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. -->
  99     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 100     <property name="application.codebase" value="*.jalview.org" />
 101     <!-- and allowing the applet to be deployed from any URL -->
 102     <property name="applet.codebase" value="*" />
 103     <property name="applet.caller-codebase" value="${applet.codebase}" />
 104
 105                 <!-- build directory configuration -->
 106                 <property name="libDir" value="lib" />
 107                 <property name="resourceDir" value="resources" />
 108                 <property name="helpDir" value="help" />
 109                 <property name="docDir" value="doc" />
 110                 <property name="sourceDir" value="src" />
 111                 <property name="schemaDir" value="schemas" />
 112                 <property name="outputDir" value="classes" />
 113                 <property name="packageDir" value="dist" />
 114                 <property name="outputJar" value="jalview.jar" />
 115                 <!-- Jalview Applet JMol Jar Dependency -->
 116                 <property name="jmolJar" value="JmolApplet-12.2.4.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                         </fileset>
 147
 148                 </path>
 149                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 150                 <!-- The Location of the java 1.1.8 jdk -->
 151                 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 152                 -->
 153                 <property name="java118.home" value="${java.home}" />
 154                     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 155                 --><!-- jre for 1.4 version -->
 156                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 157
 158                 <!-- the classpath for building the 1.1 applet -->
 159                 <path id="jalviewlite.deps">
 160                         <fileset dir="${java118.home}">
 161                                 <include name="lib/classes.zip" />
 162                         </fileset>
 163                         <fileset dir="${java.home}/lib">
 164                                 <include name="plugin.jar"/>
 165                         </fileset>
 166                         <pathelement location="appletlib/${jmolJar}" />
 167                 </path>
 168     <!-- default location for outputting javadoc -->
 169     <property name="javadocDir" value="${packageDir}/javadoc"/>
 170         </target>
 171
 172
 173         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 174         <target name="buildPropertiesFile" depends="init">
 175                 <tstamp prefix="build">
 176                         <format property="date" pattern="dd MMMM yyyy" />
 177                 </tstamp>
 178                 <properties file="${outputDir}/.build_properties">
 179                         <header>
 180           ---Jalview Build Details---
 181         </header>
 182                         <property name="VERSION" value="${JALVIEW_VERSION}" />
 183                         <property name="BUILD_DATE" value="${build.date}" />
 184                 </properties>
 185         </target>
 186
 187
 188         <target name="clean" depends="init">
 189                 <!-- not efficient yet. -->
 190                 <delete dir="${outputDir}" includes="*,**/*"/>
 191         </target>
 192
 193         <target name="distclean" depends="init, clean">
 194
 195                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 196                 <delete>
 197                         <fileset dir=".">
 198                                 <include name="${outputJar}" />
 199                                 <include name="#*#" />
 200                                 <include name="#*.*#" />
 201                                 <include name="**/#*#" />
 202                                 <include name="**/#*.*#" />
 203                                 <include name="*~" />
 204                                 <include name="*.*~" />
 205                                 <include name="**/*~" />
 206                                 <include name="**/*.*~" />
 207                         </fileset>
 208                 </delete>
 209         </target>
 210
 211         <target name="prepare" depends="init">
 212                 <mkdir dir="${outputDir}" />
 213                 <copy todir="${outputDir}">
 214                         <fileset dir=".">
 215                                 <include name="${docDir}/**/*.*" />
 216                                 <include name="${helpDir}/**/*.*" />
 217                                 <include name="${libDir}/*.jar" />
 218                         </fileset>
 219                         <fileset dir="${resourceDir}">
 220                                 <include name="**/*.*" />
 221                         </fileset>
 222                 </copy>
 223         </target>
 224
 225         <target name="build" depends="prepare">
 226                 <!-- not efficient yet. -->
 227                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 228                         <exclude name="jalview/*applet*" />
 229                         <exclude name="jalview/appletgui/**" />
 230                         <exclude name="com/stevesoft/**" />
 231                 </javac>
 232         </target>
 233         <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 234                 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 235                         <arg line="html" />
 236                 </java>
 237         </target>
 238
 239         <target name="makefulldist" depends="makedist">
 240                 <copy todir="${packageDir}">
 241                         <fileset dir="${resourceDir}/images">
 242                                 <include name="${WebStartImage}"/>
 243                         </fileset>
 244                                         </copy>
