build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   4  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   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.
  11  *
  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.
  16  *
  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.
  19 -->
  20 <project name="jalviewX" default="usage" basedir="."
  21  xmlns:if="ant:if"
  22     xmlns:unless="ant:unless">
  23   <taskdef classpath="${clover.jar}" resource="cloverlib.xml" if:set="clover.jar"/>
  24   <clover-env if:set="clover.jar"/>
  25
  26   <target name="help" depends="usage" />
  27   <target name="usage" depends="init">
  28     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  29     <echo message="Targets include:" />
  30     <echo message="usage - default target, displays this message" />
  31     <echo message="buildindices - generates JavaHelpSearch from the help files" />
  32     <echo message="build - compiles all necessary files for Application" />
  33     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  34     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  35     <echo message="              this needs a keystore and key."/>
  36     <echo message="              Add -Dtimestamp to timestamp signed jars"/>
  37     <echo message="              -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
  38     <echo message="              See docs/building.html for more information." />
  39     <echo message="compileApplet - compiles all necessary files for Applet" />
  40     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  41     <echo message="testng - run jalview's tests via testNG. Default group is '${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   </target>
  48
  49
  50   <!-- utils is a class path to additional utilities needed for
  51     building docs, jars and webstart stuff -->
  52   <!--
  53         Userdefined build property defaults
  54
  55         wsdl.server list (plus namespace mapping info ???)  - also want
  56                 ... to make this a dynamically generatable property
  57         WebStart Location
  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).
  62
  63 -->
  64
  65   <target name="init">
  66     <path id="axis.classpath">
  67       <!-->
  68       <fileset dir="/usr/local/axis/lib">
  69         <include name="**/*.jar" />
  70       </fileset>
  71       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  72         <include name="**/*.jar"/>
  73         <include name="*.jar"/>
  74       </fileset> -->
  75       </path>
  76
  77     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  78     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  79
  80     <property name="INSTALLATION" value="Source" />
  81
  82     <!-- 2.4 (VAMSAS)" -->
  83     <!-- Include debugging information in javac true or false -->
  84     <property name="javac.debug" value="true" />
  85
  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" />
  90     <!-- Key Name -->
  91     <property name="jalview.key" value="jalview" />
  92     <!-- Key Password -->
  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"/>
 102
 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="${ant.java.version}" arg2="9"/>
 108     </condition>
 109     <!-- Java 10 JVM args -->
 110     <condition property="java10">
 111       <equals arg1="${ant.java.version}" arg2="10"/>
 112     </condition>
 113     <!-- Java 11 JVM args -->
 114     <condition property="java11">
 115       <equals arg1="${ant.java.version}" arg2="11"/>
 116     </condition>
 117     <echo message="ant.java.version is ${ant.java.version}"/>
 118
 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 ${javac.target}"/>
 134
 135     <!-- Permissions for running Java applets and applications. -->
 136     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 137     <property name="application.codebase" value="*.jalview.org" />
 138     <!-- and allowing the applet to be deployed from any URL -->
 139     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
 140     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
 141     <property name="applet.caller-codebase" value="${applet.codebase}" />
 142
 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"/> -->
 169
 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" />
 183       </fileset>
 184       <fileset dir="${j11libDir}">
 185         <include name="*.jar" />
 186         <include name="**/*.jar" />
 187       </fileset>
 188       <fileset dir="${libDir}">
 189         <include name="*.jar" />
 190         <include name="**/*.jar" />
 191       </fileset>
 192       <fileset dir="${java.home}/lib">
 193         <include name="plugin.jar" />
 194       </fileset>
 195       <fileset dir="appletlib">
