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" />
47 <echo message="Useful -D flags: -Ddeprecation=true to add -Xlint:deprecation to the java compiler" />
51 <!-- utils is a class path to additional utilities needed for
52 building docs, jars and webstart stuff -->
54 Userdefined build property defaults
56 wsdl.server list (plus namespace mapping info ???) - also want
57 ... to make this a dynamically generatable property
59 Build location - provide a temporary root for speed
60 jarsigner keystore and info
61 Jakarta and axis classpath ?
62 Default argument for starting Jalview (if it exists).
67 <path id="axis.classpath">
69 <fileset dir="/usr/local/axis/lib">
70 <include name="**/*.jar" />
72 <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
73 <include name="**/*.jar"/>
74 <include name="*.jar"/>
78 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
79 <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
81 <property name="INSTALLATION" value="Source" />
83 <!-- 2.4 (VAMSAS)" -->
84 <!-- Include debugging information in javac true or false -->
85 <property name="javac.debug" value="true" />
87 <!-- JarSigner Key Store for Webstart Distribution -->
88 <property name="jalview.keystore" value="./keys/.keystore" />
89 <!-- Keystore Password -->
90 <property name="jalview.keystore.pass" value="alignmentisfun" />
92 <property name="jalview.key" value="jalview" />
94 <property name="jalview.key.pass" value="alignmentisfun" />
95 <!-- time stamp server URL -->
96 <property name="jalview.tsaurl" value="" />
97 <!-- locally valid proxy for signing with external time server -->
98 <property name="proxyPort" value="80"/>
99 <property name="proxyHost" value="sqid"/>
100 <!-- key sign/digest algorithms -->
101 <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
102 <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
104 <!-- default TestNG groups to run -->
105 <property name="testng-groups" value="Functional" />
106 <!-- Java 9 JVM args -->
107 <condition property="java9">
108 <equals arg1="${ant.java.version}" arg2="9"/>
110 <!-- Java 10 JVM args -->
111 <condition property="java10">
112 <equals arg1="${ant.java.version}" arg2="10"/>
114 <!-- Java 11 JVM args -->
115 <condition property="java11">
116 <equals arg1="${ant.java.version}" arg2="11"/>
118 <echo message="ant.java.version is ${ant.java.version}"/>
120 <!-- Don't change anything below here unless you know what you are doing! -->
121 <!-- Url path for WebStart in JNLP file -->
122 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
123 <!-- Webstart Image - looked for in resources/images -->
124 <property name="WebStartImage" value="JalviewLogo_big.png" />
125 <!-- J2SE version needed for webstart launch -->
126 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
127 <property name="j2sev" value="1.7+" />
128 <!-- Java Compilation settings - source and target javac version -->
129 <property name="javac.source" value="11" if:set="java11" />
130 <property name="javac.target" value="11" if:set="java11" />
131 <property name="javac.source" value="1.8" unless:set="java11" />
132 <property name="javac.target" value="1.8" unless:set="java11" />
133 <echo message="javac.source is ${javac.source}"/>
134 <echo message="javac.target is ${javac.target}"/>
136 <!-- Permissions for running Java applets and applications. -->
137 <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
138 <property name="application.codebase" value="*.jalview.org" />
139 <!-- and allowing the applet to be deployed from any URL -->
140 <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
141 <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
142 <property name="applet.caller-codebase" value="${applet.codebase}" />
144 <!-- build directory configuration -->
145 <property name="libDir" value="lib" />
146 <property name="j11libDir" value="j11lib" />
147 <property name="resourceDir" value="resources" />
148 <property name="helpDir" value="help" />
149 <property name="docDir" value="doc" />
150 <property name="sourceDir" value="src" />
151 <property name="schemaDir" value="schemas" />
152 <property name="outputDir" value="classes" unless:set="clover.jar"/>
153 <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
154 <property name="packageDir" value="dist" />
155 <property name="outputJar" value="jalview.jar" />
156 <!-- Jalview Applet JMol Jar Dependency -->
157 <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
158 <property name="varnaJar" value="VARNAv3-93.jar" />