 245
 246                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 247
 248     <!-- create a dummy jar which will eventually contain the jnlp template -->
 249     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 250                                 <fileset dir="${packageDir}">
 251                                         <include name="jalview.jar" />
 252                                 </fileset>
 253     </jar>
 254
 255         <mkdir dir="${packageDir}/JNLP-INF"/>
 256     <antcall target="writejnlpf">
 257        <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 258        <param name="inih" value="*" />
 259        <param name="maxh" value="*"/>
 260     </antcall>
 261
 262         <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 263                                 <fileset dir="${packageDir}">
 264                 <include name="JNLP-INF"/>
 265                                 </fileset>
 266         </jar>
 267
 268         <antcall target="writejnlpf">
 269                 <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 270                 <param name="inih" value="10M" />
 271           <param name="maxh" value="256M"/>
 272         </antcall>
 273
 274         <antcall target="writejnlpf">
 275           <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 276           <param name="inih" value="128M" />
 277                 <param name="maxh" value="512M"/>
 278         </antcall>
 279
 280         <antcall target="writejnlpf">
 281           <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 282           <param name="inih" value="256M" />
 283           <param name="maxh" value="1024M"/>
 284         </antcall>
 285
 286                         <!-- finally, need to postprocess to add in associations at end of 'information' element
 287
 288                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 289
 290                 </xslt>
 291
 292
 293                         -->
 294                                         <!--
 295                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 296         <association mime-type="application-x/ext-file" extensions="fasta"/>
 297         <association mime-type="application-x/ext-file" extensions="fastq"/>
 298         <association mime-type="application-x/ext-file" extensions="blc"/>
 299         <association mime-type="application-x/ext-file" extensions="msf"/>
 300         <association mime-type="application-x/ext-file" extensions="pfam"/>
 301         <association mime-type="application-x/ext-file" extensions="aln"/>
 302         <association mime-type="application-x/ext-file" extensions="pir"/>
 303         <association mime-type="application-x/ext-file" extensions="amsa"/>
 304         <association mime-type="application-x/ext-file" extensions="stk"/>
 305         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 306     <!-- and sign the jars -->
 307     <!-- the default keystore details might need to be edited here -->
 308     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 309         <fileset dir="${packageDir}">
 310           <include name="*.jar" />
 311         </fileset>
 312     </signjar>
 313         </target>
 314
 315         <target name="runenv" depends="init">
 316                 <path id="run.classpath">
 317                         <pathelement location="${outputDir}" />
 318                         <fileset dir="${outputDir}">
 319                                 <include name="${libDir}/*.jar" />
 320                         </fileset>
 321                 </path>
 322                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 323
 324                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 325       </echo>
 326         </target>
 327   <target name="writejnlpf">
 328         <presetdef name="jnlpf">
 329             <jnlp codebase="${WebStartLocation}">
 330               <information>
 331                 <title>Jalview</title>
 332                 <vendor>The Barton Group</vendor>
 333                 <homepage href="http://www.jalview.org" />
 334                 <description>Jalview Multiple Alignment Editor</description>
 335                 <description kind="short">Jalview</description>
 336                 <icon href="${WebStartImage}" />
 337                 <offline_allowed />
 338               </information>
 339               <resources>
 340                 <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 341                 <fileset dir="${packageDir}">
 342                   <include name="jalview.jar" />
 343                 </fileset>
 344                 <fileset dir="${packageDir}">
 345                   <include name="*.jar" />
 346                   <include name="*_*.jar" />
 347                   <exclude name="jalview.jar" />
 348                 </fileset>
 349                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 350               </resources>
 351               <application_desc main_class="jalview.bin.Jalview">
 352               </application_desc>
 353               <security>
 354                 <all_permissions />
 355               </security>
 356             </jnlp>
 357             </presetdef>
 358
 359             <jnlpf toFile="${jnlpFile}"/>
 360   </target>
 361         <target name="buildextclients" depends="init">
 362                 <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" />
 363                 <condition property="dontextbuild">
 364                         <equals arg1="n" arg2="${doextbuild.response}" />
 365                 </condition>
 366                 <condition property="dontextbuild">
 367                         <equals arg1="N" arg2="${doextbuild.response}" />
 368                 </condition>
 369                 <fail if="dontextbuild">
 370         Build External Client Code process aborted by user. Jalview source is unchanged.
 371       </fail>
 372                 <!-- Currently, this doesn't happen automatically.
