS* to
505 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
506 3. Update the jalview.ws.*WServices classes to reflect the
507 interface type, and all locations of this wsdl type that Jalview
511 <path id="axisbuild">
512 <path refid="build.classpath" />
514 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
516 <fileset dir="${sourceDir}" id="client">
517 <include name="${wsdl.ClientNS}/*.*" />
521 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
523 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
524 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
529 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
530 <!-- make the package jar if not already existing -->
531 <mkdir dir="${packageDir}" />
532 <!-- clean dir if it already existed -->
534 <fileset dir="${packageDir}">
535 <include name="*.jar" />
538 <jar destfile="${packageDir}/${outputJar}" index="true">
540 <attribute name="Main-Class" value="jalview.bin.Jalview" />
541 <attribute name="Permissions" value="all-permissions" />
542 <attribute name="Application-Name" value="Jalview Desktop" />
543 <attribute name="Codebase" value="${application.codebase}" />
545 <fileset dir="${outputDir}/">
546 <exclude name="cache*/**" />
547 <exclude name="*.jar" />
548 <exclude name="*.jar.*" />
549 <exclude name="**/*.jar" />
550 <exclude name="**/*.jar.*" />
554 <copy toDir="${packageDir}" flatten="true">
555 <fileset dir="${outputDir}">
556 <include name="*.jar" />
557 <include name="**/*.jar" />
563 <!-- jalopy code reformatter -->
564 <target name="sourcescrub" depends="init,build">
565 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
566 <fileset dir="${sourceDir}">
567 <include name="*.java" />
568 <include name="**/*.java" />
569 <include name="**/**/*.java" />
576 <!-- Compile, package and obfuscate Jalview Applet -->
577 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
579 <target name="compileApplet" depends="init,clean">
580 <mkdir dir="${outputDir}" />
581 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
584 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
585 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
586 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
587 <copy todir="${outputDir}/lang">
588 <fileset dir="${resourceDir}/lang">
589 <include name="**.*" />
592 <jar destfile="in.jar" index="true">
594 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
595 <attribute name="Application-Name" value="JalviewLite" />
596 <attribute name="Codebase" value="${applet.codebase}" />
598 <fileset dir="${outputDir}">
599 <include name="com/**" />
600 <include name="MCview/**" />
601 <include name="jalview/**" />
602 <include name=".build_properties" />
603 <include name="images/idwidth.gif" />
604 <include name="images/link.gif" />
605 <include name="lang/**" />
609 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
611 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
612 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
613 <delete file="in.jar" />
615 <target name="-obfuscatereally" unless="donotobfuscate">
617 <path id="obfuscateDeps.path">
618 <pathelement location="${applet.jre.tools}" />
619 <pathelement location="appletlib/${jmolJar}" />
620 <pathelement location="lib/${varnaJar}" />
621 <pathelement location="appletlib/${jsoup}" />
622 <pathelement location="appletlib/${jsonSimple}" />
623 <pathelement location="appletlib/${javaJson}" />
624 <fileset dir="${java.home}/lib">
625 <include name="plugin.jar" />
628 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
630 <proguard verbose="true" >
631 <injar file="in.jar" />
632 <outjar file="${jalviewLiteJar}" />
633 <libraryjar refid="obfuscateDeps.path" />
635 <keep access="public" type="class" name="jalview.bin.JalviewLite">
636 <field access="public" />
637 <method access="public" />
638 <constructor access="public" />
640 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
641 <field access="public" />
642 <method access="public" />
643 <constructor access="public" />
646 <keep name="jalview.json.binding**">
651 <keep access="public" type="class" name="MCview.PDBfile">
652 <field access="public" />
653 <method access="public" />
654 <constructor access="public" />
657 <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
658 <field access="public" />
659 <method access="public" />
660 <constructor access="public" />
663 <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
664 <field access="public" />
665 <method access="public" />
666 <constructor access="public" />
670 <!-- -libraryjars "${obfuscateDeps}"
672 -outjars jalviewApplet.jar
673 -keep public class jalview.bin.JalviewLite
676 <delete file="in.jar" />
679 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
680 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
682 <fileset dir="${sourceDir}/jalview/schemabinding/version2">
683 <include name="*.java" />
684 <include name="descriptors/*.java" />
687 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
688 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
689 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
690 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
