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                 <property name="j2sev" value="1.6+"/>
  97
  98     <!-- Permissions for running Java applets and applications. Defaults are those suitable for deploying jalview webstart/jalviewLite at www.jalview.org -->
  99     <property name="application.codebase" value="*.jalview.org"/>
 100     <property name="applet.codebase" value="*"/>
 101     <property name="applet.caller-codebase" value="${applet.codebase}"/>
 102
 103                 <!-- build directory configuration -->
 104                 <property name="libDir" value="lib" />
 105                 <property name="resourceDir" value="resources" />
 106                 <property name="helpDir" value="help" />
 107                 <property name="docDir" value="doc" />
 108                 <property name="sourceDir" value="src" />
 109                 <property name="schemaDir" value="schemas" />
 110                 <property name="outputDir" value="classes" />
 111                 <property name="packageDir" value="dist" />
 112                 <property name="outputJar" value="jalview.jar" />
 113                 <!-- Jalview Applet JMol Jar Dependency -->
 114                 <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 115                 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 116                 <!-- switch to indicate if we should obfuscate jalviewLite -->
 117                 <!--<property name="donotobfuscate" value="true"/> -->
 118
 119                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 120                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 121                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 122                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 123                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 124                 <property name="WSInterf" value="MsaWS" />
 125                 <property name="wsdl.Namespace" value="vamsas" />
 126                 <property name="wsdl.ClientNS" value="ext.vamsas" />
 127                 <!-- the class path for building the application -->
 128                 <path id="build.classpath">
 129                         <fileset dir="utils">
 130                                 <include name="*.jar" />
 131                                 <include name="**/*.jar" />
 132                         </fileset>
 133                         <fileset dir="${libDir}">
 134                                 <include name="*.jar" />
 135                                 <include name="**/*.jar" />
 136                         </fileset>
 137                         <fileset dir="${java.home}/lib">
 138                                 <include name="plugin.jar"/>
 139                         </fileset>
 140                         <fileset dir="appletlib">
 141                                 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 142                                 -->
 143                                 <include name="${jmolJar}" />
 144                         </fileset>
 145
 146                 </path>
 147                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 148                 <!-- The Location of the java 1.1.8 jdk -->
 149                 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 150                 -->
 151                 <property name="java118.home" value="${java.home}" />
 152                     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 153                 --><!-- jre for 1.4 version -->
 154                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 155
 156                 <!-- the classpath for building the 1.1 applet -->
 157                 <path id="jalviewlite.deps">
 158                         <fileset dir="${java118.home}">
 159                                 <include name="lib/classes.zip" />
 160                         </fileset>
 161                         <fileset dir="${java.home}/lib">
 162                                 <include name="plugin.jar"/>
 163                         </fileset>
 164                         <pathelement location="appletlib/${jmolJar}" />
 165                 </path>
 166     <!-- default location for outputting javadoc -->
 167     <property name="javadocDir" value="${packageDir}/javadoc"/>
 168         </target>
 169
 170
 171         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 172         <target name="buildPropertiesFile" depends="init">
 173                 <tstamp prefix="build">
 174                         <format property="date" pattern="dd MMMM yyyy" />
 175                 </tstamp>
 176                 <properties file="${outputDir}/.build_properties">
 177                         <header>
 178           ---Jalview Build Details---
 179         </header>
 180                         <property name="VERSION" value="${JALVIEW_VERSION}" />
 181                         <property name="BUILD_DATE" value="${build.date}" />
 182                 </properties>
 183         </target>
 184
 185
 186         <target name="clean" depends="init">
 187                 <!-- not efficient yet. -->
 188                 <delete dir="${outputDir}" includes="*,**/*"/>
 189         </target>
 190
 191         <target name="distclean" depends="init, clean">
 192
 193                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 194                 <delete>
 195                         <fileset dir=".">
