<?xml version="1.0"?>

<!--  $Id: build_bdk.xml,v 1.177 2009/08/06 09:56:10 tolstyh Exp $  -->

<project name="BioUML public" default="usage" basedir=".">

	<target name="usage">
		<echo>
    clean   - clean OUTDIR, RELEASEDIR, JAVADOC_OUTDIR.

    compile - compiles BioUML workbench.

    run     - starts BioUML workbench
              Alternatively you may use bdk/run.bat (Windows) or bdk/rusn.sh (Linux)

    crun    - compiles all plugins and starts BioUML workbench

    javadoc - generates documentation

    plugin.all - creates jars (compile if necessary) for all BioUML plugins

    plugin.biouml    - creates biouml.jar     for biouml.workbench_0.8.x
    plugin.workbench - creates workbench.jar  for biouml.workbench_0.8.x
    plugin.dote      - creates dote.jar       for biouml.workbench_0.8.x
    plugin.doteserver- creates doteserver.jar 
    plugin.biosoft   - creates ru.biosoft.jar for ru.biosoft.workbench_0.8.x

    plugin.cellml - creates cellml.jar for biouml.plugins.cellml_0.8.x

    plugin.sbw  - creates SBWPlugin.jar for biouml.plugins.sbw_0.8.x

    plugin.sbml - creates SBMLPlugin.jar for biouml.plugins.sbml_0.8.x

    plugin.js - creates jsplugin.jar for ru.biosoft.plugins.javascript_0.8.x

    plugin.matlab - creates matlabplugin.jar for biouml.plugins.matlab_0.8.x 

    plugin.svg - creates svg.jar
    
    plugin.biopax - creates biopax.jar for biouml.plugins.biopax_0.8.x
        
    plugin.access.javascript - creates javascript.jar for basic access javascript funcs 
    
    plugin.obo - creates obo.jar for biouml.plugins.obo_0.8.x
            
    plugin.gne - creates gne.jar for biouml.plugins.gne_0.8.x   
            
    plugin.uniprot - creates uniprot.jar for biouml.plugins.uniprot_0.8.x   
             
    plugin.miriam - creates miriam.jar for biouml.plugins.miriam_0.8.x    
    
    plugin.hemodynamics - creates hemodynamics.jar for biouml.plugins.hemodynamics_0.8.x
    
    plugin.genehub - creates genehub.jar for biouml.plugins.genehub_0.8.x
            
    plugin.chebi - creates chebi.jar for biouml.plugins.chebi_0.8.x
            
    plugin.psimi - creates psimi.jar for biouml.plugins.psimi_0.8.x
            
    plugin.simulation_test - creates simulation_test.jar for biouml.plugins.simulation_test_0.8.x

    plugin.bsa - creates bsa for ru.biosoft.bsa_0.8.x
    
    plugin.sabiork - creates sabiork.jar for biouml.plugins.sabiork_0.8.x
    
    plugin.kegg - creates kegg.jar for biouml.plugins.kegg_0.8.x
           
    plugin.analysis - creates analysis.jar for ru.biosoft.analysis_0.8.x

    plugin.optimization - creates optimization.jar for ru.biosoft.analysis.optimization_0.8.x
            
    plugin.optimization.biouml - creates optimization.jar for biouml.plugins.optimization_0.8.x
    
    plugin.genenet - creates genenet.jar for biouml.plugins.genenet_0.8.x
			
    plugin.jri - creates JRI.jar and jri_plugin.jar for ru.biosoft.plugins.jri_0.8.x
			
    plugin.creasemarks - creates creasemarks.jar for biouml.plugins.creasemarks_0.8.x
			
	plugin.explain - creates explain.jar for biouml.plugins.explain_0.8.x
			
	plugin.endonet - creates endonet.jar for biouml.plugins.endonet_0.8.x
    </echo>
	</target>

	<property name="PROJECT_NAME" value="${ant.project.name}" />

	<!-- =================================================================== -->
	<!-- Project specific properties                                         -->
	<!-- =================================================================== -->

	<property name="TOPDIR" value=".." />

	<target name="local_settings">
		<property name="SRCDIR" value="${TOPDIR}/src" />
		<property name="OUTDIR" value="${TOPDIR}/out" />
		<property name="JAVADOC_OUTDIR" value="${TOPDIR}/javadoc" />
		<property name="HELPDIR" value="${TOPDIR}/help" />
		<property name="HELPSOURCES" value="${HELPDIR}/sources" />