159 <property name="jsoup" value="jsoup-1.8.1.jar" />
160 <property name="jsonSimple" value="json_simple-1.1.jar" />
161 <property name="javaJson" value="java-json.jar" />
162 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
163 <property name="reportDir" value="test-reports" />
164 <property name="testDir" value="test" />
165 <property name="testOutputDir" value="tests" />
166 <!-- switch to indicate if we should obfuscate jalviewLite -->
167 <!-- <property name="donotobfuscate" value="true"/> -->
168 <!-- switch to exclude associations from generated jnlp files -->
169 <!-- <property name="nojnlpfileassocs" value="true"/> -->
171 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
172 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
173 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
174 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
175 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
176 <property name="WSInterf" value="MsaWS" />
177 <property name="wsdl.Namespace" value="vamsas" />
178 <property name="wsdl.ClientNS" value="ext.vamsas" />
179 <!-- the class path for building the application -->
180 <path id="build.classpath">
181 <fileset dir="utils">
182 <include name="*.jar" />
183 <include name="**/*.jar" />
185 <fileset dir="${j11libDir}">
186 <include name="*.jar" />
187 <include name="**/*.jar" />
189 <fileset dir="${libDir}">
190 <include name="*.jar" />
191 <include name="**/*.jar" />
193 <fileset dir="${java.home}/lib">
194 <include name="plugin.jar" />
196 <fileset dir="appletlib">
197 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
199 <include name="${jmolJar}" />
200 <include name="${varnaJar}" />
202 <pathelement location="${clover.jar}" if:set="clover.jar"/>
204 <path id="test.classpath">
205 <pathelement path="${outputDir}" />
206 <path refid="build.classpath" />
208 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
209 <!-- The Location of the java 1.1.8 jdk -->
210 <property name="java118.home" value="${java.home}" />
211 <!-- jre for 1.4 version -->
212 <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
214 <!-- the classpath for building the 1.1 applet -->
215 <path id="jalviewlite.deps">
216 <fileset dir="${java118.home}">
217 <include name="lib/rt.jar" />
219 <fileset dir="${java.home}/lib">
220 <include name="plugin.jar" />
222 <pathelement location="appletlib/${jmolJar}" />
223 <pathelement location="lib/${varnaJar}" />
224 <pathelement location="appletlib/${jsoup}" />
225 <pathelement location="appletlib/${jsonSimple}" />
226 <pathelement location="appletlib/${javaJson}" />
229 <!-- default location for outputting javadoc -->
230 <property name="javadocDir" value="${packageDir}/javadoc" />
234 <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
235 <target name="buildPropertiesFile" depends="init">
236 <tstamp prefix="build">
237 <format property="date" pattern="dd MMMM yyyy" />
239 <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
240 <arg value="rev-parse" />
241 <arg value="--short" />
244 <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
245 <arg value="rev-parse" />
246 <arg value="--abbrev-ref" />
249 <properties file="${outputDir}/.build_properties">
251 ---Jalview Build Details---
253 <property name="VERSION" value="${JALVIEW_VERSION}" />
254 <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
255 <property name="BUILD_DATE" value="${build.date}" />
260 <target name="clean" depends="init">
261 <!-- not efficient yet. -->
262 <delete dir="${outputDir}" includes="*,**/*" />
265 <target name="distclean" depends="init, clean">
267 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
270 <include name="${outputJar}" />
271 <include name="#*#" />
272 <include name="#*.*#" />
273 <include name="**/#*#" />
274 <include name="**/#*.*#" />
275 <include name="*~" />
276 <include name="*.*~" />
277 <include name="**/*~" />
278 <include name="**/*.*~" />
283 <target name="prepare" depends="init">
284 <mkdir dir="${outputDir}" />
285 <copy todir="${outputDir}">
287 <include name="${docDir}/**/*.*" />
288 <include name="${helpDir}/**/*.*" />
289 <include name="${libDir}/*.jar" />
291 <fileset dir="${resourceDir}">
292 <include name="**/*.*" />
297 <target name="build" depends="prepare">
298 <!-- not efficient yet. -->
299 <!-- Echo the build.classpath
300 <pathconvert property="echoClasspath" refid="build.classpath" />
301 <echo message="build.classpath is '${echoClasspath}'" />
303 <echo message="javac.target is '${javac.target}'" />
304 <echo message="adding -Xlint:deprecation to javac" if:set="deprecation"/>
