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, 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                 <!-- Don't change anything below here unless you know what you are doing! -->
  89                 <!-- Url path for WebStart in JNLP file -->
  90                 <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
  91                 <!-- J2SE version needed for webstart launch -->
  92                 <property name="j2sev" value="1.6+"/>
  93                 <!-- build directory configuration -->
  94                 <property name="libDir" value="lib" />
  95                 <property name="resourceDir" value="resources" />
  96                 <property name="helpDir" value="help" />
  97                 <property name="docDir" value="doc" />
  98                 <property name="sourceDir" value="src" />
  99                 <property name="schemaDir" value="schemas" />
 100                 <property name="outputDir" value="classes" />
 101                 <property name="packageDir" value="dist" />
 102                 <property name="outputJar" value="jalview.jar" />
 103                 <!-- Jalview Applet JMol Jar Dependency -->
 104                 <property name="jmolJar" value="JmolApplet-12.1.13.jar" />
 105                 <property name="jalviewLiteJar" value="jalviewApplet.jar" />
 106                 <!-- switch to indicate if we should obfuscate jalviewLite -->
 107                 <!--<property name="donotobfuscate" value="true"/> -->
 108
 109                 <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 110                 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 111                 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
 112                 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
 113                 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
 114                 <property name="WSInterf" value="MsaWS" />
 115                 <property name="wsdl.Namespace" value="vamsas" />
 116                 <property name="wsdl.ClientNS" value="ext.vamsas" />
 117                 <!-- the class path for building the application -->
 118                 <path id="build.classpath">
 119                         <fileset dir="utils">
 120                                 <include name="*.jar" />
 121                                 <include name="**/*.jar" />
 122                         </fileset>
 123                         <fileset dir="${libDir}">
 124                                 <include name="*.jar" />
 125                                 <include name="**/*.jar" />
 126                         </fileset>
 127                         <fileset dir="${java.home}/lib">
 128                                 <include name="plugin.jar"/>
 129                         </fileset>
 130                         <fileset dir="appletlib">
 131                                 <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
 132                                 -->
 133                                 <include name="${jmolJar}" />
 134                         </fileset>
 135
 136                 </path>
 137                 <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 138                 <!-- The Location of the java 1.1.8 jdk -->
 139                 <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 140                 -->
 141                 <property name="java118.home" value="${java.home}" />
 142                     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 143                 --><!-- jre for 1.4 version -->
 144                 <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 145
 146                 <!-- the classpath for building the 1.1 applet -->
 147                 <path id="jalviewlite.deps">
 148                         <fileset dir="${java118.home}">
 149                                 <include name="lib/classes.zip" />
 150                         </fileset>
 151                         <fileset dir="${java.home}/lib">
 152                                 <include name="plugin.jar"/>
 153                         </fileset>
 154                         <pathelement location="appletlib/${jmolJar}" />
 155                 </path>
 156     <!-- default location for outputting javadoc -->
 157     <property name="javadocDir" value="${packageDir}/javadoc"/>
 158         </target>
 159
 160
 161         <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
 162         <target name="buildPropertiesFile" depends="init">
 163                 <tstamp prefix="build">
 164                         <format property="date" pattern="dd MMMM yyyy" />
 165                 </tstamp>
 166                 <properties file="${outputDir}/.build_properties">
 167                         <header>
 168           ---Jalview Build Details---
 169         </header>
 170                         <property name="VERSION" value="${JALVIEW_VERSION}" />
 171                         <property name="BUILD_DATE" value="${build.date}" />
 172                 </properties>
 173         </target>
 174
 175
 176         <target name="clean" depends="init">
 177                 <!-- not efficient yet. -->
 178                 <delete dir="${outputDir}" includes="*,**/*"/>
 179         </target>
 180
 181         <target name="distclean" depends="init, clean">
 182
 183                 <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
 184                 <delete>
 185                         <fileset dir=".">
 186                                 <include name="${outputJar}" />
 187                                 <include name="#*#" />
 188                                 <include name="#*.*#" />
 189                                 <include name="**/#*#" />
 190                                 <include name="**/#*.*#" />