 373      1. Run WSDL2Java as below, which generates an ext.vamsas +
 374      vamsas.<datapackages> fileset.
 375      2. refactor ext.vamsas.SpecificserviceWS* to
 376      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 377      3. Update the jalview.ws.*WServices classes to reflect the
 378      interface type, and all locations of this wsdl type that Jalview
 379      might be using.
 380
 381 -->
 382                 <path id="axisbuild">
 383                         <path refid="build.classpath" />
 384                 </path>
 385                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 386                 <move todir="./bak">
 387                         <fileset dir="${sourceDir}" id="client">
 388                                 <include name="${wsdl.ClientNS}/*.*" />
 389                         </fileset>
 390                 </move>
 391
 392                 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 393                         <mappingSet>
 394                                 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 395                                 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 396                         </mappingSet>
 397                 </axis-wsdl2java>
 398         </target>
 399
 400         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 401                 <!-- make the package jar if not already existing -->
 402                 <mkdir dir="${packageDir}" />
 403                 <!-- clean dir if it already existed -->
 404                 <delete>
 405                         <fileset dir="${packageDir}">
 406                                 <include name="*.jar"/>
 407                         </fileset>
 408                 </delete>
 409                 <jar destfile="${packageDir}/${outputJar}" index="true">
 410                         <manifest>
 411                                 <attribute name="Main-Class" value="jalview.bin.Jalview" />
 412         <attribute name="Permissions" value="all-permissions" />
 413         <attribute name="Application-Name" value="Jalview Desktop" />
 414         <attribute name="Codebase" value="${application.codebase}" />
 415                         </manifest>
 416                         <fileset dir="${outputDir}/">
 417                                 <exclude name="cache*/**" />
 418                                 <exclude name="*.jar" />
 419                                 <exclude name="*.jar.*" />
 420                                 <exclude name="**/*.jar" />
 421                                 <exclude name="**/*.jar.*" />
 422                         </fileset>
 423                 </jar>
 424
 425                 <copy toDir="${packageDir}" flatten="true">
 426                         <fileset dir="${outputDir}">
 427                                 <include name="*.jar" />
 428                                 <include name="**/*.jar" />
 429                         </fileset>
 430                 </copy>
 431         </target>
 432
 433
 434         <!-- jalopy code reformatter -->
 435         <target name="sourcescrub" depends="init,build">
 436                 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 437                         <fileset dir="${sourceDir}">
 438                                 <include name="*.java" />
 439                                 <include name="**/*.java" />
 440                                 <include name="**/**/*.java" />
 441                         </fileset>
 442                 </jalopy>
 443         </target>
 444
 445
 446
 447         <!-- Compile, package and obfuscate Jalview Applet -->
 448         <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 449
 450         <target name="compileApplet" depends="init,clean">
 451                 <mkdir dir="${outputDir}" />
 452                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 453                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 454                         excludes="ext/**,MCview/**,org/**,vamsas/**" />
 455         </target>
 456
 457         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 458                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 459                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 460                 <copy todir="${outputDir}/lang">
 461                         <fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
 462                 <jar destfile="in.jar" index="true">
 463                         <manifest>
 464                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 465                 <attribute name="Application-Name" value="JalviewLite" />
 466             <attribute name="Codebase" value="${applet.codebase}" />
 467                         </manifest>
 468                         <fileset dir="${outputDir}">
 469                                 <include name="com/**" />
 470                                 <include name="MCview/**" />
 471                                 <include name="jalview/**" />
 472                                 <include name=".build_properties" />
 473                                 <include name="images/idwidth.gif" />
 474                                 <include name="images/link.gif" />
 475                                 <include name="lang/**" />
 476                         </fileset>
 477                 </jar>
 478         </target>
 479         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 480         </target>
 481         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 482                 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 483                 <delete file="in.jar" />
 484         </target>
 485         <target name="-obfuscatereally" unless="donotobfuscate">
 486
 487                 <path id="obfuscateDeps.path">
 488                         <pathelement location="${applet.jre.tools}" />