305 <javac includeantruntime="false" source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
306 <compilerarg value="-Xlint:deprecation" if:set="deprecation" />
307 <exclude name="jalview/*applet*" />
308 <exclude name="jalview/appletgui/**" />
309 <exclude name="com/stevesoft/**" />
314 <target name="testclean" depends="init">
315 <delete dir="${testOutputDir}" includes="*,**/*" />
318 <target name="prepareTests" depends="init,testclean">
319 <mkdir dir="${testOutputDir}" />
322 <target name="buildTests" depends="build,buildindices,prepareTests">
323 <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
327 <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
329 <target name="testng" depends="buildTests">
330 <loadfile property="j11modules" srcFile="modules">
335 <echo message="j11libDir is '${j11libDir}'" />
336 <echo message="j11modules is '${j11modules}'" />
337 <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
340 <pathelement location="${testOutputDir}" />
341 <pathelement location="${clover.jar}" if:set="clover.jar"/>
342 <path refid="test.classpath" />
345 <jvmarg value="DASH_DASH_module-path=${j11libDir}:${java.home}/jmods" if:set="java11"/>
347 <jvmarg value="--module-path=${j11libDir}" if:set="java11"/>
348 <jvmarg value="--add-modules=${j11modules}" if:set="java11"/>
349 <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
350 <jvmarg value="--illegal-access=warn" if:set="java9"/>
351 <classfileset dir="${testOutputDir}" includes="**/*.class" />
355 <target name="testngclass" depends="buildTests">
356 <condition property="propsSpecified">
357 <isset property="class.name" />
359 <fail unless="propsSpecified" message="class.name property not specified."/>
360 <echo message="testng-groups is '${testng-groups}'" />
361 <loadfile property="j11modules" srcFile="modules"/>
362 <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng" verbose="2">
364 <pathelement location="${testOutputDir}" />
365 <pathelement location="${clover.jar}" if:set="clover.jar"/>
366 <path refid="test.classpath" />
368 <jvmarg value="--module-path=${j11libDir}:${java.home}/jmods" if:set="java11"/>
369 <jvmarg value="--add-modules=${j11modules}" if:set="java11"/>
370 <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
371 <jvmarg value="--illegal-access=warn" if:set="java9"/>
372 <classfileset dir="${testOutputDir}" includes="${class.name}" />
376 <target name="buildindices" depends="init, prepare" unless="help.uptodate">
377 <replace value="${JALVIEW_VERSION}">
378 <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
379 <fileset dir="${outputDir}/${helpDir}">
380 <include name="help.jhm" />
384 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
389 <target name="preparejnlp" depends="makedist">
390 <copy todir="${packageDir}">
391 <fileset dir="${resourceDir}/images">
392 <include name="${WebStartImage}" />
396 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
398 <!-- create a dummy jar which will eventually contain the jnlp template -->
399 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
400 <fileset dir="${packageDir}">
401 <include name="jalview.jar" />
405 <mkdir dir="${packageDir}/JNLP-INF" />
406 <antcall target="writejnlpf">
407 <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
408 <param name="inih" value="*" />
409 <param name="maxh" value="*" />
412 <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
413 <fileset dir="${packageDir}">
414 <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
418 <antcall target="writejnlpf">
419 <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
420 <param name="inih" value="10M" />
421 <param name="maxh" value="256M" />
423 <antcall target="writejnlpf">
424 <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
425 <param name="inih" value="800M" />
426 <param name="maxh" value="1024M" />
429 <antcall target="writejnlpf">
430 <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
431 <param name="inih" value="128M" />
432 <param name="maxh" value="512M" />
435 <antcall target="writejnlpf">
436 <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
437 <param name="inih" value="800M" />
438 <param name="maxh" value="1024M" />
441 <!-- finally, need to postprocess to add in associations at end of 'information' element
443 <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
450 <association mime-type="application-x/ext-file" extensions="fa"/>
451 <association mime-type="application-x/ext-file" extensions="fasta"/>