 191                                 <include name="*~" />
 192                                 <include name="*.*~" />
 193                                 <include name="**/*~" />
 194                                 <include name="**/*.*~" />
 195                         </fileset>
 196                 </delete>
 197         </target>
 198
 199         <target name="prepare" depends="init">
 200                 <mkdir dir="${outputDir}" />
 201                 <copy todir="${outputDir}">
 202                         <fileset dir=".">
 203                                 <include name="${docDir}/**/*.*" />
 204                                 <include name="${helpDir}/**/*.*" />
 205                                 <include name="${libDir}/*.jar" />
 206                         </fileset>
 207                         <fileset dir="${resourceDir}">
 208                                 <include name="**/*.*" />
 209                         </fileset>
 210                 </copy>
 211         </target>
 212
 213         <target name="build" depends="prepare">
 214                 <!-- not efficient yet. -->
 215                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
 216                         <exclude name="jalview/*applet*" />
 217                         <exclude name="jalview/appletgui/**" />
 218                         <exclude name="com/stevesoft/**" />
 219                 </javac>
 220         </target>
 221         <target name="buildindices" depends="init, prepare" unless="help.uptodate">
 222                 <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
 223                         <arg line="html" />
 224                 </java>
 225         </target>
 226
 227         <target name="makefulldist" depends="makedist">
 228                 <!-- the default keystore details might need to be edited here -->
 229                 <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 230
 231                         <fileset dir="${packageDir}">
 232                                 <include name="*.jar" />
 233                         </fileset>
 234                 </signjar>
 235                 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 236
 237                 <!--    codebase="http://www.jalview.org/jalview/webstart" -->
 238                 <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
 239                 <jnlp toFile="${packageDir}/jalview_noa.jnlp" codebase="${WebStartLocation}">
 240                         <information>
 241                                 <title>Jalview</title>
 242                                 <vendor>The Barton Group</vendor>
 243                                 <homepage href="http://www.jalview.org" />
 244                                 <description>Jalview Multiple Alignment Editor</description>
 245                                 <description kind="short">Jalview</description>
 246                                 <icon href="logo_big.gif" />
 247                                 <offline_allowed />
 248                                 <!--
 249                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 250         <association mime-type="application-x/ext-file" extensions="fasta"/>
 251         <association mime-type="application-x/ext-file" extensions="fastq"/>
 252         <association mime-type="application-x/ext-file" extensions="blc"/>
 253         <association mime-type="application-x/ext-file" extensions="msf"/>
 254         <association mime-type="application-x/ext-file" extensions="pfam"/>
 255         <association mime-type="application-x/ext-file" extensions="aln"/>
 256         <association mime-type="application-x/ext-file" extensions="pir"/>
 257         <association mime-type="application-x/ext-file" extensions="amsa"/>
 258         <association mime-type="application-x/ext-file" extensions="stk"/>-->
 259                         </information>
 260                         <resources>
 261                                 <j2se version="${j2sev}" initial_heap_size="10M"  />
 262                                 <fileset dir="${packageDir}">
 263                                         <include name="jalview.jar" />
 264                                 </fileset>
 265                                 <fileset dir="${packageDir}">
 266                                         <include name="*.jar" />
 267                                         <include name="*_*.jar" />
 268                                         <exclude name="jalview.jar" />
 269                                 </fileset>
 270                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 271                         </resources>
 272                         <application_desc main_class="jalview.bin.Jalview">
 273                         </application_desc>
 274                         <security>
 275                                 <all_permissions />
 276                         </security>
 277                 </jnlp>
 278                 <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 279                         <information>
 280                                 <title>Jalview</title>
 281                                 <vendor>The Barton Group</vendor>
 282                                 <homepage href="http://www.jalview.org" />
 283                                 <description>Jalview Multiple Alignment Editor</description>
 284                                 <description kind="short">Jalview</description>
 285                                 <icon href="logo_big.gif" />
 286                                 <offline_allowed />
 287                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 288         <association mime-type="application-x/ext-file" extensions="fasta"/>
 289         <association mime-type="application-x/ext-file" extensions="fastq"/>
