build.xml

   1 <?xml version="1.0"?>
   2 <!--
   3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   4  * Copyright (C) 2014 The Jalview Authors
   5  *
   6  * This file is part of Jalview.
   7  *
   8  * Jalview is free software: you can redistribute it and/or
   9  * modify it under the terms of the GNU General Public License
  10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  18  * The Jalview Authors are detailed in the 'AUTHORS' file.
  19 -->
  20 <project name="jalviewX" default="usage" basedir=".">
  21         <!-- we use jalopy to format our sources -->
  22         <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
  23                 <classpath>
  24                         <fileset dir="utils/jalopy/lib">
  25                                 <include name="*.jar" />
  26                         </fileset>
  27                 </classpath>
  28         </taskdef>
  29
  30         <target name="help" depends="usage" />
  31         <target name="usage">
  32                 <echo message="~~~Jalview Ant build.xml Usage~~~~" />
  33                 <echo message="Targets include:" />
  34                 <echo message="usage - default target, displays this message" />
  35                 <echo message="buildindices - generates JavaHelpSearch from the help files" />
  36                 <echo message="build - compiles all necessary files for Application" />
  37                 <echo message="makedist - compiles and places all necessary jar files into directory dist" />
  38                 <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
  39                 <echo message="              this needs a keystore and key. See docs/building.html for more information." />
  40                 <echo message="compileApplet - compiles all necessary files for Applet" />
  41                 <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
  42                 <echo message="See docs/building.html and the comments in build file for other targets." />
  43                 <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
  44                 <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
  45         </target>
  46
  47
  48         <!-- utils is a class path to additional utilities needed for
  49     building docs, jars and webstart stuff -->
  50         <!--
  51         Userdefined build property defaults
  52
  53         wsdl.server list (plus namespace mapping info ???)  - also want
  54                 ... to make this a dynamically generatable property
  55         WebStart Location
  56         Build location - provide a temporary root for speed
  57         jarsigner keystore and info
  58         Jakarta and axis classpath ?
  59         Default argument for starting Jalview (if it exists).
  60
  61 -->
  62
  63         <target name="init">
  64                 <path id="axis.classpath">
  65                         <!-->
  66                         <fileset dir="/usr/local/axis/lib">
  67                                 <include name="**/*.jar" />
  68                         </fileset>
  69                         <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
  70                                 <include name="**/*.jar"/>
  71                                 <include name="*.jar"/>
  72                         </fileset> -->
  73       </path>
  74                 <!-- Jalview Version String displayed by application on startup and used to check for updates -->
  75                 <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
  76                 <!-- 2.4 (VAMSAS)" -->
  77                 <!-- Include debugging information in javac true or false -->
  78                 <property name="javac.debug" value="true" />
  79
  80                 <!-- JarSigner Key Store for Webstart Distribution -->
  81                 <property name="jalview.keystore" value="./keys/.keystore" />
  82                 <!-- Keystore Password -->
  83                 <property name="jalview.keystore.pass" value="alignmentisfun" />
  84                 <!-- Key Name -->
  85                 <property name="jalview.key" value="jalview" />
  86                 <!-- Key Password -->
  87                 <property name="jalview.key.pass" value="alignmentisfun" />
  88
  89
  90
  91                 <!-- Don't change anything below here unless you know what you are doing! -->
  92                 <!-- Url path for WebStart in JNLP file -->
  93                 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  94                 <!-- Webstart Image - looked for in resources/images -->
  95                 <property name="WebStartImage" value="JalviewLogo_big.png"/>
  96                 <!-- J2SE version needed for webstart launch -->
  97                 <property name="j2sev" value="1.6+"/>
  98
  99     <!-- Permissions for running Java applets and applications. -->
 100     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 101     <property name="application.codebase" value="*.jalview.org" />
 102     <!-- and allowing the applet to be deployed from any URL -->
 103     <property name="applet.codebase" value="*" />
 104     <property name="applet.caller-codebase" value="${applet.codebase}" />
 105
 106                 <!-- build directory configuration -->
 107                 <property name="libDir" value="lib" />
 108                 <property name="resourceDir" value="resources" />
 109                 <property name="helpDir" value="help" />
 110                 <property name="docDir" value="doc" />
 111                 <property name="sourceDir" value="src" />
 112                 <property name="schemaDir" value="schemas" />
 113                 <property name="outputDir" value="classes" />
 114                 <property name="packageDir" value="dist" />
 115                 <property name="outputJar" value="jalview.jar" />
