mev-4.0.01/build_script/build.xml

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3 27 Feb 07 jari 1 <!-- $Id -->
3 27 Feb 07 jari 2
2 26 Feb 07 jari 3 <project name="mev" default="build-all" basedir="./">
2 26 Feb 07 jari 4     
2 26 Feb 07 jari 5     <description>
2 26 Feb 07 jari 6        
2 26 Feb 07 jari 7     </description>
2 26 Feb 07 jari 8
2 26 Feb 07 jari 9     <!-- Directory Properties
2 26 Feb 07 jari 10          These properties specify key directories within the source
2 26 Feb 07 jari 11          and destination areas.
2 26 Feb 07 jari 12     -->
2 26 Feb 07 jari 13     <property name="dest.dir" location="${basedir}/temp"/>
2 26 Feb 07 jari 14     <property name="home.dir" location="${basedir}/.."/>
2 26 Feb 07 jari 15     <property name="source.dir" location="${basedir}/../source"/>
2 26 Feb 07 jari 16     <property name="tigr.dir" location="${source.dir}/org/tigr"/>
2 26 Feb 07 jari 17     <property name="mev.dir" location="${tigr.dir}/microarray/mev"/>
2 26 Feb 07 jari 18     <property name="cluster.dir" location="${mev.dir}/cluster"/>
2 26 Feb 07 jari 19     <property name="alg.impl.dir" location="${cluster.dir}/algorithm/impl"/>
2 26 Feb 07 jari 20     <property name="gui.impl.dir" location="${cluster.dir}/gui/impl"/>
2 26 Feb 07 jari 21     <property name="lib.dir" location="${home.dir}/lib"/>
3 27 Feb 07 jari 22     <property name="config.dir" location="${home.dir}/config"/>
3 27 Feb 07 jari 23   <property name="javac-location" location="/System/Library/Frameworks/JavaVM.framework/Versions/1.4.2/Commands/javac"/>
3 27 Feb 07 jari 24 <!--  <property name="javac-location" location="C:\j2sdk1.4.2_07\bin\javac"/> -->
2 26 Feb 07 jari 25
2 26 Feb 07 jari 26
2 26 Feb 07 jari 27     <!-- This path element contains jar files to support module compilation -->
2 26 Feb 07 jari 28     <path id="module.build.class.path">
2 26 Feb 07 jari 29         <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 30         <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 31         <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 32         <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 33         <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 34         <pathelement location="${lib.dir}/mev-base.jar"/>
2 26 Feb 07 jari 35     </path>
2 26 Feb 07 jari 36
2 26 Feb 07 jari 37
2 26 Feb 07 jari 38     <!-- Module Selection Properties     
2 26 Feb 07 jari 39      
2 26 Feb 07 jari 40      *Modules that are set (not commented out) have associated targets 
2 26 Feb 07 jari 41      that will permit module compilation
2 26 Feb 07 jari 42
2 26 Feb 07 jari 43      *module target execution includes compilation and entry of 
2 26 Feb 07 jari 44      module specfic key-value pairs into the factory.properties files        
2 26 Feb 07 jari 45
2 26 Feb 07 jari 46      *these flags control gui and algorithm side compilation, however,
2 26 Feb 07 jari 47      a separate target controls the compilation of gui and algorithm compilation.
2 26 Feb 07 jari 48
2 26 Feb 07 jari 49            **See the "algorithm-modules" target below for important information about 
2 26 Feb 07 jari 50            specification of algorithms to build and the order.
2 26 Feb 07 jari 51     -->
2 26 Feb 07 jari 52     <property name="HCL" value="y"/>
2 26 Feb 07 jari 53     <property name="TEASE" value="y"/>
2 26 Feb 07 jari 54     <property name="ST" value="y"/>
2 26 Feb 07 jari 55     <property name="SOTA" value="y"/>
2 26 Feb 07 jari 56     <property name="RN" value="y"/>
2 26 Feb 07 jari 57     <property name="KMC" value="y"/>
2 26 Feb 07 jari 58     <property name="KMCS" value="y"/>
2 26 Feb 07 jari 59     <property name="CAST" value="y"/>
2 26 Feb 07 jari 60     <property name="QTC" value="y"/>
2 26 Feb 07 jari 61     <property name="GSH" value="y"/>
2 26 Feb 07 jari 62     <property name="SOM" value="y"/>
2 26 Feb 07 jari 63     <property name="FOM" value="y"/>
2 26 Feb 07 jari 64     <property name="PTM" value="y"/>
2 26 Feb 07 jari 65     <property name="TTEST" value="y"/>
2 26 Feb 07 jari 66     <property name="BRIDGE" value="y"/>
2 26 Feb 07 jari 67     <property name="SAM" value="y"/>
2 26 Feb 07 jari 68     <property name="OWA" value="y"/>
2 26 Feb 07 jari 69     <property name="TFA" value="y"/>
2 26 Feb 07 jari 70     <property name="SVM" value="y"/>
2 26 Feb 07 jari 71     <property name="KNNC" value="y"/>
2 26 Feb 07 jari 72     <property name="DAM" value="n"/>
2 26 Feb 07 jari 73   <property name="LEM" value="y"/>
2 26 Feb 07 jari 74     <property name="GDM" value="y"/>
2 26 Feb 07 jari 75     <property name="PCA" value="y"/>
2 26 Feb 07 jari 76     <property name="COA" value="y"/>
2 26 Feb 07 jari 77     <property name="TRN" value="y"/>
2 26 Feb 07 jari 78     <property name="EASE" value="y"/>
2 26 Feb 07 jari 79   <property name="USC" value="y"/>
2 26 Feb 07 jari 80   
2 26 Feb 07 jari 81   <!-- Module category names -->
2 26 Feb 07 jari 82   <property name="CLUSTERING" value="Clustering"/>
2 26 Feb 07 jari 83   <property name="STATISTICS" value="Statistics"/>
2 26 Feb 07 jari 84   <property name="CLASSIFICATION" value="Classification"/>
2 26 Feb 07 jari 85   <property name="DATA_REDUCTION" value="Data Reduction"/>
2 26 Feb 07 jari 86   <property name="META_ANALYSIS" value="Meta Analysis"/>
2 26 Feb 07 jari 87   <property name="VISUALIZATION" value="Visualization"/>
2 26 Feb 07 jari 88   <property name="MISC" value="Miscellaneous"/>
2 26 Feb 07 jari 89
2 26 Feb 07 jari 90   <!-- Property Files, These properties identify the properties files to be constructed during module compilation -->
2 26 Feb 07 jari 91     <property name="gui.properties.file" value="${dest.dir}/org/tigr/microarray/mev/cluster/gui/impl/factory.properties"/>
2 26 Feb 07 jari 92     <property name="alg.properties.file" value="${dest.dir}/org/tigr/microarray/mev/cluster/algorithm/impl/factory.properties"/>
2 26 Feb 07 jari 93
2 26 Feb 07 jari 94     <!-- TARGET ============================================    
2 26 Feb 07 jari 95            Target Name: algorithm-modules
2 26 Feb 07 jari 96     Depends: ... build-base ... <algorithm module targets>
2 26 Feb 07 jari 97
2 26 Feb 07 jari 98            Target Description: 
2 26 Feb 07 jari 99           
2 26 Feb 07 jari 100                   This target triggers building of the base mev classes and the algorithm
2 26 Feb 07 jari 101                   module classes on both the gui.impl and the algorithm.impl areas.
2 26 Feb 07 jari 102
2 26 Feb 07 jari 103                   Note that the depends attribute of the target specifies the algorithms to
2 26 Feb 07 jari 104                   be included in the distribution.  The targets will be compiled in this order and
2 26 Feb 07 jari 105                   as a result the properties files will list the implementation names (gui.names) in
2 26 Feb 07 jari 106                   this order.  This order dictates the order in which the module buttons will appear
2 26 Feb 07 jari 107                   in the MultipleArrayViewer from left to right.
2 26 Feb 07 jari 108
2 26 Feb 07 jari 109                   In order for a module to be built it must have a property set above and must
2 26 Feb 07 jari 110                   have it's target within the list in the 'depends' attribute below. 
2 26 Feb 07 jari 111     -->   
2 26 Feb 07 jari 112     <target name="algorithm-modules"
2 26 Feb 07 jari 113 depends="build-base,HCL,TEASE,ST,SOTA,RN,KMC,KMCS,CAST,FOM,QTC,GSH,SOM,PTM,TTEST,BRIDGE,SAM,OWA,TFA,SVM,USC,LEM,KNNC,DAM,GDM,PCA,COA,TRN,EASE">
2 26 Feb 07 jari 114     </target>
2 26 Feb 07 jari 115
2 26 Feb 07 jari 116
2 26 Feb 07 jari 117     <!-- TARGET ============================================    
2 26 Feb 07 jari 118            Target Name: modules only
2 26 Feb 07 jari 119     Depends: <algorithm module targets>
2 26 Feb 07 jari 120
2 26 Feb 07 jari 121            Target Description: 
2 26 Feb 07 jari 122       This target triggers building of the algorithm module classes on both the gui.impl
2 26 Feb 07 jari 123                   and the algorithm.impl areas.
2 26 Feb 07 jari 124
2 26 Feb 07 jari 125                   Note that the depends attribute of the target specifies the algorithms to
2 26 Feb 07 jari 126                   be included in the distribution.  The targets will be compiled in this order and
2 26 Feb 07 jari 127                   as a result the properties files will list the implementation names (gui.names) in
2 26 Feb 07 jari 128                   this order.  This order dictates the order in which the module buttons will appear
2 26 Feb 07 jari 129                   in the MultipleArrayViewer from left to right.
2 26 Feb 07 jari 130
2 26 Feb 07 jari 131                   In order for a module to be built it must have a property set above and must
2 26 Feb 07 jari 132                   have it's target within the list in the 'depends' attribute below. 
2 26 Feb 07 jari 133     -->   
2 26 Feb 07 jari 134     <target name="modules-only"
2 26 Feb 07 jari 135 depends="HCL,TEASE,ST,SOTA,RN,KMC,KMCS,CAST,FOM,QTC,GSH,SOM,PTM,TTEST,BRIDGE,SAM,OWA,TFA,SVM,USC,KNNC,DAM,GDM,PCA,COA,TRN,EASE">
2 26 Feb 07 jari 136     </target>
2 26 Feb 07 jari 137
2 26 Feb 07 jari 138
2 26 Feb 07 jari 139
2 26 Feb 07 jari 140
2 26 Feb 07 jari 141
2 26 Feb 07 jari 142
2 26 Feb 07 jari 143     <!-- ====================================================================
2 26 Feb 07 jari 144      
2 26 Feb 07 jari 145          Utilities, Support, and Primary MeV Class Construction Targets
2 26 Feb 07 jari 146
2 26 Feb 07 jari 147          These targets produce mev-util.jar, mev-algorithm-support.jar, mev-gui-support.jar
2 26 Feb 07 jari 148          and mev-base.jar
2 26 Feb 07 jari 149
2 26 Feb 07 jari 150          ==================================================================== -->  
2 26 Feb 07 jari 151
2 26 Feb 07 jari 152
2 26 Feb 07 jari 153     <!-- TARGET ============================================    
2 26 Feb 07 jari 154            Target Name: init
2 26 Feb 07 jari 155     Depends: none
2 26 Feb 07 jari 156            Target Description: makes the temp directory as destination for build
2 26 Feb 07 jari 157     -->
2 26 Feb 07 jari 158     <target name="init">
2 26 Feb 07 jari 159         <tstamp/>
2 26 Feb 07 jari 160       <echo level="info" message="home.dir: ${home.dir}" />
2 26 Feb 07 jari 161       <echo level="info" message="source.dir: ${source.dir}" />
2 26 Feb 07 jari 162       <echo level="info" message="tigr.dir: ${tigr.dir}" />
2 26 Feb 07 jari 163         <echo level="info" message="mev.dir: ${mev.dir}" />
2 26 Feb 07 jari 164         <echo level="info" message="cluster.dir: ${cluster.dir}" />
2 26 Feb 07 jari 165       <echo level="info" message="alg.impl.dir: ${alg.impl.dir}" />
2 26 Feb 07 jari 166       <echo level="info" message="gui.impl.dir: ${gui.impl.dir}" />
2 26 Feb 07 jari 167       <echo level="info" message="lib.dir: ${lib.dir}" />
2 26 Feb 07 jari 168         <delete dir="${dest.dir}"/>
2 26 Feb 07 jari 169         <mkdir dir="${dest.dir}"/>
2 26 Feb 07 jari 170     </target>
2 26 Feb 07 jari 171
2 26 Feb 07 jari 172
2 26 Feb 07 jari 173
2 26 Feb 07 jari 174     <!-- TARGET ============================================    
2 26 Feb 07 jari 175            Target Name: util
2 26 Feb 07 jari 176     Depends: init
2 26 Feb 07 jari 177            Target Description: Compiles org/tigr/util and packages below
2 26 Feb 07 jari 178            Compilation Summary:
2 26 Feb 07 jari 179         org/tigr/util
2 26 Feb 07 jari 180         org/tigr/util/awt
2 26 Feb 07 jari 181         org/tigr/util/swing
2 26 Feb 07 jari 182     -->
2 26 Feb 07 jari 183     <target name="util" depends="init">
3 27 Feb 07 jari 184         <javac srcdir="${tigr.dir}/util" destdir="${dest.dir}"
3 27 Feb 07 jari 185                executable="${javac-location}">
3 27 Feb 07 jari 186
2 26 Feb 07 jari 187       <classpath>
2 26 Feb 07 jari 188                 <pathelement location="${lib.dir}/jai_core.jar"/>
2 26 Feb 07 jari 189                 <pathelement location="${lib.dir}/jai_codec.jar"/>
2 26 Feb 07 jari 190                 <pathelement location="${lib.dir}/images.jar"/>
2 26 Feb 07 jari 191             </classpath>
2 26 Feb 07 jari 192         </javac>
2 26 Feb 07 jari 193     </target>
2 26 Feb 07 jari 194
2 26 Feb 07 jari 195
2 26 Feb 07 jari 196
2 26 Feb 07 jari 197     <!-- TARGET ============================================    
2 26 Feb 07 jari 198            Target Name: graph
2 26 Feb 07 jari 199     Depends: util
2 26 Feb 07 jari 200            Target Description: Compiles graph package.
