build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   4  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
   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 -->
  19 <project name="jalviewX" default="usage" basedir=".">
  20         <!-- we use jalopy to format our sources -->
  21         <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
  22                 <classpath>
  23                         <fileset dir="utils/jalopy/lib">
  24                                 <include name="*.jar" />
  25                         </fileset>
  26                 </classpath>
  27         </taskdef>
  28
  29         <target name="help" depends="usage" />
  30         <target name="usage">
  31                 <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  32                 <echo message="Targets include:" />
  33                 <echo message="usage - default target, displays this message" />
  34                 <echo message="buildindices - generates JavaHelpSearch from the help files" />
  35                 <echo message="build - compiles all necessary files for Application" />
  36                 <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  37                 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  38                 <echo message="              this needs a keystore and key. 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="See docs/building.html and the comments in build file for other targets." />
  42                 <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  43                 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  44         </target>
  45
  46
  47         <!-- utils is a class path to additional utilities needed for
  48     building docs, jars and webstart stuff -->
  49         <!--
  50         Userdefined build property defaults
  51
  52         wsdl.server list (plus namespace mapping info ???)  - also want
  53                 ... to make this a dynamically generatable property
  54         WebStart Location
  55         Build location - provide a temporary root for speed
  56         jarsigner keystore and info
  57         Jakarta and axis classpath ?
  58         Default argument for starting Jalview (if it exists).
  59
  60 -->
  61
  62         <target name="init">
  63                 <path id="axis.classpath">
  64                         <!-->
  65                         <fileset dir="/usr/local/axis/lib">
  66                                 <include name="**/*.jar" />
  67                         </fileset>
  68                         <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  69                                 <include name="**/*.jar"/>
  70                                 <include name="*.jar"/>
  71                         </fileset> -->
  72       </path>
  73                 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  74                 <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  75                 <!-- 2.4 (VAMSAS)" -->
  76                 <!-- Include debugging information in javac true or false -->
  77                 <property name="javac.debug" value="true" />
  78
  79                 <!-- JarSigner Key Store for Webstart Distribution -->
  80                 <property name="jalview.keystore" value="./keys/.keystore" />
  81                 <!-- Keystore Password -->
  82                 <property name="jalview.keystore.pass" value="alignmentisfun" />
  83                 <!-- Key Name -->
  84                 <property name="jalview.key" value="jalview" />
  85                 <!-- Key Password -->
  86                 <property name="jalview.key.pass" value="alignmentisfun" />
  87
  88
  89
  90                 <!-- Don't change anything below here unless you know what you are doing! -->
  91                 <!-- Url path for WebStart in JNLP file -->
  92                 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  93                 <!-- Webstart Image - looked for in resources/images -->
  94                 <property name="WebStartImage" value="JalviewLogo_big.png"/>
  95                 <!-- J2SE version needed for webstart launch -->
  96 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  97                 <property name="j2sev" value="1.7+"/>
  98
  99     <!-- Permissions for running Java applets and applications. Defaults are those suitable for deploying jalview webstart/jalviewLite at www.jalview.org -->
 100     <property name="application.codebase" value="*.jalview.org"/>
 101     <property name="applet.codebase" value="*.jalview.org"/>
 102     <property name="applet.caller-codebase" value="${applet.codebase}"/>
 103
 104                 <!-- build directory configuration -->
 105                 <property name="libDir" value="lib" />
 106                 <property name="resourceDir" value="resources" />
 107                 <property name="helpDir" value="help" />
 108                 <property name="docDir" value="doc" />
 109                 <property name="sourceDir" value="src" />
 110                 <property name="schemaDir" value="schemas" />
 111                 <property name="outputDir" value="classes" />
 112                 <property name="packageDir" value="dist" />
 113                 <property name="outputJar" value="jalview.jar" />
 114                 <!-- Jalview Applet JMol Jar Dependency -->
 115                 <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 116                 <property name="varnaJar" value="VARNAv3-9.jar" />
 117                 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 118                 <!-- switch to indicate if we should obfuscate jalviewLite -->
 119                 <!--<property name="donotobfuscate" value="true"/> -->
 120
 121                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 122                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 123                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 124                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 125                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 126                 <property name="WSInterf" value="MsaWS" />
 127                 <property name="wsdl.Namespace" value="vamsas" />
 128                 <property name="wsdl.ClientNS" value="ext.vamsas" />
 129                 <!-- the class path for building the application -->
 130                 <path id="build.classpath">
 131                         <fileset dir="utils">
 132                                 <include name="*.jar" />
 133                                 <include name="**/*.jar" />
 134                         </fileset>
 135                         <fileset dir="${libDir}">
 136                                 <include name="*.jar" />
 137                                 <include name="**/*.jar" />
