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   <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" />
  41   </target>
  42
  43
  44   <!-- utils is a class path to additional utilities needed for
  45     building docs, jars and webstart stuff -->
  46   <!--
  47         Userdefined build property defaults
  48
  49         wsdl.server list (plus namespace mapping info ???)  - also want
  50                 ... to make this a dynamically generatable property
  51         WebStart Location
  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).
  56
  57 -->
  58
  59   <target name="init">
  60     <path id="axis.classpath">
  61       <!-->
  62       <fileset dir="/usr/local/axis/lib">
  63         <include name="**/*.jar" />
  64       </fileset>
  65       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  66         <include name="**/*.jar"/>
  67         <include name="*.jar"/>
  68       </fileset> -->
  69       </path>
  70
  71     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  72     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  73
  74     <property name="INSTALLATION" value="Source" />
  75
  76     <!-- 2.4 (VAMSAS)" -->
  77     <!-- Include debugging information in javac true or false -->
  78     <property name="javac.debug" value="true" />
  79
  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" />
  84     <!-- Key Name -->
  85     <property name="jalview.key" value="jalview" />
  86     <!-- Key Password -->
  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"/>
  96
  97     <!-- default TestNG groups to run -->
  98     <property name="testng-groups" value="Functional" />
  99
 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" />
 111
 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}" />
 119
 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"/> -->
 144
 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" />
 158       </fileset>
 159       <fileset dir="${libDir}">
 160         <include name="*.jar" />
 161         <include name="**/*.jar" />
 162       </fileset>
 163       <fileset dir="${java.home}/lib">
 164         <include name="plugin.jar" />
 165       </fileset>
 166       <fileset dir="appletlib">
 167         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 168                                 -->
 169         <include name="${jmolJar}" />
 170         <include name="${varnaJar}" />
 171       </fileset>
 172     </path>
 173     <path id="test.classpath">
 174       <pathelement path="${outputDir}" />
 175       <path refid="build.classpath" />
 176     </path>
 177     <property name="source.dist.name" value="${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" />
 182                 -->
 183     <!-- jre for 1.4 version -->
 184     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
 185
 186     <!-- the classpath for building the 1.1 applet -->
 187     <path id="jalviewlite.deps">
 188       <fileset dir="${java118.home}">
 189         <include name="lib/classes.zip" />
 190       </fileset>
 191       <fileset dir="${java.home}/lib">
 192         <include name="plugin.jar" />
 193       </fileset>
 194       <pathelement location="appletlib/${jmolJar}" />
 195       <pathelement location="lib/${varnaJar}" />
 196       <pathelement location="appletlib/${jsoup}" />
 197       <pathelement location="appletlib/${jsonSimple}" />
 198       <pathelement location="appletlib/${javaJson}" />
 199
 200     </path>
 201     <!-- default location for outputting javadoc -->
 202     <property name="javadocDir" value="${packageDir}/javadoc" />
 203   </target>
 204
 205
 206   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 207   <target name="buildPropertiesFile" depends="init">
 208     <tstamp prefix="build">
 209       <format property="date" pattern="dd MMMM yyyy" />
 210     </tstamp>
 211     <exec executable="/usr/bin/git" outputproperty="git.commit" failifexecutionfails="false">
 212       <arg value="rev-parse" />
 213       <arg value="--short" />
 214       <arg value="HEAD" />
 215     </exec>
 216     <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
 217       <arg value="rev-parse" />
 218       <arg value="--abbrev-ref" />
 219       <arg value="HEAD" />
 220     </exec>
 221     <properties file="${outputDir}/.build_properties">
 222       <header>
 223           ---Jalview Build Details---
 224         </header>
 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="${build.date}" />
 228     </properties>
 229   </target>
 230
 231
 232   <target name="clean" depends="init">
 233     <!-- not efficient yet. -->
 234     <delete dir="${outputDir}" includes="*,**/*" />
 235   </target>
 236