		<property name="VERSION" value="0.8.6" />

		<!-- Libraries -->
		<property name="PLUGIN_DIR" value="${TOPDIR}/plugins" />
		<property name="ECLIPSE_JARS" value="${TOPDIR}/startup.jar;${PLUGIN_DIR}/org.eclipse.core.contenttype_3.2.0.v20060603.jar;${PLUGIN_DIR}/org.eclipse.core.jobs_3.2.0.v20060603.jar;${PLUGIN_DIR}/org.eclipse.core.runtime_3.2.0.v20060603.jar;${PLUGIN_DIR}/org.eclipse.equinox.common_3.2.0.v20060603.jar;${PLUGIN_DIR}/org.eclipse.equinox.preferences_3.2.1.R32x_v20060717.jar;${PLUGIN_DIR}/org.eclipse.equinox.registry_3.2.1.R32x_v20060814.jar;${PLUGIN_DIR}/org.eclipse.osgi.services_3.1.100.v20060601.jar;${PLUGIN_DIR}/org.eclipse.osgi.util_3.1.100.v20060601.jar;${PLUGIN_DIR}/org.eclipse.osgi_3.2.2.R32x_v20070118.jar;${PLUGIN_DIR}/org.eclipse.update.configurator_3.2.2.R32x_v20070111.jar" />
		<property name="ELCIPSE_UPDATE_CORE" value="${PLUGIN_DIR}/org.eclipse.update.core_3.2.3.R32x_v20070118.jar" />
		<property name="FOXTROT" value="${PLUGIN_DIR}/foxtrot/foxtrot.jar" />
		<property name="SBW" value="${PLUGIN_DIR}/edu.caltech.sbw_2.7.6/SBWCore.jar" />
		<property name="RHINO" value="${PLUGIN_DIR}/org.mozilla.javascript_1.7.0/js.jar" />
		<property name="PLOT" value="${PLUGIN_DIR}/ptolemy.plot_2.0.0/plot.jar" />
		<property name="MATLAB" value="${PLUGIN_DIR}/biouml.plugins.matlab_${VERSION}" />
		<property name="LOG4J" value="${PLUGIN_DIR}/org.apache.log4j_1.2.12/log4j-1.2.12.jar" />
		<property name="BEANHELPERS" value="${PLUGIN_DIR}/com.beanexplorer_2.1.0/beanhelpers.jar" />
		<property name="BEANEXPLORER" value="${PLUGIN_DIR}/com.beanexplorer_2.1.0/beanexplorer.jar" />
		<property name="JHALL" value="${PLUGIN_DIR}/javax.help_2.0.05/jhall.jar" />
		<property name="JFREECHART" value="${PLUGIN_DIR}/org.jfree.chart_1.0.10/jfreechart-1.0.10.jar;${PLUGIN_DIR}/org.jfree.chart_1.0.10/jcommon-1.0.13.jar" />
		<property name="MYSQL_JAR" value="${PLUGIN_DIR}/com.mysql.jdbc_3.1.13/mysql-connector-java-3.1.13-bin.jar" />
		<property name="ENSEMBL_JAR" value="${PLUGIN_DIR}/org.ensembl.ensj_39.2/ensj-39.2.jar" />
		<property name="SQLSERVER_JAR" value="${PLUGIN_DIR}/net.sourceforge.jtds_1.0.3/jtds.jar" />
		<property name="GRAPH" value="${PLUGIN_DIR}/ru.biosoft.graph_${VERSION}/graph.jar;${PLUGIN_DIR}/ru.biosoft.graph_${VERSION}/graph2.jar" />
		<property name="JGRAPH" value="${PLUGIN_DIR}/org.jgraph.jgraph_5.1/jgraph.jar" />
		<property name="JGRAPHADDONS" value="${PLUGIN_DIR}/org.jgraph.jgraphaddons_1.0.3/jgraphaddons.jar" />
		<property name="SVGGEN" value="${PLUGIN_DIR}/org.apache.batik.svggen_1.7.0/batik-awt-util.jar;${PLUGIN_DIR}/org.apache.batik.svggen_1.7.0/batik-svggen.jar;${PLUGIN_DIR}/org.apache.batik.svggen_1.7.0/batik-util.jar" />
		<property name="LUCENE" value="${PLUGIN_DIR}/org.apache.lucene_2.3.2/lucene-core-2.3.2.jar;${PLUGIN_DIR}/org.apache.lucene_2.3.2/lucene-analyzers-2.3.2.jar;${PLUGIN_DIR}/org.apache.lucene_2.3.2/lucene-highlighter-2.3.2.jar;${PLUGIN_DIR}/org.apache.lucene_2.3.2/lucene-snowball-2.3.2.jar" />
		<property name="HIBERNATE" value="${PLUGIN_DIR}/ru.biosoft.access.hibernate_${VERSION}/hibernate/antlr-2.7.6.jar;${PLUGIN_DIR}/ru.biosoft.access.hibernate_${VERSION}/hibernate/asm-attrs.jar;${PLUGIN_DIR}/ru.biosoft.access.hibernate_${VERSION}/hibernate/asm.jar;${PLUGIN_DIR}/ru.biosoft.access.hibernate_${VERSION}/hibernate/cglib-2.1.3.jar;${PLUGIN_DIR}/ru.biosoft.access.hibernate_${VERSION}/hibernate/dom4j-1.6.1.jar;${PLUGIN_DIR}/ru.biosoft.access.hibernate_${VERSION}/hibernate/hibernate3.jar;${PLUGIN_DIR}/ru.biosoft.access.hibernate_${VERSION}/hibernate/jta.jar" />
		<!--property name="HIBERNATE" value="${PLUGIN_DIR}/org.hibernate_3.2.1/antlr-2.7.6.jar;${PLUGIN_DIR}/org.hibernate_3.2.1/asm-attrs.jar;${PLUGIN_DIR}/org.hibernate_3.2.1/asm.jar;${PLUGIN_DIR}/org.hibernate_3.2.1/cglib-2.1.3.jar;${PLUGIN_DIR}/org.hibernate_3.2.1/commons-collections-2.1.1.jar;${PLUGIN_DIR}/org.hibernate_3.2.1/commons-logging-1.0.4.jar;${PLUGIN_DIR}/org.hibernate_3.2.1/dom4j-1.6.1.jar;${PLUGIN_DIR}/org.hibernate_3.2.1/hibernate3.jar;${PLUGIN_DIR}/org.hibernate_3.2.1/jta.jar;${PLUGIN_DIR}/org.hibernate_3.2.1/log4j-1.2.11.jar"/-->
		<property name="TOMCAT" value="${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/bootstrap.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/catalina.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/commons-beanutils.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/commons-collections.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/commons-digester.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/commons-logging-api.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/commons-logging.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/commons-modeler.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/jakarta-regexp-1.3.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/jasper-compiler.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/jasper-runtime.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/mx4j-jmx.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/naming-common.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/naming-factory.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/naming-resources.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/servlet.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/servlets-common.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/servlets-default.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/servlets-invoker.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/servlets-manager.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/tomcat-coyote.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/tomcat-http11.jar;${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcat/tomcat-util.jar" />
		<!--property name="TOMCAT"               value="${PLUGIN_DIR}/org.apache.tomcat_4.1.30/bootstrap.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/catalina.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/commons-beanutils.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/commons-collections.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/commons-digester.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/commons-logging-api.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/commons-logging.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/commons-modeler.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/jakarta-regexp-1.3.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/jasper-compiler.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/jasper-runtime.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/mx4j-jmx.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/naming-common.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/naming-factory.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/naming-resources.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/servlet.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/servlets-common.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/servlets-default.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/servlets-invoker.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/servlets-manager.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/tomcat-coyote.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/tomcat-http11.jar;${PLUGIN_DIR}/org.apache.tomcat_4.1.30/tomcat-util.jar"/-->
		<property name="CERN" value="${PLUGIN_DIR}/cern.jet.random_1.3.0/colt.jar" />
		<property name="OWLAPI" value="${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/commons-lang-2.2.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-api.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-apibinding.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-debugging.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-dig1_1.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-functionalparser.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-functionalrenderer.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-impl.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-krssparser.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-oboparser.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-owlxmlparser.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-owlxmlrenderer.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-rdfapi.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-rdfxmlparser.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-rdfxmlrenderer.jar;${PLUGIN_DIR}/org.semanticweb.owl_2.1.0/owlapi-util.jar" />
		<property name="ROSUDA" value="${PLUGIN_DIR}/org.rosuda.rengine_0.6.0/rosuda.jar" />
		<property name="JAMA" value="${PLUGIN_DIR}/jama_1.0.2/Jama-1.0.2.jar" />
		<property name="DISTRIBUTION" value="${PLUGIN_DIR}/edu.uah.math_1.0.0/SOCR_plugin.jar" />
		<property name="SYNTAX" value="${PLUGIN_DIR}/com.Ostermiller.syntax_1.0.0/syntax.jar" />
		<property name="CDK" value="${PLUGIN_DIR}/org.openscience.cdk_0.9.0/cdk-core.jar;${PLUGIN_DIR}/org.openscience.cdk_0.9.0/cdk-extra.jar;${PLUGIN_DIR}/org.openscience.cdk_0.9.0/cdk-io.jar;${PLUGIN_DIR}/org.openscience.cdk_0.9.0/cdk-render.jar;${PLUGIN_DIR}/org.openscience.cdk_0.9.0/cdk-standard.jar" />
		<property name="JSON" value="${PLUGIN_DIR}/org.json_1.0.0/json.jar" />