 196         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 197                                 -->
 198         <include name="${jmolJar}" />
 199         <include name="${varnaJar}" />
 200       </fileset>
 201     </path>
 202     <path id="test.classpath">
 203       <pathelement path="${outputDir}" />
 204       <path refid="build.classpath" />
 205     </path>
 206     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 207     <!-- The Location of the java 1.1.8 jdk -->
 208     <property name="java118.home" value="${java.home}" />
 209     <!-- jre for 1.4 version -->
 210     <property name="applet.jre.tools" value="${java118.home}/lib/rt.jar" />
 211
 212     <!-- the classpath for building the 1.1 applet -->
 213     <path id="jalviewlite.deps">
 214       <fileset dir="${java118.home}">
 215         <include name="lib/rt.jar" />
 216       </fileset>
 217       <fileset dir="${java.home}/lib">
 218         <include name="plugin.jar" />
 219       </fileset>
 220       <pathelement location="appletlib/${jmolJar}" />
 221       <pathelement location="lib/${varnaJar}" />
 222       <pathelement location="appletlib/${jsoup}" />
 223       <pathelement location="appletlib/${jsonSimple}" />
 224       <pathelement location="appletlib/${javaJson}" />
 225
 226     </path>
 227     <!-- default location for outputting javadoc -->
 228     <property name="javadocDir" value="${packageDir}/javadoc" />
 229   </target>
 230
 231
 232   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 233   <target name="buildPropertiesFile" depends="init">
 234     <tstamp prefix="build">
 235       <format property="date" pattern="dd MMMM yyyy" />
 236     </tstamp>
 237     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 238       <arg value="rev-parse" />
 239       <arg value="--short" />
 240       <arg value="HEAD" />
 241     </exec>
 242     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 243       <arg value="rev-parse" />
 244       <arg value="--abbrev-ref" />
 245       <arg value="HEAD" />
 246     </exec>
 247     <properties file="${outputDir}/.build_properties">
 248       <header>
 249           ---Jalview Build Details---
 250         </header>
 251       <property name="VERSION" value="${JALVIEW_VERSION}" />
 252       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
 253       <property name="BUILD_DATE" value="${build.date}" />
 254     </properties>
 255   </target>
 256
 257
 258   <target name="clean" depends="init">
 259     <!-- not efficient yet. -->
 260     <delete dir="${outputDir}" includes="*,**/*" />
 261   </target>
 262
 263   <target name="distclean" depends="init, clean">
 264
 265     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 266     <delete>
 267       <fileset dir=".">
 268         <include name="${outputJar}" />
 269         <include name="#*#" />
 270         <include name="#*.*#" />
 271         <include name="**/#*#" />
 272         <include name="**/#*.*#" />
 273         <include name="*~" />
 274         <include name="*.*~" />
 275         <include name="**/*~" />
 276         <include name="**/*.*~" />
 277       </fileset>
 278     </delete>
 279   </target>
 280
 281   <target name="prepare" depends="init">
 282     <mkdir dir="${outputDir}" />
 283     <copy todir="${outputDir}">
 284       <fileset dir=".">
 285         <include name="${docDir}/**/*.*" />
 286         <include name="${helpDir}/**/*.*" />
 287         <include name="${libDir}/*.jar" />
 288       </fileset>
 289       <fileset dir="${resourceDir}">
 290         <include name="**/*.*" />
 291       </fileset>
 292     </copy>
 293   </target>
 294
 295   <target name="build" depends="prepare">
 296     <!-- not efficient yet. -->
 297     <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 298       <exclude name="jalview/*applet*" />
 299       <exclude name="jalview/appletgui/**" />
 300       <exclude name="com/stevesoft/**" />
 301     </javac>
 302   </target>
 303
 304
 305   <target name="testclean" depends="init">
 306     <delete dir="${testOutputDir}" includes="*,**/*" />
 307   </target>
 308
 309   <target name="prepareTests" depends="init,testclean">
 310     <mkdir dir="${testOutputDir}" />
 311   </target>
 312
 313   <target name="buildTests" depends="build,buildindices,prepareTests">
 314     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 315     </javac>
 316   </target>
 317
 318   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 319
 320   <target name="testng" depends="buildTests">
 321     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 322       verbose="2">
 323       <classpath>
 324         <pathelement location="${testOutputDir}" />
 325         <pathelement location="${clover.jar}" if:set="clover.jar"/>
 326         <path refid="test.classpath" />