 196                                 <include name="${outputJar}" />
 197                                 <include name="#*#" />
 198                                 <include name="#*.*#" />
 199                                 <include name="**/#*#" />
 200                                 <include name="**/#*.*#" />
 201                                 <include name="*~" />
 202                                 <include name="*.*~" />
 203                                 <include name="**/*~" />
 204                                 <include name="**/*.*~" />
 205                         </fileset>
 206                 </delete>
 207         </target>
 208
 209         <target name="prepare" depends="init">
 210                 <mkdir dir="${outputDir}" />
 211                 <copy todir="${outputDir}">
 212                         <fileset dir=".">
 213                                 <include name="${docDir}/**/*.*" />
 214                                 <include name="${helpDir}/**/*.*" />
 215                                 <include name="${libDir}/*.jar" />
 216                         </fileset>
 217                         <fileset dir="${resourceDir}">
 218                                 <include name="**/*.*" />
 219                         </fileset>
 220                 </copy>
 221         </target>
 222
 223         <target name="build" depends="prepare">
 224                 <!-- not efficient yet. -->
 225                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 226                         <exclude name="jalview/*applet*" />
 227                         <exclude name="jalview/appletgui/**" />
 228                         <exclude name="com/stevesoft/**" />
 229                 </javac>
 230         </target>
 231         <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 232                 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 233                         <arg line="html" />
 234                 </java>
 235         </target>
 236
 237         <target name="makefulldist" depends="makedist">
 238                 <!-- the default keystore details might need to be edited here -->
 239                 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 240
 241                         <fileset dir="${packageDir}">
 242                                 <include name="*.jar" />
 243                         </fileset>
 244                 </signjar>
 245                 <copy todir="${packageDir}">
 246                         <fileset dir="${resourceDir}/images">
 247                                 <include name="${WebStartImage}"/>
 248                         </fileset>
 249                                         </copy>
 250
 251                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 252
 253                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 254                 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 255                 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 256                         <information>
 257                                 <title>Jalview</title>
 258                                 <vendor>The Barton Group</vendor>
 259                                 <homepage href="http://www.jalview.org" />
 260                                 <description>Jalview Multiple Alignment Editor</description>
 261                                 <description kind="short">Jalview</description>
 262                                 <icon href="${WebStartImage}" />
 263                                 <offline_allowed/>
 264                         </information>
 265                         <resources>
 266                                 <j2se version="${j2sev}" initial_heap_size="10M"  />
 267                                 <fileset dir="${packageDir}">
 268                                         <include name="jalview.jar" />
 269                                 </fileset>
 270                                 <fileset dir="${packageDir}">
 271                                         <include name="*.jar" />
 272                                         <include name="*_*.jar" />
 273                                         <exclude name="jalview.jar" />
 274                                 </fileset>
 275                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 276                         </resources>
 277                         <application_desc main_class="jalview.bin.Jalview">
 278                         </application_desc>
 279                         <security>
 280                                 <all_permissions />
 281                         </security>
 282                 </jnlp>
 283                 <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 284                         <information>
 285                                 <title>Jalview</title>
 286                                 <vendor>The Barton Group</vendor>
 287                                 <homepage href="http://www.jalview.org" />
 288                                 <description>Jalview Multiple Alignment Editor</description>
 289                                 <description kind="short">Jalview</description>
 290                                 <icon href="${WebStartImage}" />
 291                                 <offline_allowed />
 292                         </information>
 293                         <resources>
 294                                 <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
 295                                 <fileset dir="${packageDir}">