 290         <association mime-type="application-x/ext-file" extensions="blc"/>
 291         <association mime-type="application-x/ext-file" extensions="msf"/>
 292         <association mime-type="application-x/ext-file" extensions="pfam"/>
 293         <association mime-type="application-x/ext-file" extensions="aln"/>
 294         <association mime-type="application-x/ext-file" extensions="pir"/>
 295         <association mime-type="application-x/ext-file" extensions="amsa"/>
 296         <association mime-type="application-x/ext-file" extensions="stk"/>
 297                         </information>
 298                         <resources>
 299                                 <j2se version="${j2sev}" initial_heap_size="10M"/>
 300                                 <fileset dir="${packageDir}">
 301                                         <include name="jalview.jar" />
 302                                 </fileset>
 303                                 <fileset dir="${packageDir}">
 304                                         <include name="*.jar" />
 305                                         <include name="*_*.jar" />
 306                                         <exclude name="jalview.jar" />
 307                                 </fileset>
 308                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 309                         </resources>
 310                         <application_desc main_class="jalview.bin.Jalview">
 311                         </application_desc>
 312                         <security>
 313                                 <all_permissions />
 314                         </security>
 315                 </jnlp>
 316
 317                 <jnlp toFile="${packageDir}/jalview_noa_1G.jnlp" codebase="${WebStartLocation}">
 318                         <information>
 319                                 <title>Jalview</title>
 320                                 <vendor>The Barton Group</vendor>
 321                                 <homepage href="http://www.jalview.org" />
 322                                 <description>Jalview Multiple Alignment Editor</description>
 323                                 <description kind="short">Jalview</description>
 324                                 <icon href="logo_big.gif" />
 325                                 <offline_allowed />
 326                                 <!--
 327                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 328         <association mime-type="application-x/ext-file" extensions="fasta"/>
 329         <association mime-type="application-x/ext-file" extensions="fastq"/>
 330         <association mime-type="application-x/ext-file" extensions="blc"/>
 331         <association mime-type="application-x/ext-file" extensions="msf"/>
 332         <association mime-type="application-x/ext-file" extensions="pfam"/>
 333         <association mime-type="application-x/ext-file" extensions="aln"/>
 334         <association mime-type="application-x/ext-file" extensions="pir"/>
 335         <association mime-type="application-x/ext-file" extensions="amsa"/>
 336         <association mime-type="application-x/ext-file" extensions="stk"/>-->
 337                         </information>
 338                         <resources>
 339                                 <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
 340                                 <fileset dir="${packageDir}">
 341                                         <include name="jalview.jar" />
 342                                 </fileset>
 343                                 <fileset dir="${packageDir}">
 344                                         <include name="*.jar" />
 345                                         <include name="*_*.jar" />
 346                                         <exclude name="jalview.jar" />
 347                                 </fileset>
 348                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 349                         </resources>
 350                         <application_desc main_class="jalview.bin.Jalview">
 351                         </application_desc>
 352                         <security>
 353                                 <all_permissions />
 354                         </security>
 355                 </jnlp>
 356                 <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 357                         <information>
 358                                 <title>Jalview</title>
 359                                 <vendor>The Barton Group</vendor>
 360                                 <homepage href="http://www.jalview.org" />
 361                                 <description>Jalview Multiple Alignment Editor</description>
 362                                 <description kind="short">Jalview</description>
 363                                 <icon href="logo_big.gif" />
 364                                 <offline_allowed />
 365                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 366         <association mime-type="application-x/ext-file" extensions="fasta"/>
 367         <association mime-type="application-x/ext-file" extensions="fastq"/>
 368         <association mime-type="application-x/ext-file" extensions="blc"/>
 369         <association mime-type="application-x/ext-file" extensions="msf"/>
 370         <association mime-type="application-x/ext-file" extensions="pfam"/>
 371         <association mime-type="application-x/ext-file" extensions="aln"/>
 372         <association mime-type="application-x/ext-file" extensions="pir"/>
 373         <association mime-type="application-x/ext-file" extensions="amsa"/>
 374         <association mime-type="application-x/ext-file" extensions="stk"/>
 375                         </information>
 376                         <resources>
 377                                 <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