		<property name="JUNIT" value="${PLUGIN_DIR}/junit_3.8.1/junit.jar" />
		<property name="testui" value="swingui" />
		<property name="COMMON" value="${PLUGIN_DIR}/org.apache.commons.cli_1.0.0/commons-cli-1.0.jar;${PLUGIN_DIR}/org.apache.commons.collections_2.1.1/commons-collections-2.1.1.jar;${PLUGIN_DIR}/org.apache.commons.logging_1.1.0/commons-logging-1.1.jar;${PLUGIN_DIR}/org.apache.commons.logging_1.1.0/commons-logging-adapters-1.1.jar;${PLUGIN_DIR}/org.apache.commons.logging_1.1.0/commons-logging-api-1.1.jar;${PLUGIN_DIR}/org.apache.axis_1.1.0/axis.jar;${PLUGIN_DIR}/org.apache.axis_1.1.0/commons-discovery.jar;${PLUGIN_DIR}/org.apache.axis_1.1.0/jaxrpc.jar;${PLUGIN_DIR}/org.apache.axis_1.1.0/saaj.jar;${PLUGIN_DIR}/org.apache.axis_1.1.0/wsdl4j.jar" />
		<!-- misc -->
		<property name="PROTECTED" value="${PLUGIN_DIR}/ru.biosoft.graph_${VERSION}/graph.jar;${PLUGIN_DIR}/biouml.workbench.graph_${VERSION}/graph.jar;${PLUGIN_DIR}/ru.biosoft.services_${VERSION}/services.jar" />



		<property name="BUILD_CLASSPATH" value=".;${ECLIPSE_JARS};${SBW};${COMMON};${RHINO};${PLOT};${MATLAB};${JHALL};${LOG4J};${BEANEXPLORER};${BEANHELPERS};${JFREECHART};${GRAPH};${JGRAPH};${JGRAPHADDONS};${SVGGEN};${PROTECTED};${JAMA};${DISTRIBUTION};${SYNTAX};${CDK};${LUCENE};${HIBERNATE};${TOMCAT};${ENSEMBL_JAR};${MYSQL_JAR};${OWLAPI};${ELCIPSE_UPDATE_CORE};${CERN};${ROSUDA};${JSON}" />
		<property name="RUN_CLASSPATH" value=".;${OUTDIR};${BEANEXPLORER};${COMMON};${BEANHELPERS};${LOG4J};${RHINO};${JHALL};${JFREECHART};${GRAPH};${JGRAPH};${JGRAPHADDONS};${JAMA};${DISTRIBUTION};${SYNTAX};${CDK};${LUCENE};${HIBERNATE};${TOMCAT};${ENSEMBL_JAR};${MYSQL_JAR};${OWLAPI};${ROSUDA};${JSON}" />

		<property name="WORKBENCH" value="${PLUGIN_DIR}/ru.biosoft.workbench_${VERSION}" />
		<property name="BIOUML_WORKBENCH" value="${PLUGIN_DIR}/biouml.workbench_${VERSION}" />
		<property name="MODULE_DATADIR" value="data" />
	</target>

	<target name="local_settings_tofile" depends="local_settings">
		<echo file=".local.properties">
TOPDIR=${TOPDIR}
SRCDIR=${SRCDIR}
OUTDIR=${OUTDIR}
HELPDIR=${HELPDIR}
HELPSOURCES=${HELPSOURCES}
JAVADOC_OUTDIR=${JAVADOC_OUTDIR}

VERSION = ${VERSION}

#Libraries
PLUGIN_DIR=${PLUGIN_DIR}
ECLIPSE_JARS=${ECLIPSE_JARS}
FOXTROT=${FOXTROT}
SBW=${SBW}
RHINO=${RHINO}
PLOT=${PLOT}
MATLAB=${MATLAB}
JHALL=${JHALL}
LOG4J=${LOG4J}
BEANHELPERS=${BEANHELPERS}
BEANEXPLORER=${BEANEXPLORER}
JFREECHART=${JFREECHART}
GRAPH=${GRAPH}
JGRAPH=${JGRAPH}
JGRAPHADDONS=${JGRAPHADDONS}
SVGGEN=${SVGGEN}
JUNIT=${JUNIT}
COMMON=${COMMON}
HIBERNATE=${HIBERNATE}
LUCENE=${LUCENE}
TOMCAT=${TOMCAT}
JAMA=${JAMA}
DISTRIBUTION=${DISTRIBUTION}
SYNTAX=${SYNTAX}
CDK=${CDK}
CERN=${CERN}
JSON=${JSON}

MYSQL_JAR=${MYSQL_JAR}
ENSEMBL_JAR=${ENSEMBL_JAR}
SQLSERVER_JAR=${SQLSERVER_JAR}

OWLAPI=${OWLAPI}

#misc
BUILD_CLASSPATH=${BUILD_CLASSPATH}
RUN_CLASSPATH=${RUN_CLASSPATH}

WORKBENCH=${WORKBENCH}
BIOUML_WORKBENCH=${BIOUML_WORKBENCH}
ELCIPSE_UPDATE_CORE=${ELCIPSE_UPDATE_CORE}          
MODULE_DATADIR=${MODULE_DATADIR}
testui=${testui}
    </echo>
	</target>

	<!-- =================================================================== -->
	<!-- Project specific targets                                            -->
	<!-- =================================================================== -->

	<target name="main" depends="prepare">
	</target>

	<target name="prepare" depends="local_settings">
		<mkdir dir="${OUTDIR}" />
		<tstamp />
	</target>

	<target name="clean" depends="local_settings">
		<delete dir="${OUTDIR}" />
		<delete dir="${JAVADOC_OUTDIR}" />
		<delete dir="${RELEASEDIR}" />
	</target>