 327       </classpath>
 328       <jvmarg value="--module-path=${j11libDir}" if:set="java11"/>
 329       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
 330       <jvmarg value="--illegal-access=warn" if:set="java9"/>
 331       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 332     </testng>
 333   </target>
 334
 335   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 336     <replace value="${JALVIEW_VERSION}">
 337       <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 338       <fileset dir="${outputDir}/${helpDir}">
 339         <include name="help.jhm" />
 340       </fileset>
 341     </replace>
 342
 343     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 344       <arg line="html" />
 345     </java>
 346   </target>
 347
 348   <target name="preparejnlp" depends="makedist">
 349     <copy todir="${packageDir}">
 350       <fileset dir="${resourceDir}/images">
 351         <include name="${WebStartImage}" />
 352       </fileset>
 353     </copy>
 354
 355     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 356
 357     <!-- create a dummy jar which will eventually contain the jnlp template -->
 358     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 359       <fileset dir="${packageDir}">
 360         <include name="jalview.jar" />
 361       </fileset>
 362     </jar>
 363
 364     <mkdir dir="${packageDir}/JNLP-INF" />
 365     <antcall target="writejnlpf">
 366       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 367       <param name="inih" value="*" />
 368       <param name="maxh" value="*" />
 369     </antcall>
 370
 371     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 372       <fileset dir="${packageDir}">
 373         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 374       </fileset>
 375     </jar>
 376
 377     <antcall target="writejnlpf">
 378       <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
 379       <param name="inih" value="10M" />
 380       <param name="maxh" value="256M" />
 381     </antcall>
 382     <antcall target="writejnlpf">
 383       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 384       <param name="inih" value="800M" />
 385       <param name="maxh" value="1024M" />
 386     </antcall>
 387
 388     <antcall target="writejnlpf">
 389       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 390       <param name="inih" value="128M" />
 391       <param name="maxh" value="512M" />
 392     </antcall>
 393
 394     <antcall target="writejnlpf">
 395       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 396       <param name="inih" value="800M" />
 397       <param name="maxh" value="1024M" />
 398     </antcall>
 399
 400     <!-- finally, need to postprocess to add in associations at end of 'information' element
 401
 402                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 403
 404                 </xslt>
 405
 406
 407                         -->
 408     <!--
 409                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 410         <association mime-type="application-x/ext-file" extensions="fasta"/>
 411         <association mime-type="application-x/ext-file" extensions="mfa"/>
 412         <association mime-type="application-x/ext-file" extensions="fastq"/>
 413         <association mime-type="application-x/ext-file" extensions="blc"/>
 414         <association mime-type="application-x/ext-file" extensions="msf"/>
 415         <association mime-type="application-x/ext-file" extensions="pfam"/>
 416         <association mime-type="application-x/ext-file" extensions="aln"/>
 417         <association mime-type="application-x/ext-file" extensions="pir"/>
 418         <association mime-type="application-x/ext-file" extensions="amsa"/>
 419         <association mime-type="application-x/ext-file" extensions="stk"/>
 420         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 421   </target>
 422
 423   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
 424     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
 425       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 426       <fileset dir="${packageDir}">
 427         <include name="*.jar" />
 428       </fileset>
 429     </signjar>
 430   </target>
 431   <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
 432     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
 433       <fileset dir="${packageDir}">
 434         <include name="*.jar" />
 435       </fileset>
 436     </signjar>
 437   </target>
 438
 439   <target name="makefulldist" depends="makedist,preparejnlp,-jarsignwithtsa,-jarsignnotsa">
 440     <!-- and sign the jars -->
 441     <!-- the default keystore details might need to be edited here -->
 442   </target>
 443
 444   <target name="runenv" depends="init">