 138                         </fileset>
 139                         <fileset dir="${java.home}/lib">
 140                                 <include name="plugin.jar"/>
 141                         </fileset>
 142                         <fileset dir="appletlib">
 143                                 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 144                                 -->
 145                                 <include name="${jmolJar}" />
 146                                 <include name="${varnaJar}" />
 147                         </fileset>
 148
 149                 </path>
 150                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 151                 <!-- The Location of the java 1.1.8 jdk -->
 152                 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 153                 -->
 154                 <property name="java118.home" value="${java.home}" />
 155                     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 156                 --><!-- jre for 1.4 version -->
 157                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 158
 159                 <!-- the classpath for building the 1.1 applet -->
 160                 <path id="jalviewlite.deps">
 161                         <fileset dir="${java118.home}">
 162                                 <include name="lib/classes.zip" />
 163                         </fileset>
 164                         <fileset dir="${java.home}/lib">
 165                                 <include name="plugin.jar"/>
 166                         </fileset>
 167                         <pathelement location="appletlib/${jmolJar}" />
 168       <pathelement location="lib/${varnaJar}" />
 169
 170                 </path>
 171     <!-- default location for outputting javadoc -->
 172     <property name="javadocDir" value="${packageDir}/javadoc"/>
 173         </target>
 174
 175
 176         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 177         <target name="buildPropertiesFile" depends="init">
 178                 <tstamp prefix="build">
 179                         <format property="date" pattern="dd MMMM yyyy" />
 180                 </tstamp>
 181                 <properties file="${outputDir}/.build_properties">
 182                         <header>
 183           ---Jalview Build Details---
 184         </header>
 185                         <property name="VERSION" value="${JALVIEW_VERSION}" />
 186                         <property name="BUILD_DATE" value="${build.date}" />
 187                 </properties>
 188         </target>
 189
 190
 191         <target name="clean" depends="init">
 192                 <!-- not efficient yet. -->
 193                 <delete dir="${outputDir}" includes="*,**/*"/>
 194         </target>
 195
 196         <target name="distclean" depends="init, clean">
 197
 198                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 199                 <delete>
 200                         <fileset dir=".">
 201                                 <include name="${outputJar}" />
 202                                 <include name="#*#" />
 203                                 <include name="#*.*#" />
 204                                 <include name="**/#*#" />
 205                                 <include name="**/#*.*#" />
 206                                 <include name="*~" />
 207                                 <include name="*.*~" />
 208                                 <include name="**/*~" />
 209                                 <include name="**/*.*~" />
 210                         </fileset>
 211                 </delete>
 212         </target>
 213
 214         <target name="prepare" depends="init">
 215                 <mkdir dir="${outputDir}" />
 216                 <copy todir="${outputDir}">
 217                         <fileset dir=".">
 218                                 <include name="${docDir}/**/*.*" />
 219                                 <include name="${helpDir}/**/*.*" />
 220                                 <include name="${libDir}/*.jar" />
 221                         </fileset>
 222                         <fileset dir="${resourceDir}">
 223                                 <include name="**/*.*" />
 224                         </fileset>
 225                 </copy>
 226         </target>
 227
 228         <target name="build" depends="prepare">
 229                 <!-- not efficient yet. -->
 230                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 231                         <exclude name="jalview/*applet*" />
 232                         <exclude name="jalview/appletgui/**" />
 233                         <exclude name="com/stevesoft/**" />
 234                 </javac>
 235         </target>
 236         <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 237                 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 238                         <arg line="html" />
 239                 </java>
 240         </target>
 241
 242         <target name="makefulldist" depends="makedist">
 243                 <!-- the default keystore details might need to be edited here -->
 244                 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 245
 246                         <fileset dir="${packageDir}">
 247                                 <include name="*.jar" />
 248                         </fileset>
 249                 </signjar>
 250                 <copy todir="${packageDir}">
 251                         <fileset dir="${resourceDir}/images">
 252                                 <include name="${WebStartImage}"/>
 253                         </fileset>
 254                                         </copy>
 255
 256                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 257
 258                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 259                 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 260                 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 261                         <information>
 262                                 <title>Jalview</title>
 263                                 <vendor>The Barton Group</vendor>
 264                                 <homepage href="http://www.jalview.org" />
 265                                 <description>Jalview Multiple Alignment Editor</description>
 266                                 <description kind="short">Jalview</description>
 267                                 <icon href="${WebStartImage}" />
 268                                 <offline_allowed/>
 269                         </information>
 270                         <resources>
 271                                 <j2se version="${j2sev}" initial_heap_size="10M"  />
 272                                 <fileset dir="${packageDir}">