 296                                         <include name="jalview.jar" />
 297                                 </fileset>
 298                                 <fileset dir="${packageDir}">
 299                                         <include name="*.jar" />
 300                                         <include name="*_*.jar" />
 301                                         <exclude name="jalview.jar" />
 302                                 </fileset>
 303                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 304                         </resources>
 305                         <application_desc main_class="jalview.bin.Jalview">
 306                         </application_desc>
 307                         <security>
 308                                 <all_permissions />
 309                         </security>
 310                 </jnlp>
 311                 <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
 312                         <information>
 313                                 <title>Jalview</title>
 314                                 <vendor>The Barton Group</vendor>
 315                                 <homepage href="http://www.jalview.org" />
 316                                 <description>Jalview Multiple Alignment Editor</description>
 317                                 <description kind="short">Jalview</description>
 318                                 <icon href="${WebStartImage}" />
 319                                 <offline_allowed />
 320                         </information>
 321                         <resources>
 322                                 <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
 323                                 <fileset dir="${packageDir}">
 324                                         <include name="jalview.jar" />
 325                                 </fileset>
 326                                 <fileset dir="${packageDir}">
 327                                         <include name="*.jar" />
 328                                         <include name="*_*.jar" />
 329                                         <exclude name="jalview.jar" />
 330                                 </fileset>
 331                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 332                         </resources>
 333                         <application_desc main_class="jalview.bin.Jalview">
 334                         </application_desc>
 335                         <security>
 336                                 <all_permissions />
 337                         </security>
 338                 </jnlp>
 339                         <!-- finally, need to postprocess to add in associations at end of 'information' element
 340
 341                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 342
 343                 </xslt>
 344
 345
 346                         -->
 347                                         <!--
 348                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 349         <association mime-type="application-x/ext-file" extensions="fasta"/>
 350         <association mime-type="application-x/ext-file" extensions="fastq"/>
 351         <association mime-type="application-x/ext-file" extensions="blc"/>
 352         <association mime-type="application-x/ext-file" extensions="msf"/>
 353         <association mime-type="application-x/ext-file" extensions="pfam"/>
 354         <association mime-type="application-x/ext-file" extensions="aln"/>
 355         <association mime-type="application-x/ext-file" extensions="pir"/>
 356         <association mime-type="application-x/ext-file" extensions="amsa"/>
 357         <association mime-type="application-x/ext-file" extensions="stk"/>
 358         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 359
 360         </target>
 361
 362         <target name="runenv" depends="init">
 363                 <path id="run.classpath">
 364                         <pathelement location="${outputDir}" />
 365                         <fileset dir="${outputDir}">
 366                                 <include name="${libDir}/*.jar" />
 367                         </fileset>
 368                 </path>
 369                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 370
 371                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 372       </echo>
 373         </target>
 374
 375         <target name="buildextclients" depends="init">
 376                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 377                 <condition property="dontextbuild">
 378                         <equals arg1="n" arg2="${doextbuild.response}" />
 379                 </condition>
 380                 <condition property="dontextbuild">
 381                         <equals arg1="N" arg2="${doextbuild.response}" />
 382                 </condition>
 383                 <fail if="dontextbuild">
 384         Build External Client Code process aborted by user. Jalview source is unchanged.
 385       </fail>
 386                 <!-- Currently, this doesn't happen automatically.
 387      1. Run WSDL2Java as below, which generates an ext.vamsas +
 388      vamsas.<datapackages> fileset.
 389      2. refactor ext.vamsas.SpecificserviceWS* to
 390      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 391      3. Update the jalview.ws.*WServices classes to reflect the
 392      interface type, and all locations of this wsdl type that Jalview
 393      might be using.
