2 <project name="jalviewX" default="build" basedir=".">
3 <!-- we use jalopy to format our sources -->
5 classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
7 <fileset dir="utils/jalopy/lib">
8 <include name="*.jar" />
14 <!-- utils is a class path to additional utilities needed for
15 building docs, jars and webstart stuff -->
18 Userdefined build property defaults
20 wsdl.server list (plus namespace mapping info ???) - also want
21 ... to make this a dynamically generatable property
23 Build location - provide a temporary root for speed
24 jarsigner keystore and info
25 Jakarta and axis classpath ?
26 Default argument for starting Jalview (if it exists).
31 <path id="axis.classpath">
32 <!--> <fileset dir="/usr/local/axis/lib">
33 <include name="**/*.jar" />
35 <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
36 <include name="**/*.jar"/>
37 <include name="*.jar"/>
41 <property name="" value=""/>
42 <property name="libDir" value="lib"/>
43 <property name="resourceDir" value="resources"/>
44 <property name="helpDir" value="help"/>
45 <property name="docDir" value="doc"/>
46 <property name="sourceDir" value="src" />
47 <property name="outputDir" value="classes" />
48 <property name="packageDir" value="dist" />
49 <property name="outputJar" value="jalview.jar" />
50 <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
51 <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
52 <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
53 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
54 <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
55 <property name="WSInterf" value="MsaWS" />
56 <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
57 <property name="wsdl.Namespace" value="vamsas" />
58 <property name="wsdl.ClientNS" value="ext.vamsas" />
60 <path id="build.classpath">
62 <include name="*.jar"/>
63 <include name="**/*.jar"/>
65 <fileset dir="${libDir}">
66 <include name="*.jar"/>
67 <include name="**/*.jar"/>
69 <!-- <fileset dir="old_lib_signed">
70 <include name="lib_axis.jar"/>
74 <!--> <uptodate property="help.uptodate"
75 targetfile="${helpDir}/helpIndex.xml">
78 includes="**/*.html" />
83 <target name="clean" depends="init">
84 <!-- not efficient yet. -->
85 <delete dir="${outputDir}"/>
88 <target name="distclean" depends="init, clean">
90 <echo message="REMOVING ALL BACKUP/AUTOSAVES!"/>
93 <include name="${outputJar}"/>
95 <include name="#*.*#"/>
96 <include name="**/#*#"/>
97 <include name="**/#*.*#"/>
99 <include name="*.*~"/>
100 <include name="**/*~"/>
101 <include name="**/*.*~"/>
106 <target name="prepare" depends="init">
107 <mkdir dir="${outputDir}"/>
108 <copy todir="${outputDir}">
110 <include name="${docDir}/**/*.*"/>
111 <include name="${helpDir}/**/*.*"/>
112 <include name="${libDir}/*.jar"/>
114 <fileset dir="${resourceDir}">
115 <include name="**/*.*"/>
120 <target name="build" depends="prepare">
121 <!-- not efficient yet. -->
122 <javac source="1.4" target="1.4"
123 srcdir ="${sourceDir}"
124 destdir="${outputDir}"
125 classpathref="build.classpath">
126 <exclude name="jalview/*applet*"/>
127 <exclude name="com/stevesoft/**"/>
130 <target name="buildindices" depends="init, prepare"
131 unless="help.uptodate">
133 classname="com.sun.java.help.search.Indexer"
134 classpathref="build.classpath"
136 dir="${outputDir}/${helpDir}"
142 <target name="makejars" depends="build, buildindices">
143 <!-- make the package jar -->
144 <mkdir dir="${packageDir}"/>
146 <jar destfile="${packageDir}/${outputJar}">
147 <fileset dir="${outputDir}/">
148 <exclude name="cache*/**"/>
149 <exclude name="*.jar" />
150 <exclude name="*.jar.*" />
151 <exclude name="**/*.jar" />
152 <exclude name="**/*.jar.*" />
156 <copy toDir="${packageDir}" flatten="true">
157 <fileset dir="${outputDir}">
158 <include name="*.jar"/>
159 <include name="**/*.jar"/>
162 <!-- the default keystore details might need to be edited here -->
164 storepass="alignmentisfun"