 237   <target name="distclean" depends="init, clean">
 238
 239     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 240     <delete>
 241       <fileset dir=".">
 242         <include name="${outputJar}" />
 243         <include name="#*#" />
 244         <include name="#*.*#" />
 245         <include name="**/#*#" />
 246         <include name="**/#*.*#" />
 247         <include name="*~" />
 248         <include name="*.*~" />
 249         <include name="**/*~" />
 250         <include name="**/*.*~" />
 251       </fileset>
 252     </delete>
 253   </target>
 254
 255   <target name="prepare" depends="init">
 256     <mkdir dir="${outputDir}" />
 257     <copy todir="${outputDir}">
 258       <fileset dir=".">
 259         <include name="${docDir}/**/*.*" />
 260         <include name="${helpDir}/**/*.*" />
 261         <include name="${libDir}/*.jar" />
 262       </fileset>
 263       <fileset dir="${resourceDir}">
 264         <include name="**/*.*" />
 265       </fileset>
 266     </copy>
 267   </target>
 268
 269   <target name="build" depends="prepare">
 270     <!-- not efficient yet. -->
 271     <javac source="${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/**" />
 275     </javac>
 276   </target>
 277
 278
 279   <target name="testclean" depends="init">
 280     <delete dir="${testOutputDir}" includes="*,**/*" />
 281   </target>
 282
 283   <target name="prepareTests" depends="init,testclean">
 284     <mkdir dir="${testOutputDir}" />
 285   </target>
 286
 287   <target name="buildTests" depends="build,buildindices,prepareTests">
 288     <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}" debug="${javac.debug}" classpathref="test.classpath" includeantruntime="false">
 289     </javac>
 290   </target>
 291
 292   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 293
 294   <target name="testng" depends="buildTests">
 295     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
 296       verbose="2">
 297       <classpath>
 298         <pathelement location="${testOutputDir}" />
 299         <path refid="test.classpath" />
 300       </classpath>
 301       <classfileset dir="${testOutputDir}" includes="**/*.class" />
 302     </testng>
 303   </target>
 304
 305   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 306     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 307       <arg line="html" />
 308     </java>
 309   </target>
 310
 311   <target name="preparejnlp" depends="makedist">
 312     <copy todir="${packageDir}">
 313       <fileset dir="${resourceDir}/images">
 314         <include name="${WebStartImage}" />
 315       </fileset>
 316     </copy>
 317
 318     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 319
 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" />
 324       </fileset>
 325     </jar>
 326
 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="*" />
 332     </antcall>
 333
 334     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 335       <fileset dir="${packageDir}">
 336         <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
 337       </fileset>
 338     </jar>
 339
 340     <antcall target="writejnlpf">
 341       <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
 342       <param name="inih" value="10M" />
 343       <param name="maxh" value="256M" />
 344     </antcall>
 345
 346     <antcall target="writejnlpf">
 347       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
 348       <param name="inih" value="128M" />
 349       <param name="maxh" value="512M" />
 350     </antcall>
 351
 352     <antcall target="writejnlpf">
 353       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
 354       <param name="inih" value="256M" />
 355       <param name="maxh" value="1024M" />
 356     </antcall>
 357
 358     <!-- finally, need to postprocess to add in associations at end of 'information' element
 359
 360                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 361
 362                 </xslt>
 363
 364
 365                         -->
 366     <!--
 367                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 368         <association mime-type="application-x/ext-file" extensions="fasta"/>
 369         <association mime-type="application-x/ext-file" extensions="mfa"/>
 370         <association mime-type="application-x/ext-file" extensions="fastq"/>
 371         <association mime-type="application-x/ext-file" extensions="blc"/>
 372         <association mime-type="application-x/ext-file" extensions="msf"/>
 373         <association mime-type="application-x/ext-file" extensions="pfam"/>
 374         <association mime-type="application-x/ext-file" extensions="aln"/>
