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" srcdir="${sourceDir}" destdir="${outputDir}"
123 classpathref="build.classpath" />
125 <target name="buildindices" depends="init, prepare"
126 unless="help.uptodate">
128 classname="com.sun.java.help.search.Indexer"
129 classpathref="build.classpath"
131 dir="${outputDir}/${helpDir}"
137 <target name="makejars" depends="build, buildindices">
138 <!-- make the package jar -->
139 <mkdir dir="${packageDir}"/>
141 <jar destfile="${packageDir}/${outputJar}">
142 <fileset dir="${outputDir}/">
143 <exclude name="cache*/**"/>
144 <exclude name="*.jar" />
145 <exclude name="*.jar.*" />
146 <exclude name="**/*.jar" />
147 <exclude name="**/*.jar.*" />
151 <copy toDir="${packageDir}" flatten="true">
152 <fileset dir="${outputDir}">
153 <include name="*.jar"/>
154 <include name="**/*.jar"/>
157 <!-- the default keystore details might need to be edited here -->
159 storepass="alignmentisfun"
160 keypass="alignmentisfun"
161 keystore="keys/.keystore"
167 <fileset dir="${packageDir}">
168 <include name="*.jar"/>
171 <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
173 <!-- codebase="http://www.jalview.org/jalview/webstart" -->
174 <jnlp toFile="${packageDir}/Jalview.jnlp" href="Jalview.jnlp"
175 codebase="${WebStartLocation}">
177 <title>Jalview</title>
178 <vendor>The Barton Group</vendor>
179 <homepage href="www.jalview.org"/>
180 <description>Jalview Multiple Alignment Editor</description>
181 <description kind="short">Jalview</description>
182 <icon href="logo_big.gif"/>
183 <association mime-type="application-x/ext-file" extensions="fa"/>
184 <association mime-type="application-x/ext-file" extensions="fasta"/>
185 <association mime-type="application-x/ext-file" extensions="fastq"/>
186 <association mime-type="application-x/ext-file" extensions="blc"/>
187 <association mime-type="application-x/ext-file" extensions="msf"/>
188 <association mime-type="application-x/ext-file" extensions="pfam"/>
189 <association mime-type="application-x/ext-file" extensions="aln"/>
190 <association mime-type="application-x/ext-file" extensions="pir"/>
193 <j2se version="1.3+"/>
194 <fileset dir="${packageDir}">
195 <include name="jalview.jar"/>
197 <fileset dir="${packageDir}">
198 <include name="*.jar"/>
199 <exclude name="jalview.jar"/>
202 <application_desc main_class="jalview.bin.Jalview">
209 <target name="runenv" depends="init">
210 <path id="run.classpath">
211 <pathelement location="${outputDir}"/>
212 <fileset dir="${outputDir}">
213 <include name="${libDir}/*.jar"/>
216 <pathconvert targetos="unix" refid="run.classpath" property="run.classpath"/>
218 <echo>java -classpath ${run.classpath} jalview.bin.Jalview
222 <target name="buildextclients" depends="init">
223 <!-- Currently, this doesn't happen automatically.
224 1. Run WSDL2Java as below, which generates an ext.vamsas +
225 vamsas.<datapackages> fileset.
226 2. refactor ext.vamsas.SpecificserviceWS* to
227 ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
228 3. Update the jalview.ws.*WServices classes to reflect the
229 interface type, and all locations of this wsdl type that Jalview
233 <path id="axisbuild">
234 <!-- <path refid="axis.classpath"/> -->
235 <path refid="build.classpath"/>
237 <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
239 <fileset dir="${sourceDir}" id="client">
240 <include name="${wsdl.ClientNS}/*.*"/>
245 output="${sourceDir}"
249 deployscope="Request"
256 namespace="${wsdl.Namespace}"
257 package="${wsdl.ClientNS}"
259 <mapping namespace="http://dataTypes.vamsas"
260 package="${wsdl.ClientNS}"/>
265 <target name="package" depends="init, build">
268 <!-- jalopy code reformatter -->
269 <target name="sourcescrub" depends="init,build">
270 <jalopy destdir="jsrc" classpathref="run.classpath"
271 convention="jalview-jalopy.xml">
272 <fileset dir="${sourceDir}">
273 <include name="*.java"/>
274 <include name="**/*.java"/>
275 <include name="**/**/*.java"/>
282 <!-- Compile, package and obfuscate Jalview Applet -->
283 <target name="makeApplet" depends="obfuscate"/>
285 <target name="compileApplet" depends="init,clean">
286 <mkdir dir="${outputDir}"/>
287 <javac source="1.2" target="1.1" srcdir="${sourceDir}" destdir="${outputDir}"
288 includes="jalview/analysis/**,jalview/appletgui/**,jalview/datamodel/**jalview/jbappletgui/**,jalview/math/**,jalview/schemes/**"
289 excludes="ext/**,MCview/**,org/**,vamsas/**"/>
292 <target name="packageApplet" depends="compileApplet">
293 <jar destfile="in.jar">
294 <fileset dir="${outputDir}">
295 <include name="com/**"/>
296 <include name="jalview/**"/>
297 <include name="${resourceDir}/images/idwidth.gif"/>
302 <target name="obfuscate" depends="packageApplet">
303 <taskdef resource="proguard/ant/task.properties" classpath="C:/JalviewX/utils/proguard.jar" />
305 -libraryjars "${java.home}/lib/rt.jar"
307 -outjars jalviewApplet.jar
308 -keep public class jalview.bin.JalviewLite
310 <delete file="in.jar"/>