2 26 Feb 07 jari 201            Compilation Summary: org/tigr/graph
2 26 Feb 07 jari 202     -->
2 26 Feb 07 jari 203     <target name="graph" depends="util">
3 27 Feb 07 jari 204         <javac srcdir="${tigr.dir}/graph" destdir="${dest.dir}"
3 27 Feb 07 jari 205                executable="${javac-location}">
2 26 Feb 07 jari 206       <classpath>
2 26 Feb 07 jari 207                 <pathelement location="${lib.dir}/jai_core.jar"/>
2 26 Feb 07 jari 208                 <pathelement location="${lib.dir}/jai_codec.jar"/>
2 26 Feb 07 jari 209                 <pathelement location="${lib.dir}/images.jar"/>
2 26 Feb 07 jari 210             </classpath>
2 26 Feb 07 jari 211         </javac>
2 26 Feb 07 jari 212     </target>
2 26 Feb 07 jari 213
2 26 Feb 07 jari 214
2 26 Feb 07 jari 215
2 26 Feb 07 jari 216     <!-- TARGET ============================================    
2 26 Feb 07 jari 217            Target Name: jar-util
2 26 Feb 07 jari 218     Depends: graph
2 26 Feb 07 jari 219            Target Description: jars org/tigr/util and sub-directories
2 26 Feb 07 jari 220            Jar Contents: 
2 26 Feb 07 jari 221         org/tigr/graph
2 26 Feb 07 jari 222         org/tigr/util
2 26 Feb 07 jari 223         org/tigr/util/awt
2 26 Feb 07 jari 224         org/tigr/util/swing
2 26 Feb 07 jari 225     -->
2 26 Feb 07 jari 226     <target name="jar-util" depends="graph">
2 26 Feb 07 jari 227         <jar destfile="${lib.dir}/mev-util.jar"
2 26 Feb 07 jari 228              basedir="${dest.dir}"
2 26 Feb 07 jari 229          includes="org/tigr/util/**, org/tigr/graph/**"
2 26 Feb 07 jari 230   
2 26 Feb 07 jari 231         />        
2 26 Feb 07 jari 232     </target>
2 26 Feb 07 jari 233
2 26 Feb 07 jari 234
2 26 Feb 07 jari 235
2 26 Feb 07 jari 236
2 26 Feb 07 jari 237     <!-- TARGET ============================================    
2 26 Feb 07 jari 238            Target Name: algorithm-support
2 26 Feb 07 jari 239     Depends: jar-util
2 26 Feb 07 jari 240            Target Description: Compiles non-module specific support on algorithm side
2 26 Feb 07 jari 241            Compilation Summary:
2 26 Feb 07 jari 242         mev/cluster
2 26 Feb 07 jari 243         mev/cluster/algorithm
2 26 Feb 07 jari 244         mev/cluster/algorithm/impl (non-module classes)
2 26 Feb 07 jari 245         mev/cluster/algorithm/impl/util
2 26 Feb 07 jari 246     -->
2 26 Feb 07 jari 247     <target name="algorithm-support" depends="jar-util">
3 27 Feb 07 jari 248         <javac sourcepath="" srcdir="${cluster.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 249                executable="${javac-location}">
2 26 Feb 07 jari 250             <include name="*.java"/>            
2 26 Feb 07 jari 251         </javac>
3 27 Feb 07 jari 252         <javac sourcepath="" srcdir="${cluster.dir}/algorithm" destdir="${dest.dir}"
3 27 Feb 07 jari 253                executable="${javac-location}">
2 26 Feb 07 jari 254             <include name="*.java"/>            
2 26 Feb 07 jari 255         </javac>
3 27 Feb 07 jari 256         <javac sourcepath="" srcdir="${cluster.dir}/algorithm/impl" destdir="${dest.dir}"
3 27 Feb 07 jari 257                executable="${javac-location}">
2 26 Feb 07 jari 258             <include name="ExperimentUtil.java"/>            
2 26 Feb 07 jari 259             <include name="AlgorithmFactoryImpl.java"/>
2 26 Feb 07 jari 260             <include name="util/*.java"/>              
2 26 Feb 07 jari 261         </javac>
2 26 Feb 07 jari 262     </target>
2 26 Feb 07 jari 263
2 26 Feb 07 jari 264
2 26 Feb 07 jari 265
2 26 Feb 07 jari 266     <!-- TARGET ============================================    
2 26 Feb 07 jari 267            Target Name: jar-algorithm-support
2 26 Feb 07 jari 268     Depends: algorithm-support
2 26 Feb 07 jari 269            Target Description: jars algorithm support classes
2 26 Feb 07 jari 270     -->
2 26 Feb 07 jari 271     <target name="jar-algorithm-support" depends="algorithm-support">
2 26 Feb 07 jari 272         <jar destfile="${lib.dir}/mev-algorithm-support.jar"
2 26 Feb 07 jari 273              basedir="${dest.dir}"
2 26 Feb 07 jari 274          includes="org/tigr/microarray/mev/cluster/*.class,
2 26 Feb 07 jari 275                        org/tigr/microarray/mev/cluster/algorithm/*.class,
2 26 Feb 07 jari 276                    org/tigr/microarray/mev/cluster/algorithm/impl/*.class,            
2 26 Feb 07 jari 277                    org/tigr/microarray/mev/cluster/algorithm/impl/util/*.class"            
2 26 Feb 07 jari 278         /> 
2 26 Feb 07 jari 279     </target>
2 26 Feb 07 jari 280     
2 26 Feb 07 jari 281    
2 26 Feb 07 jari 282
2 26 Feb 07 jari 283
2 26 Feb 07 jari 284     <!-- TARGET ============================================    
2 26 Feb 07 jari 285            Target Name: base
2 26 Feb 07 jari 286     Depends: jar-algorithm-support
2 26 Feb 07 jari 287            Target Description: This is the main target for compilation of non-module code.
2 26 Feb 07 jari 288            Compilation Summary: 
2 26 Feb 07 jari 289           tigr/remote
2 26 Feb 07 jari 290           mev/r/**
2 26 Feb 07 jari 291                         microarray/file/**
2 26 Feb 07 jari 292                 microarray/util/**
2 26 Feb 07 jari 293           mev
2 26 Feb 07 jari 294           mev/action
2 26 Feb 07 jari 295           mev/file/**
2 26 Feb 07 jari 296                                         mev/cgh/**
2 26 Feb 07 jari 297           mev/script/**
2 26 Feb 07 jari 298     -->
2 26 Feb 07 jari 299     <target name="base" depends="jar-algorithm-support">
2 26 Feb 07 jari 300         <javac srcdir="${tigr.dir}/microarray:${tigr.dir}" destdir="${dest.dir}"
2 26 Feb 07 jari 301           fork="yes" 
2 26 Feb 07 jari 302         executable="${javac-location}"
2 26 Feb 07 jari 303         memoryMaximumSize="256m"
2 26 Feb 07 jari 304             includes=
2 26 Feb 07 jari 305             "mev/r/**, 
2 26 Feb 07 jari 306             file/**, 
2 26 Feb 07 jari 307             remote/**, 
2 26 Feb 07 jari 308             util/**, 
2 26 Feb 07 jari 309             mev/**, 
2 26 Feb 07 jari 310             mev/action/*.java, 
2 26 Feb 07 jari 311             mev/persistence/**, 
2 26 Feb 07 jari 312             mev/file/**, 
2 26 Feb 07 jari 313             mev/script/**,
2 26 Feb 07 jari 314       mev/cluster/gui/impl/**, 
2 26 Feb 07 jari 315       mev/cgh/**,
2 26 Feb 07 jari 316       mev/cluster/gui/impl/dialogs/**, 
2 26 Feb 07 jari 317       mev/cluster/gui/impl/util/*.java, 
2 26 Feb 07 jari 318       mev/cluster/gui/*.java,
2 26 Feb 07 jari 319       mev/cluster/clusterUtil/**, 
2 26 Feb 07 jari 320       mev/cluster/gui/helpers/**, 
2 26 Feb 07 jari 321       ${source.dir}/edu/washington/cea/r/*.java">
2 26 Feb 07 jari 322             <classpath>
2 26 Feb 07 jari 323                 <pathelement location="${lib.dir}/normalization.jar"/>  
2 26 Feb 07 jari 324                 <pathelement location="${lib.dir}/jai_codec.jar"/>  
2 26 Feb 07 jari 325                 <pathelement location="${lib.dir}/jama.jar"/>  
2 26 Feb 07 jari 326                 <pathelement location="${lib.dir}/JSciCore.jar"/>  
2 26 Feb 07 jari 327
2 26 Feb 07 jari 328                 <pathelement location="${lib.dir}/jai_core.jar"/>  
2 26 Feb 07 jari 329                 <pathelement location="${lib.dir}/vecmath.jar"/>  
2 26 Feb 07 jari 330
2 26 Feb 07 jari 331                 <pathelement location="${lib.dir}/j3dcore.jar"/>  
2 26 Feb 07 jari 332                 <pathelement location="${lib.dir}/j3dutils.jar"/>  
2 26 Feb 07 jari 333                  <pathelement location="${lib.dir}/colt.jar"/>
2 26 Feb 07 jari 334                 <pathelement location="${lib.dir}/comcgh.jar"/>
2 26 Feb 07 jari 335                 <pathelement location="${lib.dir}/educgh.jar"/>
3 27 Feb 07 jari 336                 <pathelement location="${lib.dir}/jnlp.jar"/>
2 26 Feb 07 jari 337                 <pathelement location="${lib.dir}/Text_JDBC30.jar"/>
2 26 Feb 07 jari 338                 <pathelement location="${lib.dir}/xerces.jar"/>
2 26 Feb 07 jari 339                 <pathelement location="${lib.dir}/base64.jar"/>
2 26 Feb 07 jari 340                 <pathelement location="${lib.dir}/HTTPClient.jar"/>
2 26 Feb 07 jari 341                 <pathelement location="${lib.dir}/servlet.jar"/>
2 26 Feb 07 jari 342                 <pathelement location="${lib.dir}/ftpbean.jar"/>
2 26 Feb 07 jari 343                 <pathelement location="${tigr.dir}/microarray/file"/>
2 26 Feb 07 jari 344             </classpath>      
2 26 Feb 07 jari 345         </javac>
2 26 Feb 07 jari 346     </target>
2 26 Feb 07 jari 347
2 26 Feb 07 jari 348
2 26 Feb 07 jari 349
2 26 Feb 07 jari 350
2 26 Feb 07 jari 351     <!-- TARGET ============================================    
2 26 Feb 07 jari 352            Target Name: jar-gui-support
2 26 Feb 07 jari 353     Depends: base
2 26 Feb 07 jari 354            Target Description: jars mev base classes
2 26 Feb 07 jari 355     Note:  Calling this target will produce the following jars:
2 26 Feb 07 jari 356       mev-util.jar, mev-algorithm-support.jar,
2 26 Feb 07 jari 357       mev-gui-support.jar, mev-base.jar
2 26 Feb 07 jari 358     -->
2 26 Feb 07 jari 359     <target name="jar-gui-support" depends="base">
2 26 Feb 07 jari 360         
2 26 Feb 07 jari 361         <!-- make the images directory within the destination area -->
2 26 Feb 07 jari 362         <mkdir dir="${dest.dir}/org/tigr/microarray/mev/cluster/gui/impl/images"/>       
2 26 Feb 07 jari 363         
2 26 Feb 07 jari 364         <!-- copy images (gifs) to images directory for inclusion in the jar -->        
2 26 Feb 07 jari 365         <copy todir="${dest.dir}/org/tigr/microarray/mev/cluster/gui/impl/images">
2 26 Feb 07 jari 366             <fileset dir="${gui.impl.dir}/images"/>
2 26 Feb 07 jari 367         </copy>
2 26 Feb 07 jari 368
2 26 Feb 07 jari 369
2 26 Feb 07 jari 370         <jar destfile="${lib.dir}/mev-gui-support.jar"
2 26 Feb 07 jari 371             basedir="${dest.dir}"
2 26 Feb 07 jari 372         includes="org/tigr/microarray/mev/cluster/gui/*.class,                        
2 26 Feb 07 jari 373               org/tigr/microarray/mev/cluster/gui/helpers/*.class,
2 26 Feb 07 jari 374              org/tigr/microarray/mev/cluster/gui/helpers/ktree/*.class"                    
2 26 Feb 07 jari 375         />
2 26 Feb 07 jari 376     </target>
2 26 Feb 07 jari 377
2 26 Feb 07 jari 378
2 26 Feb 07 jari 379
2 26 Feb 07 jari 380     <!-- TARGET ============================================
2 26 Feb 07 jari 381            Target Name: jar-images
2 26 Feb 07 jari 382     Depends: None
2 26 Feb 07 jari 383            Target Description: jars org/tigr/images for gui support
2 26 Feb 07 jari 384                                 creates images.jar
2 26 Feb 07 jari 385     -->
2 26 Feb 07 jari 386     <target name="jar-images">
2 26 Feb 07 jari 387         
2 26 Feb 07 jari 388         <!-- make the images directory within the destination area -->
2 26 Feb 07 jari 389         <mkdir dir="${dest.dir}/org/tigr/images"/>       
2 26 Feb 07 jari 390         
2 26 Feb 07 jari 391         <!-- copy images (gifs) to images directory for inclusion in the jar -->        
2 26 Feb 07 jari 392         <copy todir="${dest.dir}/org/tigr/images">
2 26 Feb 07 jari 393             <fileset dir="${tigr.dir}/images"/>
2 26 Feb 07 jari 394         </copy>
2 26 Feb 07 jari 395
2 26 Feb 07 jari 396         <jar destfile="${lib.dir}/images.jar"
2 26 Feb 07 jari 397             basedir="${dest.dir}"
2 26 Feb 07 jari 398         includes="org/tigr/images/*"
2 26 Feb 07 jari 399         />
2 26 Feb 07 jari 400     </target>
2 26 Feb 07 jari 401
2 26 Feb 07 jari 402
2 26 Feb 07 jari 403
2 26 Feb 07 jari 404     <!-- TARGET ============================================
2 26 Feb 07 jari 405            Target Name: jar-dialog-help
2 26 Feb 07 jari 406     Depends: None
2 26 Feb 07 jari 407            Target Description: creates dialogHelp.jar from the html pages
2 26 Feb 07 jari 408     within .../gui/impl/dialogs/dialogHelpUtil/dialogHelpPages