 116                 <!-- Jalview Applet JMol Jar Dependency -->
 117                 <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 118                 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 119                 <!-- switch to indicate if we should obfuscate jalviewLite -->
 120                 <!--<property name="donotobfuscate" value="true"/> -->
 121
 122                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 123                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 124                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 125                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 126                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 127                 <property name="WSInterf" value="MsaWS" />
 128                 <property name="wsdl.Namespace" value="vamsas" />
 129                 <property name="wsdl.ClientNS" value="ext.vamsas" />
 130                 <!-- the class path for building the application -->
 131                 <path id="build.classpath">
 132                         <fileset dir="utils">
 133                                 <include name="*.jar" />
 134                                 <include name="**/*.jar" />
 135                         </fileset>
 136                         <fileset dir="${libDir}">
 137                                 <include name="*.jar" />
 138                                 <include name="**/*.jar" />
 139                         </fileset>
 140                         <fileset dir="${java.home}/lib">
 141                                 <include name="plugin.jar"/>
 142                         </fileset>
 143                         <fileset dir="appletlib">
 144                                 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 145                                 -->
 146                                 <include name="${jmolJar}" />
 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/${jmolJar}" />
 168                 </path>
 169     <!-- default location for outputting javadoc -->
 170     <property name="javadocDir" value="${packageDir}/javadoc"/>
 171         </target>
 172
 173
 174         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 175         <target name="buildPropertiesFile" depends="init">
 176                 <tstamp prefix="build">
 177                         <format property="date" pattern="dd MMMM yyyy" />
 178                 </tstamp>
 179                 <properties file="${outputDir}/.build_properties">
 180                         <header>
 181           ---Jalview Build Details---
 182         </header>
 183                         <property name="VERSION" value="${JALVIEW_VERSION}" />
 184                         <property name="BUILD_DATE" value="${build.date}" />
 185                 </properties>
 186         </target>
 187
 188
 189         <target name="clean" depends="init">
 190                 <!-- not efficient yet. -->
 191                 <delete dir="${outputDir}" includes="*,**/*"/>
 192         </target>
 193
 194         <target name="distclean" depends="init, clean">
 195
 196                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 197                 <delete>
 198                         <fileset dir=".">
 199                                 <include name="${outputJar}" />
 200                                 <include name="#*#" />
 201                                 <include name="#*.*#" />
 202                                 <include name="**/#*#" />
 203                                 <include name="**/#*.*#" />
 204                                 <include name="*~" />
 205                                 <include name="*.*~" />
 206                                 <include name="**/*~" />
 207                                 <include name="**/*.*~" />
 208                         </fileset>
 209                 </delete>
 210         </target>
 211
 212         <target name="prepare" depends="init">
 213                 <mkdir dir="${outputDir}" />
 214                 <copy todir="${outputDir}">
 215                         <fileset dir=".">
 216                                 <include name="${docDir}/**/*.*" />
 217                                 <include name="${helpDir}/**/*.*" />
 218                                 <include name="${libDir}/*.jar" />
 219                         </fileset>
 220                         <fileset dir="${resourceDir}">
 221                                 <include name="**/*.*" />
 222                         </fileset>
 223                 </copy>
 224         </target>
 225
 226         <target name="build" depends="prepare">
 227                 <!-- not efficient yet. -->
 228                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 229                         <exclude name="jalview/*applet*" />
 230                         <exclude name="jalview/appletgui/**" />
 231                         <exclude name="com/stevesoft/**" />
 232                 </javac>
 233         </target>
 234         <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 235                 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 236                         <arg line="html" />
 237                 </java>
 238         </target>
 239
 240         <target name="makefulldist" depends="makedist">
 241                 <copy todir="${packageDir}">
 242                         <fileset dir="${resourceDir}/images">
 243                                 <include name="${WebStartImage}"/>
 244                         </fileset>
 245                                         </copy>
 246
 247                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 248
 249     <!-- create a dummy jar which will eventually contain the jnlp template -->