165 keypass="alignmentisfun"
166 keystore="keys/.keystore"
172 <fileset dir="${packageDir}">
173 <include name="*.jar"/>
176 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
178 <!-- codebase="http://www.jalview.org/jalview/webstart" -->
179 <jnlp toFile="${packageDir}/Jalview.jnlp" href="Jalview.jnlp"
180 codebase="${WebStartLocation}">
182 <title>Jalview</title>
183 <vendor>The Barton Group</vendor>
184 <homepage href="www.jalview.org"/>
185 <description>Jalview Multiple Alignment Editor</description>
186 <description kind="short">Jalview</description>
187 <icon href="logo_big.gif"/>
189 <association mime-type="application-x/ext-file" extensions="fa"/>
190 <association mime-type="application-x/ext-file" extensions="fasta"/>
191 <association mime-type="application-x/ext-file" extensions="fastq"/>
192 <association mime-type="application-x/ext-file" extensions="blc"/>
193 <association mime-type="application-x/ext-file" extensions="msf"/>
194 <association mime-type="application-x/ext-file" extensions="pfam"/>
195 <association mime-type="application-x/ext-file" extensions="aln"/>
196 <association mime-type="application-x/ext-file" extensions="pir"/>
200 <j2se version="1.3+"/>
201 <fileset dir="${packageDir}">
202 <include name="jalview.jar"/>
204 <fileset dir="${packageDir}">
205 <include name="*.jar"/>
206 <exclude name="jalview.jar"/>
209 <application_desc main_class="jalview.bin.Jalview">
216 <target name="runenv" depends="init">
217 <path id="run.classpath">
218 <pathelement location="${outputDir}"/>
219 <fileset dir="${outputDir}">
220 <include name="${libDir}/*.jar"/>
223 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
225 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
229 <target name="buildextclients" depends="init">
230 <!-- Currently, this doesn't happen automatically.
231 1. Run WSDL2Java as below, which generates an ext.vamsas +
232 vamsas.<datapackages> fileset.
233 2. refactor ext.vamsas.SpecificserviceWS* to
234 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
235 3. Update the jalview.ws.*WServices classes to reflect the
236 interface type, and all locations of this wsdl type that Jalview
240 <path id="axisbuild">
241 <!-- <path refid="axis.classpath"/> -->
242 <path refid="build.classpath"/>
244 <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
246 <fileset dir="${sourceDir}" id="client">
247 <include name="${wsdl.ClientNS}/*.*"/>
252 output="${sourceDir}"
256 deployscope="Request"
263 namespace="${wsdl.Namespace}"
264 package="${wsdl.ClientNS}"
266 <mapping namespace="http://dataTypes.vamsas"
267 package="${wsdl.ClientNS}"/>
272 <target name="package" depends="init, build">
275 <!-- jalopy code reformatter -->
276 <target name="sourcescrub" depends="init,build">
277 <jalopy destdir="jsrc" classpathref="run.classpath"
278 convention="jalview-jalopy.xml">
279 <fileset dir="${sourceDir}">
280 <include name="*.java"/>
281 <include name="**/*.java"/>
282 <include name="**/**/*.java"/>
289 <!-- Compile, package and obfuscate Jalview Applet -->
290 <target name="makeApplet" depends="obfuscate"/>
292 <target name="compileApplet" depends="init,clean">
293 <mkdir dir="${outputDir}"/>
294 <javac source="1.2" target="1.1" srcdir="${sourceDir}" destdir="${outputDir}"
295 includes="jalview/analysis/**,jalview/appletgui/**,jalview/datamodel/**jalview/jbappletgui/**,jalview/math/**,jalview/schemes/**"
296 excludes="ext/**,MCview/**,org/**,vamsas/**"/>
299 <target name="packageApplet" depends="compileApplet">
300 <jar destfile="in.jar">
301 <fileset dir="${outputDir}">
302 <include name="com/**"/>
303 <include name="jalview/**"/>
304 <include name="${resourceDir}/images/idwidth.gif"/>
309 <target name="obfuscate" depends="packageApplet">
310 <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
312 -libraryjars "${java.home}/lib/rt.jar"
314 -outjars jalviewApplet.jar
315 -keep public class jalview.bin.JalviewLite
317 <delete file="in.jar"/>