2 26 Feb 07 jari 409     -->
2 26 Feb 07 jari 410     <target name="jar-dialog-help">
2 26 Feb 07 jari 411         
2 26 Feb 07 jari 412         <!-- make the images directory within the destination area -->
2 26 Feb 07 jari 413         <mkdir dir="${dest.dir}/org/tigr/microarray/mev/cluster/gui/impl/dialogs/dialogHelpUtil/dialogHelpPages"/>       
2 26 Feb 07 jari 414         
2 26 Feb 07 jari 415         <!-- copy images (gifs) to images directory for inclusion in the jar -->        
2 26 Feb 07 jari 416         <copy todir="${dest.dir}/org/tigr/microarray/mev/cluster/gui/impl/dialogs/dialogHelpUtil/dialogHelpPages">
2 26 Feb 07 jari 417             <fileset dir="${gui.impl.dir}/dialogs/dialogHelpUtil/dialogHelpPages"/>
2 26 Feb 07 jari 418         </copy>
2 26 Feb 07 jari 419
2 26 Feb 07 jari 420         <jar destfile="${lib.dir}/dialogHelp.jar"
2 26 Feb 07 jari 421              basedir="${dest.dir}"
2 26 Feb 07 jari 422        includes="org/tigr/microarray/mev/cluster/gui/impl/dialogs/dialogHelpUtil/dialogHelpPages/*"
2 26 Feb 07 jari 423         />
2 26 Feb 07 jari 424     </target>
2 26 Feb 07 jari 425
2 26 Feb 07 jari 426
2 26 Feb 07 jari 427
2 26 Feb 07 jari 428     <!-- TARGET ============================================    
2 26 Feb 07 jari 429            Target Name: build-base
2 26 Feb 07 jari 430     Depends: jar-gui-support, jar-images, jar-dialog-help
2 26 Feb 07 jari 431            Target Description: jars mev base classes
2 26 Feb 07 jari 432     Note:  Calling this target will produce the following jars:
2 26 Feb 07 jari 433       mev-util.jar, mev-algorithm-support.jar,
2 26 Feb 07 jari 434       mev-gui-support.jar, mev-base.jar
2 26 Feb 07 jari 435     -->
2 26 Feb 07 jari 436     <target name="build-base" depends="jar-gui-support, jar-images, jar-dialog-help">
3 27 Feb 07 jari 437         <!-- make the config directory within the destination area -->
3 27 Feb 07 jari 438         <mkdir dir="${dest.dir}/org/tigr/config"/>
3 27 Feb 07 jari 439         <!-- copy tmev.cfg to config directory for inclusion in the jar -->
3 27 Feb 07 jari 440         <copy todir="${dest.dir}/org/tigr/config">
3 27 Feb 07 jari 441           <fileset file="${config.dir}/tmev.cfg"/>
3 27 Feb 07 jari 442         </copy>
3 27 Feb 07 jari 443
2 26 Feb 07 jari 444         <jar destfile="${lib.dir}/mev-base.jar"
2 26 Feb 07 jari 445              basedir="${dest.dir}"
2 26 Feb 07 jari 446          includes= 
2 26 Feb 07 jari 447           "org/tigr/remote/**,
2 26 Feb 07 jari 448             org/tigr/microarray/file/*.class,
2 26 Feb 07 jari 449         org/tigr/microarray/util/**,
2 26 Feb 07 jari 450       org/tigr/microarray/mev/r/*.class,
2 26 Feb 07 jari 451           org/tigr/microarray/mev/*.html,  
2 26 Feb 07 jari 452       org/tigr/microarray/mev/cgh/**,
2 26 Feb 07 jari 453             org/tigr/microarray/mev/*.class,
2 26 Feb 07 jari 454       org/tigr/microarray/mev/action/*.class,
2 26 Feb 07 jari 455       org/tigr/microarray/mev/file/**,
2 26 Feb 07 jari 456       org/tigr/microarray/mev/script/**,
2 26 Feb 07 jari 457           org/tigr/microarray/mev/persistence/**,
3 27 Feb 07 jari 458       org/tigr/microarray/mev/cluster/clusterUtil/**,
3 27 Feb 07 jari 459       org/tigr/config/tmev.cfg"
2 26 Feb 07 jari 460           update="true"
2 26 Feb 07 jari 461         />
2 26 Feb 07 jari 462     </target>
2 26 Feb 07 jari 463
2 26 Feb 07 jari 464
2 26 Feb 07 jari 465
2 26 Feb 07 jari 466
2 26 Feb 07 jari 467
2 26 Feb 07 jari 468     <!-- ====================================================================
2 26 Feb 07 jari 469      
2 26 Feb 07 jari 470          Module Targets
2 26 Feb 07 jari 471
2 26 Feb 07 jari 472          These targets produce mev-algorithm-impl.jar and mev-gui-impl.jar
2 26 Feb 07 jari 473          Each algorithm's target is dependent on the corresponding GUI target and
2 26 Feb 07 jari 474      so for each 'algorithm' target a corresponding 'gui' target is executed.
2 26 Feb 07 jari 475
2 26 Feb 07 jari 476          Each module target's execution is triggered by the 'algorithm-modules' target
2 26 Feb 07 jari 477          near the top of this script below the properties.  Each of these targets
2 26 Feb 07 jari 478          also is executed on the condition that the corresponding module property
2 26 Feb 07 jari 479          is set module properties list, also at the top of this script.
2 26 Feb 07 jari 480
2 26 Feb 07 jari 481          ==================================================================== -->
2 26 Feb 07 jari 482
2 26 Feb 07 jari 483     <target name="HCL" depends="HCL-GUI" if="HCL">
3 27 Feb 07 jari 484         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 485                executable="${javac-location}">
2 26 Feb 07 jari 486     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 487             <include name="HCL.java"/>
2 26 Feb 07 jari 488     </javac>
2 26 Feb 07 jari 489     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 490     <entry key="HCL" value="org.tigr.microarray.mev.cluster.algorithm.impl.HCL"/>
2 26 Feb 07 jari 491         </propertyfile>
2 26 Feb 07 jari 492     </target>
2 26 Feb 07 jari 493
2 26 Feb 07 jari 494     <target name="HCL-GUI">
3 27 Feb 07 jari 495         <javac srcdir="${gui.impl.dir}/hcl" destdir="${dest.dir}"
3 27 Feb 07 jari 496                executable="${javac-location}">
2 26 Feb 07 jari 497     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 498     </javac>
2 26 Feb 07 jari 499     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 500     <entry key="gui.names" value="HCL:" operation="+"/>            
2 26 Feb 07 jari 501             <entry key="HCL.name" value="HCL"/>
2 26 Feb 07 jari 502             <entry key="HCL.class" value="org.tigr.microarray.mev.cluster.gui.impl.hcl.HCLGUI"/>
2 26 Feb 07 jari 503         <entry key="HCL.category" value="${CLUSTERING}"/>
2 26 Feb 07 jari 504             <entry key="HCL.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 505             <entry key="HCL.largeIcon" value="hcl_button.gif"/>
2 26 Feb 07 jari 506             <entry key="HCL.tooltip" value="Hierarchical Clustering"/>
2 26 Feb 07 jari 507         </propertyfile>
2 26 Feb 07 jari 508     </target>
2 26 Feb 07 jari 509
2 26 Feb 07 jari 510
2 26 Feb 07 jari 511
2 26 Feb 07 jari 512     <target name="ST" depends="ST-GUI" if="ST">
3 27 Feb 07 jari 513         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 514                executable="${javac-location}">
2 26 Feb 07 jari 515     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 516             <include name="NodeSupports.java"/>
2 26 Feb 07 jari 517     </javac>
2 26 Feb 07 jari 518     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 519             <entry key="ST" value="org.tigr.microarray.mev.cluster.algorithm.impl.NodeSupports"/>
2 26 Feb 07 jari 520         </propertyfile>
2 26 Feb 07 jari 521     </target>
2 26 Feb 07 jari 522
2 26 Feb 07 jari 523     <target name="ST-GUI">
3 27 Feb 07 jari 524         <javac srcdir="${gui.impl.dir}/st" destdir="${dest.dir}"
3 27 Feb 07 jari 525                executable="${javac-location}">
2 26 Feb 07 jari 526     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 527     </javac>
2 26 Feb 07 jari 528     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 529     <entry key="gui.names" value="ST:" operation="+"/>
2 26 Feb 07 jari 530             <entry key="ST.name" value="ST"/>
2 26 Feb 07 jari 531             <entry key="ST.class" value="org.tigr.microarray.mev.cluster.gui.impl.st.STGUI"/>
2 26 Feb 07 jari 532       <entry key="ST.category" value="${CLUSTERING}"/>
2 26 Feb 07 jari 533             <entry key="ST.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 534             <entry key="ST.largeIcon" value="st_button.gif"/>
2 26 Feb 07 jari 535             <entry key="ST.tooltip" value="HCL Support Trees"/>
2 26 Feb 07 jari 536         </propertyfile>
2 26 Feb 07 jari 537     </target>
2 26 Feb 07 jari 538
2 26 Feb 07 jari 539
2 26 Feb 07 jari 540
2 26 Feb 07 jari 541     <target name="SOTA" depends="SOTA-GUI" if="SOTA">
3 27 Feb 07 jari 542         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 543                executable="${javac-location}">
2 26 Feb 07 jari 544     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 545             <include name="SOTACell.java"/>
2 26 Feb 07 jari 546             <include name="SOTA.java"/>
2 26 Feb 07 jari 547     </javac>
2 26 Feb 07 jari 548     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 549             <entry key="SOTA" value="org.tigr.microarray.mev.cluster.algorithm.impl.SOTA"/>
2 26 Feb 07 jari 550         </propertyfile>
2 26 Feb 07 jari 551     </target>
2 26 Feb 07 jari 552
2 26 Feb 07 jari 553     <target name="SOTA-GUI" if="SOTA">
3 27 Feb 07 jari 554         <javac srcdir="${gui.impl.dir}/sota" destdir="${dest.dir}"
3 27 Feb 07 jari 555                executable="${javac-location}">
2 26 Feb 07 jari 556     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 557     </javac>
2 26 Feb 07 jari 558     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 559     <entry key="gui.names" value="SOTA:" operation="+"/>            
2 26 Feb 07 jari 560             <entry key="SOTA.name" value="SOTA"/>
2 26 Feb 07 jari 561             <entry key="SOTA.class" value="org.tigr.microarray.mev.cluster.gui.impl.sota.SOTAGUI"/>
2 26 Feb 07 jari 562         <entry key="SOTA.category" value="${CLUSTERING}"/>
2 26 Feb 07 jari 563           <entry key="SOTA.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 564             <entry key="SOTA.largeIcon" value="sota_button.gif"/>
2 26 Feb 07 jari 565             <entry key="SOTA.tooltip" value="Self Organizing Tree Algorithm"/>
2 26 Feb 07 jari 566         </propertyfile>
2 26 Feb 07 jari 567     </target>
2 26 Feb 07 jari 568
2 26 Feb 07 jari 569
2 26 Feb 07 jari 570
2 26 Feb 07 jari 571     <target name="RN" depends="RN-GUI" if="RN">
3 27 Feb 07 jari 572         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 573                executable="${javac-location}">
2 26 Feb 07 jari 574     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 575             <include name="RelNetComparator.java"/>
2 26 Feb 07 jari 576             <include name="PermutationTest.java"/>
2 26 Feb 07 jari 577             <include name="RN.java"/>
2 26 Feb 07 jari 578     </javac>
2 26 Feb 07 jari 579     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 580             <entry key="RN" value="org.tigr.microarray.mev.cluster.algorithm.impl.RN"/>
2 26 Feb 07 jari 581         </propertyfile>
2 26 Feb 07 jari 582     </target>
2 26 Feb 07 jari 583
2 26 Feb 07 jari 584     <target name="RN-GUI">
3 27 Feb 07 jari 585         <javac srcdir="${gui.impl.dir}/rn" destdir="${dest.dir}"
3 27 Feb 07 jari 586                executable="${javac-location}">
2 26 Feb 07 jari 587     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 588     </javac>
2 26 Feb 07 jari 589     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 590     <entry key="gui.names" value="RN:" operation="+"/>            
2 26 Feb 07 jari 591             <entry key="RN.name" value="RN"/>
2 26 Feb 07 jari 592             <entry key="RN.class" value="org.tigr.microarray.mev.cluster.gui.impl.rn.RNGUI"/>
2 26 Feb 07 jari 593       <entry key="RN.category" value="${DATA_REDUCTION}"/>
2 26 Feb 07 jari 594          <entry key="RN.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 595             <entry key="RN.largeIcon" value="rn_button.gif"/>
2 26 Feb 07 jari 596             <entry key="RN.tooltip" value="Relevance Networks"/>
2 26 Feb 07 jari 597         </propertyfile>
2 26 Feb 07 jari 598     </target>
2 26 Feb 07 jari 599
2 26 Feb 07 jari 600
2 26 Feb 07 jari 601
2 26 Feb 07 jari 602     <target name="KMC" depends="KMC-GUI" if="KMC">
3 27 Feb 07 jari 603         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 604                executable="${javac-location}">
2 26 Feb 07 jari 605     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 606             <include name="KMC.java"/>
2 26 Feb 07 jari 607     </javac>