 378                                 <fileset dir="${packageDir}">
 379                                         <include name="jalview.jar" />
 380                                 </fileset>
 381                                 <fileset dir="${packageDir}">
 382                                         <include name="*.jar" />
 383                                         <include name="*_*.jar" />
 384                                         <exclude name="jalview.jar" />
 385                                 </fileset>
 386                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 387                         </resources>
 388                         <application_desc main_class="jalview.bin.Jalview">
 389                         </application_desc>
 390                         <security>
 391                                 <all_permissions />
 392                         </security>
 393                 </jnlp>
 394                 <jnlp toFile="${packageDir}/jalview_noac_2G.jnlp" codebase="${WebStartLocation}">
 395                         <information>
 396                                 <title>Jalview</title>
 397                                 <vendor>The Barton Group</vendor>
 398                                 <homepage href="http://www.jalview.org" />
 399                                 <description>Jalview Multiple Alignment Editor</description>
 400                                 <description kind="short">Jalview</description>
 401                                 <icon href="logo_big.gif" />
 402                                 <offline_allowed />
 403                                 <!--
 404                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 405         <association mime-type="application-x/ext-file" extensions="fasta"/>
 406         <association mime-type="application-x/ext-file" extensions="fastq"/>
 407         <association mime-type="application-x/ext-file" extensions="blc"/>
 408         <association mime-type="application-x/ext-file" extensions="msf"/>
 409         <association mime-type="application-x/ext-file" extensions="pfam"/>
 410         <association mime-type="application-x/ext-file" extensions="aln"/>
 411         <association mime-type="application-x/ext-file" extensions="pir"/>
 412         <association mime-type="application-x/ext-file" extensions="amsa"/>
 413         <association mime-type="application-x/ext-file" extensions="stk"/>
 414                         -->
 415                         </information>
 416                         <resources>
 417                                 <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
 418                                 <fileset dir="${packageDir}">
 419                                         <include name="jalview.jar" />
 420                                 </fileset>
 421                                 <fileset dir="${packageDir}">
 422                                         <include name="*.jar" />
 423                                         <include name="*_*.jar" />
 424                                         <exclude name="jalview.jar" />
 425                                 </fileset>
 426                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 427                         </resources>
 428                         <application_desc main_class="jalview.bin.Jalview">
 429                         </application_desc>
 430                         <security>
 431                                 <all_permissions />
 432                         </security>
 433                 </jnlp>
 434                 <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
 435                         <information>
 436                                 <title>Jalview</title>
 437                                 <vendor>The Barton Group</vendor>
 438                                 <homepage href="http://www.jalview.org" />
 439                                 <description>Jalview Multiple Alignment Editor</description>
 440                                 <description kind="short">Jalview</description>
 441                                 <icon href="logo_big.gif" />
 442                                 <offline_allowed />
 443                                 <association mime-type="application-x/ext-file" extensions="fa"/>
 444         <association mime-type="application-x/ext-file" extensions="fasta"/>
 445         <association mime-type="application-x/ext-file" extensions="fastq"/>
 446         <association mime-type="application-x/ext-file" extensions="blc"/>
 447         <association mime-type="application-x/ext-file" extensions="msf"/>
 448         <association mime-type="application-x/ext-file" extensions="pfam"/>
 449         <association mime-type="application-x/ext-file" extensions="aln"/>
 450         <association mime-type="application-x/ext-file" extensions="pir"/>
 451         <association mime-type="application-x/ext-file" extensions="amsa"/>
 452         <association mime-type="application-x/ext-file" extensions="stk"/>
 453                         </information>
 454                         <resources>
 455                                 <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
 456                                 <fileset dir="${packageDir}">
 457                                         <include name="jalview.jar" />
 458                                 </fileset>
 459                                 <fileset dir="${packageDir}">
 460                                         <include name="*.jar" />
 461                                         <include name="*_*.jar" />
 462                                         <exclude name="jalview.jar" />
 463                                 </fileset>
 464                                 <property name="jalview.version" value="${JALVIEW_VERSION}" />