 445     <path id="run.classpath">
 446       <pathelement location="${outputDir}" />
 447       <fileset dir="${outputDir}">
 448         <include name="${libDir}/*.jar" />
 449       </fileset>
 450     </path>
 451     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 452
 453     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 454       </echo>
 455   </target>
 456
 457   <target name="-generatejnlpf">
 458     <presetdef name="jnlpf">
 459       <jnlp codebase="${WebStartLocation}">
 460         <information>
 461           <title>Jalview</title>
 462           <vendor>The Barton Group</vendor>
 463           <homepage href="http://www.jalview.org" />
 464           <description>Jalview Multiple Alignment Editor</description>
 465           <description kind="short">Jalview</description>
 466           <icon href="${WebStartImage}" />
 467           <offline_allowed />
 468         </information>
 469         <resources>
 470           <j2se version="1.8+" />
 471           <jar main="true" href="jalview.jar"/>
 472           <fileset dir="${packageDir}">
 473             <exclude name="jalview.jar" />
 474             <include name="*.jar" />
 475             <include name="*_*.jar" />
 476             <exclude name="*quaqua*.jar" />
 477           </fileset>
 478           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 479         </resources>
 480         <resources os="Mac OS X">
 481           <fileset dir="${packageDir}">
 482                  <include name="quaqua-filechooser-only-8.0.jar"/>
 483             <include name="*quaqua64*.jnilib.jar" />
 484           </fileset>
 485         </resources>
 486
 487         <application_desc main_class="jalview.bin.Jalview">
 488         </application_desc>
 489         <security>
 490           <all_permissions />
 491         </security>
 492       </jnlp>
 493     </presetdef>
 494
 495     <jnlpf toFile="${jnlpFile}" />
 496     <!-- add the add-modules j2se attribute for java 9 -->
 497     <replace file="${jnlpFile}" value="j2se version=&quot;1.8+&quot; initial-heap-size=&quot;${inih}&quot; max-heap-size=&quot;${maxh}&quot; java-vm-args=&quot;--add-modules=java.se.ee --illegal-access=warn&quot;">
 498           <replacetoken>j2se version="1.8+"</replacetoken>
 499     </replace>
 500   </target>
 501
 502   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 503     <echo message="Not adding JNLP File Associations" />
 504   </target>
 505
 506   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 507     <replace file="${jnlpFile}">
 508       <replacetoken>
 509         <![CDATA[</information>]]></replacetoken>
 510       <replacevalue>
 511         <![CDATA[
 512           <association mime-type="application-x/ext-file" extensions="fa" />
 513         <association mime-type="application-x/ext-file" extensions="fasta" />
 514         <association mime-type="application-x/ext-file" extensions="mfa" />
 515         <association mime-type="application-x/ext-file" extensions="fastq" />
 516         <association mime-type="application-x/ext-file" extensions="blc" />
 517         <association mime-type="application-x/ext-file" extensions="msf" />
 518         <association mime-type="application-x/ext-file" extensions="pfam" />
 519         <association mime-type="application-x/ext-file" extensions="aln"/>
 520         <association mime-type="application-x/ext-file" extensions="pir"/>
 521         <association mime-type="application-x/ext-file" extensions="amsa"/>
 522         <association mime-type="application-x/ext-file" extensions="stk"/>
 523         <association mime-type="application-x/ext-file" extensions="jvp"/>
 524       </information>]]></replacevalue>
 525   </replace>
 526   <echo message="Added file associations to JNLP file" />
 527 </target>
 528 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 529 </target>
 530
 531 <target name="buildextclients" depends="init">
 532   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 533   <condition property="dontextbuild">
 534     <equals arg1="n" arg2="${doextbuild.response}" />
 535   </condition>
 536   <condition property="dontextbuild">
 537     <equals arg1="N" arg2="${doextbuild.response}" />
 538   </condition>
 539   <fail if="dontextbuild">
 540         Build External Client Code process aborted by user. Jalview source is unchanged.
 541       </fail>
 542   <!-- Currently, this doesn't happen automatically.
 543      1. Run WSDL2Java as below, which generates an ext.vamsas +
 544      vamsas.<datapackages> fileset.
 545      2. refactor ext.vamsas.SpecificserviceWS* to
 546      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 547      3. Update the jalview.ws.*WServices classes to reflect the
 548      interface type, and all locations of this wsdl type that Jalview
 549      might be using.