2 26 Feb 07 jari 608     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 609             <entry key="KMC" value="org.tigr.microarray.mev.cluster.algorithm.impl.KMC"/>
2 26 Feb 07 jari 610         </propertyfile>
2 26 Feb 07 jari 611     </target>
2 26 Feb 07 jari 612
2 26 Feb 07 jari 613     <target name="KMC-GUI">
3 27 Feb 07 jari 614         <javac srcdir="${gui.impl.dir}/kmc" destdir="${dest.dir}"
3 27 Feb 07 jari 615                executable="${javac-location}">
2 26 Feb 07 jari 616     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 617     </javac>
2 26 Feb 07 jari 618     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 619     <entry key="gui.names" value="KMC:" operation="+"/>
2 26 Feb 07 jari 620             <entry key="KMC.name" value="KMC"/>
2 26 Feb 07 jari 621             <entry key="KMC.class" value="org.tigr.microarray.mev.cluster.gui.impl.kmc.KMCGUI"/>
2 26 Feb 07 jari 622       <entry key="KMC.category" value="${CLUSTERING}"/> 
2 26 Feb 07 jari 623          <entry key="KMC.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 624             <entry key="KMC.largeIcon" value="kmc_button.gif"/>
2 26 Feb 07 jari 625             <entry key="KMC.tooltip" value="k-Means/Medians Clustering"/>
2 26 Feb 07 jari 626         </propertyfile>
2 26 Feb 07 jari 627     </target>
2 26 Feb 07 jari 628
2 26 Feb 07 jari 629
2 26 Feb 07 jari 630
2 26 Feb 07 jari 631     <target name="KMCS" depends="KMCS-GUI" if="KMCS">
3 27 Feb 07 jari 632         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 633                executable="${javac-location}">
2 26 Feb 07 jari 634     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 635             <include name="KMCSupport.java"/>
2 26 Feb 07 jari 636     </javac>
2 26 Feb 07 jari 637     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 638             <entry key="KMCS" value="org.tigr.microarray.mev.cluster.algorithm.impl.KMCSupport"/>
2 26 Feb 07 jari 639         </propertyfile>
2 26 Feb 07 jari 640     </target>
2 26 Feb 07 jari 641
2 26 Feb 07 jari 642     <target name="KMCS-GUI">
3 27 Feb 07 jari 643         <javac srcdir="${gui.impl.dir}/kmcs" destdir="${dest.dir}"
3 27 Feb 07 jari 644                executable="${javac-location}">
2 26 Feb 07 jari 645     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 646   </javac>
2 26 Feb 07 jari 647   <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 648     <entry key="gui.names" value="KMCS:" operation="+"/>
2 26 Feb 07 jari 649             <entry key="KMCS.name" value="KMS"/>
2 26 Feb 07 jari 650             <entry key="KMCS.class" value="org.tigr.microarray.mev.cluster.gui.impl.kmcs.KMCSuppGUI"/>
2 26 Feb 07 jari 651     <entry key="KMCS.category" value="${CLUSTERING}"/>
2 26 Feb 07 jari 652             <entry key="KMCS.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 653             <entry key="KMCS.largeIcon" value="kms_button.gif"/>
2 26 Feb 07 jari 654             <entry key="KMCS.tooltip" value="KMC Support"/>
2 26 Feb 07 jari 655         </propertyfile>
2 26 Feb 07 jari 656     </target>
2 26 Feb 07 jari 657
2 26 Feb 07 jari 658
2 26 Feb 07 jari 659
2 26 Feb 07 jari 660     <target name="CAST" depends="CAST-GUI" if="CAST">
3 27 Feb 07 jari 661         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 662                executable="${javac-location}">
2 26 Feb 07 jari 663     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 664             <include name="CastClust.java"/>
2 26 Feb 07 jari 665     </javac>
2 26 Feb 07 jari 666     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 667             <entry key="CAST" value="org.tigr.microarray.mev.cluster.algorithm.impl.CastClust"/>
2 26 Feb 07 jari 668         </propertyfile>
2 26 Feb 07 jari 669     </target>
2 26 Feb 07 jari 670
2 26 Feb 07 jari 671     <target name="CAST-GUI">
3 27 Feb 07 jari 672         <javac srcdir="${gui.impl.dir}/cast" destdir="${dest.dir}"
3 27 Feb 07 jari 673                executable="${javac-location}">
2 26 Feb 07 jari 674     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 675     </javac>
2 26 Feb 07 jari 676     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 677     <entry key="gui.names" value="CAST:" operation="+"/>
2 26 Feb 07 jari 678             <entry key="CAST.name" value="CAST"/>
2 26 Feb 07 jari 679             <entry key="CAST.class" value="org.tigr.microarray.mev.cluster.gui.impl.cast.CASTGUI"/>    
2 26 Feb 07 jari 680       <entry key="CAST.category" value="${CLUSTERING}"/>
2 26 Feb 07 jari 681       <entry key="CAST.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 682             <entry key="CAST.largeIcon" value="cast_button.gif"/>
2 26 Feb 07 jari 683             <entry key="CAST.tooltip" value="Cluster Affinity Search Technique"/>
2 26 Feb 07 jari 684         </propertyfile>
2 26 Feb 07 jari 685     </target>
2 26 Feb 07 jari 686
2 26 Feb 07 jari 687
2 26 Feb 07 jari 688
2 26 Feb 07 jari 689     <target name="QTC" depends="QTC-GUI" if="QTC">
3 27 Feb 07 jari 690         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 691                executable="${javac-location}">
2 26 Feb 07 jari 692     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 693             <include name="QTC.java"/>
2 26 Feb 07 jari 694     </javac>
2 26 Feb 07 jari 695     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 696             <entry key="QTC" value="org.tigr.microarray.mev.cluster.algorithm.impl.QTC"/>
2 26 Feb 07 jari 697         </propertyfile>
2 26 Feb 07 jari 698     </target>
2 26 Feb 07 jari 699
2 26 Feb 07 jari 700     <target name="QTC-GUI">
3 27 Feb 07 jari 701         <javac srcdir="${gui.impl.dir}/qtc" destdir="${dest.dir}"
3 27 Feb 07 jari 702                executable="${javac-location}">
2 26 Feb 07 jari 703     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 704     </javac>
2 26 Feb 07 jari 705     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 706     <entry key="gui.names" value="QTC:" operation="+"/>
2 26 Feb 07 jari 707             <entry key="QTC.name" value="QTC"/>
2 26 Feb 07 jari 708             <entry key="QTC.class" value="org.tigr.microarray.mev.cluster.gui.impl.qtc.QTCGUI"/>
2 26 Feb 07 jari 709       <entry key="QTC.category" value="${CLUSTERING}"/>
2 26 Feb 07 jari 710           <entry key="QTC.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 711             <entry key="QTC.largeIcon" value="qtc_button.gif"/>
2 26 Feb 07 jari 712             <entry key="QTC.tooltip" value="QT Cluster"/>
2 26 Feb 07 jari 713         </propertyfile>
2 26 Feb 07 jari 714     </target>
2 26 Feb 07 jari 715
2 26 Feb 07 jari 716
2 26 Feb 07 jari 717
2 26 Feb 07 jari 718     <target name="GSH" depends="GSH-GUI" if="GSH">
3 27 Feb 07 jari 719         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 720                executable="${javac-location}">
2 26 Feb 07 jari 721             <include name="GSH.java"/>  
2 26 Feb 07 jari 722             <classpath>
2 26 Feb 07 jari 723                 <pathelement location="${lib.dir}/jama.jar"/>
2 26 Feb 07 jari 724
2 26 Feb 07 jari 725                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 726                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 727                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 728                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 729                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 730                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 731                 <pathelement location="${lib.dir}/mev-base.jar"/>            
2 26 Feb 07 jari 732             </classpath>
2 26 Feb 07 jari 733     </javac>
2 26 Feb 07 jari 734     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 735             <entry key="GSH" value="org.tigr.microarray.mev.cluster.algorithm.impl.GSH"/>
2 26 Feb 07 jari 736         </propertyfile>
2 26 Feb 07 jari 737     </target>
2 26 Feb 07 jari 738
2 26 Feb 07 jari 739     <target name="GSH-GUI">
3 27 Feb 07 jari 740         <javac srcdir="${gui.impl.dir}/gsh" destdir="${dest.dir}"
3 27 Feb 07 jari 741                executable="${javac-location}">
2 26 Feb 07 jari 742             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 743     </javac>
2 26 Feb 07 jari 744     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 745     <entry key="gui.names" value="GSH:" operation="+"/>
2 26 Feb 07 jari 746             <entry key="GSH.name" value="GSH"/>
2 26 Feb 07 jari 747             <entry key="GSH.class" value="org.tigr.microarray.mev.cluster.gui.impl.gsh.GSHGUI"/>
2 26 Feb 07 jari 748       <entry key="GSH.category" value="${MISC}"/>
2 26 Feb 07 jari 749           <entry key="GSH.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 750             <entry key="GSH.largeIcon" value="gsh_button.gif"/>
2 26 Feb 07 jari 751             <entry key="GSH.tooltip" value="Gene Shaving"/>
2 26 Feb 07 jari 752         </propertyfile>
2 26 Feb 07 jari 753     </target>
2 26 Feb 07 jari 754
2 26 Feb 07 jari 755
2 26 Feb 07 jari 756
2 26 Feb 07 jari 757     <target name="SOM" depends="SOM-GUI" if="SOM">
3 27 Feb 07 jari 758         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 759                executable="${javac-location}">
2 26 Feb 07 jari 760             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 761             <include name="SOMMatrix.java"/>
2 26 Feb 07 jari 762             <include name="SOM.java"/>
2 26 Feb 07 jari 763     </javac>
2 26 Feb 07 jari 764     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 765             <entry key="SOM" value="org.tigr.microarray.mev.cluster.algorithm.impl.SOM"/>
2 26 Feb 07 jari 766         </propertyfile>
2 26 Feb 07 jari 767     </target>
2 26 Feb 07 jari 768
2 26 Feb 07 jari 769     <target name="SOM-GUI">
3 27 Feb 07 jari 770         <javac srcdir="${gui.impl.dir}/som" destdir="${dest.dir}"
3 27 Feb 07 jari 771                executable="${javac-location}">
2 26 Feb 07 jari 772             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 773     </javac>
2 26 Feb 07 jari 774     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 775     <entry key="gui.names" value="SOM:" operation="+"/>
2 26 Feb 07 jari 776             <entry key="SOM.name" value="SOM"/>
2 26 Feb 07 jari 777             <entry key="SOM.class" value="org.tigr.microarray.mev.cluster.gui.impl.som.SOMGUI"/>
2 26 Feb 07 jari 778       <entry key="SOM.category" value="${CLUSTERING}"/>
2 26 Feb 07 jari 779           <entry key="SOM.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 780             <entry key="SOM.largeIcon" value="som_button.gif"/>
2 26 Feb 07 jari 781             <entry key="SOM.tooltip" value="Self Organizing Map"/>
2 26 Feb 07 jari 782         </propertyfile>
2 26 Feb 07 jari 783     </target>
2 26 Feb 07 jari 784
2 26 Feb 07 jari 785
2 26 Feb 07 jari 786
2 26 Feb 07 jari 787     <target name="FOM" depends="FOM-GUI" if="FOM">
3 27 Feb 07 jari 788         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 789                executable="${javac-location}">
2 26 Feb 07 jari 790             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 791             <include name="FOM.java"/>
2 26 Feb 07 jari 792     </javac>
2 26 Feb 07 jari 793     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 794             <entry key="FOM" value="org.tigr.microarray.mev.cluster.algorithm.impl.FOM"/>
2 26 Feb 07 jari 795         </propertyfile>
2 26 Feb 07 jari 796     </target>
2 26 Feb 07 jari 797
2 26 Feb 07 jari 798     <target name="FOM-GUI">
3 27 Feb 07 jari 799         <javac srcdir="${gui.impl.dir}/fom" destdir="${dest.dir}"
3 27 Feb 07 jari 800                executable="${javac-location}">
2 26 Feb 07 jari 801             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 802     </javac>
2 26 Feb 07 jari 803     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 804     <entry key="gui.names" value="FOM:" operation="+"/>
2 26 Feb 07 jari 805             <entry key="FOM.name" value="FOM"/>
2 26 Feb 07 jari 806             <entry key="FOM.class" value="org.tigr.microarray.mev.cluster.gui.impl.fom.FOMGUI"/>