 273                                         <include name="jalview.jar" />
 274                                 </fileset>
 275                                 <fileset dir="${packageDir}">
 276                                         <include name="*.jar" />
 277                                         <include name="*_*.jar" />
 278                                         <exclude name="jalview.jar" />
 279                                 </fileset>
 280                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 281                         </resources>
 282                         <application_desc main_class="jalview.bin.Jalview">
 283                         </application_desc>
 284                         <security>
 285                                 <all_permissions />
 286                         </security>
 287                 </jnlp>
 288                 <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 289                         <information>
 290                                 <title>Jalview</title>
 291                                 <vendor>The Barton Group</vendor>
 292                                 <homepage href="http://www.jalview.org" />
 293                                 <description>Jalview Multiple Alignment Editor</description>
 294                                 <description kind="short">Jalview</description>
 295                                 <icon href="${WebStartImage}" />
 296                                 <offline_allowed />
 297                         </information>
 298                         <resources>
 299                                 <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
 300                                 <fileset dir="${packageDir}">
 301                                         <include name="jalview.jar" />
 302                                 </fileset>
 303                                 <fileset dir="${packageDir}">
 304                                         <include name="*.jar" />
 305                                         <include name="*_*.jar" />
 306                                         <exclude name="jalview.jar" />
 307                                 </fileset>
 308                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 309                         </resources>
 310                         <application_desc main_class="jalview.bin.Jalview">
 311                         </application_desc>
 312                         <security>
 313                                 <all_permissions />
 314                         </security>
 315                 </jnlp>
 316                 <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
 317                         <information>
 318                                 <title>Jalview</title>
 319                                 <vendor>The Barton Group</vendor>
 320                                 <homepage href="http://www.jalview.org" />
 321                                 <description>Jalview Multiple Alignment Editor</description>
 322                                 <description kind="short">Jalview</description>
 323                                 <icon href="${WebStartImage}" />
 324                                 <offline_allowed />
 325                         </information>
 326                         <resources>
 327                                 <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
 328                                 <fileset dir="${packageDir}">
 329                                         <include name="jalview.jar" />
 330                                 </fileset>
 331                                 <fileset dir="${packageDir}">
 332                                         <include name="*.jar" />
 333                                         <include name="*_*.jar" />
 334                                         <exclude name="jalview.jar" />
 335                                 </fileset>
 336                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 337                         </resources>
 338                         <application_desc main_class="jalview.bin.Jalview">
 339                         </application_desc>
 340                         <security>
 341                                 <all_permissions />
 342                         </security>
 343                 </jnlp>
 344                         <!-- finally, need to postprocess to add in associations at end of 'information' element
 345
 346                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 347
 348                 </xslt>
 349
 350
 351                         -->
 352                                         <!--
 353                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 354         <association mime-type="application-x/ext-file" extensions="fasta"/>
 355         <association mime-type="application-x/ext-file" extensions="fastq"/>
 356         <association mime-type="application-x/ext-file" extensions="blc"/>
 357         <association mime-type="application-x/ext-file" extensions="msf"/>
 358         <association mime-type="application-x/ext-file" extensions="pfam"/>
 359         <association mime-type="application-x/ext-file" extensions="aln"/>
 360         <association mime-type="application-x/ext-file" extensions="pir"/>
 361         <association mime-type="application-x/ext-file" extensions="amsa"/>
 362         <association mime-type="application-x/ext-file" extensions="stk"/>
 363         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 364
 365         </target>
 366
 367         <target name="runenv" depends="init">
 368                 <path id="run.classpath">
 369                         <pathelement location="${outputDir}" />
 370                         <fileset dir="${outputDir}">
 371                                 <include name="${libDir}/*.jar" />
 372                         </fileset>
 373                 </path>
 374                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 375
 376                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 377       </echo>
 378         </target>
 379
 380         <target name="buildextclients" depends="init">
 381                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 382                 <condition property="dontextbuild">
 383                         <equals arg1="n" arg2="${doextbuild.response}" />
 384                 </condition>
 385                 <condition property="dontextbuild">
 386                         <equals arg1="N" arg2="${doextbuild.response}" />
 387                 </condition>
 388                 <fail if="dontextbuild">
 389         Build External Client Code process aborted by user. Jalview source is unchanged.
 390       </fail>
 391                 <!-- Currently, this doesn't happen automatically.
