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 <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
  98                 <property name="j2sev" value="1.7+"/>
  99
 100     <!-- Permissions for running Java applets and applications. -->
 101     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
 102     <property name="application.codebase" value="*.jalview.org" />
 103     <!-- and allowing the applet to be deployed from any URL -->
 104     <property name="applet.codebase" value="*" />
 105     <property name="applet.caller-codebase" value="${applet.codebase}" />
 106
 107                 <!-- build directory configuration -->
 108                 <property name="libDir" value="lib" />
 109                 <property name="resourceDir" value="resources" />
 110                 <property name="helpDir" value="help" />
 111                 <property name="docDir" value="doc" />
 112                 <property name="sourceDir" value="src" />
 113                 <property name="schemaDir" value="schemas" />
 114                 <property name="outputDir" value="classes" />
 115                 <property name="packageDir" value="dist" />
 116                 <property name="outputJar" value="jalview.jar" />
 117                 <!-- Jalview Applet JMol Jar Dependency -->
 118                 <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
 119                 <property name="varnaJar" value="VARNAv3-9.jar" />
 120                 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 121                 <!-- switch to indicate if we should obfuscate jalviewLite -->
 122                 <!--<property name="donotobfuscate" value="true"/> -->
 123
 124                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 125                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 126                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 127                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 128                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 129                 <property name="WSInterf" value="MsaWS" />
 130                 <property name="wsdl.Namespace" value="vamsas" />
 131                 <property name="wsdl.ClientNS" value="ext.vamsas" />
 132                 <!-- the class path for building the application -->
 133                 <path id="build.classpath">
 134                         <fileset dir="utils">
 135                                 <include name="*.jar" />
 136                                 <include name="**/*.jar" />
 137                         </fileset>
 138                         <fileset dir="${libDir}">
 139                                 <include name="*.jar" />
 140                                 <include name="**/*.jar" />
 141                         </fileset>
 142                         <fileset dir="${java.home}/lib">
 143                                 <include name="plugin.jar"/>
 144                         </fileset>
 145                         <fileset dir="appletlib">
 146                                 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 147                                 -->
 148                                 <include name="${jmolJar}" />
 149                                 <include name="${varnaJar}" />
 150                         </fileset>
 151
 152                 </path>
 153                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 154                 <!-- The Location of the java 1.1.8 jdk -->
 155                 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 156                 -->
 157                 <property name="java118.home" value="${java.home}" />
 158                     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 159                 --><!-- jre for 1.4 version -->
 160                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 161
 162                 <!-- the classpath for building the 1.1 applet -->
 163                 <path id="jalviewlite.deps">
 164                         <fileset dir="${java118.home}">
 165                                 <include name="lib/classes.zip" />
 166                         </fileset>
 167                         <fileset dir="${java.home}/lib">
 168                                 <include name="plugin.jar"/>
 169                         </fileset>
 170                         <pathelement location="appletlib/${jmolJar}" />
 171       <pathelement location="lib/${varnaJar}" />
 172
 173                 </path>
 174     <!-- default location for outputting javadoc -->
 175     <property name="javadocDir" value="${packageDir}/javadoc"/>
 176         </target>
 177
 178
 179         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 180         <target name="buildPropertiesFile" depends="init">
 181                 <tstamp prefix="build">
 182                         <format property="date" pattern="dd MMMM yyyy" />
 183                 </tstamp>
 184                 <properties file="${outputDir}/.build_properties">
 185                         <header>
 186           ---Jalview Build Details---
 187         </header>
 188                         <property name="VERSION" value="${JALVIEW_VERSION}" />
 189                         <property name="BUILD_DATE" value="${build.date}" />
 190                 </properties>
 191         </target>
 192
 193
 194         <target name="clean" depends="init">
 195                 <!-- not efficient yet. -->
 196                 <delete dir="${outputDir}" includes="*,**/*"/>
 197         </target>
 198
 199         <target name="distclean" depends="init, clean">
 200
 201                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 202                 <delete>
 203                         <fileset dir=".">
 204                                 <include name="${outputJar}" />
 205                                 <include name="#*#" />
 206                                 <include name="#*.*#" />
 207                                 <include name="**/#*#" />
 208                                 <include name="**/#*.*#" />
 209                                 <include name="*~" />
 210                                 <include name="*.*~" />
 211                                 <include name="**/*~" />
 212                                 <include name="**/*.*~" />
 213                         </fileset>
 214                 </delete>