 375         <association mime-type="application-x/ext-file" extensions="pir"/>
 376         <association mime-type="application-x/ext-file" extensions="amsa"/>
 377         <association mime-type="application-x/ext-file" extensions="stk"/>
 378         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 379   </target>
 380
 381   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
 382     <signjar storepass="${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="${packageDir}">
 385         <include name="*.jar" />
 386       </fileset>
 387     </signjar>
 388   </target>
 389   <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
 390     <signjar storepass="${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" />
 393       </fileset>
 394     </signjar>
 395   </target>
 396
 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 -->
 400   </target>
 401
 402   <target name="runenv" depends="init">
 403     <path id="run.classpath">
 404       <pathelement location="${outputDir}" />
 405       <fileset dir="${outputDir}">
 406         <include name="${libDir}/*.jar" />
 407       </fileset>
 408     </path>
 409     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 410
 411     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 412       </echo>
 413   </target>
 414
 415   <target name="-generatejnlpf">
 416     <presetdef name="jnlpf">
 417       <jnlp codebase="${WebStartLocation}">
 418         <information>
 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="${WebStartImage}" />
 425           <offline_allowed />
 426         </information>
 427         <resources>
 428           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 429           <jar main="true" href="jalview.jar"/>
 430           <fileset dir="${packageDir}">
 431             <exclude name="jalview.jar" />
 432             <include name="*.jar" />
 433             <include name="*_*.jar" />
 434             <exclude name="*jnilib.jar" />
 435           </fileset>
 436           <property name="jalview.version" value="${JALVIEW_VERSION}" />
 437         </resources>
 438         <resources os="Mac OS X">
 439           <fileset dir="${packageDir}">
 440             <include name="*quaqua*.jnilib.jar" />
 441           </fileset>
 442         </resources>
 443
 444         <application_desc main_class="jalview.bin.Jalview">
 445         </application_desc>
 446         <security>
 447           <all_permissions />
 448         </security>
 449       </jnlp>
 450     </presetdef>
 451
 452     <jnlpf toFile="${jnlpFile}" />
 453
 454   </target>
 455
 456   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
 457     <echo message="Not adding JNLP File Associations" />
 458   </target>
 459
 460   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
 461     <replace file="${jnlpFile}">
 462       <replacetoken>
 463         <![CDATA[</information>]]></replacetoken>
 464       <replacevalue>
 465         <![CDATA[
 466           <association mime-type="application-x/ext-file" extensions="fa" />
 467         <association mime-type="application-x/ext-file" extensions="fasta" />
 468         <association mime-type="application-x/ext-file" extensions="mfa" />
 469         <association mime-type="application-x/ext-file" extensions="fastq" />
 470         <association mime-type="application-x/ext-file" extensions="blc" />
 471         <association mime-type="application-x/ext-file" extensions="msf" />
 472         <association mime-type="application-x/ext-file" extensions="pfam" />
 473         <association mime-type="application-x/ext-file" extensions="aln"/>
 474         <association mime-type="application-x/ext-file" extensions="pir"/>
 475         <association mime-type="application-x/ext-file" extensions="amsa"/>
 476         <association mime-type="application-x/ext-file" extensions="stk"/>
 477         <association mime-type="application-x/ext-file" extensions="jvp"/>
 478       </information>]]></replacevalue>
 479   </replace>
 480   <echo message="Added file associations to JNLP file" />
 481 </target>
 482 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 483 </target>
 484
 485 <target name="buildextclients" depends="init">
 486   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 487   <condition property="dontextbuild">
 488     <equals arg1="n" arg2="${doextbuild.response}" />
 489   </condition>
 490   <condition property="dontextbuild">
 491     <equals arg1="N" arg2="${doextbuild.response}" />
 492   </condition>
 493   <fail if="dontextbuild">
 494         Build External Client Code process aborted by user. Jalview source is unchanged.
 495       </fail>
 496   <!-- Currently, this doesn't happen automatically.