	<target name="compile" depends="main">
		<echo message="Compiling BioUML Library..." />
		<javac srcdir="${SRCDIR}" destdir="${OUTDIR}" classpath="${BUILD_CLASSPATH}" debug="on" deprecation="off" optimize="off">
			<include name="**/*.java" />
			<exclude name="**/_test/*.java" />
			<exclude name="**/TestProxy.java" />
			<exclude name="**/ru/biosoft/microarray/*.java" />
		</javac>
		<copy todir="${OUTDIR}">
			<fileset dir="${SRCDIR}" includes="**/*.gif,**/*.jpg" />
		</copy>
	</target>


	<target name="run" depends="main">
		<echo message="Run BioUML as Eclipse application" />
		<java classname="org.eclipse.core.launcher.Main" dir=".." fork="yes">
			<jvmarg value="-Xmx256m" />
			<classpath>
				<pathelement path="../startup.jar" />
			</classpath>
			<arg line="-application biouml.workbench.launcher ./data ./data_resources" />
		</java>
	</target>

	<target name="run.debug" depends="main">
		<echo message="Run BioUML as Eclipse application" />
		<java classname="org.eclipse.core.launcher.Main" dir=".." fork="yes">
			<jvmarg value="-Xmx256m" />
			<jvmarg value="-Xdebug" />
			<jvmarg value="-Xnoagent" />
			<jvmarg value="-Djava.compiler=NONE" />
			<jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=5006" />
			<classpath>
				<pathelement path="../startup.jar" />
			</classpath>
			<arg value="./data" />
		</java>
	</target>

	<target name="crun" depends="plugin.all,run">
	</target>

	<target name="javadoc" depends="local_settings">
		<property name="JAVADOC_OUTDIR" value="./javadoc" />

		<echo message="Building javadocs..." />
		<mkdir dir="${JAVADOC_OUTDIR}" />
		<javadoc maxmemory="512m" sourcepath="${SRCDIR}" packagenames="biouml.*,ru.biosoft.*,com.developmentontheedge.*" link="http://java.sun.com/j2se/1.4/docs/api" classpath="${BUILD_CLASSPATH}" destdir="${JAVADOC_OUTDIR}" public="false" noindex="true" Use="true" bottom="&lt;i&gt;Copyright &#169; 2001-2009 Biosof.Ru. All Rights Reserved.&lt;/i&gt;">
			<tag name="todo" scope="all" description="To do:" />
			<tag name="pending" scope="all" description="Pending:" />
			<group title="BioUML workbench" packages="biouml,biouml.*,biouml.model.*" />
			<group title="Biosoft.Ru libraries" packages="ru.biosoft,ru.biosoft.*" />
			<group title="DevelopmentOnTheEdge.com utility libraries" packages="com.developmentontheedge.*" />
		</javadoc>
	</target>

	<target name="javadoc.plugin" depends="local_settings">
		<delete dir="${PLUGIN_OUTDIR}" />
		<javadoc maxmemory="512m" sourcepath="${SRCDIR}" packagenames="${PLUGIN_PACKAGES}" link="http://java.sun.com/j2se/1.4/docs/api" classpath="${BUILD_CLASSPATH}" destdir="${PLUGIN_OUTDIR}" public="true" noindex="true" notree="true" nonavbar="true" nohelp="true" noqualifier="true" Use="false" bottom="&lt;i&gt;Copyright &#169; 2001-2009 Biosof.Ru. All Rights Reserved.&lt;/i&gt;">
		</javadoc>
	</target>

	<!-- =================================================================== -->
	<!-- Create plugins                                                      -->
	<!-- =================================================================== -->

	<target name="plugin.all" depends="plugin.ginsim,plugin.biouml.graph,plugin.gxl,plugin.services,plugin.biouml,plugin.workbench,plugin.dote,plugin.doteserver,plugin.biosoft,plugin.access,plugin.table,plugin.datasearch,plugin.lucene,plugin.server,plugin.hibernate,plugin.tomcat,plugin.access.server,plugin.biosoft.math,plugin.cellml,plugin.sbw,plugin.sbml,plugin.js,plugin.simulation,plugin.matlab,plugin.svg,plugin.ensembl,plugin.bioserver,plugin.biopax,plugin.obo,plugin.microarray,plugin.gne,plugin.genehub,plugin.uniprot,plugin.miriam,plugin.chebi,plugin.psimi,plugin.simulation_test,plugin.hemodynamics,plugin.access.javascript,plugin.bsa,plugin.sabiork,plugin.kegg,plugin.analysis,plugin.optimization,plugin.optimization.biouml,plugin.genenet,plugin.jri,plugin.creasemarks,plugin.explain,plugin.endonet" />

	<target name="plugin.biouml" depends="compile">
		<echo message="Making biouml.jar ..." />
		<jar jarfile="${BIOUML_WORKBENCH}/biouml.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/model/**/*.class" />
					<include name="biouml/standard/**/*.class" />
					<include name="biouml/Framework.class" />
					<exclude name="biouml/**/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/model/**/*.gif" />
					<include name="biouml/standard/**/*.gif" />
					<include name="biouml/standard/**/*.jpg" />
					<include name="biouml/standard/diagram/resources/**/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.workbench" depends="compile">
		<echo message="Making workbench.jar ..." />
		<copy todir="${OUTDIR}">
			<fileset dir="${SRCDIR}">
				<include name="biouml/workbench/resources/*.html" />
			</fileset>
			<filterset begintoken="$" endtoken="$">
				<filter token="build_no" value="${DSTAMP}" />
			</filterset>
		</copy>
		<jar jarfile="${BIOUML_WORKBENCH}/workbench.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/workbench/**/*.class" />
					<include name="biouml/workbench/resources/*.html" />
					<include name="biouml/plugins/*.class" />
					<exclude name="biouml/**/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/workbench/**/*.gif" />
					<include name="biouml/workbench/**/*.jpg" />
					<include name="biouml/workbench/**/*.png" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.dote" depends="compile">
		<echo message="Making dote.jar ..." />
		<jar jarfile="${PLUGIN_DIR}/com.developmentontheedge.util_${VERSION}/dote.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="com/developmentontheedge/**/*.class" />
					<exclude name="com/developmentontheedge/**/_test/**/*.class" />
					<exclude name="com/developmentontheedge/server/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="com/developmentontheedge/**/*.gif" />
					<exclude name="com/developmentontheedge/server/**/*.class" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.doteserver" depends="compile">
		<echo message="Making doteserver.jar ..." />
		<jar jarfile="${PLUGIN_DIR}/com.developmentontheedge.server_${VERSION}/doteserver.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="com/developmentontheedge/server/**/*.class" />
					<exclude name="com/developmentontheedge/**/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="com/developmentontheedge/server/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>