 215         </target>
 216
 217         <target name="prepare" depends="init">
 218                 <mkdir dir="${outputDir}" />
 219                 <copy todir="${outputDir}">
 220                         <fileset dir=".">
 221                                 <include name="${docDir}/**/*.*" />
 222                                 <include name="${helpDir}/**/*.*" />
 223                                 <include name="${libDir}/*.jar" />
 224                         </fileset>
 225                         <fileset dir="${resourceDir}">
 226                                 <include name="**/*.*" />
 227                         </fileset>
 228                 </copy>
 229         </target>
 230
 231         <target name="build" depends="prepare">
 232                 <!-- not efficient yet. -->
 233                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 234                         <exclude name="jalview/*applet*" />
 235                         <exclude name="jalview/appletgui/**" />
 236                         <exclude name="com/stevesoft/**" />
 237                 </javac>
 238         </target>
 239         <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 240                 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 241                         <arg line="html" />
 242                 </java>
 243         </target>
 244
 245         <target name="makefulldist" depends="makedist">
 246                 <copy todir="${packageDir}">
 247                         <fileset dir="${resourceDir}/images">
 248                                 <include name="${WebStartImage}"/>
 249                         </fileset>
 250                                         </copy>
 251
 252                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 253
 254     <!-- create a dummy jar which will eventually contain the jnlp template -->
 255     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 256                                 <fileset dir="${packageDir}">
 257                                         <include name="jalview.jar" />
 258                                 </fileset>
 259     </jar>
 260
 261         <mkdir dir="${packageDir}/JNLP-INF"/>
 262     <antcall target="writejnlpf">
 263        <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
 264        <param name="inih" value="*" />
 265        <param name="maxh" value="*"/>
 266     </antcall>
 267
 268         <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
 269                                 <fileset dir="${packageDir}">
 270                 <include name="JNLP-INF"/>
 271                                 </fileset>
 272         </jar>
 273
 274         <antcall target="writejnlpf">
 275                 <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
 276                 <param name="inih" value="10M" />
 277           <param name="maxh" value="256M"/>
 278         </antcall>
 279
 280         <antcall target="writejnlpf">
 281           <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
 282           <param name="inih" value="128M" />
 283                 <param name="maxh" value="512M"/>
 284         </antcall>
 285
 286         <antcall target="writejnlpf">
 287           <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
 288           <param name="inih" value="256M" />
 289           <param name="maxh" value="1024M"/>
 290         </antcall>
 291
 292                         <!-- finally, need to postprocess to add in associations at end of 'information' element
 293
 294                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 295
 296                 </xslt>
 297
 298
 299                         -->
 300                                         <!--
 301                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 302         <association mime-type="application-x/ext-file" extensions="fasta"/>
 303         <association mime-type="application-x/ext-file" extensions="mfa"/>
 304         <association mime-type="application-x/ext-file" extensions="fastq"/>
 305         <association mime-type="application-x/ext-file" extensions="blc"/>
 306         <association mime-type="application-x/ext-file" extensions="msf"/>
 307         <association mime-type="application-x/ext-file" extensions="pfam"/>
 308         <association mime-type="application-x/ext-file" extensions="aln"/>
 309         <association mime-type="application-x/ext-file" extensions="pir"/>
 310         <association mime-type="application-x/ext-file" extensions="amsa"/>
 311         <association mime-type="application-x/ext-file" extensions="stk"/>
 312         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 313     <!-- and sign the jars -->
 314     <!-- the default keystore details might need to be edited here -->
 315     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 316         <fileset dir="${packageDir}">
 317           <include name="*.jar" />
 318         </fileset>
 319     </signjar>
 320         </target>
 321
 322         <target name="runenv" depends="init">
 323                 <path id="run.classpath">
 324                         <pathelement location="${outputDir}" />
 325                         <fileset dir="${outputDir}">
 326                                 <include name="${libDir}/*.jar" />
 327                         </fileset>
 328                 </path>
 329                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 330
 331                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 332       </echo>
 333         </target>
 334   <target name="writejnlpf">
 335         <presetdef name="jnlpf">
 336             <jnlp codebase="${WebStartLocation}">
 337               <information>
 338                 <title>Jalview</title>
 339                 <vendor>The Barton Group</vendor>
 340                 <homepage href="http://www.jalview.org" />
 341                 <description>Jalview Multiple Alignment Editor</description>
 342                 <description kind="short">Jalview</description>
 343                 <icon href="${WebStartImage}" />
 344                 <offline_allowed />
 345               </information>
 346               <resources>
 347                 <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
 348                 <fileset dir="${packageDir}">
 349                   <include name="jalview.jar" />
 350                 </fileset>