 489                         <pathelement location="appletlib/${jmolJar}" />
 490                 </path>
 491                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 492
 493                 <proguard>
 494                         <injar file="in.jar" />
 495                         <outjar file="${jalviewLiteJar}" />
 496                         <libraryjar refid="obfuscateDeps.path" />
 497                         <dontwarn/>
 498                         <keep access="public" type="class" name="jalview.bin.JalviewLite">
 499                                 <field access="public" />
 500                                 <method access="public" />
 501                                 <constructor access="public" />
 502                         </keep>
 503                         <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 504                                 <field access="public" />
 505                                 <method access="public" />
 506                                 <constructor access="public" />
 507                         </keep>
 508                         <!--      -libraryjars "${obfuscateDeps}"
 509       -injars      in.jar
 510       -outjars     jalviewApplet.jar
 511       -keep public class jalview.bin.JalviewLite
 512        { public * ; } -->
 513                 </proguard>
 514                 <delete file="in.jar" />
 515         </target>
 516
 517         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 518                 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 519                 <delete>
 520                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 521                                 <include name="*.java" />
 522                                 <include name="descriptors/*.java" />
 523                         </fileset>
 524                 </delete>
 525                 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 526                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 527                 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 528                 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 529                 <!--
 530                 now build the jalview.binding package with the old schema set
 531                 -->
 532                 <delete>
 533                         <fileset dir="${sourceDir}/jalview/binding/">
 534                                 <include name="**" />
 535                         </fileset>
 536                 </delete>
 537                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 538                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 539                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 540         </target>
 541         <target name="sourcedist" description="create jalview source distribution" depends="init">
 542                 <delete file="${source.dist.name}" />
 543                 <tar destfile="${source.dist.name}" compression="gzip">
 544                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 545                                 <include name="LICENSE" />
 546                                 <include name="README" />
 547                                 <include name="build.xml" />
 548                                 <include name="jalview-jalopy.xml" />
 549                                 <include name="JalviewApplet.jpx" />
 550                                 <include name="JalviewX.jpx" />
 551                                 <include name="nbbuild.xml"/>
 552                                 <include name="nbproject/genfiles.properties"/>
 553         <include name="nbproject/project.properties"/>
 554         <include name="nbproject/project.xml"/>
 555                                 <include name="${sourceDir}/*.java" />
 556                                 <include name="${sourceDir}/**/*.java" />
 557                                 <include name="${sourceDir}/**/*.cdr" />
 558                                 <include name="${libDir}/**/*" />
 559                                 <include name="${resourceDir}/**/*" />
 560                                 <include name="${helpDir}/**/*" />
 561                                 <include name="appletlib/${jmolJar}" />
 562                                 <exclude name="**/*locales" />
 563                                 <exclude name="*locales/**" />
 564                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 565                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 566                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 567                                 <exclude name="utils/InstallAnywhere/**locale*" />
 568                                 <exclude name="utils/InstallAnywhere/**locale*/**" />
 569                                 <include name="${schemaDir}/**/*" />
 570                                 <include name="utils/**/*" />
 571                                 <include name="${docDir}/**/*" />
 572                                 <include name="examples/**/*" />
 573                         </tarfileset>
 574                 </tar>
 575         </target>
 576         <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 577           <copy todir="${packageDir}/examples">
 578           <fileset dir="examples">
 579                 <include name="**/*"/>
 580                 <include name="javascript/*"/>
 581       <include name="jmol/*"/>
 582           </fileset>
 583                 <fileset dir=".">
 584         <include name="${jalviewLiteJar}" />
 585                         </fileset>
 586                 <fileset dir="appletlib">
 587                       <include name="**/*"/>
 588                         </fileset>
 589           </copy>
 590             <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 591             <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 592                 <manifest>