	<target name="plugin.biosoft" depends="compile">
		<echo message="Making ru.biosoft.jar ..." />
		<jar jarfile="${WORKBENCH}/ru.biosoft.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/**/*.class" />
					<exclude name="ru/biosoft/access/**/*.class" />
					<exclude name="ru/biosoft/bsa/**/*.class" />
					<exclude name="ru/biosoft/graph/**/*.class" />
					<exclude name="ru/biosoft/math/**/*.class" />
					<exclude name="ru/biosoft/plugins/javascript/**/*.class" />
					<exclude name="ru/biosoft/plugins/jri/**/*.class" />
					<exclude name="ru/biosoft/services/**/*.class" />
					<exclude name="ru/biosoft/util/**/*.class" />
					<exclude name="ru/biosoft/server/**/*.class" />
					<exclude name="ru/biosoft/**/_test/**/*.class" />
					<exclude name="ru/biosoft/analysis/**/*.class" />
					<exclude name="ru/biosoft/analysis/optimization/**/*.class" />
					<exclude name="ru/biosoft/table/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="ru/biosoft/**/*.gif" />
					<exclude name="ru/biosoft/access/**/*.*" />
					<exclude name="ru/biosoft/bsa/**/*.*" />
					<exclude name="ru/biosoft/graph/**/*.*" />
					<exclude name="ru/biosoft/math/**/*.*" />
					<exclude name="ru/biosoft/plugins/javascript/**/*.*" />
					<exclude name="ru/biosoft/plugins/jri/**/*.*" />
					<exclude name="ru/biosoft/services/**/*.*" />
					<exclude name="ru/biosoft/util/**/*.*" />
					<exclude name="ru/biosoft/**/_test/**/*.*" />
					<exclude name="ru/biosoft/analysis/**/*.*" />
					<exclude name="ru/biosoft/analysis/optimization/**/*.*" />
					<exclude name="ru/biosoft/table/**/*.*" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.access" depends="compile">
		<echo message="Making access.jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.access_${VERSION}/access.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/access/**/*.class" />
					<include name="ru/biosoft/util/**/*.class" />
					<exclude name="ru/biosoft/access/javascript/**/*.class" />
					<exclude name="ru/biosoft/access/search/**/*.class" />
					<exclude name="ru/biosoft/access/server/**/*.class" />
					<exclude name="ru/biosoft/access/hibernate/**/*.class" />
					<exclude name="ru/biosoft/access/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="ru/biosoft/access/**/*.gif" />
					<include name="ru/biosoft/util/**/*.gif" />
					<exclude name="ru/biosoft/access/javascript/**/*.*" />
					<exclude name="ru/biosoft/access/search/**/*.*" />
					<exclude name="ru/biosoft/access/server/**/*.*" />
					<exclude name="ru/biosoft/access/hibernate/**/*.*" />
					<exclude name="ru/biosoft/access/_test/**/*.*" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.table" depends="compile">
		<echo message="Making table.jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.table_${VERSION}/table.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/table/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="ru/biosoft/table/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.access.javascript" depends="compile">
		<echo message="Making javascript.jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.access.javascript_${VERSION}/javascript.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/access/javascript/**/*.class" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.bsa" depends="local_settings,compile">
		<echo message="Making bsa.jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.bsa_${VERSION}/bsa.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/bsa/**/*.class" />
					<exclude name="ru/biosoft/bsa/**/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="ru/biosoft/bsa/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.hibernate" depends="compile">
		<echo message="Making hiberaccess.jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.access.hibernate_${VERSION}/hiberaccess.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/access/hibernate/**/*.class" />
					<exclude name="ru/biosoft/access/hibernate/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="ru/biosoft/access/hibernate/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.datasearch" depends="local_settings,compile">
		<echo message="Making ru.biosoft.access.search jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.access.search_${VERSION}/search.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/access/search/*.class" />
					<exclude name="ru/biosoft/access/search/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="ru/biosoft/access/search/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.lucene" depends="local_settings,compile">
		<echo message="Making biouml.plugins.lucene jar ..." />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.lucene_${VERSION}/lucene.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/lucene/*.class" />
					<exclude name="biouml/plugins/lucene/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/lucene/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.microarray" depends="local_settings,compile">
		<echo message="Making biouml.plugins.microarray jar ..." />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.microarray_${VERSION}/microarray.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/microarray/*.class" />
					<include name="biouml/plugins/microarray/*/*.class" />
					<include name="biouml/plugins/microarray/analysis/*/*.class" />

					<exclude name="biouml/plugins/microarray/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/microarray/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.bioserver" depends="local_settings,compile">
		<echo message="Making biouml.plugins.server jar ..." />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.server_${VERSION}/bioserver.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/server/*.class" />
					<exclude name="biouml/plugins/server/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/server/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.server" depends="local_settings,compile">
		<echo message="Making ru.biosoft.server jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.server_${VERSION}/server.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/server/**/*.class" />
					<exclude name="ru/biosoft/server/**/_test/**/*.class" />
					<exclude name="ru/biosoft/server/tomcat/**/*.class" />
					<exclude name="ru/biosoft/server/servlets/**/*.class" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.tomcat" depends="local_settings,compile">
		<echo message="Making ru.biosoft.server jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/tomcatserver.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/server/tomcat/**/*.class" />
					<exclude name="ru/biosoft/server/**/_test/**/*.class" />
					<exclude name="ru/biosoft/server/tomcat/ConnectionServlet.class" />
					<exclude name="ru/biosoft/server/tomcat/ServerConnectionServlet.class" />
				</patternset>
			</fileset>
		</jar>
		<copy file="${OUTDIR}/ru/biosoft/server/tomcat/ConnectionServlet.class" tofile="${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/webapps/ROOT/WEB-INF/classes/ru/biosoft/server/tomcat/ConnectionServlet.class" />
		<copy file="${OUTDIR}/ru/biosoft/server/tomcat/ServerConnectionServlet.class" tofile="${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/webapps/ROOT/WEB-INF/classes/ru/biosoft/server/tomcat/ServerConnectionServlet.class" />
		<copy file="${OUTDIR}/ru/biosoft/server/Response.class" tofile="${PLUGIN_DIR}/ru.biosoft.server.tomcat_${VERSION}/webapps/ROOT/WEB-INF/classes/ru/biosoft/server/Response.class" />
	</target>