 465                         </resources>
 466                         <application_desc main_class="jalview.bin.Jalview">
 467                         </application_desc>
 468                         <security>
 469                                 <all_permissions />
 470                         </security>
 471                 </jnlp>
 472
 473         </target>
 474
 475         <target name="runenv" depends="init">
 476                 <path id="run.classpath">
 477                         <pathelement location="${outputDir}" />
 478                         <fileset dir="${outputDir}">
 479                                 <include name="${libDir}/*.jar" />
 480                         </fileset>
 481                 </path>
 482                 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
 483
 484                 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
 485       </echo>
 486         </target>
 487
 488         <target name="buildextclients" depends="init">
 489                 <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
 490                 <condition property="dontextbuild">
 491                         <equals arg1="n" arg2="${doextbuild.response}" />
 492                 </condition>
 493                 <condition property="dontextbuild">
 494                         <equals arg1="N" arg2="${doextbuild.response}" />
 495                 </condition>
 496                 <fail if="dontextbuild">
 497         Build External Client Code process aborted by user. Jalview source is unchanged.
 498       </fail>
 499                 <!-- Currently, this doesn't happen automatically.
 500      1. Run WSDL2Java as below, which generates an ext.vamsas +
 501      vamsas.<datapackages> fileset.
 502      2. refactor ext.vamsas.SpecificserviceWS* to
 503      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
 504      3. Update the jalview.ws.*WServices classes to reflect the
 505      interface type, and all locations of this wsdl type that Jalview
 506      might be using.
 507
 508 -->
 509                 <path id="axisbuild">
 510                         <path refid="build.classpath" />
 511                 </path>
 512                 <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
 513                 <move todir="./bak">
 514                         <fileset dir="${sourceDir}" id="client">
 515                                 <include name="${wsdl.ClientNS}/*.*" />
 516                         </fileset>
 517                 </move>
 518
 519                 <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
 520                         <mappingSet>
 521                                 <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
 522                                 <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
 523                         </mappingSet>
 524                 </axis-wsdl2java>
 525         </target>
 526
 527         <target name="makedist" depends="build, buildPropertiesFile, buildindices">
 528                 <!-- make the package jar if not already existing -->
 529                 <mkdir dir="${packageDir}" />
 530                 <!-- clean dir if it already existed -->
 531                 <delete>
 532                         <fileset dir="${packageDir}">
 533                                 <include name="*.jar"/>
 534                         </fileset>
 535                 </delete>
 536                 <jar destfile="${packageDir}/${outputJar}">
 537                         <manifest>
 538                                 <attribute name="Main-Class" value="jalview.bin.Jalview" />
 539                         </manifest>
 540                         <fileset dir="${outputDir}/">
 541                                 <exclude name="cache*/**" />
 542                                 <exclude name="*.jar" />
 543                                 <exclude name="*.jar.*" />
 544                                 <exclude name="**/*.jar" />
 545                                 <exclude name="**/*.jar.*" />
 546                         </fileset>
 547                 </jar>
 548
 549                 <copy toDir="${packageDir}" flatten="true">
 550                         <fileset dir="${outputDir}">
 551                                 <include name="*.jar" />
 552                                 <include name="**/*.jar" />
 553                         </fileset>
 554                 </copy>
 555         </target>
 556
 557
 558         <!-- jalopy code reformatter -->
 559         <target name="sourcescrub" depends="init,build">
 560                 <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
 561                         <fileset dir="${sourceDir}">
 562                                 <include name="*.java" />
 563                                 <include name="**/*.java" />
 564                                 <include name="**/**/*.java" />
 565                         </fileset>
 566                 </jalopy>
 567         </target>
 568
 569
 570
 571         <!-- Compile, package and obfuscate Jalview Applet -->
 572         <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 573
 574         <target name="compileApplet" depends="init,clean">
 575                 <mkdir dir="${outputDir}" />
 576                 <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
 577                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
 578                         excludes="ext/**,MCview/**,org/**,vamsas/**" />
 579         </target>
 580
 581         <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
 582                 <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 583                 <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
 584                 <jar destfile="in.jar">
 585                         <manifest>
 586                                 <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
 587                         </manifest>
 588                         <fileset dir="${outputDir}">
 589                                 <include name="com/**" />
 590                                 <include name="MCview/**" />
 591                                 <include name="jalview/**" />
 592                                 <include name=".build_properties" />
 593                                 <include name="images/idwidth.gif" />
 594                                 <include name="images/link.gif" />