692 now build the jalview.binding package with the old schema set
695 <fileset dir="${sourceDir}/jalview/binding/">
696 <include name="**" />
699 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
700 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
701 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
703 <target name="sourcedist" description="create jalview source distribution" depends="init">
704 <delete file="${source.dist.name}" />
705 <!-- temporary copy of source to update timestamps -->
706 <copy todir="_sourcedist">
708 <exclude name=".*" />
709 <exclude name="**/.*" />
710 <exclude name="*.class" />
711 <exclude name="**/*.class" />
712 <include name="LICENSE" />
713 <include name="README" />
714 <include name="build.xml" />
715 <include name="jalview-jalopy.xml" />
716 <include name="JalviewApplet.jpx" />
717 <include name="JalviewX.jpx" />
718 <include name="nbbuild.xml" />
719 <include name="nbproject/genfiles.properties" />
720 <include name="nbproject/project.properties" />
721 <include name="nbproject/project.xml" />
722 <include name="${sourceDir}/*.java" />
723 <include name="${sourceDir}/**/*.java" />
724 <include name="${sourceDir}/**/*.cdr" />
725 <include name="${libDir}/**/*" />
726 <include name="${resourceDir}/**/*" />
727 <include name="${helpDir}/**/*" />
728 <include name="appletlib/${jmolJar}" />
729 <include name="appletlib/${jsonSimple}" />
730 <include name="appletlib/${javaJson}" />
731 <exclude name="**/*locales" />
732 <exclude name="*locales/**" />
733 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
734 <exclude name="utils/InstallAnywhere/**Build*/**" />
735 <exclude name="utils/InstallAnywhere/**Build*/**" />
736 <exclude name="utils/InstallAnywhere/.build*.*/**" />
737 <exclude name="utils/InstallAnywhere/**locale*" />
738 <exclude name="utils/InstallAnywhere/**locale*/**" />
739 <exclude name="utils/InstallAnywhere/**locale*/**" />
740 <include name="${schemaDir}/**/*" />
741 <include name="utils/**/*" />
742 <include name="${docDir}/**/*" />
743 <include name="examples/**/*" />
747 <tstamp prefix="build">
748 <format property="year" pattern="yyyy" />
750 <!-- each replacetoken CDATA body must be on one line -
751 otherwise the pattern doesn't match -->
752 <replace value="${JALVIEW_VERSION}">
753 <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
754 <fileset dir="_sourcedist">
755 <include name="**/*" />
758 <replace dir="_sourcedist" value="${build.year}">
759 <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
760 <fileset dir="_sourcedist">
761 <include name="**/*" />
765 <tar destfile="${source.dist.name}" compression="gzip">
766 <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
770 <delete dir="_sourcedist" />
772 <target name="prepubapplet_1" depends="makeApplet">
773 <copy todir="${packageDir}/examples">
774 <fileset dir="examples">
775 <include name="**/*" />
776 <include name="javascript/*" />
777 <include name="jmol/*" />
780 <include name="${jalviewLiteJar}" />
782 <fileset dir="appletlib">
783 <include name="**/*" />
786 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
787 <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
788 <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
789 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
791 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
792 <!-- <attribute name="Permissions" value="sandbox" /> -->
793 <!--<attribute name="Trusted-Lib" value="true" /> -->
794 <attribute name="Codebase" value="${applet.codebase}" />
795 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
799 <presetdef name="ap_applet.jar">
800 <!-- build a signed applet with 'all-permissions' -
801 Needs 'param name="permissions' value="all-permissions"' in applet tag
802 JalviewLite+JmolApplet linked sequence/structure fails
803 Mixed code warnings are raised
805 <jar update="true" index="true">
807 <attribute name="Application-Name" value="JalviewLite" />
808 <attribute name="Permissions" value="all-permissions" />
809 <attribute name="Codebase" value="${applet.codebase}" />
810 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
811 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
815 <presetdef name="applet.jar">
816 <!-- build signed applet with sandbox permissions -
817 Needs 'param name="permissions' value="sandbox"' in applet tag
818 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
821 <jar update="true" index="true">
823 <attribute name="Application-Name" value="JalviewLite" />
824 <attribute name="Permissions" value="sandbox" />
825 <attribute name="Codebase" value="${applet.codebase}" />
826 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
827 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
831 <presetdef name="tl_applet.jar">
832 <!-- build signed applet with trusted library/trusted permissions -
833 Needs 'param name="permissions' value="all-permissions"' in applet tag
835 No mixed code warnings raised
836 Jmol/JalviewLite sequence/structure example doesn't link structures
837 Raises dialog asking user to allow page to control applet via LiveConnect javascript