	<target name="plugin.access.server" depends="local_settings,compile">
		<echo message="Making ru.biosoft.access.server jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.access.server_${VERSION}/server.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/access/server/*.class" />
					<exclude name="ru/biosoft/access/server/_test/**/*.class" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.biosoft.math" depends="compile">
		<echo message="Making math.jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.math_${VERSION}/math.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/math/**/*.class" />
					<exclude name="ru/biosoft/math/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="ru/biosoft/math/**/*.gif" />
					<exclude name="ru/biosoft/math/_test/**/*.*" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.cellml" depends="compile">
		<echo message="  cellml plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.cellml_${VERSION}/cellml.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/cellml/**/*.class" />
					<exclude name="biouml/plugins/cellml/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/cellml/**/*.gif" />
					<include name="biouml/plugins/cellml/**/*.jpg" />
					<include name="biouml/plugins/cellml/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.sbml" depends="compile">
		<echo message="  sbml plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.sbml_${VERSION}/SBMLPlugin.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/sbml/**/*.class" />
					<exclude name="biouml/plugins/sbml/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/sbml/**/*.gif" />
					<include name="biouml/plugins/sbml/**/*.jpg" />
					<include name="biouml/plugins/sbml/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.sbw" depends="compile">
		<echo message="  sbw plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.sbw_${VERSION}/sbwplugin.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/sbw/**/*.class" />
					<exclude name="biouml/plugins/sbw/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/sbw/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.js" depends="compile">
		<echo message="  JavaScript plugin" />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.plugins.javascript_${VERSION}/jsplugin.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/plugins/javascript/**/*.class" />
					<exclude name="ru/biosoft/plugins/javascript/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="ru/biosoft/plugins/javascript/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>


	<target name="plugin.matlab" depends="compile">
		<echo message="  matlab plugin" />
		<javac srcdir="${PLUGIN_DIR}/biouml.plugins.matlab_${VERSION}" classpath="${BUILD_CLASSPATH}" debug="on" deprecation="off" optimize="off">
			<include name="JMatLink.java" />
		</javac>
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.matlab_${VERSION}/matlabplugin.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/matlab/**/*.class" />
					<exclude name="biouml/plugins/matlab/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/matlab/**/*.gif" />
				</patternset>
			</fileset>
			<fileset dir="${MATLAB}">
				<patternset>
					<include name="JMatLink.class" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.ginsim" depends="local_settings,compile">
		<echo message="  GinSim plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.ginsim_${VERSION}/ginsim.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/ginsim/**/*.class" />
					<exclude name="biouml/plugins/ginsim/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/ginsim/**/*.gif" />
					<include name="biouml/plugins/ginsim/**/*.jpg" />
					<include name="biouml/plugins/ginsim/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.gxl" depends="compile">
		<echo message="  GXL plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.gxl_${VERSION}/gxl.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/gxl/**/*.class" />
					<exclude name="biouml/plugins/gxl/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/gxl/**/*.gif" />
					<include name="biouml/plugins/gxl/**/*.jpg" />
					<include name="biouml/plugins/gxl/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.svg" depends="compile">
		<echo message="  sbml plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.svg_${VERSION}/svg.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/svg/**/*.class" />
					<exclude name="biouml/plugins/svg/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/svg/**/*.gif" />
					<include name="biouml/plugins/svg/**/*.jpg" />
					<include name="biouml/plugins/svg/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.simulation" depends="compile">
		<echo message="simulation plug-in" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.simulation_${VERSION}/simulation.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/simulation/**/*.*" />
					<exclude name="biouml/plugins/simulation/hybrid/**/*.*" />
				</patternset>
			</fileset>
		</jar>

		<echo message="  src jar" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.simulation_${VERSION}/src.jar" compress="true">
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/simulation/Model.java" />
					<include name="biouml/plugins/simulation/ode/OdeModel.java" />
					<include name="biouml/plugins/simulation/ae/AeModel.java" />
					<include name="biouml/plugins/simulation/ae/NewtonSolver.java" />
					<include name="biouml/plugins/simulation/java/JavaBaseModel.java" />
					<include name="ru/biosoft/math/MathRoutines.java" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.simulation_test" depends="plugin.simulation">
		<echo message="simulation plug-in" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.simulation_test_${VERSION}/simulation_test.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/simulation_test/**/*.*" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.themes" depends="main">
		<echo message="  metal themes" />
		<mkdir dir="${OUTDIR}/themes" />
		<javac srcdir="${PLUGIN_DIR}/plaf.metal_1.5.0/src" destdir="${OUTDIR}/themes" debug="on" deprecation="off" optimize="off">
			<include name="*.java" />
		</javac>