 550
 551 -->
 552   <path id="axisbuild">
 553     <path refid="build.classpath" />
 554   </path>
 555   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 556   <move todir="./bak">
 557     <fileset dir="${sourceDir}" id="client">
 558       <include name="${wsdl.ClientNS}/*.*" />
 559     </fileset>
 560   </move>
 561
 562   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 563     <mappingSet>
 564       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 565       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 566     </mappingSet>
 567   </axis-wsdl2java>
 568 </target>
 569
 570 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
 571   <fail if="clover.jar">
 572     Ignoring request to build jalview distribution with clover-instrumented classes
 573   </fail>
 574   <!-- make the package jar if not already existing -->
 575   <mkdir dir="${packageDir}" />
 576   <!-- clean dir if it already existed -->
 577   <delete>
 578     <fileset dir="${packageDir}">
 579       <include name="*.jar" />
 580     </fileset>
 581   </delete>
 582   <jar destfile="${packageDir}/${outputJar}" index="true">
 583     <manifest>
 584       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 585       <attribute name="Permissions" value="all-permissions" />
 586       <attribute name="Application-Name" value="Jalview Desktop" />
 587       <attribute name="Codebase" value="${application.codebase}" />
 588     </manifest>
 589     <fileset dir="${outputDir}/">
 590       <exclude name="cache*/**" />
 591       <exclude name="*.jar" />
 592       <exclude name="*.jar.*" />
 593       <exclude name="**/*.jar" />
 594       <exclude name="**/*.jar.*" />
 595     </fileset>
 596   </jar>
 597
 598   <copy toDir="${packageDir}" flatten="true">
 599     <fileset dir="${outputDir}">
 600       <include name="*.jar" />
 601       <include name="**/*.jar" />
 602     </fileset>
 603   </copy>
 604 </target>
 605
 606
 607 <!-- jalopy code reformatter -->
 608 <target name="sourcescrub" depends="init,build">
 609   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 610     <fileset dir="${sourceDir}">
 611       <include name="*.java" />
 612       <include name="**/*.java" />
 613       <include name="**/**/*.java" />
 614     </fileset>
 615   </jalopy>
 616 </target>
 617
 618
 619
 620 <!-- Compile, package and obfuscate Jalview Applet -->
 621 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 622
 623 <target name="compileApplet" depends="init,clean">
 624   <mkdir dir="${outputDir}" />
 625   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 626 </target>
 627
 628 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 629   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 630   <copy todir="${outputDir}/lang">
 631     <fileset dir="${resourceDir}/lang">
 632       <include name="**.*" />
 633     </fileset>
 634   </copy>
 635   <jar destfile="in.jar" index="true">
 636     <manifest>
 637       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 638       <attribute name="Application-Name" value="JalviewLite" />
 639       <attribute name="Codebase" value="${applet.codebase}" />
 640     </manifest>
 641     <fileset dir="${outputDir}">
 642       <include name="com/**" />
 643       <include name="MCview/**" />
 644       <include name="jalview/**" />
 645       <include name=".build_properties" />
 646       <include name="images/link.gif" />
 647       <include name="lang/**" />
 648     </fileset>
 649   </jar>
 650 </target>
 651 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 652 </target>
 653 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 654   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 655   <delete file="in.jar" />
 656 </target>
 657 <target name="-obfuscatereally" unless="donotobfuscate">
 658
 659   <path id="obfuscateDeps.path">
 660     <pathelement location="${applet.jre.tools}" />
 661     <pathelement location="appletlib/${jmolJar}" />
 662     <pathelement location="lib/${varnaJar}" />
 663     <pathelement location="appletlib/${jsoup}" />
 664     <pathelement location="appletlib/${jsonSimple}" />
 665     <pathelement location="appletlib/${javaJson}" />
 666     <fileset dir="${java.home}/lib">
 667       <include name="plugin.jar" />
 668     </fileset>
 669   </path>
 670   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard_5.3.3.jar" />
 671
 672   <proguard verbose="true" >
 673     <injar file="in.jar" />
 674     <outjar file="${jalviewLiteJar}" />
 675     <libraryjar refid="obfuscateDeps.path" />
 676     <dontwarn />
 677     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 678       <field access="public" />
 679       <method access="public" />
 680       <constructor access="public" />
 681     </keep>
 682     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 683       <field access="public" />
 684       <method access="public" />
 685       <constructor access="public" />
 686     </keep>
 687
 688     <keep name="jalview.json.binding**">
 689       <constructor/>
 690       <method name="*"/>
 691     </keep>
 692
 693     <keep access="public" type="class" name="MCview.PDBfile">
 694       <field access="public" />
 695       <method access="public" />
 696       <constructor access="public" />
 697     </keep>
 698
 699     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 700       <field access="public" />
 701       <method access="public" />
 702       <constructor access="public" />
 703     </keep>
 704
 705     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 706       <field access="public" />
 707       <method access="public" />
 708       <constructor access="public" />
 709     </keep>
 710
 711
 712     <!--      -libraryjars "${obfuscateDeps}"
 713       -injars      in.jar
 714       -outjars     jalviewApplet.jar
 715       -keep public class jalview.bin.JalviewLite
 716        { public * ; } -->
 717   </proguard>
 718   <delete file="in.jar" />
 719 </target>
 720
 721 <target name="sourcedist" description="create jalview source distribution" depends="init">