452 <association mime-type="application-x/ext-file" extensions="mfa"/>
453 <association mime-type="application-x/ext-file" extensions="fastq"/>
454 <association mime-type="application-x/ext-file" extensions="blc"/>
455 <association mime-type="application-x/ext-file" extensions="msf"/>
456 <association mime-type="application-x/ext-file" extensions="pfam"/>
457 <association mime-type="application-x/ext-file" extensions="aln"/>
458 <association mime-type="application-x/ext-file" extensions="pir"/>
459 <association mime-type="application-x/ext-file" extensions="amsa"/>
460 <association mime-type="application-x/ext-file" extensions="stk"/>
461 <association mime-type="application-x/ext-file" extensions="jar"/>-->
464 <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
465 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
466 tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
467 <fileset dir="${packageDir}">
468 <include name="*.jar" />
472 <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
473 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
474 <fileset dir="${packageDir}">
475 <include name="*.jar" />
480 <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
481 <!-- and sign the jars -->
482 <!-- the default keystore details might need to be edited here -->
485 <target name="runenv" depends="init">
486 <path id="run.classpath">
487 <pathelement location="${outputDir}" />
488 <fileset dir="${outputDir}">
489 <include name="${libDir}/*.jar" />
492 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
494 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
498 <target name="-generatejnlpf">
499 <presetdef name="jnlpf">
500 <jnlp codebase="${WebStartLocation}">
502 <title>Jalview</title>
503 <vendor>The Barton Group</vendor>
504 <homepage href="http://www.jalview.org" />
505 <description>Jalview Multiple Alignment Editor</description>
506 <description kind="short">Jalview</description>
507 <icon href="${WebStartImage}" />
511 <j2se version="1.8+" />
512 <jar main="true" href="jalview.jar"/>
513 <fileset dir="${packageDir}">
514 <exclude name="jalview.jar" />
515 <include name="*.jar" />
516 <include name="*_*.jar" />
517 <exclude name="*quaqua*.jar" />
519 <property name="jalview.version" value="${JALVIEW_VERSION}" />
521 <resources os="Mac OS X">
522 <fileset dir="${packageDir}">
523 <include name="quaqua-filechooser-only-8.0.jar"/>
524 <include name="*quaqua64*.jnilib.jar" />
528 <application_desc main_class="jalview.bin.Jalview">
536 <jnlpf toFile="${jnlpFile}" />
537 <!-- add the add-modules j2se attribute for java 9 -->
538 <replace file="${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"">
539 <replacetoken>j2se version="1.8+"</replacetoken>
543 <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
544 <echo message="Not adding JNLP File Associations" />
547 <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
548 <replace file="${jnlpFile}">
550 <![CDATA[</information>]]></replacetoken>
553 <association mime-type="application-x/ext-file" extensions="fa" />
554 <association mime-type="application-x/ext-file" extensions="fasta" />
555 <association mime-type="application-x/ext-file" extensions="mfa" />
556 <association mime-type="application-x/ext-file" extensions="fastq" />
557 <association mime-type="application-x/ext-file" extensions="blc" />
558 <association mime-type="application-x/ext-file" extensions="msf" />
559 <association mime-type="application-x/ext-file" extensions="pfam" />
560 <association mime-type="application-x/ext-file" extensions="aln"/>
561 <association mime-type="application-x/ext-file" extensions="pir"/>
562 <association mime-type="application-x/ext-file" extensions="amsa"/>
563 <association mime-type="application-x/ext-file" extensions="stk"/>
564 <association mime-type="application-x/ext-file" extensions="jvp"/>
565 </information>]]></replacevalue>
567 <echo message="Added file associations to JNLP file" />
569 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
572 <target name="buildextclients" depends="init">
573 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
574 <condition property="dontextbuild">
575 <equals arg1="n" arg2="${doextbuild.response}" />
577 <condition property="dontextbuild">
578 <equals arg1="N" arg2="${doextbuild.response}" />
580 <fail if="dontextbuild">
581 Build External Client Code process aborted by user. Jalview source is unchanged.
583 <!-- Currently, this doesn't happen automatically.
584 1. Run WSDL2Java as below, which generates an ext.vamsas +
585 vamsas.<datapackages> fileset.