		<jar jarfile="${PLUGIN_DIR}/plaf.metal_1.5.0/themes.jar" compress="true">
			<fileset dir="${OUTDIR}/themes">
				<patternset>
					<include name="*.class" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.ensembl" depends="compile">
		<echo message="  Ensembl plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.ensembl_${VERSION}/ensembl.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/ensembl/**/*.class" />
					<exclude name="biouml/plugins/ensembl/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/ensembl/**/*.gif" />
					<include name="biouml/plugins/ensembl/**/*.jpg" />
					<include name="biouml/plugins/ensembl/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.services" depends="local_settings,compile">
		<echo message="Making services.jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.services_${VERSION}/services.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/services/**/*.class" />
					<exclude name="ru/biosoft/services/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="ru/biosoft/services/**/*.gif" />
					<exclude name="ru/biosoft/services/_test/**/*.*" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.biouml.graph" depends="local_settings,compile">
		<echo message="Making biouml.workbench.graph jar ..." />
		<jar jarfile="${PLUGIN_DIR}/biouml.workbench.graph_${VERSION}/graph.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/workbench/graph/*.class" />
					<exclude name="biouml/workbench/graph/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/workbench/graph/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.biopax" depends="local_settings,compile">
		<echo message=" BioPAX plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.biopax_${VERSION}/biopax.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/biopax/**/*.class" />
					<exclude name="biouml/plugins/biopax/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/biopax/**/*.gif" />
					<include name="biouml/plugins/biopax/**/*.jpg" />
					<include name="biouml/plugins/biopax/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.gne" depends="local_settings,compile">
		<echo message=" GNE plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.gne_${VERSION}/gne.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/gne/**/*.class" />
					<exclude name="biouml/plugins/gne/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/gne/**/*.gif" />
					<include name="biouml/plugins/gne/**/*.jpg" />
					<include name="biouml/plugins/gne/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.uniprot" depends="local_settings,compile">
		<echo message=" UniProt plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.uniprot_${VERSION}/uniprot.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/uniprot/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/uniprot/**/*.gif" />
					<include name="biouml/plugins/uniprot/**/*.jpg" />
					<include name="biouml/plugins/uniprot/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.miriam" depends="local_settings,compile">
		<echo message=" Miriam plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.miriam_${VERSION}/miriam.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/miriam/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/miriam/**/*.gif" />
					<include name="biouml/plugins/miriam/**/*.jpg" />
					<include name="biouml/plugins/miriam/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.obo" depends="local_settings,compile">
		<echo message=" OBO plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.obo_${VERSION}/obo.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/obo/**/*.class" />
					<exclude name="biouml/plugins/obo/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/obo/**/*.gif" />
					<include name="biouml/plugins/obo/**/*.jpg" />
					<include name="biouml/plugins/obo/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.hemodynamics" depends="local_settings,compile">
		<echo message=" Hemodynamics plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.hemodynamics_${VERSION}/hemodynamics.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/hemodynamics/**/*.class" />
					<exclude name="biouml/plugins/hemodynamics/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/hemodynamics/**/*.gif" />
					<include name="biouml/plugins/hemodynamics/**/*.jpg" />
					<include name="biouml/plugins/hemodynamics/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.genehub" depends="plugin.microarray">
		<echo message=" GeneHub plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.genehub_${VERSION}/genehub.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/genehub/**/*.class" />
					<exclude name="biouml/plugins/genehub/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/genehub/**/*.gif" />
					<include name="biouml/plugins/genehub/**/*.jpg" />
					<include name="biouml/plugins/genehub/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.chebi" depends="local_settings,compile">
		<echo message=" ChEBI plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.chebi_${VERSION}/chebi.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/chebi/**/*.class" />
					<exclude name="biouml/plugins/chebi/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/chebi/**/*.gif" />
					<include name="biouml/plugins/chebi/**/*.jpg" />
					<include name="biouml/plugins/chebi/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.psimi" depends="local_settings,compile">
		<echo message=" PSI-MI plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.psimi_${VERSION}/psimi.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/psimi/**/*.class" />
					<exclude name="biouml/plugins/psimi/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/psimi/**/*.gif" />
					<include name="biouml/plugins/psimi/**/*.jpg" />
					<include name="biouml/plugins/psimi/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.sabiork" depends="local_settings,compile">
		<echo message=" SABIO-RK plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.sabiork_${VERSION}/sabiork.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/sabiork/**/*.class" />
					<exclude name="biouml/plugins/sabiork/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/sabiork/**/*.gif" />
					<include name="biouml/plugins/sabiork/**/*.jpg" />
					<include name="biouml/plugins/sabiork/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.kegg" depends="local_settings,compile">
		<echo message="KEGG plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.kegg_${VERSION}/kegg.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/kegg/**/*.class" />
					<exclude name="biouml/plugins/kegg/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/kegg/**/*.gif" />
					<include name="biouml/plugins/kegg/**/*.jpg" />
					<include name="biouml/plugins/kegg/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.analysis" depends="local_settings,compile">
		<echo message="Making analysis.jar ..." />
		<copy todir="${OUTDIR}">
			<fileset dir="${SRCDIR}">
				<include name="ru/biosoft/analysis/resources/*.html" />
			</fileset>
		</copy>
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.analysis_${VERSION}/analysis.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/analysis/**/*.class" />
					<include name="ru/biosoft/analysis/resources/*.html" />
					<exclude name="ru/biosoft/analysis/**/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="ru/biosoft/analysis/**/*.gif" />
					<include name="ru/biosoft/analysis/resources/*.png" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.optimization" depends="local_settings,compile">
		<echo message="Making optimization.jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.analysis.optimization_${VERSION}/optimization.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/analysis/optimization/**/*.class" />
					<exclude name="ru/biosoft/analysis/optimization/**/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="ru/biosoft/analysis/optimization/**/*.gif" />
					<include name="ru/biosoft/analysis/optimization/**/*.html" />
					<include name="ru/biosoft/analysis/optimization/**/*.png" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.optimization.biouml" depends="local_settings,compile">
		<echo message="Making optimization.jar ..." />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.optimization_${VERSION}/optimization.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/optimization/**/*.class" />
					<exclude name="biouml/plugins/optimization/**/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/optimization/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.genenet" depends="local_settings,compile">
		<echo message="GeneNet plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.genenet_${VERSION}/genenet.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/genenet/**/*.class" />
					<exclude name="biouml/plugins/genenet/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/genenet/**/*.gif" />
					<include name="biouml/plugins/genenet/**/*.jpg" />
					<include name="biouml/plugins/genenet/resources/*.html" />
				</patternset>
			</fileset>
		</jar>
		<copy file="${SRCDIR}/biouml/plugins/genenet/license" todir="${PLUGIN_DIR}/biouml.plugins.genenet_${VERSION}/" />
	</target>

	<target name="plugin.jri" depends="local_settings,compile">
		<echo message="JRI plugin" />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.plugins.jri_${VERSION}/jri.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="org/rosuda/JRI/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/plugins/jri/**/*.class" />
					<exclude name="ru/biosoft/plugins/jri/**/_test/**/*.class" />
				</patternset>
			</fileset>
		</jar>
		<antcall target="javadoc.plugin">
			<param name="PLUGIN_PACKAGES" value="ru.biosoft.plugins.jri,ru.biosoft.plugins.jri.protocol,ru.biosoft.plugins.jri.server" />
			<param name="PLUGIN_OUTDIR" value="${PLUGIN_DIR}/ru.biosoft.plugins.jri_${VERSION}/javadoc" />
		</antcall>
	</target>

	<target name="plugin.creasemarks" depends="local_settings,compile">
		<echo message="Making biouml.plugins.creasemarks jar ..." />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.creasemarks_${VERSION}/creasemarks.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/creasemarks/**/*.class" />
					<exclude name="biouml/plugins/creasemarks/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/creasemarks/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.explain" depends="local_settings,compile">
		<echo message="Making biouml.plugins.explain jar ..." />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.explain_${VERSION}/explain.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/explain/*.class" />
					<include name="biouml/plugins/explain/*/*.class" />
					<include name="biouml/plugins/explain/analysis/*/*.class" />
					<exclude name="biouml/plugins/explain/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="biouml/plugins/explain/**/*.gif" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<target name="plugin.endonet" depends="local_settings,compile">
		<echo message=" Endonet plugin" />
		<jar jarfile="${PLUGIN_DIR}/biouml.plugins.endonet_${VERSION}/endonet.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="biouml/plugins/endonet/**/*.class" />
					<exclude name="biouml/plugins/endonet/_test/**/*.class" />
				</patternset>
			</fileset>
		</jar>
	</target>