 722   <delete file="${source.dist.name}" />
 723   <!-- temporary copy of source to update timestamps -->
 724   <copy todir="_sourcedist">
 725     <fileset dir=".">
 726       <exclude name=".*" />
 727       <exclude name="**/.*" />
 728       <exclude name="*.class" />
 729       <exclude name="**/*.class" />
 730       <include name="LICENSE" />
 731       <include name="README" />
 732       <include name="build.xml" />
 733       <include name="jalview-jalopy.xml" />
 734       <include name="JalviewApplet.jpx" />
 735       <include name="JalviewX.jpx" />
 736       <include name="nbbuild.xml" />
 737       <include name="nbproject/genfiles.properties" />
 738       <include name="nbproject/project.properties" />
 739       <include name="nbproject/project.xml" />
 740       <include name="${sourceDir}/*.java" />
 741       <include name="${sourceDir}/**/*.java" />
 742       <include name="${sourceDir}/**/*.cdr" />
 743       <include name="${libDir}/**/*" />
 744       <include name="${resourceDir}/**/*" />
 745       <include name="${helpDir}/**/*" />
 746       <include name="appletlib/${jmolJar}" />
 747       <include name="appletlib/${jsonSimple}" />
 748       <include name="appletlib/${javaJson}" />
 749       <exclude name="**/*locales" />
 750       <exclude name="*locales/**" />
 751       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 752       <exclude name="utils/InstallAnywhere/**Build*/**" />
 753       <exclude name="utils/InstallAnywhere/**Build*/**" />
 754       <exclude name="utils/InstallAnywhere/.build*.*/**" />
 755       <exclude name="utils/InstallAnywhere/**locale*" />
 756       <exclude name="utils/InstallAnywhere/**locale*/**" />
 757       <exclude name="utils/InstallAnywhere/**locale*/**" />
 758       <include name="${schemaDir}/**/*" />
 759       <include name="utils/**/*" />
 760       <include name="${docDir}/**/*" />
 761       <include name="examples/**/*" />
 762     </fileset>
 763   </copy>
 764
 765   <tstamp prefix="build">
 766     <format property="year" pattern="yyyy" />
 767   </tstamp>
 768   <!-- each replacetoken CDATA body must be on one line -
 769        otherwise the pattern doesn't match -->
 770   <replace value="${JALVIEW_VERSION}">
 771     <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 772     <fileset dir="_sourcedist">
 773       <include name="**/*" />
 774     </fileset>
 775   </replace>
 776   <replace dir="_sourcedist" value="${build.year}">
 777     <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
 778     <fileset dir="_sourcedist">
 779       <include name="**/*" />
 780     </fileset>
 781   </replace>
 782
 783   <tar destfile="${source.dist.name}" compression="gzip">
 784     <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
 785     </tarfileset>
 786   </tar>
 787
 788   <delete dir="_sourcedist" />
 789 </target>
 790 <target name="prepubapplet_1" depends="makeApplet">
 791   <copy todir="${packageDir}/examples">
 792     <fileset dir="examples">
 793       <include name="**/*" />
 794       <include name="javascript/*" />
 795       <include name="jmol/*" />
 796     </fileset>
 797     <fileset dir=".">
 798       <include name="${jalviewLiteJar}" />
 799     </fileset>
 800     <fileset dir="appletlib">
 801       <include name="**/*" />
 802     </fileset>
 803   </copy>
 804   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 805   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 806   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 807   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 808     <manifest>
 809       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 810       <!--          <attribute name="Permissions" value="sandbox" /> -->
 811       <!--<attribute name="Trusted-Lib" value="true" /> -->
 812       <attribute name="Codebase" value="${applet.codebase}" />
 813       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 814     </manifest>
 815   </jar>
 816
 817   <presetdef name="ap_applet.jar">
 818     <!-- build a signed applet with 'all-permissions' -
 819                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 820                           JalviewLite+JmolApplet linked sequence/structure fails
 821                           Mixed code warnings are raised
 822                           -->
 823     <jar update="true" index="true">
 824       <manifest>
 825         <attribute name="Application-Name" value="JalviewLite" />
 826         <attribute name="Permissions" value="all-permissions" />
 827         <attribute name="Codebase" value="${applet.codebase}" />
 828         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 829         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 830       </manifest>
 831     </jar>
 832   </presetdef>
 833   <presetdef name="applet.jar">
 834     <!-- build signed applet with sandbox permissions -
 835                           Needs 'param name="permissions' value="sandbox"' in applet tag
 836                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 837                         -->
 838
 839     <jar update="true" index="true">
 840       <manifest>
 841         <attribute name="Application-Name" value="JalviewLite" />
 842         <attribute name="Permissions" value="sandbox" />
 843         <attribute name="Codebase" value="${applet.codebase}" />
 844         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 845         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 846       </manifest>
 847     </jar>
 848   </presetdef>
 849   <presetdef name="tl_applet.jar">
 850     <!-- build signed applet with trusted library/trusted permissions -
 851                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 852                                j1.7_45:
 853                                No mixed code warnings raised
 854                                Jmol/JalviewLite sequence/structure example doesn't link structures
 855                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 856
 857                               -->