 392      1. Run WSDL2Java as below, which generates an ext.vamsas +
 393      vamsas.<datapackages> fileset.
 394      2. refactor ext.vamsas.SpecificserviceWS* to
 395      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 396      3. Update the jalview.ws.*WServices classes to reflect the
 397      interface type, and all locations of this wsdl type that Jalview
 398      might be using.
 399
 400 -->
 401                 <path id="axisbuild">
 402                         <path refid="build.classpath" />
 403                 </path>
 404                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 405                 <move todir="./bak">
 406                         <fileset dir="${sourceDir}" id="client">
 407                                 <include name="${wsdl.ClientNS}/*.*" />
 408                         </fileset>
 409                 </move>
 410
 411                 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 412                         <mappingSet>
 413                                 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 414                                 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 415                         </mappingSet>
 416                 </axis-wsdl2java>
 417         </target>
 418
 419         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 420                 <!-- make the package jar if not already existing -->
 421                 <mkdir dir="${packageDir}" />
 422                 <!-- clean dir if it already existed -->
 423                 <delete>
 424                         <fileset dir="${packageDir}">
 425                                 <include name="*.jar"/>
 426                         </fileset>
 427                 </delete>
 428                 <jar destfile="${packageDir}/${outputJar}" index="true">
 429                         <manifest>
 430                                 <attribute name="Main-Class" value="jalview.bin.Jalview" />
 431         <attribute name="Permissions" value="all-permissions" />
 432         <!--<attribute name="Trusted-Lib" value="true" /> -->
 433         <attribute name="Application-Name" value="Jalview Desktop"/>
 434         <attribute name="Codebase" value="${application.codebase}"/>
 435                         </manifest>
 436                         <fileset dir="${outputDir}/">
 437                                 <exclude name="cache*/**" />
 438                                 <exclude name="*.jar" />
 439                                 <exclude name="*.jar.*" />
 440                                 <exclude name="**/*.jar" />
 441                                 <exclude name="**/*.jar.*" />
 442                         </fileset>
 443                 </jar>
 444
 445                 <copy toDir="${packageDir}" flatten="true">
 446                         <fileset dir="${outputDir}">
 447                                 <include name="*.jar" />
 448                                 <include name="**/*.jar" />
 449                         </fileset>
 450                 </copy>
 451         </target>
 452
 453
 454         <!-- jalopy code reformatter -->
 455         <target name="sourcescrub" depends="init,build">
 456                 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 457                         <fileset dir="${sourceDir}">
 458                                 <include name="*.java" />
 459                                 <include name="**/*.java" />
 460                                 <include name="**/**/*.java" />
 461                         </fileset>
 462                 </jalopy>
 463         </target>
 464
 465
 466
 467         <!-- Compile, package and obfuscate Jalview Applet -->
 468         <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 469
 470         <target name="compileApplet" depends="init,clean">
 471                 <mkdir dir="${outputDir}" />
 472                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 473                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 474                         excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 475         </target>
 476
 477         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 478                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 479                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 480                 <copy todir="${outputDir}/lang">
 481                         <fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
 482                 <jar destfile="in.jar" index="true">
 483                         <manifest>
 484                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 485                                 <attribute name="Application-Name" value="JalviewLite Applet"/>
 486                                 <!--            <attribute name="Permissions" value="sandbox" /> -->
 487                                 <!--<attribute name="Trusted-Lib" value="true" /> -->
 488                                 <attribute name="Codebase" value="${applet.codebase}"/>
 489                                 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 490                         </manifest>
 491                         <fileset dir="${outputDir}">
 492                                 <include name="com/**" />
 493                                 <include name="MCview/**" />
 494                                 <include name="jalview/**" />
 495                                 <include name=".build_properties" />
 496                                 <include name="images/idwidth.gif" />
 497                                 <include name="images/link.gif" />
 498                                 <include name="lang/**" />
 499                         </fileset>
 500                 </jar>
 501         </target>
 502         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 503         </target>
 504         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 505                 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 506                 <delete file="in.jar" />
 507         </target>
 508         <target name="-obfuscatereally" unless="donotobfuscate">
 509
 510                 <path id="obfuscateDeps.path">
 511                         <pathelement location="${applet.jre.tools}" />
 512                         <pathelement location="appletlib/${jmolJar}" />
 513                 </path>
 514                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 515
 516                 <proguard>
 517                         <injar file="in.jar" />
 518                         <outjar file="${jalviewLiteJar}" />