 250     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 251                                 <fileset dir="${packageDir}">
 252                                         <include name="jalview.jar" />
 253                                 </fileset>
 254     </jar>
 255
 256         <mkdir dir="${packageDir}/JNLP-INF"/>
 257     <antcall target="writejnlpf">
 258        <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 259        <param name="inih" value="*" />
 260        <param name="maxh" value="*"/>
 261     </antcall>
 262
 263         <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 264                                 <fileset dir="${packageDir}">
 265                 <include name="JNLP-INF"/>
 266                                 </fileset>
 267         </jar>
 268
 269         <antcall target="writejnlpf">
 270                 <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 271                 <param name="inih" value="10M" />
 272           <param name="maxh" value="256M"/>
 273         </antcall>
 274
 275         <antcall target="writejnlpf">
 276           <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 277           <param name="inih" value="128M" />
 278                 <param name="maxh" value="512M"/>
 279         </antcall>
 280
 281         <antcall target="writejnlpf">
 282           <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 283           <param name="inih" value="256M" />
 284           <param name="maxh" value="1024M"/>
 285         </antcall>
 286
 287                         <!-- finally, need to postprocess to add in associations at end of 'information' element
 288
 289                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 290
 291                 </xslt>
 292
 293
 294                         -->
 295                                         <!--
 296                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 297         <association mime-type="application-x/ext-file" extensions="fasta"/>
 298         <association mime-type="application-x/ext-file" extensions="mfa"/>
 299         <association mime-type="application-x/ext-file" extensions="fastq"/>
 300         <association mime-type="application-x/ext-file" extensions="blc"/>
 301         <association mime-type="application-x/ext-file" extensions="msf"/>
 302         <association mime-type="application-x/ext-file" extensions="pfam"/>
 303         <association mime-type="application-x/ext-file" extensions="aln"/>
 304         <association mime-type="application-x/ext-file" extensions="pir"/>
 305         <association mime-type="application-x/ext-file" extensions="amsa"/>
 306         <association mime-type="application-x/ext-file" extensions="stk"/>
 307         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 308     <!-- and sign the jars -->
 309     <!-- the default keystore details might need to be edited here -->
 310     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 311         <fileset dir="${packageDir}">
 312           <include name="*.jar" />
 313         </fileset>
 314     </signjar>
 315         </target>
 316
 317         <target name="runenv" depends="init">
 318                 <path id="run.classpath">
 319                         <pathelement location="${outputDir}" />
 320                         <fileset dir="${outputDir}">
 321                                 <include name="${libDir}/*.jar" />
 322                         </fileset>
 323                 </path>
 324                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 325
 326                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 327       </echo>
 328         </target>
 329   <target name="writejnlpf">
 330         <presetdef name="jnlpf">
 331             <jnlp codebase="${WebStartLocation}">
 332               <information>
 333                 <title>Jalview</title>
 334                 <vendor>The Barton Group</vendor>
 335                 <homepage href="http://www.jalview.org" />
 336                 <description>Jalview Multiple Alignment Editor</description>
 337                 <description kind="short">Jalview</description>
 338                 <icon href="${WebStartImage}" />
 339                 <offline_allowed />
 340               </information>
 341               <resources>
 342                 <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 343                 <fileset dir="${packageDir}">
 344                   <include name="jalview.jar" />
 345                 </fileset>
 346                 <fileset dir="${packageDir}">
 347                   <include name="*.jar" />
 348                   <include name="*_*.jar" />
 349                   <exclude name="jalview.jar" />
 350                 </fileset>
 351                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 352               </resources>
 353               <application_desc main_class="jalview.bin.Jalview">
 354               </application_desc>
 355               <security>
 356                 <all_permissions />
 357               </security>
 358             </jnlp>
 359             </presetdef>
 360
 361             <jnlpf toFile="${jnlpFile}"/>
 362   </target>
 363         <target name="buildextclients" depends="init">
 364                 <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" />
 365                 <condition property="dontextbuild">
 366                         <equals arg1="n" arg2="${doextbuild.response}" />
 367                 </condition>
 368                 <condition property="dontextbuild">
 369                         <equals arg1="N" arg2="${doextbuild.response}" />
 370                 </condition>
 371                 <fail if="dontextbuild">
 372         Build External Client Code process aborted by user. Jalview source is unchanged.
 373       </fail>
 374                 <!-- Currently, this doesn't happen automatically.