586 2. refactor ext.vamsas.SpecificserviceWS* to
587 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
588 3. Update the jalview.ws.*WServices classes to reflect the
589 interface type, and all locations of this wsdl type that Jalview
593 <path id="axisbuild">
594 <path refid="build.classpath" />
596 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
598 <fileset dir="${sourceDir}" id="client">
599 <include name="${wsdl.ClientNS}/*.*" />
603 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
605 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
606 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
611 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
612 <fail if="clover.jar">
613 Ignoring request to build jalview distribution with clover-instrumented classes
615 <!-- make the package jar if not already existing -->
616 <mkdir dir="${packageDir}" />
617 <!-- clean dir if it already existed -->
619 <fileset dir="${packageDir}">
620 <include name="*.jar" />
623 <jar destfile="${packageDir}/${outputJar}" index="true">
625 <attribute name="Main-Class" value="jalview.bin.Jalview" />
626 <attribute name="Permissions" value="all-permissions" />
627 <attribute name="Application-Name" value="Jalview Desktop" />
628 <attribute name="Codebase" value="${application.codebase}" />
630 <fileset dir="${outputDir}/">
631 <exclude name="cache*/**" />
632 <exclude name="*.jar" />
633 <exclude name="*.jar.*" />
634 <exclude name="**/*.jar" />
635 <exclude name="**/*.jar.*" />
639 <copy toDir="${packageDir}" flatten="true">
640 <fileset dir="${outputDir}">
641 <include name="*.jar" />
642 <include name="**/*.jar" />
648 <!-- jalopy code reformatter -->
649 <target name="sourcescrub" depends="init,build">
650 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
651 <fileset dir="${sourceDir}">
652 <include name="*.java" />
653 <include name="**/*.java" />
654 <include name="**/**/*.java" />
661 <!-- Compile, package and obfuscate Jalview Applet -->
662 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
664 <target name="compileApplet" depends="init,clean">
665 <mkdir dir="${outputDir}" />
666 <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
669 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
670 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
671 <copy todir="${outputDir}/lang">
672 <fileset dir="${resourceDir}/lang">
673 <include name="**.*" />
676 <jar destfile="in.jar" index="true">
678 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
679 <attribute name="Application-Name" value="JalviewLite" />
680 <attribute name="Codebase" value="${applet.codebase}" />
682 <fileset dir="${outputDir}">
683 <include name="com/**" />
684 <include name="MCview/**" />
685 <include name="jalview/**" />
686 <include name=".build_properties" />
687 <include name="images/link.gif" />
688 <include name="lang/**" />
692 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
694 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
695 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
696 <delete file="in.jar" />
698 <target name="-obfuscatereally" unless="donotobfuscate">
700 <path id="obfuscateDeps.path">
701 <pathelement location="${applet.jre.tools}" />
702 <pathelement location="appletlib/${jmolJar}" />
703 <pathelement location="lib/${varnaJar}" />
704 <pathelement location="appletlib/${jsoup}" />
705 <pathelement location="appletlib/${jsonSimple}" />
706 <pathelement location="appletlib/${javaJson}" />
707 <fileset dir="${java.home}/lib">
708 <include name="plugin.jar" />
711 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
713 <proguard verbose="true" >
714 <injar file="in.jar" />
715 <outjar file="${jalviewLiteJar}" />
716 <libraryjar refid="obfuscateDeps.path" />
718 <keep access="public" type="class" name="jalview.bin.JalviewLite">
719 <field access="public" />
720 <method access="public" />
721 <constructor access="public" />
723 <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
724 <field access="public" />
725 <method access="public" />
726 <constructor access="public" />
729 <keep name="jalview.json.binding**">
734 <keep access="public" type="class" name="MCview.PDBfile">
735 <field access="public" />
736 <method access="public" />
737 <constructor access="public" />
740 <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
741 <field access="public" />
742 <method access="public" />
743 <constructor access="public" />
746 <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
747 <field access="public" />
748 <method access="public" />
749 <constructor access="public" />
753 <!-- -libraryjars "${obfuscateDeps}"
755 -outjars jalviewApplet.jar
756 -keep public class jalview.bin.JalviewLite
759 <delete file="in.jar" />
762 <target name="jaxb-bindings" depends="init" description="Generates JAXB bindings for supported Jalview XML models (needs xjc on the path)">
764 <fileset dir="${sourceDir}/jalview/xml/binding/jalview">
765 <include name="*.java" />
768 <exec executable="xjc">
769 <arg value="${schemaDir}/jalview.xsd"/>
771 <arg value="${sourceDir}"/>
773 <arg value="jalview.xml.binding.jalview"/>
776 <fileset dir="${sourceDir}/jalview/xml/binding/embl">
777 <include name="*.java" />
781 <exec executable="xjc">
782 <arg value="${schemaDir}/embl.xsd"/>