	<!-- =================================================================== -->
	<!-- Servlets                                                            -->
	<!-- =================================================================== -->
	<target name="server.servlets" depends="local_settings,compile">
		<echo message="Making ru.biosoft.server.servlets jar ..." />
		<jar jarfile="${PLUGIN_DIR}/ru.biosoft.server.servlets_${VERSION}/servlets.jar" compress="true">
			<fileset dir="${OUTDIR}">
				<patternset>
					<include name="ru/biosoft/server/servlets/**/*.class" />
					<exclude name="ru/biosoft/server/servlets/**/_test/**/*.class" />
				</patternset>
			</fileset>
			<fileset dir="${SRCDIR}">
				<patternset>
					<include name="ru/biosoft/server/servlets/**/data/*.txt" />
					<include name="ru/biosoft/server/servlets/**/files/**/*.*" />
				</patternset>
			</fileset>
		</jar>
	</target>

	<!-- =================================================================== -->
	<!-- Server                                                              -->
	<!-- =================================================================== -->

	<target name="deploy.server">

		<!-- Full path to BioUML server repository (for example, "C:/BioUML_Server_0.8.6") -->
		<property name="SERVER_PATH" value="../server/BioUML_Server" />

		<!-- Full path to Tomcat application (for example, "C:\jakarta-tomcat-4.1.30\webapps\biouml") -->
		<property name="TOMCAT_PROJECT_PATH" value="../server/Tomcat_Application/biouml" />

		<ant target="server" />
	</target>

	<target name="server" depends="plugin.all, server.servlets" description="deploys tomcat application, server files and data repository">
		<echo message="Deploying repository..." />

		<property name="WAR_PATH" value="${TOMCAT_PROJECT_PATH}/../biouml.war" />

		<delete dir="${SERVER_PATH}/repo" />
		<copy todir="${SERVER_PATH}/repo">
			<fileset dir="${TOPDIR}/data" includes="default.config" />
		</copy>

		<delete dir="${SERVER_PATH}/resources" />
		<copy todir="${SERVER_PATH}/resources">
			<fileset dir="${TOPDIR}/data_resources">
				<include name="default.config" />
			</fileset>
			<fileset dir="${TOPDIR}/data_resources">
				<include name="graphic notations/**/*" />
				<include name="microarray/**/*" />
				<include name="microarray results/**/*" />
			</fileset>
		</copy>

		<echo message="Deploying conf required for server operations..." />
		<delete dir="${SERVER_PATH}/configuration" />
		<copy todir="${SERVER_PATH}/configuration">
			<fileset dir="${TOPDIR}/configuration" includes="config.ini" />
		</copy>

		<echo message="Deploying plugins required for server operations..." />
		<delete dir="${SERVER_PATH}/plugins" />
		<copy todir="${SERVER_PATH}/plugins">
			<fileset dir="${PLUGIN_DIR}">
				<include name="**/**/*" />
				<include name="*.jar" />
			</fileset>
		</copy>
		<!-- Special properties only for server version -->
		<copy file="${SRCDIR}/ru/biosoft/plugins/jri/server_properties/access.properties" todir="${SERVER_PATH}/plugins/ru.biosoft.plugins.jri_${VERSION}/" />


		<delete file="${WAR_PATH}" />
		<delete dir="${TOMCAT_PROJECT_PATH}" />

		<echo message="Copying classes for war..." />
		<copy todir="${TOMCAT_PROJECT_PATH}/WEB-INF/classes">
			<fileset dir="${OUTDIR}">
				<include name="biouml/launcher/*.class" />
				<include name="ru/biosoft/server/tomcat/ConnectionServlet.class" />
				<include name="ru/biosoft/server/Response.class" />
			</fileset>
		</copy>

		<copy file="${TOPDIR}/startup.jar" tofile="${TOMCAT_PROJECT_PATH}/WEB-INF/lib/startup.jar" />
		<copy file="${TOPDIR}/plugins/org.apache.log4j_1.2.12/log4j-1.2.12.jar" todir="${TOMCAT_PROJECT_PATH}/WEB-INF/lib" />

		<copy file="${TOPDIR}/server.lcf" tofile="${TOMCAT_PROJECT_PATH}/../../bin/server.lcf" />

		<echo message="Parametrizing context and creating war..." />
		<copy file="${TOPDIR}/web.xml" tofile="${TOMCAT_PROJECT_PATH}/web.xml" />
		<replace file="${TOMCAT_PROJECT_PATH}/web.xml" token="@@server.path.absolute@@" value="${SERVER_PATH}" />

		<war warfile="${WAR_PATH}" webxml="${TOMCAT_PROJECT_PATH}/web.xml">
			<fileset dir="${TOMCAT_PROJECT_PATH}">
				<exclude name="web.xml" />
			</fileset>
		</war>

		<echo message="Deploying descriptor..." />

		<echo message="Cleaning up..." />
		<delete dir="${TOMCAT_PROJECT_PATH}" />
	</target>

	<!-- =================================================================== -->
	<!-- Compiles and run regression tests                                   -->
	<!-- =================================================================== -->

	<target name="ctest" depends="prepare,compile">
		<property name="TEST_CLASSPATH" value="${BUILD_CLASSPATH};${JUNIT};${COMMON}" />
		<echo message="Building Tests..." />
		<javac srcdir="${SRCDIR}" destdir="${OUTDIR}" classpath="${TEST_CLASSPATH}" debug="on" deprecation="off" optimize="off">
			<include name="**/_test/*.java" />
			<include name="**/TestProxy.java" />
		</javac>
	</target>

	<target name="rtest" depends="ctest">
		<echo message="Running tests in ${test}...${PLUGIN_DIR}/biouml.plugins.matlab_${VERSION}" />
		<java classname="junit.${testui}.TestRunner" fork="yes">
			<classpath>
				<pathelement path="${RUN_CLASSPATH};${JUNIT};${JUNITX};${ECLIPSE_JARS};${ENSEMBL_JAR};${MYSQL_JAR};${SQLSERVER_JAR};${PLUGIN_DIR}/biouml.plugins.matlab_${VERSION}" />
			</classpath>
			<jvmarg value="-Drepository=${projects.java.dir}/${PROJECT_NAME}/data" />
			<arg value="-noloading" />
			<arg value="${test}" />
		</java>
	</target>

</project>