 593                 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 594                 <!--          <attribute name="Permissions" value="sandbox" /> -->
 595                 <!--<attribute name="Trusted-Lib" value="true" /> -->
 596                 <attribute name="Codebase" value="${applet.codebase}"/>
 597                 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 598                   </manifest>
 599                 </jar>
 600     <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 601       <fileset dir="${packageDir}/examples">
 602         <include name="*.jar" />
 603       </fileset>
 604     </signjar>
 605     <presetdef name="ap_applet.jar">
 606       <!-- build a signed applet with 'all-permissions' -
 607                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 608                           JalviewLite+JmolApplet linked sequence/structure fails
 609                           Mixed code warnings are raised
 610                           -->
 611       <jar update="true" index="true">
 612         <manifest>
 613           <attribute name="Application-Name" value="JalviewLite" />
 614           <attribute name="Permissions" value="all-permissions" />
 615           <attribute name="Codebase" value="${applet.codebase}" />
 616           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 617           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 618         </manifest>
 619       </jar>
 620     </presetdef>
 621     <presetdef name="applet.jar">
 622       <!-- build signed applet with sandbox permissions -
 623                           Needs 'param name="permissions' value="sandbox"' in applet tag
 624                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 625                         -->
 626
 627       <jar update="true" index="true">
 628         <manifest>
 629           <attribute name="Application-Name" value="JalviewLite" />
 630           <attribute name="Permissions" value="sandbox" />
 631           <attribute name="Codebase" value="${applet.codebase}" />
 632           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 633           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 634         </manifest>
 635       </jar>
 636     </presetdef>
 637     <presetdef name="tl_applet.jar">
 638       <!-- build signed applet with trusted library/trusted permissions -
 639                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 640                                j1.7_45:
 641                                No mixed code warnings raised
 642                                Jmol/JalviewLite sequence/structure example doesn't link structures
 643                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 644
 645                               -->
 646
 647       <jar update="true" index="true">
 648         <manifest>
 649           <attribute name="Application-Name" value="JalviewLite" />
 650           <attribute name="Permissions" value="all-permissions" />
 651           <attribute name="Codebase" value="${applet.codebase}" />
 652           <attribute name="Trusted-Only" value="true" />
 653           <attribute name="Trusted-Library" value="true" />
 654         </manifest>
 655       </jar>
 656     </presetdef>
 657     <presetdef name="to_applet.jar">
 658       <!-- not fully test variant (yet) -->
 659       <jar update="true" index="true">
 660         <manifest>
 661           <attribute name="Application-Name" value="JalviewLite" />
 662           <attribute name="Permissions" value="all-permissions" />
 663           <attribute name="Codebase" value="${applet.codebase}" />
 664           <attribute name="Trusted-Only" value="true" />
 665         </manifest>
 666       </jar>
 667     </presetdef>
 668     <!-- create differently privileged artefacts -->
 669     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 670     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}"/>
 671     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 672     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 673     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 674     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 675     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 676     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 677     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 678     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 679     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 680     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 681     <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 682     <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 683     <!-- finally, create manifest for original jars -->
 684     <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 685     <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 686
 687     <!-- todo - write examples/downloads for alternate versions of the applet -->
 688     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 689
 690       <fileset dir="${packageDir}/examples">
 691         <include name="${jalviewLiteJar}" />
 692         <include name="${jmolJar}" />
 693         <include name="to_${jalviewLiteJar}" />
 694         <include name="to_${jmolJar}" />
 695         <include name="tl_${jalviewLiteJar}" />
 696         <include name="tl_${jmolJar}" />
 697         <include name="ap_${jalviewLiteJar}" />
 698         <include name="ap_${jmolJar}" />
 699       </fileset>
 700     </signjar>
 701         </target>
 702         <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 703          <javadoc destdir="${javadocDir}">
 704                 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 705                 </packageset>
 706                 </javadoc>
 707         </target>
 708
 709 </project>