 375      1. Run WSDL2Java as below, which generates an ext.vamsas +
 376      vamsas.<datapackages> fileset.
 377      2. refactor ext.vamsas.SpecificserviceWS* to
 378      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 379      3. Update the jalview.ws.*WServices classes to reflect the
 380      interface type, and all locations of this wsdl type that Jalview
 381      might be using.
 382
 383 -->
 384                 <path id="axisbuild">
 385                         <path refid="build.classpath" />
 386                 </path>
 387                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 388                 <move todir="./bak">
 389                         <fileset dir="${sourceDir}" id="client">
 390                                 <include name="${wsdl.ClientNS}/*.*" />
 391                         </fileset>
 392                 </move>
 393
 394                 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 395                         <mappingSet>
 396                                 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 397                                 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 398                         </mappingSet>
 399                 </axis-wsdl2java>
 400         </target>
 401
 402         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 403                 <!-- make the package jar if not already existing -->
 404                 <mkdir dir="${packageDir}" />
 405                 <!-- clean dir if it already existed -->
 406                 <delete>
 407                         <fileset dir="${packageDir}">
 408                                 <include name="*.jar"/>
 409                         </fileset>
 410                 </delete>
 411                 <jar destfile="${packageDir}/${outputJar}" index="true">
 412                         <manifest>
 413                                 <attribute name="Main-Class" value="jalview.bin.Jalview" />
 414         <attribute name="Permissions" value="all-permissions" />
 415         <attribute name="Application-Name" value="Jalview Desktop" />
 416         <attribute name="Codebase" value="${application.codebase}" />
 417                         </manifest>
 418                         <fileset dir="${outputDir}/">
 419                                 <exclude name="cache*/**" />
 420                                 <exclude name="*.jar" />
 421                                 <exclude name="*.jar.*" />
 422                                 <exclude name="**/*.jar" />
 423                                 <exclude name="**/*.jar.*" />
 424                         </fileset>
 425                 </jar>
 426
 427                 <copy toDir="${packageDir}" flatten="true">
 428                         <fileset dir="${outputDir}">
 429                                 <include name="*.jar" />
 430                                 <include name="**/*.jar" />
 431                         </fileset>
 432                 </copy>
 433         </target>
 434
 435
 436         <!-- jalopy code reformatter -->
 437         <target name="sourcescrub" depends="init,build">
 438                 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 439                         <fileset dir="${sourceDir}">
 440                                 <include name="*.java" />
 441                                 <include name="**/*.java" />
 442                                 <include name="**/**/*.java" />
 443                         </fileset>
 444                 </jalopy>
 445         </target>
 446
 447
 448
 449         <!-- Compile, package and obfuscate Jalview Applet -->
 450         <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 451
 452         <target name="compileApplet" depends="init,clean">
 453                 <mkdir dir="${outputDir}" />
 454                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 455                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 456                         excludes="ext/**,MCview/**,org/**,vamsas/**" />
 457         </target>
 458
 459         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 460                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 461                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 462                 <copy todir="${outputDir}/lang">
 463                         <fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
 464                 <jar destfile="in.jar" index="true">
 465                         <manifest>
 466                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 467                 <attribute name="Application-Name" value="JalviewLite" />
 468             <attribute name="Codebase" value="${applet.codebase}" />
 469                         </manifest>
 470                         <fileset dir="${outputDir}">
 471                                 <include name="com/**" />
 472                                 <include name="MCview/**" />
 473                                 <include name="jalview/**" />
 474                                 <include name=".build_properties" />
 475                                 <include name="images/idwidth.gif" />
 476                                 <include name="images/link.gif" />
 477                                 <include name="lang/**" />
 478                         </fileset>
 479                 </jar>
 480         </target>
 481         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 482         </target>
 483         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 484                 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 485                 <delete file="in.jar" />
 486         </target>
 487         <target name="-obfuscatereally" unless="donotobfuscate">
 488
 489                 <path id="obfuscateDeps.path">
 490                         <pathelement location="${applet.jre.tools}" />