2 26 Feb 07 jari 807       <entry key="FOM.category" value="${CLUSTERING}"/>
2 26 Feb 07 jari 808         <entry key="FOM.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 809             <entry key="FOM.largeIcon" value="fom_button.gif"/>
2 26 Feb 07 jari 810             <entry key="FOM.tooltip" value="Figure of Merit"/>
2 26 Feb 07 jari 811         </propertyfile>
2 26 Feb 07 jari 812     </target>
2 26 Feb 07 jari 813
2 26 Feb 07 jari 814
2 26 Feb 07 jari 815     <target name="PTM" depends="PTM-GUI" if="PTM">
3 27 Feb 07 jari 816         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 817                executable="${javac-location}">
2 26 Feb 07 jari 818             <classpath> 
2 26 Feb 07 jari 819             <pathelement location="${lib.dir}/JSciCore.jar"/>
2 26 Feb 07 jari 820
2 26 Feb 07 jari 821                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 822                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 823                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 824                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 825                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 826                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 827                 <pathelement location="${lib.dir}/mev-base.jar"/> 
2 26 Feb 07 jari 828             </classpath>
2 26 Feb 07 jari 829             <include name="PavlidisTemplateMatching.java"/>
2 26 Feb 07 jari 830     </javac>
2 26 Feb 07 jari 831     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 832             <entry key="PTM" value="org.tigr.microarray.mev.cluster.algorithm.impl.PavlidisTemplateMatching"/>
2 26 Feb 07 jari 833         </propertyfile>
2 26 Feb 07 jari 834     </target>
2 26 Feb 07 jari 835
2 26 Feb 07 jari 836     <target name="PTM-GUI">
3 27 Feb 07 jari 837         <javac srcdir="${gui.impl.dir}/ptm" destdir="${dest.dir}"
3 27 Feb 07 jari 838                executable="${javac-location}">
2 26 Feb 07 jari 839             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 840     </javac>
2 26 Feb 07 jari 841     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 842     <entry key="gui.names" value="PTM:" operation="+"/>
2 26 Feb 07 jari 843             <entry key="PTM.name" value="PTM"/>
2 26 Feb 07 jari 844             <entry key="PTM.class" value="org.tigr.microarray.mev.cluster.gui.impl.ptm.PTMGUI"/>
2 26 Feb 07 jari 845       <entry key="PTM.category" value="${STATISTICS}"/> 
2 26 Feb 07 jari 846          <entry key="PTM.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 847             <entry key="PTM.largeIcon" value="ptm_button.gif"/>
2 26 Feb 07 jari 848             <entry key="PTM.tooltip" value="Pavlidis Template Matching"/>
2 26 Feb 07 jari 849         </propertyfile>
2 26 Feb 07 jari 850     </target>
2 26 Feb 07 jari 851
2 26 Feb 07 jari 852
2 26 Feb 07 jari 853
2 26 Feb 07 jari 854     <target name="TTEST" depends="TTEST-GUI" if="TTEST">
3 27 Feb 07 jari 855         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 856                executable="${javac-location}">
2 26 Feb 07 jari 857             <include name="Ttest.java"/>
2 26 Feb 07 jari 858             <classpath>
2 26 Feb 07 jari 859                 <pathelement location="${lib.dir}/JSciCore.jar"/>
2 26 Feb 07 jari 860
2 26 Feb 07 jari 861                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 862                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 863                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 864                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 865                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 866                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 867                 <pathelement location="${lib.dir}/mev-base.jar"/>            
2 26 Feb 07 jari 868             </classpath>
2 26 Feb 07 jari 869     </javac>
2 26 Feb 07 jari 870     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 871             <entry key="TTEST" value="org.tigr.microarray.mev.cluster.algorithm.impl.Ttest"/>
2 26 Feb 07 jari 872         </propertyfile>
2 26 Feb 07 jari 873     </target>
2 26 Feb 07 jari 874
2 26 Feb 07 jari 875     <target name="TTEST-GUI">
3 27 Feb 07 jari 876         <javac srcdir="${gui.impl.dir}/ttest" destdir="${dest.dir}"
3 27 Feb 07 jari 877                executable="${javac-location}">
2 26 Feb 07 jari 878             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 879     </javac>
2 26 Feb 07 jari 880     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 881     <entry key="gui.names" value="TTEST:" operation="+"/>
2 26 Feb 07 jari 882             <entry key="TTEST.name" value="TTEST"/>
2 26 Feb 07 jari 883             <entry key="TTEST.class" value="org.tigr.microarray.mev.cluster.gui.impl.ttest.TtestGUI"/>
2 26 Feb 07 jari 884       <entry key="TTEST.category" value="${STATISTICS}"/> 
2 26 Feb 07 jari 885       <entry key="TTEST.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 886             <entry key="TTEST.largeIcon" value="ttest_button.gif"/>
2 26 Feb 07 jari 887             <entry key="TTEST.tooltip" value="t Tests"/>
2 26 Feb 07 jari 888         </propertyfile>
2 26 Feb 07 jari 889     </target>
2 26 Feb 07 jari 890
2 26 Feb 07 jari 891
2 26 Feb 07 jari 892
2 26 Feb 07 jari 893     <target name="BRIDGE" depends="BRIDGE-GUI" if="BRIDGE">
3 27 Feb 07 jari 894         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 895                executable="${javac-location}">
2 26 Feb 07 jari 896             <include name="Bridge.java"/>
2 26 Feb 07 jari 897             <classpath>
2 26 Feb 07 jari 898                 <pathelement location="${lib.dir}/JSciCore.jar"/>
2 26 Feb 07 jari 899
2 26 Feb 07 jari 900                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 901                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 902                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 903                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 904                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 905                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 906                 <pathelement location="${lib.dir}/mev-base.jar"/>            
2 26 Feb 07 jari 907             </classpath>
2 26 Feb 07 jari 908     </javac>
2 26 Feb 07 jari 909     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 910             <entry key="BRIDGE" value="org.tigr.microarray.mev.cluster.algorithm.impl.bridge"/>
2 26 Feb 07 jari 911         </propertyfile>
2 26 Feb 07 jari 912     </target>
2 26 Feb 07 jari 913
2 26 Feb 07 jari 914     <target name="BRIDGE-GUI">
3 27 Feb 07 jari 915         <javac srcdir="${gui.impl.dir}/bridge" destdir="${dest.dir}"
3 27 Feb 07 jari 916                executable="${javac-location}">
2 26 Feb 07 jari 917             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 918     </javac>
2 26 Feb 07 jari 919     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 920     <entry key="gui.names" value="BRIDGE:" operation="+"/>
2 26 Feb 07 jari 921             <entry key="BRIDGE.name" value="BRIDGE"/>
2 26 Feb 07 jari 922             <entry key="BRIDGE.class" value="org.tigr.microarray.mev.cluster.gui.impl.bridge.BridgeGUI"/>
2 26 Feb 07 jari 923       <entry key="BRIDGE.category" value="${STATISTICS}"/> 
2 26 Feb 07 jari 924       <entry key="BRIDGE.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 925             <entry key="BRIDGE.largeIcon" value="bridge_button.gif"/>
2 26 Feb 07 jari 926             <entry key="BRIDGE.tooltip" value="BRIDGE"/>
2 26 Feb 07 jari 927         </propertyfile>
2 26 Feb 07 jari 928     </target>
2 26 Feb 07 jari 929
2 26 Feb 07 jari 930
2 26 Feb 07 jari 931
2 26 Feb 07 jari 932     <target name="SAM" depends="SAM-GUI" if="SAM">
3 27 Feb 07 jari 933         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 934                executable="${javac-location}">
2 26 Feb 07 jari 935             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 936             <include name="SAM.java"/>
2 26 Feb 07 jari 937     </javac>
2 26 Feb 07 jari 938     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 939             <entry key="SAM" value="org.tigr.microarray.mev.cluster.algorithm.impl.SAM"/>
2 26 Feb 07 jari 940         </propertyfile>
2 26 Feb 07 jari 941     </target>
2 26 Feb 07 jari 942
2 26 Feb 07 jari 943     <target name="SAM-GUI">
3 27 Feb 07 jari 944         <javac srcdir="${gui.impl.dir}/sam" destdir="${dest.dir}"
3 27 Feb 07 jari 945                executable="${javac-location}">
2 26 Feb 07 jari 946             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 947     </javac>
2 26 Feb 07 jari 948     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 949     <entry key="gui.names" value="SAM:" operation="+"/>
2 26 Feb 07 jari 950             <entry key="SAM.name" value="SAM"/>
2 26 Feb 07 jari 951             <entry key="SAM.class" value="org.tigr.microarray.mev.cluster.gui.impl.sam.SAMGUI"/>
2 26 Feb 07 jari 952       <entry key="SAM.category" value="${STATISTICS}"/>  
2 26 Feb 07 jari 953          <entry key="SAM.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 954             <entry key="SAM.largeIcon" value="sam_button.gif"/>
2 26 Feb 07 jari 955             <entry key="SAM.tooltip" value="Significance Analysis for Microarrays"/>
2 26 Feb 07 jari 956         </propertyfile>
2 26 Feb 07 jari 957     </target>
2 26 Feb 07 jari 958
2 26 Feb 07 jari 959
2 26 Feb 07 jari 960
2 26 Feb 07 jari 961     <target name="OWA" depends="OWA-GUI" if="OWA">
3 27 Feb 07 jari 962         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 963                executable="${javac-location}">
2 26 Feb 07 jari 964             <include name="OneWayANOVA.java"/>
2 26 Feb 07 jari 965             <classpath>
2 26 Feb 07 jari 966                 <pathelement location="${lib.dir}/JSciCore.jar"/>
2 26 Feb 07 jari 967
2 26 Feb 07 jari 968                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 969                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 970                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 971                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 972                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 973                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 974                 <pathelement location="${lib.dir}/mev-base.jar"/>            
2 26 Feb 07 jari 975             </classpath>
2 26 Feb 07 jari 976     </javac>
2 26 Feb 07 jari 977     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 978             <entry key="OWA" value="org.tigr.microarray.mev.cluster.algorithm.impl.OneWayANOVA"/>
2 26 Feb 07 jari 979         </propertyfile>
2 26 Feb 07 jari 980     </target>
2 26 Feb 07 jari 981
2 26 Feb 07 jari 982     <target name="OWA-GUI">
3 27 Feb 07 jari 983         <javac srcdir="${gui.impl.dir}/owa" destdir="${dest.dir}"
3 27 Feb 07 jari 984                executable="${javac-location}">
2 26 Feb 07 jari 985             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 986     </javac>
2 26 Feb 07 jari 987     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 988     <entry key="gui.names" value="OWA:" operation="+"/>
2 26 Feb 07 jari 989             <entry key="OWA.name" value="ANOVA"/>
2 26 Feb 07 jari 990             <entry key="OWA.class" value="org.tigr.microarray.mev.cluster.gui.impl.owa.OWAGUI"/>
2 26 Feb 07 jari 991       <entry key="OWA.category" value="${STATISTICS}"/>  
2 26 Feb 07 jari 992          <entry key="OWA.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 993             <entry key="OWA.largeIcon" value="owa_button.gif"/>
2 26 Feb 07 jari 994             <entry key="OWA.tooltip" value="One-way ANOVA"/>
2 26 Feb 07 jari 995         </propertyfile>
2 26 Feb 07 jari 996     </target>
2 26 Feb 07 jari 997
2 26 Feb 07 jari 998
2 26 Feb 07 jari 999
2 26 Feb 07 jari 1000     <target name="TFA" depends="TFA-GUI" if="TFA">