 519                         <libraryjar refid="obfuscateDeps.path" />
 520                         <dontwarn/>
 521                         <keep access="public" type="class" name="jalview.bin.JalviewLite">
 522                                 <field access="public" />
 523                                 <method access="public" />
 524                                 <constructor access="public" />
 525                         </keep>
 526                         <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 527                                 <field access="public" />
 528                                 <method access="public" />
 529                                 <constructor access="public" />
 530                         </keep>
 531                         <!--      -libraryjars "${obfuscateDeps}"
 532       -injars      in.jar
 533       -outjars     jalviewApplet.jar
 534       -keep public class jalview.bin.JalviewLite
 535        { public * ; } -->
 536                 </proguard>
 537                 <delete file="in.jar" />
 538         </target>
 539
 540         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 541                 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 542                 <delete>
 543                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 544                                 <include name="*.java" />
 545                                 <include name="descriptors/*.java" />
 546                         </fileset>
 547                 </delete>
 548                 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 549                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 550                 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 551                 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 552                 <!--
 553                 now build the jalview.binding package with the old schema set
 554                 -->
 555                 <delete>
 556                         <fileset dir="${sourceDir}/jalview/binding/">
 557                                 <include name="**" />
 558                         </fileset>
 559                 </delete>
 560                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 561                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 562                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 563         </target>
 564         <target name="sourcedist" description="create jalview source distribution" depends="init">
 565                 <delete file="${source.dist.name}" />
 566                 <tar destfile="${source.dist.name}" compression="gzip">
 567                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 568                                 <include name="LICENSE" />
 569                                 <include name="README" />
 570                                 <include name="build.xml" />
 571                                 <include name="jalview-jalopy.xml" />
 572                                 <include name="JalviewApplet.jpx" />
 573                                 <include name="JalviewX.jpx" />
 574                                 <include name="nbbuild.xml"/>
 575                                 <include name="nbproject/genfiles.properties"/>
 576         <include name="nbproject/project.properties"/>
 577         <include name="nbproject/project.xml"/>
 578                                 <include name="${sourceDir}/*.java" />
 579                                 <include name="${sourceDir}/**/*.java" />
 580                                 <include name="${sourceDir}/**/*.cdr" />
 581                                 <include name="${libDir}/**/*" />
 582                                 <include name="${resourceDir}/**/*" />
 583                                 <include name="${helpDir}/**/*" />
 584                                 <include name="appletlib/${jmolJar}" />
 585                                 <exclude name="**/*locales" />
 586                                 <exclude name="*locales/**" />
 587                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 588                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 589                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 590                                 <exclude name="utils/InstallAnywhere/**locale*" />
 591                                 <exclude name="utils/InstallAnywhere/**locale*/**" />
 592                                 <include name="${schemaDir}/**/*" />
 593                                 <include name="utils/**/*" />
 594                                 <include name="${docDir}/**/*" />
 595                                 <include name="examples/**/*" />
 596                         </tarfileset>
 597                 </tar>
 598         </target>
 599         <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 600           <copy todir="${packageDir}/examples">
 601           <fileset dir="examples">
 602                 <include name="**/*"/>
 603                 <include name="javascript/*"/>
 604       <include name="jmol/*"/>
 605           </fileset>
 606                 <fileset dir=".">
 607                 <include name="jalviewApplet.jar"/>
 608                         </fileset>
 609                 <fileset dir="appletlib">
 610                       <include name="**/*"/>
 611                         </fileset>
 612           </copy>
 613             <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 614             <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 615                 <manifest>
 616                 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 617                 <!--          <attribute name="Permissions" value="sandbox" /> -->
 618                 <!--<attribute name="Trusted-Lib" value="true" /> -->
 619                 <attribute name="Codebase" value="${applet.codebase}"/>
 620                 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 621                   </manifest>
 622                 </jar>
 623     <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 624       <fileset dir="${packageDir}/examples">
 625         <include name="*.jar" />
 626       </fileset>
 627     </signjar>
 628         </target>
 629         <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 630          <javadoc destdir="${javadocDir}">
 631                 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 632                 </packageset>
 633                 </javadoc>
 634         </target>
 635
 636 </project>