 491                         <pathelement location="appletlib/${jmolJar}" />
 492                 </path>
 493                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 494
 495                 <proguard>
 496                         <injar file="in.jar" />
 497                         <outjar file="${jalviewLiteJar}" />
 498                         <libraryjar refid="obfuscateDeps.path" />
 499                         <dontwarn/>
 500                         <keep access="public" type="class" name="jalview.bin.JalviewLite">
 501                                 <field access="public" />
 502                                 <method access="public" />
 503                                 <constructor access="public" />
 504                         </keep>
 505                         <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 506                                 <field access="public" />
 507                                 <method access="public" />
 508                                 <constructor access="public" />
 509                         </keep>
 510                         <!--      -libraryjars "${obfuscateDeps}"
 511       -injars      in.jar
 512       -outjars     jalviewApplet.jar
 513       -keep public class jalview.bin.JalviewLite
 514        { public * ; } -->
 515                 </proguard>
 516                 <delete file="in.jar" />
 517         </target>
 518
 519         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 520                 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 521                 <delete>
 522                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 523                                 <include name="*.java" />
 524                                 <include name="descriptors/*.java" />
 525                         </fileset>
 526                 </delete>
 527                 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 528                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 529                 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 530                 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 531                 <!--
 532                 now build the jalview.binding package with the old schema set
 533                 -->
 534                 <delete>
 535                         <fileset dir="${sourceDir}/jalview/binding/">
 536                                 <include name="**" />
 537                         </fileset>
 538                 </delete>
 539                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 540                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 541                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 542         </target>
 543         <target name="sourcedist" description="create jalview source distribution" depends="init">
 544                 <delete file="${source.dist.name}" />
 545                 <tar destfile="${source.dist.name}" compression="gzip">
 546                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 547                                 <include name="LICENSE" />
 548                                 <include name="README" />
 549                                 <include name="build.xml" />
 550                                 <include name="jalview-jalopy.xml" />
 551                                 <include name="JalviewApplet.jpx" />
 552                                 <include name="JalviewX.jpx" />
 553                                 <include name="nbbuild.xml"/>
 554                                 <include name="nbproject/genfiles.properties"/>
 555         <include name="nbproject/project.properties"/>
 556         <include name="nbproject/project.xml"/>
 557                                 <include name="${sourceDir}/*.java" />
 558                                 <include name="${sourceDir}/**/*.java" />
 559                                 <include name="${sourceDir}/**/*.cdr" />
 560                                 <include name="${libDir}/**/*" />
 561                                 <include name="${resourceDir}/**/*" />
 562                                 <include name="${helpDir}/**/*" />
 563                                 <include name="appletlib/${jmolJar}" />
 564                                 <exclude name="**/*locales" />
 565                                 <exclude name="*locales/**" />
 566                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 567                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 568                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 569                                 <exclude name="utils/InstallAnywhere/**locale*" />
 570                                 <exclude name="utils/InstallAnywhere/**locale*/**" />
 571                                 <include name="${schemaDir}/**/*" />
 572                                 <include name="utils/**/*" />
 573                                 <include name="${docDir}/**/*" />
 574                                 <include name="examples/**/*" />
 575                         </tarfileset>
 576                 </tar>
 577         </target>
 578         <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 579           <copy todir="${packageDir}/examples">
 580           <fileset dir="examples">
 581                 <include name="**/*"/>
 582                 <include name="javascript/*"/>
 583       <include name="jmol/*"/>
 584           </fileset>
 585                 <fileset dir=".">
 586         <include name="${jalviewLiteJar}" />
 587                         </fileset>
 588                 <fileset dir="appletlib">
 589                       <include name="**/*"/>
 590                         </fileset>
 591           </copy>
 592             <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 593             <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 594                 <manifest>