784 <arg value="${sourceDir}"/>
786 <arg value="${schemaDir}/embl_bindings.xml"/>
788 <arg value="jalview.xml.binding.embl"/>
792 <fileset dir="${sourceDir}/jalview/xml/binding/uniprot">
793 <include name="*.java" />
797 <exec executable="xjc">
798 <arg value="${schemaDir}/uniprot.xsd"/>
800 <arg value="${sourceDir}"/>
802 <arg value="jalview.xml.binding.uniprot"/>
806 <target name="sourcedist" description="create jalview source distribution" depends="init">
807 <delete file="${source.dist.name}" />
808 <!-- temporary copy of source to update timestamps -->
809 <copy todir="_sourcedist">
811 <exclude name=".*" />
812 <exclude name="**/.*" />
813 <exclude name="*.class" />
814 <exclude name="**/*.class" />
815 <include name="LICENSE" />
816 <include name="README" />
817 <include name="build.xml" />
818 <include name="jalview-jalopy.xml" />
819 <include name="JalviewApplet.jpx" />
820 <include name="JalviewX.jpx" />
821 <include name="nbbuild.xml" />
822 <include name="nbproject/genfiles.properties" />
823 <include name="nbproject/project.properties" />
824 <include name="nbproject/project.xml" />
825 <include name="${sourceDir}/*.java" />
826 <include name="${sourceDir}/**/*.java" />
827 <include name="${sourceDir}/**/*.cdr" />
828 <include name="${libDir}/**/*" />
829 <include name="${resourceDir}/**/*" />
830 <include name="${helpDir}/**/*" />
831 <include name="appletlib/${jmolJar}" />
832 <include name="appletlib/${jsonSimple}" />
833 <include name="appletlib/${javaJson}" />
834 <exclude name="**/*locales" />
835 <exclude name="*locales/**" />
836 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
837 <exclude name="utils/InstallAnywhere/**Build*/**" />
838 <exclude name="utils/InstallAnywhere/**Build*/**" />
839 <exclude name="utils/InstallAnywhere/.build*.*/**" />
840 <exclude name="utils/InstallAnywhere/**locale*" />
841 <exclude name="utils/InstallAnywhere/**locale*/**" />
842 <exclude name="utils/InstallAnywhere/**locale*/**" />
843 <include name="${schemaDir}/**/*" />
844 <include name="utils/**/*" />
845 <include name="${docDir}/**/*" />
846 <include name="examples/**/*" />
850 <tstamp prefix="build">
851 <format property="year" pattern="yyyy" />
853 <!-- each replacetoken CDATA body must be on one line -
854 otherwise the pattern doesn't match -->
855 <replace value="${JALVIEW_VERSION}">
856 <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
857 <fileset dir="_sourcedist">
858 <include name="**/*" />
861 <replace dir="_sourcedist" value="${build.year}">
862 <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
863 <fileset dir="_sourcedist">
864 <include name="**/*" />
868 <tar destfile="${source.dist.name}" compression="gzip">
869 <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
873 <delete dir="_sourcedist" />
875 <target name="prepubapplet_1" depends="makeApplet">
876 <copy todir="${packageDir}/examples">
877 <fileset dir="examples">
878 <include name="**/*" />
879 <include name="javascript/*" />
880 <include name="jmol/*" />
883 <include name="${jalviewLiteJar}" />
885 <fileset dir="appletlib">
886 <include name="**/*" />
889 <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
890 <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
891 <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
892 <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
894 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
895 <!-- <attribute name="Permissions" value="sandbox" /> -->
896 <!--<attribute name="Trusted-Lib" value="true" /> -->
897 <attribute name="Codebase" value="${applet.codebase}" />
898 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
902 <presetdef name="ap_applet.jar">
903 <!-- build a signed applet with 'all-permissions' -
904 Needs 'param name="permissions' value="all-permissions"' in applet tag
905 JalviewLite+JmolApplet linked sequence/structure fails
906 Mixed code warnings are raised
908 <jar update="true" index="true">
910 <attribute name="Application-Name" value="JalviewLite" />
911 <attribute name="Permissions" value="all-permissions" />
912 <attribute name="Codebase" value="${applet.codebase}" />
913 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
914 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
918 <presetdef name="applet.jar">
919 <!-- build signed applet with sandbox permissions -
920 Needs 'param name="permissions' value="sandbox"' in applet tag
921 Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
924 <jar update="true" index="true">
926 <attribute name="Application-Name" value="JalviewLite" />
927 <attribute name="Permissions" value="sandbox" />
928 <attribute name="Codebase" value="${applet.codebase}" />
929 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
930 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
934 <presetdef name="tl_applet.jar">
935 <!-- build signed applet with trusted library/trusted permissions -
936 Needs 'param name="permissions' value="all-permissions"' in applet tag
938 No mixed code warnings raised
939 Jmol/JalviewLite sequence/structure example doesn't link structures
940 Raises dialog asking user to allow page to control applet via LiveConnect javascript
944 <jar update="true" index="true">
946 <attribute name="Application-Name" value="JalviewLite" />