841 <jar update="true" index="true">
843 <attribute name="Application-Name" value="JalviewLite" />
844 <attribute name="Permissions" value="all-permissions" />
845 <attribute name="Codebase" value="${applet.codebase}" />
846 <attribute name="Trusted-Only" value="true" />
847 <attribute name="Trusted-Library" value="true" />
851 <presetdef name="to_applet.jar">
852 <!-- not fully test variant (yet) -->
853 <jar update="true" index="true">
855 <attribute name="Application-Name" value="JalviewLite" />
856 <attribute name="Permissions" value="all-permissions" />
857 <attribute name="Codebase" value="${applet.codebase}" />
858 <attribute name="Trusted-Only" value="true" />
862 <!-- create differently privileged artefacts -->
863 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
864 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
865 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
866 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
867 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
868 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
869 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
870 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
871 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
872 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
873 <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
874 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
875 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
876 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
877 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
878 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
879 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
880 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
881 <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
882 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
883 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
884 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
885 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
886 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
887 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
888 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
889 <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
890 <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
891 <!-- finally, create manifest for original jars -->
892 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
893 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
894 <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
895 <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
897 <!-- todo - write examples/downloads for alternate versions of the applet
898 probably don't need to do this now since we don't have alternate versions anymore !-->
900 <target name="-signapplet" depends="prepubapplet_1">
901 <fileset id="signappletjarset" dir="${packageDir}/examples">
902 <exclude name="u_*.jar" />
903 <include name="${jalviewLiteJar}" />
904 <include name="${jmolJar}" />
905 <include name="${javaJson}" />
906 <include name="${jsonSimple}" />
907 <include name="to_${jalviewLiteJar}" />
908 <include name="to_${jmolJar}" />
909 <include name="to_${javaJson}" />
910 <include name="to_${jsonSimple}" />
911 <include name="tl_${jalviewLiteJar}" />
912 <include name="tl_${jmolJar}" />
913 <include name="tl_${javaJson}" />
914 <include name="tl_${jsonSimple}" />
915 <include name="ap_${jalviewLiteJar}" />
916 <include name="ap_${jmolJar}" />
917 <include name="ap_${javaJson}" />
918 <include name="ap_${jsonSimple}" />
921 <target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
922 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
923 <fileset refid="signappletjarset" />
927 <target name="-signapplettsa" if="timestamp" depends="-signapplet">
928 <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}">
929 <fileset refid="signappletjarset" />
933 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
935 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
937 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
938 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
939 <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
940 <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
941 <!-- finally, replace any launchApp servlet tags with a version specification -->
942 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
944 <![CDATA[http://www.jalview.org/services/launchApp"]]>
946 <fileset dir="${packageDir}/examples">
947 <include name="**/*.html" />
950 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
952 <![CDATA[http://www.jalview.org/services/launchApp']]>
954 <fileset dir="${packageDir}/examples">
955 <include name="**/*.html" />
960 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
961 <javadoc destdir="${javadocDir}">
962 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
966 <target name="linkcheck" depends="init,prepare">
967 <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
968 <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
969 <arg file="${helpDir}"/>
970 <arg value="-nointernet"/>