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                 <!-- the default keystore details might need to be edited here -->
 241                 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 242
 243                         <fileset dir="${packageDir}">
 244                                 <include name="*.jar" />
 245                         </fileset>
 246                 </signjar>
 247                 <copy todir="${packageDir}">
 248                         <fileset dir="${resourceDir}/images">
 249                                 <include name="${WebStartImage}"/>
 250                         </fileset>
 251                                         </copy>
 252
 253                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 254
 255                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 256                 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 257                 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 258                         <information>
 259                                 <title>Jalview</title>
 260                                 <vendor>The Barton Group</vendor>
 261                                 <homepage href="http://www.jalview.org" />
 262                                 <description>Jalview Multiple Alignment Editor</description>
 263                                 <description kind="short">Jalview</description>
 264                                 <icon href="${WebStartImage}" />
 265                                 <offline_allowed/>
 266                         </information>
 267                         <resources>
 268                                 <j2se version="${j2sev}" initial_heap_size="10M"  />
 269                                 <fileset dir="${packageDir}">
 270                                         <include name="jalview.jar" />
 271                                 </fileset>
 272                                 <fileset dir="${packageDir}">
 273                                         <include name="*.jar" />
 274                                         <include name="*_*.jar" />
 275                                         <exclude name="jalview.jar" />
 276                                 </fileset>
 277                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 278                         </resources>
 279                         <application_desc main_class="jalview.bin.Jalview">
 280                         </application_desc>
 281                         <security>
 282                                 <all_permissions />
 283                         </security>
 284                 </jnlp>
 285                 <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 286                         <information>
 287                                 <title>Jalview</title>
 288                                 <vendor>The Barton Group</vendor>
 289                                 <homepage href="http://www.jalview.org" />
 290                                 <description>Jalview Multiple Alignment Editor</description>
 291                                 <description kind="short">Jalview</description>
 292                                 <icon href="${WebStartImage}" />
 293                                 <offline_allowed />
 294                         </information>
 295                         <resources>
 296                                 <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
 297                                 <fileset dir="${packageDir}">
 298                                         <include name="jalview.jar" />
 299                                 </fileset>
 300                                 <fileset dir="${packageDir}">
 301                                         <include name="*.jar" />
 302                                         <include name="*_*.jar" />
 303                                         <exclude name="jalview.jar" />
 304                                 </fileset>
 305                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 306                         </resources>
 307                         <application_desc main_class="jalview.bin.Jalview">
 308                         </application_desc>
 309                         <security>
 310                                 <all_permissions />
 311                         </security>
 312                 </jnlp>
 313                 <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
 314                         <information>
 315                                 <title>Jalview</title>
 316                                 <vendor>The Barton Group</vendor>
 317                                 <homepage href="http://www.jalview.org" />
 318                                 <description>Jalview Multiple Alignment Editor</description>
 319                                 <description kind="short">Jalview</description>
 320                                 <icon href="${WebStartImage}" />
 321                                 <offline_allowed />
 322                         </information>
 323                         <resources>
 324                                 <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
 325                                 <fileset dir="${packageDir}">
 326                                         <include name="jalview.jar" />
 327                                 </fileset>
 328                                 <fileset dir="${packageDir}">
 329                                         <include name="*.jar" />
 330                                         <include name="*_*.jar" />
 331                                         <exclude name="jalview.jar" />
 332                                 </fileset>
 333                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 334                         </resources>
 335                         <application_desc main_class="jalview.bin.Jalview">
 336                         </application_desc>
 337                         <security>
 338                                 <all_permissions />
 339                         </security>
 340                 </jnlp>
 341                         <!-- finally, need to postprocess to add in associations at end of 'information' element
 342
 343                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 344
 345                 </xslt>
 346
 347
 348                         -->
 349                                         <!--
 350                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 351         <association mime-type="application-x/ext-file" extensions="fasta"/>
 352         <association mime-type="application-x/ext-file" extensions="fastq"/>
 353         <association mime-type="application-x/ext-file" extensions="blc"/>
 354         <association mime-type="application-x/ext-file" extensions="msf"/>
 355         <association mime-type="application-x/ext-file" extensions="pfam"/>
 356         <association mime-type="application-x/ext-file" extensions="aln"/>
 357         <association mime-type="application-x/ext-file" extensions="pir"/>
 358         <association mime-type="application-x/ext-file" extensions="amsa"/>
 359         <association mime-type="application-x/ext-file" extensions="stk"/>
 360         <association mime-type="application-x/ext-file" extensions="jar"/>-->
 361
 362         </target>
 363
 364         <target name="runenv" depends="init">
 365                 <path id="run.classpath">
 366                         <pathelement location="${outputDir}" />
 367                         <fileset dir="${outputDir}">
 368                                 <include name="${libDir}/*.jar" />
 369                         </fileset>
 370                 </path>
 371                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 372
 373                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 374       </echo>
 375         </target>
 376
 377         <target name="buildextclients" depends="init">
 378                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 379                 <condition property="dontextbuild">