947 <attribute name="Permissions" value="all-permissions" />
948 <attribute name="Codebase" value="${applet.codebase}" />
949 <attribute name="Trusted-Only" value="true" />
950 <attribute name="Trusted-Library" value="true" />
954 <presetdef name="to_applet.jar">
955 <!-- not fully test variant (yet) -->
956 <jar update="true" index="true">
958 <attribute name="Application-Name" value="JalviewLite" />
959 <attribute name="Permissions" value="all-permissions" />
960 <attribute name="Codebase" value="${applet.codebase}" />
961 <attribute name="Trusted-Only" value="true" />
965 <!-- create differently privileged artefacts -->
966 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
967 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
968 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
969 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
970 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
971 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
972 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
973 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
974 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
975 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
976 <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
977 <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
978 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
979 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
980 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
981 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
982 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
983 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
984 <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
985 <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
986 <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
987 <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
988 <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
989 <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
990 <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
991 <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
992 <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
993 <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
994 <!-- finally, create manifest for original jars -->
995 <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
996 <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
997 <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
998 <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
1000 <!-- todo - write examples/downloads for alternate versions of the applet
1001 probably don't need to do this now since we don't have alternate versions anymore !-->
1003 <target name="-signapplet" depends="prepubapplet_1">
1004 <fileset id="signappletjarset" dir="${packageDir}/examples">
1005 <exclude name="u_*.jar" />
1006 <include name="${jalviewLiteJar}" />
1007 <include name="${jmolJar}" />
1008 <include name="${javaJson}" />
1009 <include name="${jsonSimple}" />
1010 <include name="to_${jalviewLiteJar}" />
1011 <include name="to_${jmolJar}" />
1012 <include name="to_${javaJson}" />
1013 <include name="to_${jsonSimple}" />
1014 <include name="tl_${jalviewLiteJar}" />
1015 <include name="tl_${jmolJar}" />
1016 <include name="tl_${javaJson}" />
1017 <include name="tl_${jsonSimple}" />
1018 <include name="ap_${jalviewLiteJar}" />
1019 <include name="ap_${jmolJar}" />
1020 <include name="ap_${javaJson}" />
1021 <include name="ap_${jsonSimple}" />
1024 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
1025 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
1026 <fileset refid="signappletjarset" />
1030 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
1031 <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}">
1032 <fileset refid="signappletjarset" />
1036 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
1037 <target name="pubapplet" description="Dummy target to keep legacy Jalview build system happy. We don't actually publish the applet anymore."/>
1039 <target name="_pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
1041 <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
1042 <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
1043 <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
1044 <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
1045 <!-- finally, replace any launchApp servlet tags with a version specification -->
1046 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
1048 <![CDATA[http://www.jalview.org/services/launchApp"]]>
1050 <fileset dir="${packageDir}/examples">
1051 <include name="**/*.html" />
1054 <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
1056 <![CDATA[http://www.jalview.org/services/launchApp']]>
1058 <fileset dir="${packageDir}/examples">
1059 <include name="**/*.html" />
1064 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
1065 <javadoc destdir="${javadocDir}">
1066 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
1070 <target name="linkcheck" depends="init,prepare">
1071 <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
1072 <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
1073 <arg file="${helpDir}"/>
1074 <arg value="-nointernet"/>