 351                 <fileset dir="${packageDir}">
 352                   <include name="*.jar" />
 353                   <include name="*_*.jar" />
 354                   <exclude name="jalview.jar" />
 355                 </fileset>
 356                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 357               </resources>
 358               <application_desc main_class="jalview.bin.Jalview">
 359               </application_desc>
 360               <security>
 361                 <all_permissions />
 362               </security>
 363             </jnlp>
 364             </presetdef>
 365
 366             <jnlpf toFile="${jnlpFile}"/>
 367   </target>
 368         <target name="buildextclients" depends="init">
 369                 <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" />
 370                 <condition property="dontextbuild">
 371                         <equals arg1="n" arg2="${doextbuild.response}" />
 372                 </condition>
 373                 <condition property="dontextbuild">
 374                         <equals arg1="N" arg2="${doextbuild.response}" />
 375                 </condition>
 376                 <fail if="dontextbuild">
 377         Build External Client Code process aborted by user. Jalview source is unchanged.
 378       </fail>
 379                 <!-- Currently, this doesn't happen automatically.
 380      1. Run WSDL2Java as below, which generates an ext.vamsas +
 381      vamsas.<datapackages> fileset.
 382      2. refactor ext.vamsas.SpecificserviceWS* to
 383      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 384      3. Update the jalview.ws.*WServices classes to reflect the
 385      interface type, and all locations of this wsdl type that Jalview
 386      might be using.
 387
 388 -->
 389                 <path id="axisbuild">
 390                         <path refid="build.classpath" />
 391                 </path>
 392                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 393                 <move todir="./bak">
 394                         <fileset dir="${sourceDir}" id="client">
 395                                 <include name="${wsdl.ClientNS}/*.*" />
 396                         </fileset>
 397                 </move>
 398
 399                 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 400                         <mappingSet>
 401                                 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 402                                 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 403                         </mappingSet>
 404                 </axis-wsdl2java>
 405         </target>
 406
 407         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 408                 <!-- make the package jar if not already existing -->
 409                 <mkdir dir="${packageDir}" />
 410                 <!-- clean dir if it already existed -->
 411                 <delete>
 412                         <fileset dir="${packageDir}">
 413                                 <include name="*.jar"/>
 414                         </fileset>
 415                 </delete>
 416                 <jar destfile="${packageDir}/${outputJar}" index="true">
 417                         <manifest>
 418                                 <attribute name="Main-Class" value="jalview.bin.Jalview" />
 419         <attribute name="Permissions" value="all-permissions" />
 420         <attribute name="Application-Name" value="Jalview Desktop" />
 421         <attribute name="Codebase" value="${application.codebase}" />
 422                         </manifest>
 423                         <fileset dir="${outputDir}/">
 424                                 <exclude name="cache*/**" />
 425                                 <exclude name="*.jar" />
 426                                 <exclude name="*.jar.*" />
 427                                 <exclude name="**/*.jar" />
 428                                 <exclude name="**/*.jar.*" />
 429                         </fileset>
 430                 </jar>
 431
 432                 <copy toDir="${packageDir}" flatten="true">
 433                         <fileset dir="${outputDir}">
 434                                 <include name="*.jar" />
 435                                 <include name="**/*.jar" />
 436                         </fileset>
 437                 </copy>
 438         </target>
 439
 440
 441         <!-- jalopy code reformatter -->
 442         <target name="sourcescrub" depends="init,build">
 443                 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 444                         <fileset dir="${sourceDir}">
 445                                 <include name="*.java" />
 446                                 <include name="**/*.java" />
 447                                 <include name="**/**/*.java" />
 448                         </fileset>
 449                 </jalopy>
 450         </target>
 451
 452
 453
 454         <!-- Compile, package and obfuscate Jalview Applet -->
 455         <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 456
 457         <target name="compileApplet" depends="init,clean">
 458                 <mkdir dir="${outputDir}" />
 459                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 460                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 461                         excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 462         </target>
 463
 464         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 465                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 466                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 467                 <copy todir="${outputDir}/lang">
 468                         <fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
 469                 <jar destfile="in.jar" index="true">
 470                         <manifest>
 471                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 472                 <attribute name="Application-Name" value="JalviewLite" />
 473             <attribute name="Codebase" value="${applet.codebase}" />
 474                         </manifest>
 475                         <fileset dir="${outputDir}">
 476                                 <include name="com/**" />
 477                                 <include name="MCview/**" />
 478                                 <include name="jalview/**" />