 380                         <equals arg1="n" arg2="${doextbuild.response}" />
 381                 </condition>
 382                 <condition property="dontextbuild">
 383                         <equals arg1="N" arg2="${doextbuild.response}" />
 384                 </condition>
 385                 <fail if="dontextbuild">
 386         Build External Client Code process aborted by user. Jalview source is unchanged.
 387       </fail>
 388                 <!-- Currently, this doesn't happen automatically.
 389      1. Run WSDL2Java as below, which generates an ext.vamsas +
 390      vamsas.<datapackages> fileset.
 391      2. refactor ext.vamsas.SpecificserviceWS* to
 392      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 393      3. Update the jalview.ws.*WServices classes to reflect the
 394      interface type, and all locations of this wsdl type that Jalview
 395      might be using.
 396
 397 -->
 398                 <path id="axisbuild">
 399                         <path refid="build.classpath" />
 400                 </path>
 401                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 402                 <move todir="./bak">
 403                         <fileset dir="${sourceDir}" id="client">
 404                                 <include name="${wsdl.ClientNS}/*.*" />
 405                         </fileset>
 406                 </move>
 407
 408                 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 409                         <mappingSet>
 410                                 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 411                                 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 412                         </mappingSet>
 413                 </axis-wsdl2java>
 414         </target>
 415
 416         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 417                 <!-- make the package jar if not already existing -->
 418                 <mkdir dir="${packageDir}" />
 419                 <!-- clean dir if it already existed -->
 420                 <delete>
 421                         <fileset dir="${packageDir}">
 422                                 <include name="*.jar"/>
 423                         </fileset>
 424                 </delete>
 425                 <jar destfile="${packageDir}/${outputJar}" index="true">
 426                         <manifest>
 427                                 <attribute name="Main-Class" value="jalview.bin.Jalview" />
 428         <attribute name="Permissions" value="all-permissions" />
 429         <attribute name="Application-Name" value="Jalview Desktop"/>
 430         <attribute name="Codebase" value="${application.codebase}"/>
 431                         </manifest>
 432                         <fileset dir="${outputDir}/">
 433                                 <exclude name="cache*/**" />
 434                                 <exclude name="*.jar" />
 435                                 <exclude name="*.jar.*" />
 436                                 <exclude name="**/*.jar" />
 437                                 <exclude name="**/*.jar.*" />
 438                         </fileset>
 439                 </jar>
 440
 441                 <copy toDir="${packageDir}" flatten="true">
 442                         <fileset dir="${outputDir}">
 443                                 <include name="*.jar" />
 444                                 <include name="**/*.jar" />
 445                         </fileset>
 446                 </copy>
 447         </target>
 448
 449
 450         <!-- jalopy code reformatter -->
 451         <target name="sourcescrub" depends="init,build">
 452                 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 453                         <fileset dir="${sourceDir}">
 454                                 <include name="*.java" />
 455                                 <include name="**/*.java" />
 456                                 <include name="**/**/*.java" />
 457                         </fileset>
 458                 </jalopy>
 459         </target>
 460
 461
 462
 463         <!-- Compile, package and obfuscate Jalview Applet -->
 464         <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 465
 466         <target name="compileApplet" depends="init,clean">
 467                 <mkdir dir="${outputDir}" />
 468                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 469                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 470                         excludes="ext/**,MCview/**,org/**,vamsas/**" />
 471         </target>
 472
 473         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 474                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 475                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 476                 <jar destfile="in.jar" index="true">
 477                         <manifest>
 478                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 479                                 <attribute name="Application-Name" value="JalviewLite"/>
 480                                 <attribute name="Codebase" value="${applet.codebase}"/>
 481                         </manifest>
 482                         <fileset dir="${outputDir}">
 483                                 <include name="com/**" />
 484                                 <include name="MCview/**" />
 485                                 <include name="jalview/**" />
 486                                 <include name=".build_properties" />
 487                                 <include name="images/idwidth.gif" />
 488                                 <include name="images/link.gif" />
 489                         </fileset>