 394
 395 -->
 396                 <path id="axisbuild">
 397                         <path refid="build.classpath" />
 398                 </path>
 399                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 400                 <move todir="./bak">
 401                         <fileset dir="${sourceDir}" id="client">
 402                                 <include name="${wsdl.ClientNS}/*.*" />
 403                         </fileset>
 404                 </move>
 405
 406                 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 407                         <mappingSet>
 408                                 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 409                                 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 410                         </mappingSet>
 411                 </axis-wsdl2java>
 412         </target>
 413
 414         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 415                 <!-- make the package jar if not already existing -->
 416                 <mkdir dir="${packageDir}" />
 417                 <!-- clean dir if it already existed -->
 418                 <delete>
 419                         <fileset dir="${packageDir}">
 420                                 <include name="*.jar"/>
 421                         </fileset>
 422                 </delete>
 423                 <jar destfile="${packageDir}/${outputJar}" index="true">
 424                         <manifest>
 425                                 <attribute name="Main-Class" value="jalview.bin.Jalview" />
 426         <attribute name="Permissions" value="all-permissions" />
 427         <attribute name="Application-Name" value="Jalview Desktop"/>
 428         <attribute name="Codebase" value="${application.codebase}"/>
 429                         </manifest>
 430                         <fileset dir="${outputDir}/">
 431                                 <exclude name="cache*/**" />
 432                                 <exclude name="*.jar" />
 433                                 <exclude name="*.jar.*" />
 434                                 <exclude name="**/*.jar" />
 435                                 <exclude name="**/*.jar.*" />
 436                         </fileset>
 437                 </jar>
 438
 439                 <copy toDir="${packageDir}" flatten="true">
 440                         <fileset dir="${outputDir}">
 441                                 <include name="*.jar" />
 442                                 <include name="**/*.jar" />
 443                         </fileset>
 444                 </copy>
 445         </target>
 446
 447
 448         <!-- jalopy code reformatter -->
 449         <target name="sourcescrub" depends="init,build">
 450                 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 451                         <fileset dir="${sourceDir}">
 452                                 <include name="*.java" />
 453                                 <include name="**/*.java" />
 454                                 <include name="**/**/*.java" />
 455                         </fileset>
 456                 </jalopy>
 457         </target>
 458
 459
 460
 461         <!-- Compile, package and obfuscate Jalview Applet -->
 462         <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 463
 464         <target name="compileApplet" depends="init,clean">
 465                 <mkdir dir="${outputDir}" />
 466                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 467                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 468                         excludes="ext/**,MCview/**,org/**,vamsas/**" />
 469         </target>
 470
 471         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 472                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 473                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 474                 <jar destfile="in.jar" index="true">
 475                         <manifest>
 476                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 477                                 <attribute name="Application-Name" value="JalviewLite"/>
 478                                 <attribute name="Permissions" value="all-permissions" />
 479                                 <attribute name="Codebase" value="${applet.codebase}"/>
 480                         </manifest>
 481                         <fileset dir="${outputDir}">
 482                                 <include name="com/**" />
 483                                 <include name="MCview/**" />
 484                                 <include name="jalview/**" />
 485                                 <include name=".build_properties" />
 486                                 <include name="images/idwidth.gif" />
 487                                 <include name="images/link.gif" />
 488                         </fileset>
 489                 </jar>
 490         </target>
 491         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 492         </target>
 493         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 494                 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 495                 <delete file="in.jar" />
 496         </target>
 497         <target name="-obfuscatereally" unless="donotobfuscate">
 498
 499                 <path id="obfuscateDeps.path">
 500                         <pathelement location="${applet.jre.tools}" />
 501                         <pathelement location="appletlib/${jmolJar}" />
 502                 </path>
 503                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 504
 505                 <proguard>
 506                         <injar file="in.jar" />
 507                         <outjar file="${jalviewLiteJar}" />
 508                         <libraryjar refid="obfuscateDeps.path" />
 509                         <dontwarn/>
 510                         <keep access="public" type="class" name="jalview.bin.JalviewLite">
 511                                 <field access="public" />
 512                                 <method access="public" />
 513                                 <constructor access="public" />
 514                         </keep>
 515                         <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 516                                 <field access="public" />
 517                                 <method access="public" />
 518                                 <constructor access="public" />
 519                         </keep>
 520                         <!--      -libraryjars "${obfuscateDeps}"
 521       -injars      in.jar
 522       -outjars     jalviewApplet.jar
 523       -keep public class jalview.bin.JalviewLite
 524        { public * ; } -->
 525                 </proguard>
 526                 <delete file="in.jar" />