 497      1. Run WSDL2Java as below, which generates an ext.vamsas +
 498      vamsas.<datapackages> fileset.
 499      2. refactor ext.vamsas.SpecificserviceWS* to
 500      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 501      3. Update the jalview.ws.*WServices classes to reflect the
 502      interface type, and all locations of this wsdl type that Jalview
 503      might be using.
 504
 505 -->
 506   <path id="axisbuild">
 507     <path refid="build.classpath" />
 508   </path>
 509   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 510   <move todir="./bak">
 511     <fileset dir="${sourceDir}" id="client">
 512       <include name="${wsdl.ClientNS}/*.*" />
 513     </fileset>
 514   </move>
 515
 516   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 517     <mappingSet>
 518       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 519       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 520     </mappingSet>
 521   </axis-wsdl2java>
 522 </target>
 523
 524 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
 525   <!-- make the package jar if not already existing -->
 526   <mkdir dir="${packageDir}" />
 527   <!-- clean dir if it already existed -->
 528   <delete>
 529     <fileset dir="${packageDir}">
 530       <include name="*.jar" />
 531     </fileset>
 532   </delete>
 533   <jar destfile="${packageDir}/${outputJar}" index="true">
 534     <manifest>
 535       <attribute name="Main-Class" value="jalview.bin.Jalview" />
 536       <attribute name="Permissions" value="all-permissions" />
 537       <attribute name="Application-Name" value="Jalview Desktop" />
 538       <attribute name="Codebase" value="${application.codebase}" />
 539     </manifest>
 540     <fileset dir="${outputDir}/">
 541       <exclude name="cache*/**" />
 542       <exclude name="*.jar" />
 543       <exclude name="*.jar.*" />
 544       <exclude name="**/*.jar" />
 545       <exclude name="**/*.jar.*" />
 546     </fileset>
 547   </jar>
 548
 549   <copy toDir="${packageDir}" flatten="true">
 550     <fileset dir="${outputDir}">
 551       <include name="*.jar" />
 552       <include name="**/*.jar" />
 553     </fileset>
 554   </copy>
 555 </target>
 556
 557
 558 <!-- jalopy code reformatter -->
 559 <target name="sourcescrub" depends="init,build">
 560   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 561     <fileset dir="${sourceDir}">
 562       <include name="*.java" />
 563       <include name="**/*.java" />
 564       <include name="**/**/*.java" />
 565     </fileset>
 566   </jalopy>
 567 </target>
 568
 569
 570
 571 <!-- Compile, package and obfuscate Jalview Applet -->
 572 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
 573
 574 <target name="compileApplet" depends="init,clean">
 575   <mkdir dir="${outputDir}" />
 576   <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 577 </target>
 578
 579 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 580   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 581   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 582   <copy todir="${outputDir}/lang">
 583     <fileset dir="${resourceDir}/lang">
 584       <include name="**.*" />
 585     </fileset>
 586   </copy>
 587   <jar destfile="in.jar" index="true">
 588     <manifest>
 589       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 590       <attribute name="Application-Name" value="JalviewLite" />
 591       <attribute name="Codebase" value="${applet.codebase}" />
 592     </manifest>
 593     <fileset dir="${outputDir}">
 594       <include name="com/**" />
 595       <include name="MCview/**" />
 596       <include name="jalview/**" />
 597       <include name=".build_properties" />
 598       <include name="images/idwidth.gif" />
 599       <include name="images/link.gif" />
 600       <include name="lang/**" />
 601     </fileset>
 602   </jar>
 603 </target>
 604 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 605 </target>
 606 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 607   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 608   <delete file="in.jar" />
 609 </target>
 610 <target name="-obfuscatereally" unless="donotobfuscate">
 611
 612   <path id="obfuscateDeps.path">
 613     <pathelement location="${applet.jre.tools}" />
 614     <pathelement location="appletlib/${jmolJar}" />
 615     <pathelement location="lib/${varnaJar}" />
 616     <pathelement location="appletlib/${jsoup}" />
 617     <pathelement location="appletlib/${jsonSimple}" />
 618     <pathelement location="appletlib/${javaJson}" />
 619     <fileset dir="${java.home}/lib">
 620       <include name="plugin.jar" />
 621     </fileset>
 622   </path>
 623   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 624
 625   <proguard verbose="true" >
 626     <injar file="in.jar" />
 627     <outjar file="${jalviewLiteJar}" />
 628     <libraryjar refid="obfuscateDeps.path" />