 490                 </jar>
 491         </target>
 492         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 493         </target>
 494         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 495                 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 496                 <delete file="in.jar" />
 497         </target>
 498         <target name="-obfuscatereally" unless="donotobfuscate">
 499
 500                 <path id="obfuscateDeps.path">
 501                         <pathelement location="${applet.jre.tools}" />
 502                         <pathelement location="appletlib/${jmolJar}" />
 503                 </path>
 504                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 505
 506                 <proguard>
 507                         <injar file="in.jar" />
 508                         <outjar file="${jalviewLiteJar}" />
 509                         <libraryjar refid="obfuscateDeps.path" />
 510                         <dontwarn/>
 511                         <keep access="public" type="class" name="jalview.bin.JalviewLite">
 512                                 <field access="public" />
 513                                 <method access="public" />
 514                                 <constructor access="public" />
 515                         </keep>
 516                         <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
 517                                 <field access="public" />
 518                                 <method access="public" />
 519                                 <constructor access="public" />
 520                         </keep>
 521                         <!--      -libraryjars "${obfuscateDeps}"
 522       -injars      in.jar
 523       -outjars     jalviewApplet.jar
 524       -keep public class jalview.bin.JalviewLite
 525        { public * ; } -->
 526                 </proguard>
 527                 <delete file="in.jar" />
 528         </target>
 529
 530         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 531                 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 532                 <delete>
 533                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 534                                 <include name="*.java" />
 535                                 <include name="descriptors/*.java" />
 536                         </fileset>
 537                 </delete>
 538                 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 539                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 540                 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 541                 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 542                 <!--
 543                 now build the jalview.binding package with the old schema set
 544                 -->
 545                 <delete>
 546                         <fileset dir="${sourceDir}/jalview/binding/">
 547                                 <include name="**" />
 548                         </fileset>
 549                 </delete>
 550                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 551                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 552                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 553         </target>
 554         <target name="sourcedist" description="create jalview source distribution" depends="init">
 555                 <delete file="${source.dist.name}" />
 556                 <tar destfile="${source.dist.name}" compression="gzip">
 557                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 558                                 <include name="LICENSE" />
 559                                 <include name="README" />
 560                                 <include name="build.xml" />
 561                                 <include name="jalview-jalopy.xml" />
 562                                 <include name="JalviewApplet.jpx" />
 563                                 <include name="JalviewX.jpx" />
 564                                 <include name="nbbuild.xml"/>
 565                                 <include name="nbproject/genfiles.properties"/>
 566         <include name="nbproject/project.properties"/>
 567         <include name="nbproject/project.xml"/>
 568                                 <include name="${sourceDir}/*.java" />
 569                                 <include name="${sourceDir}/**/*.java" />
 570                                 <include name="${sourceDir}/**/*.cdr" />
 571                                 <include name="${libDir}/**/*" />
 572                                 <include name="${resourceDir}/**/*" />
 573                                 <include name="${helpDir}/**/*" />
 574                                 <include name="appletlib/${jmolJar}" />
 575                                 <exclude name="**/*locales" />
 576                                 <exclude name="*locales/**" />
 577                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 578                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 579                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 580                                 <exclude name="utils/InstallAnywhere/**locale*" />
 581                                 <exclude name="utils/InstallAnywhere/**locale*/**" />
 582                                 <include name="${schemaDir}/**/*" />
 583                                 <include name="utils/**/*" />
 584                                 <include name="${docDir}/**/*" />
 585                                 <include name="examples/**/*" />
 586                         </tarfileset>