 527         </target>
 528
 529         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 530                 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 531                 <delete>
 532                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 533                                 <include name="*.java" />
 534                                 <include name="descriptors/*.java" />
 535                         </fileset>
 536                 </delete>
 537                 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 538                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 539                 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 540                 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 541                 <!--
 542                 now build the jalview.binding package with the old schema set
 543                 -->
 544                 <delete>
 545                         <fileset dir="${sourceDir}/jalview/binding/">
 546                                 <include name="**" />
 547                         </fileset>
 548                 </delete>
 549                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 550                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 551                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 552         </target>
 553         <target name="sourcedist" description="create jalview source distribution" depends="init">
 554                 <delete file="${source.dist.name}" />
 555                 <tar destfile="${source.dist.name}" compression="gzip">
 556                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 557                                 <include name="LICENSE" />
 558                                 <include name="README" />
 559                                 <include name="build.xml" />
 560                                 <include name="jalview-jalopy.xml" />
 561                                 <include name="JalviewApplet.jpx" />
 562                                 <include name="JalviewX.jpx" />
 563                                 <include name="nbbuild.xml"/>
 564                                 <include name="nbproject/genfiles.properties"/>
 565         <include name="nbproject/project.properties"/>
 566         <include name="nbproject/project.xml"/>
 567                                 <include name="${sourceDir}/*.java" />
 568                                 <include name="${sourceDir}/**/*.java" />
 569                                 <include name="${sourceDir}/**/*.cdr" />
 570                                 <include name="${libDir}/**/*" />
 571                                 <include name="${resourceDir}/**/*" />
 572                                 <include name="${helpDir}/**/*" />
 573                                 <include name="appletlib/${jmolJar}" />
 574                                 <exclude name="**/*locales" />
 575                                 <exclude name="*locales/**" />
 576                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 577                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 578                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 579                                 <exclude name="utils/InstallAnywhere/**locale*" />
 580                                 <exclude name="utils/InstallAnywhere/**locale*/**" />
 581                                 <include name="${schemaDir}/**/*" />
 582                                 <include name="utils/**/*" />
 583                                 <include name="${docDir}/**/*" />
 584                                 <include name="examples/**/*" />
 585                         </tarfileset>
 586                 </tar>
 587         </target>
 588         <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 589           <copy todir="${packageDir}/examples">
 590           <fileset dir="examples">
 591                 <include name="**/*"/>
 592                 <include name="javascript/*"/>
 593       <include name="jmol/*"/>
 594           </fileset>
 595                 <fileset dir=".">
 596                 <include name="${jalviewLiteJar}"/>
 597                         </fileset>
 598                 <fileset dir="appletlib">
 599                       <include name="**/*"/>
 600                         </fileset>
 601           </copy>
 602           <presetdef name="applet.jar">
 603             <jar update="true" index="true">
 604                 <manifest>
 605                 <attribute name="Application-Name" value="JalviewLite"/>
 606                 <attribute name="Permissions" value="all-permissions"/>
 607                 <attribute name="Codebase" value="${applet.codebase}"/>
 608                 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 609                 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}"/>
 610                 <!--
 611                 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}"/>
 612                 -->
 613 <!--            <attribute name="Trusted-Only" value="true"/>
 614 -->
 615 <!--            <attribute name="Trusted-Library" value="true"/>
 616 -->
 617                 </manifest>
 618           </jar>
 619           </presetdef>
 620           <presetdef name="applet_tl.jar">
 621             <jar update="true" index="true" jarfile="@{jarfile}">
 622                 <manifest>
 623                 <attribute name="Application-Name" value="JalviewLite"/>
 624                 <attribute name="Permissions" value="all-permissions" />
 625                 <attribute name="Codebase" value="${applet.codebase}"/>
 626                 <attribute name="Trusted-Only" value="true"/>
 627                 <attribute name="Trusted-Library" value="true"/>
 628                 </manifest>
 629           </jar>
 630
 631           </presetdef>
 632           <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}"/>
 633           <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}"/>
 634           <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 635           <applet_tl.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}"/>
 636           <applet.jar jarfile="${packageDir}/examples/${jmolJar}"/>
 637           <applet_tl.jar jarfile="${packageDir}/examples/tl_${jmolJar}"/>
 638     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 639
 640       <fileset dir="${packageDir}/examples">
 641         <include name="*.jar" />
 642       </fileset>
 643     </signjar>
 644         </target>
 645         <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 646          <javadoc destdir="${javadocDir}">
 647                 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 648                 </packageset>
 649                 </javadoc>
 650         </target>
 651
 652 </project>