 479                                 <include name=".build_properties" />
 480                                 <include name="images/idwidth.gif" />
 481                                 <include name="images/link.gif" />
 482                                 <include name="lang/**" />
 483                         </fileset>
 484                 </jar>
 485         </target>
 486         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 487         </target>
 488         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 489                 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 490                 <delete file="in.jar" />
 491         </target>
 492         <target name="-obfuscatereally" unless="donotobfuscate">
 493
 494                 <path id="obfuscateDeps.path">
 495                         <pathelement location="${applet.jre.tools}" />
 496                         <pathelement location="appletlib/${jmolJar}" />
 497                 </path>
 498                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 499
 500                 <proguard>
 501                         <injar file="in.jar" />
 502                         <outjar file="${jalviewLiteJar}" />
 503                         <libraryjar refid="obfuscateDeps.path" />
 504                         <dontwarn/>
 505                         <keep access="public" type="class" name="jalview.bin.JalviewLite">
 506                                 <field access="public" />
 507                                 <method access="public" />
 508                                 <constructor access="public" />
 509                         </keep>
 510                         <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 511                                 <field access="public" />
 512                                 <method access="public" />
 513                                 <constructor access="public" />
 514                         </keep>
 515                         <!--      -libraryjars "${obfuscateDeps}"
 516       -injars      in.jar
 517       -outjars     jalviewApplet.jar
 518       -keep public class jalview.bin.JalviewLite
 519        { public * ; } -->
 520                 </proguard>
 521                 <delete file="in.jar" />
 522         </target>
 523
 524         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 525                 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 526                 <delete>
 527                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 528                                 <include name="*.java" />
 529                                 <include name="descriptors/*.java" />
 530                         </fileset>
 531                 </delete>
 532                 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 533                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 534                 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 535                 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 536                 <!--
 537                 now build the jalview.binding package with the old schema set
 538                 -->
 539                 <delete>
 540                         <fileset dir="${sourceDir}/jalview/binding/">
 541                                 <include name="**" />
 542                         </fileset>
 543                 </delete>
 544                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 545                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 546                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 547         </target>
 548         <target name="sourcedist" description="create jalview source distribution" depends="init">
 549                 <delete file="${source.dist.name}" />
 550                 <tar destfile="${source.dist.name}" compression="gzip">
 551                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 552                                 <include name="LICENSE" />
 553                                 <include name="README" />
 554                                 <include name="build.xml" />
 555                                 <include name="jalview-jalopy.xml" />
 556                                 <include name="JalviewApplet.jpx" />
 557                                 <include name="JalviewX.jpx" />
 558                                 <include name="nbbuild.xml"/>
 559                                 <include name="nbproject/genfiles.properties"/>
 560         <include name="nbproject/project.properties"/>
 561         <include name="nbproject/project.xml"/>
 562                                 <include name="${sourceDir}/*.java" />
 563                                 <include name="${sourceDir}/**/*.java" />
 564                                 <include name="${sourceDir}/**/*.cdr" />
 565                                 <include name="${libDir}/**/*" />
 566                                 <include name="${resourceDir}/**/*" />
 567                                 <include name="${helpDir}/**/*" />
 568                                 <include name="appletlib/${jmolJar}" />
 569                                 <exclude name="**/*locales" />
 570                                 <exclude name="*locales/**" />
 571                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 572                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 573                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 574                                 <exclude name="utils/InstallAnywhere/**locale*" />
 575                                 <exclude name="utils/InstallAnywhere/**locale*/**" />
 576                                 <include name="${schemaDir}/**/*" />
 577                                 <include name="utils/**/*" />
 578                                 <include name="${docDir}/**/*" />
 579                                 <include name="examples/**/*" />
 580                         </tarfileset>
 581                 </tar>
 582         </target>
 583         <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 584           <copy todir="${packageDir}/examples">
 585           <fileset dir="examples">
 586                 <include name="**/*"/>
 587                 <include name="javascript/*"/>
 588       <include name="jmol/*"/>
 589           </fileset>