 587                 </tar>
 588         </target>
 589         <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 590           <copy todir="${packageDir}/examples">
 591           <fileset dir="examples">
 592                 <include name="**/*"/>
 593                 <include name="javascript/*"/>
 594       <include name="jmol/*"/>
 595           </fileset>
 596                 <fileset dir=".">
 597                 <include name="${jalviewLiteJar}"/>
 598                         </fileset>
 599                 <fileset dir="appletlib">
 600                       <include name="**/*"/>
 601                         </fileset>
 602           </copy>
 603           <presetdef name="applet.jar">
 604       <!-- build a signed applet with 'all-permissions' -
 605                           Needs 'param name="permissions' value="all-permissions"' in applet tag
 606                           JalviewLite+JmolApplet linked sequence/structure fails
 607                           Mixed code warnings are raised
 608                           -->
 609             <jar update="true" index="true">
 610                 <manifest>
 611                 <attribute name="Application-Name" value="JalviewLite"/>
 612                 <attribute name="Permissions" value="all-permissions"/>
 613                 <attribute name="Codebase" value="${applet.codebase}"/>
 614                 <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
 615                 <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}"/>
 616         </manifest>
 617       </jar>
 618     </presetdef>
 619     <presetdef name="s_applet.jar">
 620       <!-- build signed applet with sandbox permissions -
 621                           Needs 'param name="permissions' value="sandbox"' in applet tag
 622                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
 623 -->
 624
 625       <jar update="true" index="true" jarfile="@{jarfile}">
 626         <manifest>
 627           <attribute name="Application-Name" value="JalviewLite" />
 628           <attribute name="Permissions" value="sandbox" />
 629           <attribute name="Codebase" value="${applet.codebase}" />
 630           <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
 631           <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
 632                 </manifest>
 633           </jar>
 634           </presetdef>
 635           <presetdef name="applet_tl.jar">
 636       <!-- build signed applet with trusted library/trusted permissions -
 637                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
 638                                j1.7_45:
 639                                No mixed code warnings raised
 640                                Jmol/JalviewLite sequence/structure example doesn't link structures
 641                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
 642
 643                               -->
 644
 645             <jar update="true" index="true" jarfile="@{jarfile}">
 646                 <manifest>
 647                 <attribute name="Application-Name" value="JalviewLite"/>
 648                 <attribute name="Permissions" value="all-permissions" />
 649                 <attribute name="Codebase" value="${applet.codebase}"/>
 650                 <attribute name="Trusted-Only" value="true"/>
 651                 <attribute name="Trusted-Library" value="true"/>
 652                 </manifest>
 653           </jar>
 654
 655           </presetdef>
 656     <presetdef name="applet_to.jar">
 657       <!-- not fully test variant (yet) -->
 658       <jar update="true" index="true" jarfile="@{jarfile}">
 659         <manifest>
 660           <attribute name="Application-Name" value="JalviewLite" />
 661           <attribute name="Permissions" value="all-permissions" />
 662           <attribute name="Codebase" value="${applet.codebase}" />
 663           <attribute name="Trusted-Only" value="true" />
 664         </manifest>
 665       </jar>
 666     </presetdef>
 667     <!-- create differently privileged artefacts -->
 668           <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}"/>
 669           <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}"/>
 670     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
 671     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
 672     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/s_${jalviewLiteJar}" />
 673     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/s_${jmolJar}" />
 674     <applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
 675     <applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
 676           <applet_tl.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}"/>
 677           <applet_tl.jar jarfile="${packageDir}/examples/tl_${jmolJar}"/>
 678     <s_applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
 679     <s_applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
 680     <applet_to.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
 681     <applet_to.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
 682     <!-- todo - write examples/downloads for alternate versions of the applet -->
 683     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 684
 685       <fileset dir="${packageDir}/examples">
 686         <include name="*.jar" />
 687       </fileset>
 688     </signjar>
 689         </target>
 690         <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 691          <javadoc destdir="${javadocDir}">
 692                 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 693                 </packageset>
 694                 </javadoc>
 695         </target>
 696
 697 </project>