 629     <dontwarn />
 630     <keep access="public" type="class" name="jalview.bin.JalviewLite">
 631       <field access="public" />
 632       <method access="public" />
 633       <constructor access="public" />
 634     </keep>
 635     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 636       <field access="public" />
 637       <method access="public" />
 638       <constructor access="public" />
 639     </keep>
 640
 641     <keep name="jalview.json.binding**">
 642       <constructor/>
 643       <method name="*"/>
 644     </keep>
 645
 646     <keep access="public" type="class" name="MCview.PDBfile">
 647       <field access="public" />
 648       <method access="public" />
 649       <constructor access="public" />
 650     </keep>
 651
 652     <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
 653       <field access="public" />
 654       <method access="public" />
 655       <constructor access="public" />
 656     </keep>
 657
 658     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
 659       <field access="public" />
 660       <method access="public" />
 661       <constructor access="public" />
 662     </keep>
 663
 664
 665     <!--      -libraryjars "${obfuscateDeps}"
 666       -injars      in.jar
 667       -outjars     jalviewApplet.jar
 668       -keep public class jalview.bin.JalviewLite
 669        { public * ; } -->
 670   </proguard>
 671   <delete file="in.jar" />
 672 </target>
 673
 674 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 675   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 676   <delete>
 677     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 678       <include name="*.java" />
 679       <include name="descriptors/*.java" />
 680     </fileset>
 681   </delete>
 682   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 683   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 684   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 685   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 686   <!--
 687                 now build the jalview.binding package with the old schema set
 688                 -->
 689   <delete>
 690     <fileset dir="${sourceDir}/jalview/binding/">
 691       <include name="**" />
 692     </fileset>
 693   </delete>
 694   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 695   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 696   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 697 </target>
 698 <target name="sourcedist" description="create jalview source distribution" depends="init">
 699   <delete file="${source.dist.name}" />
 700   <!-- temporary copy of source to update timestamps -->
 701   <copy todir="_sourcedist">
 702     <fileset dir=".">
 703       <exclude name=".*" />
 704       <exclude name="**/.*" />
 705       <exclude name="*.class" />
 706       <exclude name="**/*.class" />
 707       <include name="LICENSE" />
 708       <include name="README" />
 709       <include name="build.xml" />
 710       <include name="jalview-jalopy.xml" />
 711       <include name="JalviewApplet.jpx" />
 712       <include name="JalviewX.jpx" />
 713       <include name="nbbuild.xml" />
 714       <include name="nbproject/genfiles.properties" />
 715       <include name="nbproject/project.properties" />
 716       <include name="nbproject/project.xml" />
 717       <include name="${sourceDir}/*.java" />
 718       <include name="${sourceDir}/**/*.java" />
 719       <include name="${sourceDir}/**/*.cdr" />
 720       <include name="${libDir}/**/*" />
 721       <include name="${resourceDir}/**/*" />
 722       <include name="${helpDir}/**/*" />
 723       <include name="appletlib/${jmolJar}" />
 724       <include name="appletlib/${jsonSimple}" />
 725       <include name="appletlib/${javaJson}" />
 726       <exclude name="**/*locales" />
 727       <exclude name="*locales/**" />
 728       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 729       <exclude name="utils/InstallAnywhere/**Build*/**" />
 730       <exclude name="utils/InstallAnywhere/**Build*/**" />
 731       <exclude name="utils/InstallAnywhere/.build*.*/**" />
 732       <exclude name="utils/InstallAnywhere/**locale*" />
 733       <exclude name="utils/InstallAnywhere/**locale*/**" />
 734       <exclude name="utils/InstallAnywhere/**locale*/**" />
 735       <include name="${schemaDir}/**/*" />
 736       <include name="utils/**/*" />
 737       <include name="${docDir}/**/*" />
 738       <include name="examples/**/*" />
 739     </fileset>
 740   </copy>
 741
 742   <tstamp prefix="build">
 743     <format property="year" pattern="yyyy" />
 744   </tstamp>
 745   <!-- each replacetoken CDATA body must be on one line -
 746        otherwise the pattern doesn't match -->
 747   <replace value="${JALVIEW_VERSION}">
 748     <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
 749     <fileset dir="_sourcedist">