 858
 859     <jar update="true" index="true">
 860       <manifest>
 861         <attribute name="Application-Name" value="JalviewLite" />
 862         <attribute name="Permissions" value="all-permissions" />
 863         <attribute name="Codebase" value="${applet.codebase}" />
 864         <attribute name="Trusted-Only" value="true" />
 865         <attribute name="Trusted-Library" value="true" />
 866       </manifest>
 867     </jar>
 868   </presetdef>
 869   <presetdef name="to_applet.jar">
 870     <!-- not fully test variant (yet) -->
 871     <jar update="true" index="true">
 872       <manifest>
 873         <attribute name="Application-Name" value="JalviewLite" />
 874         <attribute name="Permissions" value="all-permissions" />
 875         <attribute name="Codebase" value="${applet.codebase}" />
 876         <attribute name="Trusted-Only" value="true" />
 877       </manifest>
 878     </jar>
 879   </presetdef>
 880   <!-- create differently privileged artefacts -->
 881   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 882   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 883   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 884   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 885   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 886   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 887   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 888   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 889   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 890   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 891   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 892   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 893   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 894   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 895   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 896   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 897   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 898   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 899   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 900   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 901   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 902   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 903   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 904   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 905   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 906   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 907   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 908   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 909   <!-- finally, create manifest for original jars -->
 910   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 911   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 912   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 913   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 914
 915   <!-- todo - write examples/downloads for alternate versions of the applet
 916     probably don't need to do this now since we don't have alternate versions anymore !-->
 917 </target>
 918 <target name="-signapplet" depends="prepubapplet_1">
 919   <fileset id="signappletjarset" dir="${packageDir}/examples">
 920     <exclude name="u_*.jar" />
 921     <include name="${jalviewLiteJar}" />
 922     <include name="${jmolJar}" />
 923     <include name="${javaJson}" />
 924     <include name="${jsonSimple}" />
 925     <include name="to_${jalviewLiteJar}" />
 926     <include name="to_${jmolJar}" />
 927     <include name="to_${javaJson}" />
 928     <include name="to_${jsonSimple}" />
 929     <include name="tl_${jalviewLiteJar}" />
 930     <include name="tl_${jmolJar}" />
 931     <include name="tl_${javaJson}" />
 932     <include name="tl_${jsonSimple}" />
 933     <include name="ap_${jalviewLiteJar}" />
 934     <include name="ap_${jmolJar}" />
 935     <include name="ap_${javaJson}" />
 936     <include name="ap_${jsonSimple}" />
 937   </fileset>
 938 </target>
 939 <target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
 940   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 941     <fileset refid="signappletjarset" />
 942   </signjar>
 943 </target>
 944
 945 <target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
 946   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
 947     <fileset refid="signappletjarset" />
 948   </signjar>
 949 </target>
 950
 951 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
 952
 953 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 954
 955   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 956   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 957   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 958   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 959   <!-- finally, replace any launchApp servlet tags with a version specification -->
 960   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 961     <replacetoken>
 962       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 963     </replacetoken>
 964     <fileset dir="${packageDir}/examples">
 965       <include name="**/*.html" />
 966     </fileset>
 967   </replace>
 968   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 969     <replacetoken>
 970       <![CDATA[http://www.jalview.org/services/launchApp']]>
 971     </replacetoken>
 972     <fileset dir="${packageDir}/examples">
 973       <include name="**/*.html" />
 974     </fileset>
 975   </replace>
 976
 977 </target>
 978 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 979   <javadoc destdir="${javadocDir}">
 980     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 981     </packageset>
 982   </javadoc>
 983 </target>
 984 <target name="linkcheck" depends="init,prepare">
 985   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
 986   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
 987     <arg file="${helpDir}"/>
 988     <arg value="-nointernet"/>
 989   </java>
 990 </target>
 991 </project>