 595                 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 596                 <!--          <attribute name="Permissions" value="sandbox" /> -->
 597                 <!--<attribute name="Trusted-Lib" value="true" /> -->
 598                 <attribute name="Codebase" value="${applet.codebase}"/>
 599                 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 600                   </manifest>
 601                 </jar>
 602     <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 603       <fileset dir="${packageDir}/examples">
 604         <include name="*.jar" />
 605       </fileset>
 606     </signjar>
 607     <presetdef name="ap_applet.jar">
 608       <!-- build a signed applet with 'all-permissions' -
 609                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 610                           JalviewLite+JmolApplet linked sequence/structure fails
 611                           Mixed code warnings are raised
 612                           -->
 613       <jar update="true" index="true">
 614         <manifest>
 615           <attribute name="Application-Name" value="JalviewLite" />
 616           <attribute name="Permissions" value="all-permissions" />
 617           <attribute name="Codebase" value="${applet.codebase}" />
 618           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 619           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 620         </manifest>
 621       </jar>
 622     </presetdef>
 623     <presetdef name="applet.jar">
 624       <!-- build signed applet with sandbox permissions -
 625                           Needs 'param name="permissions' value="sandbox"' in applet tag
 626                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 627                         -->
 628
 629       <jar update="true" index="true">
 630         <manifest>
 631           <attribute name="Application-Name" value="JalviewLite" />
 632           <attribute name="Permissions" value="sandbox" />
 633           <attribute name="Codebase" value="${applet.codebase}" />
 634           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 635           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 636         </manifest>
 637       </jar>
 638     </presetdef>
 639     <presetdef name="tl_applet.jar">
 640       <!-- build signed applet with trusted library/trusted permissions -
 641                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 642                                j1.7_45:
 643                                No mixed code warnings raised
 644                                Jmol/JalviewLite sequence/structure example doesn't link structures
 645                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 646
 647                               -->
 648
 649       <jar update="true" index="true">
 650         <manifest>
 651           <attribute name="Application-Name" value="JalviewLite" />
 652           <attribute name="Permissions" value="all-permissions" />
 653           <attribute name="Codebase" value="${applet.codebase}" />
 654           <attribute name="Trusted-Only" value="true" />
 655           <attribute name="Trusted-Library" value="true" />
 656         </manifest>
 657       </jar>
 658     </presetdef>
 659     <presetdef name="to_applet.jar">
 660       <!-- not fully test variant (yet) -->
 661       <jar update="true" index="true">
 662         <manifest>
 663           <attribute name="Application-Name" value="JalviewLite" />
 664           <attribute name="Permissions" value="all-permissions" />
 665           <attribute name="Codebase" value="${applet.codebase}" />
 666           <attribute name="Trusted-Only" value="true" />
 667         </manifest>
 668       </jar>
 669     </presetdef>
 670     <!-- create differently privileged artefacts -->
 671     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 672     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 673     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 674     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 675     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 676     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 677     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 678     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 679     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 680     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 681     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 682     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 683     <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 684     <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 685     <!-- finally, create manifest for original jars -->
 686     <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 687     <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 688
 689     <!-- todo - write examples/downloads for alternate versions of the applet -->
 690     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 691
 692       <fileset dir="${packageDir}/examples">
 693         <exclude name="u_*.jar"/>
 694         <include name="${jalviewLiteJar}" />
 695         <include name="${jmolJar}" />
 696         <include name="to_${jalviewLiteJar}" />
 697         <include name="to_${jmolJar}" />
 698         <include name="tl_${jalviewLiteJar}" />
 699         <include name="tl_${jmolJar}" />
 700         <include name="ap_${jalviewLiteJar}" />
 701         <include name="ap_${jmolJar}" />
 702       </fileset>
 703     </signjar>
 704     <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 705     <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 706   </target>
 707   <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 708     <javadoc destdir="${javadocDir}">
 709       <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 710       </packageset>
 711     </javadoc>
 712   </target>
 713 </project>