3 27 Feb 07 jari 1001         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1002                executable="${javac-location}">
2 26 Feb 07 jari 1003             <include name="TFA.java"/>
2 26 Feb 07 jari 1004             <classpath>
2 26 Feb 07 jari 1005                 <pathelement location="${lib.dir}/JSciCore.jar"/>
2 26 Feb 07 jari 1006
2 26 Feb 07 jari 1007                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 1008                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 1009                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 1010                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 1011                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 1012                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 1013                 <pathelement location="${lib.dir}/mev-base.jar"/>            
2 26 Feb 07 jari 1014             </classpath>
2 26 Feb 07 jari 1015     </javac>
2 26 Feb 07 jari 1016     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1017             <entry key="TFA" value="org.tigr.microarray.mev.cluster.algorithm.impl.TFA"/>
2 26 Feb 07 jari 1018         </propertyfile>
2 26 Feb 07 jari 1019     </target>
2 26 Feb 07 jari 1020
2 26 Feb 07 jari 1021     <target name="TFA-GUI">
3 27 Feb 07 jari 1022         <javac srcdir="${gui.impl.dir}/tfa" destdir="${dest.dir}"
3 27 Feb 07 jari 1023                executable="${javac-location}">
2 26 Feb 07 jari 1024             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1025     </javac>
2 26 Feb 07 jari 1026     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1027     <entry key="gui.names" value="TFA:" operation="+"/>
2 26 Feb 07 jari 1028             <entry key="TFA.name" value="2 Fact. ANOVA"/>
2 26 Feb 07 jari 1029             <entry key="TFA.class" value="org.tigr.microarray.mev.cluster.gui.impl.tfa.TFAGUI"/>
2 26 Feb 07 jari 1030       <entry key="TFA.category" value="${STATISTICS}"/> 
2 26 Feb 07 jari 1031           <entry key="TFA.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1032             <entry key="TFA.largeIcon" value="tfa_button.gif"/>
2 26 Feb 07 jari 1033             <entry key="TFA.tooltip" value="Two-factor ANOVA"/>
2 26 Feb 07 jari 1034         </propertyfile>
2 26 Feb 07 jari 1035     </target>
2 26 Feb 07 jari 1036
2 26 Feb 07 jari 1037
2 26 Feb 07 jari 1038
2 26 Feb 07 jari 1039     <target name="SVM" depends="SVM-GUI" if="SVM">
3 27 Feb 07 jari 1040         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1041                executable="${javac-location}">
2 26 Feb 07 jari 1042             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1043             <include name="SVM.java"/>
2 26 Feb 07 jari 1044     </javac>
2 26 Feb 07 jari 1045     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1046             <entry key="SVM" value="org.tigr.microarray.mev.cluster.algorithm.impl.SVM"/>
2 26 Feb 07 jari 1047         </propertyfile>
2 26 Feb 07 jari 1048     </target>
2 26 Feb 07 jari 1049
2 26 Feb 07 jari 1050     <target name="SVM-GUI">
3 27 Feb 07 jari 1051         <javac srcdir="${gui.impl.dir}/svm" destdir="${dest.dir}"
3 27 Feb 07 jari 1052                executable="${javac-location}">
2 26 Feb 07 jari 1053             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1054     </javac>
2 26 Feb 07 jari 1055     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1056     <entry key="gui.names" value="SVM:" operation="+"/>
2 26 Feb 07 jari 1057             <entry key="SVM.name" value="SVM"/>
2 26 Feb 07 jari 1058             <entry key="SVM.class" value="org.tigr.microarray.mev.cluster.gui.impl.svm.SVMGUI"/>
2 26 Feb 07 jari 1059       <entry key="SVM.category" value="${CLASSIFICATION}"/> 
2 26 Feb 07 jari 1060           <entry key="SVM.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1061             <entry key="SVM.largeIcon" value="svm_button.gif"/>
2 26 Feb 07 jari 1062             <entry key="SVM.tooltip" value="Support Vector Machines"/>
2 26 Feb 07 jari 1063         </propertyfile>
2 26 Feb 07 jari 1064     </target>
2 26 Feb 07 jari 1065
2 26 Feb 07 jari 1066
2 26 Feb 07 jari 1067
2 26 Feb 07 jari 1068 <target name="USC" depends="USC-GUI" if="USC">
3 27 Feb 07 jari 1069         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1070                executable="${javac-location}">
2 26 Feb 07 jari 1071             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1072             <include name="USC.java"/>
2 26 Feb 07 jari 1073     </javac>
2 26 Feb 07 jari 1074     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1075             <entry key="USC" value="org.tigr.microarray.mev.cluster.algorithm.impl.usc"/>
2 26 Feb 07 jari 1076         </propertyfile>
2 26 Feb 07 jari 1077     </target>
2 26 Feb 07 jari 1078
2 26 Feb 07 jari 1079     <target name="USC-GUI">
3 27 Feb 07 jari 1080         <javac srcdir="${gui.impl.dir}/usc" destdir="${dest.dir}"
3 27 Feb 07 jari 1081                executable="${javac-location}">
2 26 Feb 07 jari 1082             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1083     </javac>
2 26 Feb 07 jari 1084     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1085     <entry key="gui.names" value="USC:" operation="+"/>
2 26 Feb 07 jari 1086             <entry key="USC.name" value="USC"/>
2 26 Feb 07 jari 1087             <entry key="USC.class" value="org.tigr.microarray.mev.cluster.gui.impl.usc.USCGUI"/>
2 26 Feb 07 jari 1088       <entry key="USC.category" value="${CLASSIFICATION}"/>
2 26 Feb 07 jari 1089             <entry key="USC.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1090             <entry key="USC.largeIcon" value="usc_button.gif"/>
2 26 Feb 07 jari 1091             <entry key="USC.tooltip" value="Uncorrelated Shrunken Centroid Classification"/>
2 26 Feb 07 jari 1092         </propertyfile>
2 26 Feb 07 jari 1093     </target>
2 26 Feb 07 jari 1094   
2 26 Feb 07 jari 1095
2 26 Feb 07 jari 1096     <target name="TEASE" depends="TEASE-GUI" if="TEASE">
2 26 Feb 07 jari 1097       <!-- Compile HCL classes along with TEASE classes -->
3 27 Feb 07 jari 1098         <javac srcdir="${gui.impl.dir}/hcl" destdir="${dest.dir}"
3 27 Feb 07 jari 1099                executable="${javac-location}">
2 26 Feb 07 jari 1100       <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1101          </javac>
2 26 Feb 07 jari 1102       
3 27 Feb 07 jari 1103         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1104                executable="${javac-location}">
2 26 Feb 07 jari 1105     <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1106             <include name="tease/**"/>
2 26 Feb 07 jari 1107             <include name="ease/**"/>
2 26 Feb 07 jari 1108             <include name="HCL.java"/>
2 26 Feb 07 jari 1109     </javac>
2 26 Feb 07 jari 1110       
2 26 Feb 07 jari 1111     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1112     <entry key="TEASE" value="org.tigr.microarray.mev.cluster.algorithm.impl.tease.TEASE"/>
2 26 Feb 07 jari 1113         </propertyfile>
2 26 Feb 07 jari 1114     </target>
2 26 Feb 07 jari 1115
2 26 Feb 07 jari 1116     <target name="TEASE-GUI">
3 27 Feb 07 jari 1117         <javac srcdir="${gui.impl.dir}/tease" destdir="${dest.dir}"
3 27 Feb 07 jari 1118                executable="${javac-location}">
2 26 Feb 07 jari 1119     <classpath>
2 26 Feb 07 jari 1120
2 26 Feb 07 jari 1121                 <pathelement location="${lib.dir}/ftpbean.jar"/>
2 26 Feb 07 jari 1122
2 26 Feb 07 jari 1123
2 26 Feb 07 jari 1124
2 26 Feb 07 jari 1125                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 1126                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 1127                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 1128                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 1129                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 1130                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 1131                 <pathelement location="${lib.dir}/mev-base.jar"/> 
2 26 Feb 07 jari 1132
2 26 Feb 07 jari 1133
2 26 Feb 07 jari 1134     </classpath>
2 26 Feb 07 jari 1135     </javac>
2 26 Feb 07 jari 1136     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1137     <entry key="gui.names" value="TEASE:" operation="+"/>            
2 26 Feb 07 jari 1138             <entry key="TEASE.name" value="TEASE"/>
2 26 Feb 07 jari 1139             <entry key="TEASE.class" value="org.tigr.microarray.mev.cluster.gui.impl.tease.TEASEGUI"/>
2 26 Feb 07 jari 1140         <entry key="TEASE.category" value="${CLUSTERING}"/>
2 26 Feb 07 jari 1141             <entry key="TEASE.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1142             <entry key="TEASE.largeIcon" value="tease_button.gif"/>
2 26 Feb 07 jari 1143             <entry key="TEASE.tooltip" value="Tree EASE"/>
2 26 Feb 07 jari 1144         </propertyfile>
2 26 Feb 07 jari 1145     </target>
2 26 Feb 07 jari 1146
2 26 Feb 07 jari 1147     <target name="KNNC" depends="KNNC-GUI" if="KNNC">
3 27 Feb 07 jari 1148         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1149                executable="${javac-location}">
2 26 Feb 07 jari 1150             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1151             <include name="KNNClassify.java"/>
2 26 Feb 07 jari 1152     </javac>
2 26 Feb 07 jari 1153     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1154             <entry key="KNNC" value="org.tigr.microarray.mev.cluster.algorithm.impl.KNNClassify"/>
2 26 Feb 07 jari 1155         </propertyfile>
2 26 Feb 07 jari 1156     </target>
2 26 Feb 07 jari 1157
2 26 Feb 07 jari 1158     <target name="KNNC-GUI">
3 27 Feb 07 jari 1159         <javac srcdir="${gui.impl.dir}/knnc" destdir="${dest.dir}"
3 27 Feb 07 jari 1160                executable="${javac-location}">
2 26 Feb 07 jari 1161             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1162     </javac>
2 26 Feb 07 jari 1163     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1164     <entry key="gui.names" value="KNNC:" operation="+"/>
2 26 Feb 07 jari 1165             <entry key="KNNC.name" value="KNNC"/>
2 26 Feb 07 jari 1166             <entry key="KNNC.class" value="org.tigr.microarray.mev.cluster.gui.impl.knnc.KNNCGUI"/>
2 26 Feb 07 jari 1167       <entry key="KNNC.category" value="${CLASSIFICATION}"/>  
2 26 Feb 07 jari 1168          <entry key="KNNC.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1169             <entry key="KNNC.largeIcon" value="knnc_button.gif"/>
2 26 Feb 07 jari 1170             <entry key="KNNC.tooltip" value="K-Nearest Neighbors Classification"/>
2 26 Feb 07 jari 1171         </propertyfile>
2 26 Feb 07 jari 1172     </target>
2 26 Feb 07 jari 1173
2 26 Feb 07 jari 1174
2 26 Feb 07 jari 1175
2 26 Feb 07 jari 1176     <target name="DAM" depends="DAM-GUI" if="DAM">
3 27 Feb 07 jari 1177         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1178                executable="${javac-location}">
2 26 Feb 07 jari 1179             <include name="DAM.java"/>
2 26 Feb 07 jari 1180             <classpath>
2 26 Feb 07 jari 1181                 <pathelement location="${lib.dir}/jama.jar"/>  
2 26 Feb 07 jari 1182                 <pathelement location="${lib.dir}/JSciCore.jar"/>  
2 26 Feb 07 jari 1183
2 26 Feb 07 jari 1184                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 1185                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 1186                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 1187                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 1188                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 1189                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 1190                 <pathelement location="${lib.dir}/mev-base.jar"/>            
2 26 Feb 07 jari 1191             </classpath>
2 26 Feb 07 jari 1192     </javac>
2 26 Feb 07 jari 1193     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1194             <entry key="DAM" value="org.tigr.microarray.mev.cluster.algorithm.impl.DAM"/>