 590                 <fileset dir=".">
 591         <include name="${jalviewLiteJar}" />
 592                         </fileset>
 593                 <fileset dir="appletlib">
 594                       <include name="**/*"/>
 595                         </fileset>
 596           </copy>
 597             <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
 598             <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
 599                 <manifest>
 600                 <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
 601                 <!--          <attribute name="Permissions" value="sandbox" /> -->
 602                 <!--<attribute name="Trusted-Lib" value="true" /> -->
 603                 <attribute name="Codebase" value="${applet.codebase}"/>
 604                 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 605                   </manifest>
 606                 </jar>
 607     <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 608       <fileset dir="${packageDir}/examples">
 609         <include name="*.jar" />
 610       </fileset>
 611     </signjar>
 612     <presetdef name="ap_applet.jar">
 613       <!-- build a signed applet with 'all-permissions' -
 614                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 615                           JalviewLite+JmolApplet linked sequence/structure fails
 616                           Mixed code warnings are raised
 617                           -->
 618       <jar update="true" index="true">
 619         <manifest>
 620           <attribute name="Application-Name" value="JalviewLite" />
 621           <attribute name="Permissions" value="all-permissions" />
 622           <attribute name="Codebase" value="${applet.codebase}" />
 623           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 624           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 625         </manifest>
 626       </jar>
 627     </presetdef>
 628     <presetdef name="applet.jar">
 629       <!-- build signed applet with sandbox permissions -
 630                           Needs 'param name="permissions' value="sandbox"' in applet tag
 631                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 632                         -->
 633
 634       <jar update="true" index="true">
 635         <manifest>
 636           <attribute name="Application-Name" value="JalviewLite" />
 637           <attribute name="Permissions" value="sandbox" />
 638           <attribute name="Codebase" value="${applet.codebase}" />
 639           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 640           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 641         </manifest>
 642       </jar>
 643     </presetdef>
 644     <presetdef name="tl_applet.jar">
 645       <!-- build signed applet with trusted library/trusted permissions -
 646                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 647                                j1.7_45:
 648                                No mixed code warnings raised
 649                                Jmol/JalviewLite sequence/structure example doesn't link structures
 650                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 651
 652                               -->
 653
 654       <jar update="true" index="true">
 655         <manifest>
 656           <attribute name="Application-Name" value="JalviewLite" />
 657           <attribute name="Permissions" value="all-permissions" />
 658           <attribute name="Codebase" value="${applet.codebase}" />
 659           <attribute name="Trusted-Only" value="true" />
 660           <attribute name="Trusted-Library" value="true" />
 661         </manifest>
 662       </jar>
 663     </presetdef>
 664     <presetdef name="to_applet.jar">
 665       <!-- not fully test variant (yet) -->
 666       <jar update="true" index="true">
 667         <manifest>
 668           <attribute name="Application-Name" value="JalviewLite" />
 669           <attribute name="Permissions" value="all-permissions" />
 670           <attribute name="Codebase" value="${applet.codebase}" />
 671           <attribute name="Trusted-Only" value="true" />
 672         </manifest>
 673       </jar>
 674     </presetdef>
 675     <!-- create differently privileged artefacts -->
 676     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
 677     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
 678     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 679     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
 680     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 681     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 682     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 683     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
 684     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
 685     <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
 686     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 687     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 688     <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 689     <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 690     <!-- finally, create manifest for original jars -->
 691     <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 692     <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 693
 694     <!-- todo - write examples/downloads for alternate versions of the applet -->
 695     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 696
 697       <fileset dir="${packageDir}/examples">
 698         <exclude name="u_*.jar"/>
 699         <include name="${jalviewLiteJar}" />
 700         <include name="${jmolJar}" />
 701         <include name="to_${jalviewLiteJar}" />
 702         <include name="to_${jmolJar}" />
 703         <include name="tl_${jalviewLiteJar}" />
 704         <include name="tl_${jmolJar}" />
 705         <include name="ap_${jalviewLiteJar}" />
 706         <include name="ap_${jmolJar}" />
 707       </fileset>
 708     </signjar>
 709     <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
 710     <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
 711   </target>
 712   <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 713     <javadoc destdir="${javadocDir}">
 714       <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 715       </packageset>
 716     </javadoc>
 717   </target>
 718 </project>