 750       <include name="**/*" />
 751     </fileset>
 752   </replace>
 753   <replace dir="_sourcedist" value="${build.year}">
 754     <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
 755     <fileset dir="_sourcedist">
 756       <include name="**/*" />
 757     </fileset>
 758   </replace>
 759
 760   <tar destfile="${source.dist.name}" compression="gzip">
 761     <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
 762     </tarfileset>
 763   </tar>
 764
 765   <delete dir="_sourcedist" />
 766 </target>
 767 <target name="prepubapplet_1" depends="makeApplet">
 768   <copy todir="${packageDir}/examples">
 769     <fileset dir="examples">
 770       <include name="**/*" />
 771       <include name="javascript/*" />
 772       <include name="jmol/*" />
 773     </fileset>
 774     <fileset dir=".">
 775       <include name="${jalviewLiteJar}" />
 776     </fileset>
 777     <fileset dir="appletlib">
 778       <include name="**/*" />
 779     </fileset>
 780   </copy>
 781   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 782   <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
 783   <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
 784   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 785     <manifest>
 786       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
 787       <!--          <attribute name="Permissions" value="sandbox" /> -->
 788       <!--<attribute name="Trusted-Lib" value="true" /> -->
 789       <attribute name="Codebase" value="${applet.codebase}" />
 790       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 791     </manifest>
 792   </jar>
 793
 794   <presetdef name="ap_applet.jar">
 795     <!-- build a signed applet with 'all-permissions' -
 796                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 797                           JalviewLite+JmolApplet linked sequence/structure fails
 798                           Mixed code warnings are raised
 799                           -->
 800     <jar update="true" index="true">
 801       <manifest>
 802         <attribute name="Application-Name" value="JalviewLite" />
 803         <attribute name="Permissions" value="all-permissions" />
 804         <attribute name="Codebase" value="${applet.codebase}" />
 805         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 806         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 807       </manifest>
 808     </jar>
 809   </presetdef>
 810   <presetdef name="applet.jar">
 811     <!-- build signed applet with sandbox permissions -
 812                           Needs 'param name="permissions' value="sandbox"' in applet tag
 813                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 814                         -->
 815
 816     <jar update="true" index="true">
 817       <manifest>
 818         <attribute name="Application-Name" value="JalviewLite" />
 819         <attribute name="Permissions" value="sandbox" />
 820         <attribute name="Codebase" value="${applet.codebase}" />
 821         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 822         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 823       </manifest>
 824     </jar>
 825   </presetdef>
 826   <presetdef name="tl_applet.jar">
 827     <!-- build signed applet with trusted library/trusted permissions -
 828                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 829                                j1.7_45:
 830                                No mixed code warnings raised
 831                                Jmol/JalviewLite sequence/structure example doesn't link structures
 832                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 833
 834                               -->
 835
 836     <jar update="true" index="true">
 837       <manifest>
 838         <attribute name="Application-Name" value="JalviewLite" />
 839         <attribute name="Permissions" value="all-permissions" />
 840         <attribute name="Codebase" value="${applet.codebase}" />
 841         <attribute name="Trusted-Only" value="true" />
 842         <attribute name="Trusted-Library" value="true" />
 843       </manifest>
 844     </jar>
 845   </presetdef>
 846   <presetdef name="to_applet.jar">
 847     <!-- not fully test variant (yet) -->
 848     <jar update="true" index="true">
 849       <manifest>
 850         <attribute name="Application-Name" value="JalviewLite" />
 851         <attribute name="Permissions" value="all-permissions" />
 852         <attribute name="Codebase" value="${applet.codebase}" />
 853         <attribute name="Trusted-Only" value="true" />
 854       </manifest>
 855     </jar>
 856   </presetdef>
 857   <!-- create differently privileged artefacts -->
 858   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 859   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 860   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 861   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 862   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 863   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