2 26 Feb 07 jari 1195         </propertyfile>
2 26 Feb 07 jari 1196     </target>
2 26 Feb 07 jari 1197
2 26 Feb 07 jari 1198     <target name="DAM-GUI">
3 27 Feb 07 jari 1199         <javac srcdir="${gui.impl.dir}/dam" destdir="${dest.dir}"
3 27 Feb 07 jari 1200                executable="${javac-location}">
2 26 Feb 07 jari 1201             <classpath>
2 26 Feb 07 jari 1202                 <pathelement location="${lib.dir}/vecmath.jar"/>  
2 26 Feb 07 jari 1203                 <pathelement location="${lib.dir}/j3dcore.jar"/>  
2 26 Feb 07 jari 1204                 <pathelement location="${lib.dir}/j3dutils.jar"/>
2 26 Feb 07 jari 1205
2 26 Feb 07 jari 1206                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 1207                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 1208                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 1209                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 1210                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 1211                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 1212                 <pathelement location="${lib.dir}/mev-base.jar"/>            
2 26 Feb 07 jari 1213             </classpath>
2 26 Feb 07 jari 1214     </javac>
2 26 Feb 07 jari 1215     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1216     <entry key="gui.names" value="DAM:" operation="+"/>
2 26 Feb 07 jari 1217             <entry key="DAM.name" value="DAM"/>
2 26 Feb 07 jari 1218             <entry key="DAM.class" value="org.tigr.microarray.mev.cluster.gui.impl.dam.DAMGUI"/>
2 26 Feb 07 jari 1219       <entry key="DAM.category" value="${CLASSIFICATION}"/>  
2 26 Feb 07 jari 1220           <entry key="DAM.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1221             <entry key="DAM.largeIcon" value="dam_button.gif"/>
2 26 Feb 07 jari 1222             <entry key="DAM.tooltip" value="Discriminant Analysis Classifier"/>
2 26 Feb 07 jari 1223         </propertyfile>
2 26 Feb 07 jari 1224     </target>
2 26 Feb 07 jari 1225
2 26 Feb 07 jari 1226
2 26 Feb 07 jari 1227
2 26 Feb 07 jari 1228  <target name="LEM" depends="LEM-GUI" if="LEM">
3 27 Feb 07 jari 1229         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1230                executable="${javac-location}">
2 26 Feb 07 jari 1231             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1232             <include name="LEM.java"/>
2 26 Feb 07 jari 1233     </javac>
2 26 Feb 07 jari 1234     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1235             <entry key="LEM" value="org.tigr.microarray.mev.cluster.algorithm.impl.LEM"/>
2 26 Feb 07 jari 1236         </propertyfile>
2 26 Feb 07 jari 1237     </target>
2 26 Feb 07 jari 1238
2 26 Feb 07 jari 1239     <target name="LEM-GUI">
3 27 Feb 07 jari 1240         <javac srcdir="${gui.impl.dir}/lem" destdir="${dest.dir}"
3 27 Feb 07 jari 1241                executable="${javac-location}">
2 26 Feb 07 jari 1242             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1243     </javac>
2 26 Feb 07 jari 1244     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1245     <entry key="gui.names" value="LEM:" operation="+"/>
2 26 Feb 07 jari 1246             <entry key="LEM.name" value="LEM"/>
2 26 Feb 07 jari 1247             <entry key="LEM.class" value="org.tigr.microarray.mev.cluster.gui.impl.lem.LEMGUI"/>
2 26 Feb 07 jari 1248       <entry key="LEM.category" value="${VISUALIZATION}"/>
2 26 Feb 07 jari 1249             <entry key="LEM.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1250             <entry key="LEM.largeIcon" value="lem_button.gif"/>
2 26 Feb 07 jari 1251             <entry key="LEM.tooltip" value="Linear Expression Map"/>
2 26 Feb 07 jari 1252         </propertyfile>
2 26 Feb 07 jari 1253     </target>
2 26 Feb 07 jari 1254     <target name="GDM" depends="GDM-GUI" if="GDM">
3 27 Feb 07 jari 1255         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1256                executable="${javac-location}">
2 26 Feb 07 jari 1257             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1258             <include name="GDM.java"/>
2 26 Feb 07 jari 1259     </javac>
2 26 Feb 07 jari 1260     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1261             <entry key="GDM" value="org.tigr.microarray.mev.cluster.algorithm.impl.GDM"/>
2 26 Feb 07 jari 1262         </propertyfile>
2 26 Feb 07 jari 1263     </target>
2 26 Feb 07 jari 1264
2 26 Feb 07 jari 1265     <target name="GDM-GUI">
3 27 Feb 07 jari 1266         <javac srcdir="${gui.impl.dir}/gdm" destdir="${dest.dir}"
3 27 Feb 07 jari 1267                executable="${javac-location}">
2 26 Feb 07 jari 1268             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1269     </javac>
2 26 Feb 07 jari 1270     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1271     <entry key="gui.names" value="GDM:" operation="+"/>
2 26 Feb 07 jari 1272             <entry key="GDM.name" value="GDM"/>
2 26 Feb 07 jari 1273             <entry key="GDM.class" value="org.tigr.microarray.mev.cluster.gui.impl.gdm.GDMGUI"/>
2 26 Feb 07 jari 1274       <entry key="GDM.category" value="${VISUALIZATION}"/>   
2 26 Feb 07 jari 1275          <entry key="GDM.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1276             <entry key="GDM.largeIcon" value="gdm_button.gif"/>
2 26 Feb 07 jari 1277             <entry key="GDM.tooltip" value="Gene Distance Matrix"/>
2 26 Feb 07 jari 1278         </propertyfile>
2 26 Feb 07 jari 1279     </target>
2 26 Feb 07 jari 1280
2 26 Feb 07 jari 1281
2 26 Feb 07 jari 1282
2 26 Feb 07 jari 1283     <target name="PCA" depends="PCA-GUI" if="PCA">
3 27 Feb 07 jari 1284         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1285                executable="${javac-location}">
2 26 Feb 07 jari 1286             <classpath refid="module.build.class.path"/>
2 26 Feb 07 jari 1287             <include name="PCA.java"/>
2 26 Feb 07 jari 1288     </javac>
2 26 Feb 07 jari 1289     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1290             <entry key="PCA" value="org.tigr.microarray.mev.cluster.algorithm.impl.PCA"/>
2 26 Feb 07 jari 1291         </propertyfile>
2 26 Feb 07 jari 1292     </target>
2 26 Feb 07 jari 1293
2 26 Feb 07 jari 1294     <target name="PCA-GUI">
3 27 Feb 07 jari 1295         <javac srcdir="${gui.impl.dir}/pca" destdir="${dest.dir}"
3 27 Feb 07 jari 1296                executable="${javac-location}">
2 26 Feb 07 jari 1297             <classpath>
2 26 Feb 07 jari 1298             <pathelement location="${lib.dir}/vecmath.jar"/>
2 26 Feb 07 jari 1299                 <pathelement location="${lib.dir}/j3dcore.jar"/>  
2 26 Feb 07 jari 1300                 <pathelement location="${lib.dir}/j3dutils.jar"/>
2 26 Feb 07 jari 1301
2 26 Feb 07 jari 1302                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 1303                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 1304                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 1305                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 1306                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 1307                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 1308                 <pathelement location="${lib.dir}/mev-base.jar"/>            
2 26 Feb 07 jari 1309             </classpath>
2 26 Feb 07 jari 1310     </javac>
2 26 Feb 07 jari 1311     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1312     <entry key="gui.names" value="PCA:" operation="+"/>
2 26 Feb 07 jari 1313             <entry key="PCA.name" value="PCA"/>
2 26 Feb 07 jari 1314             <entry key="PCA.class" value="org.tigr.microarray.mev.cluster.gui.impl.pca.PCAGUI"/>
2 26 Feb 07 jari 1315       <entry key="PCA.category" value="${DATA_REDUCTION}"/>  
2 26 Feb 07 jari 1316          <entry key="PCA.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1317             <entry key="PCA.largeIcon" value="pca_button.gif"/>
2 26 Feb 07 jari 1318             <entry key="PCA.tooltip" value="Principal Component Analysis"/>
2 26 Feb 07 jari 1319         </propertyfile>
2 26 Feb 07 jari 1320     </target>
2 26 Feb 07 jari 1321
2 26 Feb 07 jari 1322
2 26 Feb 07 jari 1323
2 26 Feb 07 jari 1324     <target name="COA" depends="COA-GUI" if="COA">
3 27 Feb 07 jari 1325         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1326                executable="${javac-location}">
2 26 Feb 07 jari 1327             <classpath>
2 26 Feb 07 jari 1328             <pathelement location="${lib.dir}/vecmath.jar"/>
2 26 Feb 07 jari 1329             <pathelement location="${lib.dir}/jama.jar"/>
2 26 Feb 07 jari 1330
2 26 Feb 07 jari 1331                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 1332                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 1333                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 1334                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 1335                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 1336                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 1337                 <pathelement location="${lib.dir}/mev-base.jar"/>            
2 26 Feb 07 jari 1338             </classpath>
2 26 Feb 07 jari 1339             <include name="COA.java"/>
2 26 Feb 07 jari 1340     </javac>
2 26 Feb 07 jari 1341     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1342             <entry key="COA" value="org.tigr.microarray.mev.cluster.algorithm.impl.COA"/>
2 26 Feb 07 jari 1343         </propertyfile>
2 26 Feb 07 jari 1344     </target>
2 26 Feb 07 jari 1345
2 26 Feb 07 jari 1346     <target name="COA-GUI">
3 27 Feb 07 jari 1347         <javac srcdir="${gui.impl.dir}/coa" destdir="${dest.dir}"
3 27 Feb 07 jari 1348                executable="${javac-location}">
2 26 Feb 07 jari 1349             <classpath>
2 26 Feb 07 jari 1350             <pathelement location="${lib.dir}/vecmath.jar"/>
2 26 Feb 07 jari 1351                 <pathelement location="${lib.dir}/j3dcore.jar"/>  
2 26 Feb 07 jari 1352                 <pathelement location="${lib.dir}/j3dutils.jar"/>
2 26 Feb 07 jari 1353
2 26 Feb 07 jari 1354                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 1355                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 1356                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 1357                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 1358                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 1359                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 1360                 <pathelement location="${lib.dir}/mev-base.jar"/>            
2 26 Feb 07 jari 1361             </classpath>
2 26 Feb 07 jari 1362     </javac>
2 26 Feb 07 jari 1363     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1364     <entry key="gui.names" value="COA:" operation="+"/>
2 26 Feb 07 jari 1365             <entry key="COA.name" value="COA"/>
2 26 Feb 07 jari 1366             <entry key="COA.class" value="org.tigr.microarray.mev.cluster.gui.impl.coa.COAGUI"/>
2 26 Feb 07 jari 1367       <entry key="COA.category" value="${DATA_REDUCTION}"/>   
2 26 Feb 07 jari 1368          <entry key="COA.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1369             <entry key="COA.largeIcon" value="coa_button.gif"/>
2 26 Feb 07 jari 1370             <entry key="COA.tooltip" value="Correspondence Analysis"/>
2 26 Feb 07 jari 1371         </propertyfile>
2 26 Feb 07 jari 1372     </target>
2 26 Feb 07 jari 1373
2 26 Feb 07 jari 1374
2 26 Feb 07 jari 1375
2 26 Feb 07 jari 1376     <target name="TRN" depends="TRN-GUI" if="TRN">
3 27 Feb 07 jari 1377         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1378                executable="${javac-location}">
2 26 Feb 07 jari 1379             <include name="terrain/**"/>
2 26 Feb 07 jari 1380             <classpath>
2 26 Feb 07 jari 1381             <pathelement location="${lib.dir}/vecmath.jar"/>
2 26 Feb 07 jari 1382