 595                         </fileset>
 596                 </jar>
 597         </target>
 598         <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 599         </target>
 600         <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 601                 <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
 602                 <delete file="in.jar" />
 603         </target>
 604         <target name="-obfuscatereally" unless="donotobfuscate">
 605
 606                 <path id="obfuscateDeps.path">
 607                         <pathelement location="${applet.jre.tools}" />
 608                         <pathelement location="appletlib/${jmolJar}" />
 609                 </path>
 610                 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 611
 612                 <proguard>
 613                         <injar file="in.jar" />
 614                         <outjar file="${jalviewLiteJar}" />
 615                         <libraryjar refid="obfuscateDeps.path" />
 616                         <keep access="public" type="class" name="jalview.bin.JalviewLite">
 617                                 <field access="public" />
 618                                 <method access="public" />
 619                                 <constructor access="public" />
 620                         </keep>
 621                         <!--      -libraryjars "${obfuscateDeps}"
 622       -injars      in.jar
 623       -outjars     jalviewApplet.jar
 624       -keep public class jalview.bin.JalviewLite
 625        { public * ; } -->
 626                 </proguard>
 627                 <delete file="in.jar" />
 628         </target>
 629
 630         <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 631                 <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 632                 <delete>
 633                         <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 634                                 <include name="*.java" />
 635                                 <include name="descriptors/*.java" />
 636                         </fileset>
 637                 </delete>
 638                 <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 639                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 640                 <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 641                 <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
 642                 <!--
 643                 now build the jalview.binding package with the old schema set
 644                 -->
 645                 <delete>
 646                         <fileset dir="${sourceDir}/jalview/binding/">
 647                                 <include name="**" />
 648                         </fileset>
 649                 </delete>
 650                 <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 651                 <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 652                 <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
 653         </target>
 654         <target name="sourcedist" description="create jalview source distribution" depends="init">
 655                 <delete file="${source.dist.name}" />
 656                 <tar destfile="${source.dist.name}" compression="gzip">
 657                         <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
 658                                 <include name="LICENSE" />
 659                                 <include name="README" />
 660                                 <include name="build.xml" />
 661                                 <include name="jalview-jalopy.xml" />
 662                                 <include name="JalviewApplet.jpx" />
 663                                 <include name="JalviewX.jpx" />
 664                                 <include name="nbbuild.xml"/>
 665                                 <include name="nbproject/genfiles.properties"/>
 666         <include name="nbproject/project.properties"/>
 667         <include name="nbproject/project.xml"/>
 668                                 <include name="${sourceDir}/*.java" />
 669                                 <include name="${sourceDir}/**/*.java" />
 670                                 <include name="${sourceDir}/**/*.cdr" />
 671                                 <include name="${libDir}/**/*" />
 672                                 <include name="${resourceDir}/**/*" />
 673                                 <include name="${helpDir}/**/*" />
 674                                 <include name="appletlib/${jmolJar}" />
 675                                 <exclude name="**/*locales" />
 676                                 <exclude name="*locales/**" />
 677                                 <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
 678                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 679                                 <exclude name="utils/InstallAnywhere/**Build*/**" />
 680                                 <exclude name="utils/InstallAnywhere/**locale*" />
 681                                 <exclude name="utils/InstallAnywhere/**locale*/**" />
 682                                 <include name="${schemaDir}/**/*" />
 683                                 <include name="utils/**/*" />
 684                                 <include name="${docDir}/**/*" />
 685                                 <include name="examples/**/*" />
 686                         </tarfileset>
 687                 </tar>
 688         </target>
 689         <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
 690           <copy todir="${packageDir}/examples">
 691           <fileset dir="examples">
 692                 <include name="**/*"/>
 693                 <include name="javascript/*"/>
 694       <include name="jmol/*"/>
 695           </fileset>
 696                 <fileset dir=".">
 697                 <include name="jalviewApplet.jar"/>
 698                         </fileset>
 699                 <fileset dir="appletlib">
 700                       <include name="**/*"/>
 701                         </fileset>
 702           </copy>
 703
 704         </target>
 705         <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
 706          <javadoc destdir="${javadocDir}">
 707                 <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
 708                 </packageset>
 709                 </javadoc>
 710         </target>
 711
 712 </project>