 864   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
 865   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
 866   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 867   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 868   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
 869   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
 870   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 871   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 872   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
 873   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
 874   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 875   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 876   <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
 877   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
 878   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 879   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 880   <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
 881   <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
 882   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 883   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 884   <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
 885   <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
 886   <!-- finally, create manifest for original jars -->
 887   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 888   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 889   <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
 890   <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 891
 892   <!-- todo - write examples/downloads for alternate versions of the applet
 893     probably don't need to do this now since we don't have alternate versions anymore !-->
 894 </target>
 895 <target name="-signapplet" depends="prepubapplet_1">
 896   <fileset id="signappletjarset" dir="${packageDir}/examples">
 897     <exclude name="u_*.jar" />
 898     <include name="${jalviewLiteJar}" />
 899     <include name="${jmolJar}" />
 900     <include name="${javaJson}" />
 901     <include name="${jsonSimple}" />
 902     <include name="to_${jalviewLiteJar}" />
 903     <include name="to_${jmolJar}" />
 904     <include name="to_${javaJson}" />
 905     <include name="to_${jsonSimple}" />
 906     <include name="tl_${jalviewLiteJar}" />
 907     <include name="tl_${jmolJar}" />
 908     <include name="tl_${javaJson}" />
 909     <include name="tl_${jsonSimple}" />
 910     <include name="ap_${jalviewLiteJar}" />
 911     <include name="ap_${jmolJar}" />
 912     <include name="ap_${javaJson}" />
 913     <include name="ap_${jsonSimple}" />
 914   </fileset>
 915 </target>
 916 <target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
 917   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 918     <fileset refid="signappletjarset" />
 919   </signjar>
 920 </target>
 921
 922 <target name="-signapplettsa" if="timestamp" depends="-signapplet">
 923   <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}">
 924     <fileset refid="signappletjarset" />
 925   </signjar>
 926 </target>
 927
 928 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
 929
 930 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 931
 932   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 933   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 934   <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
 935   <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
 936   <!-- finally, replace any launchApp servlet tags with a version specification -->
 937   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
 938     <replacetoken>
 939       <![CDATA[http://www.jalview.org/services/launchApp"]]>
 940     </replacetoken>
 941     <fileset dir="${packageDir}/examples">
 942       <include name="**/*.html" />
 943     </fileset>
 944   </replace>
 945   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
 946     <replacetoken>
 947       <![CDATA[http://www.jalview.org/services/launchApp']]>
 948     </replacetoken>
 949     <fileset dir="${packageDir}/examples">
 950       <include name="**/*.html" />
 951     </fileset>
 952   </replace>
 953
 954 </target>
 955 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 956   <javadoc destdir="${javadocDir}">
 957     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 958     </packageset>
 959   </javadoc>
 960 </target>
 961 <target name="linkcheck" depends="init,prepare">
 962   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
 963   <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
 964     <arg file="${helpDir}"/>
 965     <arg value="-nointernet"/>
 966   </java>
 967 </target>
 968 </project>