2 26 Feb 07 jari 1383                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 1384                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 1385                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 1386                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 1387                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 1388                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 1389                 <pathelement location="${lib.dir}/mev-base.jar"/>            
2 26 Feb 07 jari 1390             </classpath>
2 26 Feb 07 jari 1391     </javac>
2 26 Feb 07 jari 1392     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1393             <entry key="Terrain" value="org.tigr.microarray.mev.cluster.algorithm.impl.terrain.Terrain"/>
2 26 Feb 07 jari 1394         </propertyfile>
2 26 Feb 07 jari 1395     </target>
2 26 Feb 07 jari 1396
2 26 Feb 07 jari 1397
2 26 Feb 07 jari 1398     <target name="TRN-GUI">
3 27 Feb 07 jari 1399         <javac srcdir="${gui.impl.dir}/terrain" destdir="${dest.dir}"
3 27 Feb 07 jari 1400                executable="${javac-location}">
2 26 Feb 07 jari 1401             <classpath>
2 26 Feb 07 jari 1402             <pathelement location="${lib.dir}/vecmath.jar"/>
2 26 Feb 07 jari 1403                 <pathelement location="${lib.dir}/j3dcore.jar"/>  
2 26 Feb 07 jari 1404                 <pathelement location="${lib.dir}/j3dutils.jar"/>
2 26 Feb 07 jari 1405
2 26 Feb 07 jari 1406                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 1407                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 1408                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 1409                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 1410                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 1411                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 1412                 <pathelement location="${lib.dir}/mev-base.jar"/>            
2 26 Feb 07 jari 1413             </classpath>
2 26 Feb 07 jari 1414     </javac>
2 26 Feb 07 jari 1415     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1416     <entry key="gui.names" value="Terrain:" operation="+"/>
2 26 Feb 07 jari 1417             <entry key="Terrain.name" value="TRN"/>
2 26 Feb 07 jari 1418             <entry key="Terrain.class" value="org.tigr.microarray.mev.cluster.gui.impl.terrain.TerrainGUI"/>
2 26 Feb 07 jari 1419       <entry key="Terrain.category" value="${DATA_REDUCTION}"/>  
2 26 Feb 07 jari 1420           <entry key="Terrain.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1421             <entry key="Terrain.largeIcon" value="trn_button.gif"/>
2 26 Feb 07 jari 1422             <entry key="Terrain.tooltip" value="Expression Terrain Map"/>
2 26 Feb 07 jari 1423         </propertyfile>
2 26 Feb 07 jari 1424     </target>
2 26 Feb 07 jari 1425
2 26 Feb 07 jari 1426
2 26 Feb 07 jari 1427
2 26 Feb 07 jari 1428     <target name="EASE" depends="EASE-GUI" if="EASE">
3 27 Feb 07 jari 1429         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1430                executable="${javac-location}">
2 26 Feb 07 jari 1431             <classpath refid="module.build.class.path">
2 26 Feb 07 jari 1432     </classpath>
2 26 Feb 07 jari 1433             <include name="ease/**"/>
2 26 Feb 07 jari 1434     </javac>
2 26 Feb 07 jari 1435     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1436             <entry key="EASE" value="org.tigr.microarray.mev.cluster.algorithm.impl.ease.EASE"/>
2 26 Feb 07 jari 1437         </propertyfile>
2 26 Feb 07 jari 1438     </target>
2 26 Feb 07 jari 1439
2 26 Feb 07 jari 1440     <target name="EASE-GUI">
3 27 Feb 07 jari 1441         <javac srcdir="${gui.impl.dir}/ease" destdir="${dest.dir}"
3 27 Feb 07 jari 1442                executable="${javac-location}">
2 26 Feb 07 jari 1443             <classpath>
2 26 Feb 07 jari 1444                 <pathelement location="${lib.dir}/ftpbean.jar"/>
2 26 Feb 07 jari 1445
2 26 Feb 07 jari 1446
2 26 Feb 07 jari 1447                 <!-- jars to support module compilation -->
2 26 Feb 07 jari 1448                 <pathelement location="${lib.dir}/mev-util.jar"/>
2 26 Feb 07 jari 1449                 <pathelement location="${lib.dir}/mev-gui-impl.jar"/>
2 26 Feb 07 jari 1450                 <pathelement location="${lib.dir}/mev-gui-support.jar"/>
2 26 Feb 07 jari 1451                 <pathelement location="${lib.dir}/mev-algorithm-impl.jar"/>
2 26 Feb 07 jari 1452                 <pathelement location="${lib.dir}/mev-algorithm-support.jar"/>
2 26 Feb 07 jari 1453                 <pathelement location="${lib.dir}/mev-base.jar"/> 
2 26 Feb 07 jari 1454     </classpath>
2 26 Feb 07 jari 1455     </javac>
2 26 Feb 07 jari 1456     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1457       <entry key="gui.names" value="EASE:" operation="+"/>
2 26 Feb 07 jari 1458             <entry key="EASE.name" value="EASE"/>
2 26 Feb 07 jari 1459             <entry key="EASE.class" value="org.tigr.microarray.mev.cluster.gui.impl.ease.EASEGUI"/>
2 26 Feb 07 jari 1460         <entry key="EASE.category" value="${META_ANALYSIS}"/>  
2 26 Feb 07 jari 1461           <entry key="EASE.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1462             <entry key="EASE.largeIcon" value="ease_button.gif"/>
2 26 Feb 07 jari 1463             <entry key="EASE.tooltip" value="EASE Cluster Analysis"/>
2 26 Feb 07 jari 1464         </propertyfile>
2 26 Feb 07 jari 1465     </target>
2 26 Feb 07 jari 1466
2 26 Feb 07 jari 1467
2 26 Feb 07 jari 1468
2 26 Feb 07 jari 1469     <!-- Generic Algorithm Module Target Pair
2 26 Feb 07 jari 1470      For new modules that require compilation targets, this generic target
2 26 Feb 07 jari 1471          pair can be used as a template by replacing *** with the package name
2 26 Feb 07 jari 1472          or appropriate class names.
2 26 Feb 07 jari 1473     -->
2 26 Feb 07 jari 1474     <target name="***" depends="***-GUI">
3 27 Feb 07 jari 1475         <javac sourcepath="" srcdir="${alg.impl.dir}" destdir="${dest.dir}"
3 27 Feb 07 jari 1476                executable="${javac-location}">
2 26 Feb 07 jari 1477             <include name="***.java"/>
2 26 Feb 07 jari 1478     </javac>
2 26 Feb 07 jari 1479     <propertyfile file="${alg.properties.file}">
2 26 Feb 07 jari 1480             <entry key="***" value="org.tigr.microarray.mev.cluster.algorithm.impl.***"/>
2 26 Feb 07 jari 1481         </propertyfile>
2 26 Feb 07 jari 1482     </target>
2 26 Feb 07 jari 1483
2 26 Feb 07 jari 1484     <!--Generic Model GUI module build -->
2 26 Feb 07 jari 1485     <target name="***-GUI">
3 27 Feb 07 jari 1486         <javac srcdir="${gui.impl.dir}/***" destdir="${dest.dir}"
3 27 Feb 07 jari 1487                executable="${javac-location}">
2 26 Feb 07 jari 1488     </javac>
2 26 Feb 07 jari 1489     <propertyfile file="${gui.properties.file}">
2 26 Feb 07 jari 1490     <entry key="gui.names" value="***:" operation="+"/>
2 26 Feb 07 jari 1491             <entry key="***.name" value="***"/>
2 26 Feb 07 jari 1492             <entry key="***.class" value="org.tigr.microarray.mev.cluster.gui.impl.***"/>    
2 26 Feb 07 jari 1493       <entry key="***.category" value="${DATA_REDUCTION}"/>  
2 26 Feb 07 jari 1494       <entry key="***.smallIcon" value="analysis16.gif"/>
2 26 Feb 07 jari 1495             <entry key="***.largeIcon" value="***_button.gif"/>
2 26 Feb 07 jari 1496             <entry key="***.tooltip" value=" "/>
2 26 Feb 07 jari 1497         </propertyfile>
2 26 Feb 07 jari 1498     </target>
2 26 Feb 07 jari 1499
2 26 Feb 07 jari 1500
2 26 Feb 07 jari 1501
2 26 Feb 07 jari 1502     <!-- TARGET ============================================    
2 26 Feb 07 jari 1503            Target Name: jar-modules
2 26 Feb 07 jari 1504     Depends: algorithm-modules
2 26 Feb 07 jari 1505            Target Description: jars algorithm and gui module implemenations
2 26 Feb 07 jari 1506     Note:  Calling this target will produce the following jars:
2 26 Feb 07 jari 1507           mev-algorithm-impl.jar, mev-gui-impl.jar
2 26 Feb 07 jari 1508     --> 
2 26 Feb 07 jari 1509     <target name="jar-modules" depends="algorithm-modules">                
2 26 Feb 07 jari 1510
2 26 Feb 07 jari 1511         <!-- Jar the Algorithm Implementations -->
2 26 Feb 07 jari 1512         <jar destfile="${lib.dir}/mev-algorithm-impl.jar"
2 26 Feb 07 jari 1513             basedir="${dest.dir}"
2 26 Feb 07 jari 1514         includes="org/tigr/microarray/mev/cluster/algorithm/impl/**"
2 26 Feb 07 jari 1515    
2 26 Feb 07 jari 1516         />
2 26 Feb 07 jari 1517
2 26 Feb 07 jari 1518         <!-- Jar the GUI Implementations -->
2 26 Feb 07 jari 1519         <jar destfile="${lib.dir}/mev-gui-impl.jar"
2 26 Feb 07 jari 1520             basedir="${dest.dir}"
2 26 Feb 07 jari 1521         includes="org/tigr/microarray/mev/cluster/gui/impl/**"
2 26 Feb 07 jari 1522         />
2 26 Feb 07 jari 1523     </target>
2 26 Feb 07 jari 1524
2 26 Feb 07 jari 1525
2 26 Feb 07 jari 1526
2 26 Feb 07 jari 1527
2 26 Feb 07 jari 1528     <!-- TARGET ============================================    
2 26 Feb 07 jari 1529            Target Name: build-all
2 26 Feb 07 jari 1530     Depends: jar-modules
2 26 Feb 07 jari 1531            Target Description: Initial target to trigger full mev compilation.
2 26 Feb 07 jari 1532                                 Following compilation and jar activities the temp
2 26 Feb 07 jari 1533             destination file system is deleted.
2 26 Feb 07 jari 1534     -->   
2 26 Feb 07 jari 1535     <target name="build-all" depends="jar-modules">
2 26 Feb 07 jari 1536         <delete dir="${dest.dir}"/> 
2 26 Feb 07 jari 1537     </target>
2 26 Feb 07 jari 1538
2 26 Feb 07 jari 1539
2 26 Feb 07 jari 1540
2 26 Feb 07 jari 1541     <target name="init-module-build">
2 26 Feb 07 jari 1542         <tstamp/>
2 26 Feb 07 jari 1543         <delete dir="${dest.dir}"/>
2 26 Feb 07 jari 1544         <mkdir dir="${dest.dir}"/>         
2 26 Feb 07 jari 1545     </target>
2 26 Feb 07 jari 1546
2 26 Feb 07 jari 1547
2 26 Feb 07 jari 1548     <!-- TARGET ============================================    
2 26 Feb 07 jari 1549            Target Name: jar-modules-build-only
2 26 Feb 07 jari 1550     Depends: modules-only
2 26 Feb 07 jari 1551            Target Description: jars algorithm and gui module implemenations
2 26 Feb 07 jari 1552     Note:  Calling this target will produce the following jars:
2 26 Feb 07 jari 1553           mev-algorithm-impl.jar, mev-gui-impl.jar
2 26 Feb 07 jari 1554     --> 
2 26 Feb 07 jari 1555     <target name="jar-module-build-only" depends="modules-only">                
2 26 Feb 07 jari 1556
2 26 Feb 07 jari 1557         <!-- Jar the Algorithm Implementations -->
2 26 Feb 07 jari 1558         <jar destfile="${lib.dir}/mev-algorithm-impl.jar"
2 26 Feb 07 jari 1559              basedir="${dest.dir}"
2 26 Feb 07 jari 1560              includes="org/tigr/microarray/mev/cluster/algorithm/impl/**"
2 26 Feb 07 jari 1561         />
2 26 Feb 07 jari 1562         
2 26 Feb 07 jari 1563         <!-- Jar the GUI Implementations -->
2 26 Feb 07 jari 1564         <jar destfile="${lib.dir}/mev-gui-impl.jar"
2 26 Feb 07 jari 1565              basedir="${dest.dir}"
2 26 Feb 07 jari 1566          includes="org/tigr/microarray/mev/cluster/gui/impl/**"
2 26 Feb 07 jari 1567         />
2 26 Feb 07 jari 1568     </target>
2 26 Feb 07 jari 1569  
2 26 Feb 07 jari 1570 <!--
2 26 Feb 07 jari 1571     <target name="build-modules" depends="init-module-build, jar-module-build-only">
2 26 Feb 07 jari 1572         <delete dir="${dest.dir}"/> 
2 26 Feb 07 jari 1573     </target>
2 26 Feb 07 jari 1574 -->
2 26 Feb 07 jari 1575   <target name="build_deploy" depends="build-all">
2 26 Feb 07 jari 1576     
2 26 Feb 07 jari 1577     <!--
2 26 Feb 07 jari 1578     zip lib dir, source dir, docs, config, sampledata, bat file into releasable zip file
2 26 Feb 07 jari 1579     -->
2 26 Feb 07 jari 1580   </target>
2 26 Feb 07 jari 1581 </project>
2 26 Feb 07 jari 1582

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