build.xml

<?xml version="1.0" encoding="UTF-8" ?>

<project name="Smiles2Monomers" default="compile" basedir=".">

	<property name="lib.home"     value="${basedir}/lib"/>
	<property name="build.home"   value="${basedir}/build"/>
	<property name="src.home"     value="${basedir}/src"/>
	<property name="tests.home"   value="${basedir}/tests"/>
	<property name="reports.home" value="${build.home}/reports"/>

	<property name="exec.monomers" value="data/monomers.json"/>
	<property name="exec.learning" value="data/learning.json"/>
	<property name="exec.polymers" value="data/polymers.json"/>
	<property name="exec.rules" value="data/rules.json"/>
	<property name="exec.residues" value="data/residues.json"/>
	<property name="exec.chains" value="data/chains.json"/>
	<property name="jarfile" value="${build.home}/s2m.jar"/>

	<property name="exec.blocSize" value="2"/>
	
	<property name="exec.outfolder" value="${build.home}/results" />

	<path id="compile.classpath">
		<fileset dir="${build.home}/lib">
			<include name="*.jar"/>
		</fileset>
	</path>

	<path id="exec.classpath">
		<fileset dir="${build.home}/lib">
			<include name="*.jar"/>
		</fileset>
		<fileset dir="${build.home}">
			<include name="s2m.jar"/>
		</fileset>
	</path>



	<target name="clean" description="Delete old build and dist directories">
		<delete dir="${build.home}"/>
	</target>



	<target name="prepare" depends="clean">
		<mkdir  dir="${build.home}"/>
		<mkdir  dir="${build.home}/classes"/>
		<mkdir  dir="${build.home}/tests"/>
		<mkdir  dir="${build.home}/reports"/>
		<mkdir  dir="${build.home}/lib"/>
		<mkdir  dir="${exec.outfolder}"/>
	</target>

	<target name="copy" depends="prepare">
		<copy file="${lib.home}/hamcrest-core.jar" tofile="${build.home}/lib/hamcrest-core.jar"/>
		<copy file="${lib.home}/junit.jar" tofile="${build.home}/lib/junit.jar"/>
		<copy file="${lib.home}/libtw.jar" tofile="${build.home}/lib/libtw.jar"/>
		<copy file="${lib.home}/cdk-1.4.19.jar" tofile="${build.home}/lib/cdk.jar"/>
		<copy file="${lib.home}/json-simple-1.1.1.jar" tofile="${build.home}/lib/json.jar"/>
		<copy file="${lib.home}/xerces.jar" tofile="${build.home}/lib/xerces.jar"/>
	</target>



	<target name="compile" depends="copy">
		<javac srcdir="${src.home}" destdir="${build.home}/classes" deprecation="true" includeAntRuntime="no">
			<classpath refid="compile.classpath"/>
		</javac>
	</target>

	<target name="translateSmiles" depends="">
		<java classname="main.PeptidesToCanonicalSmiles" failonerror="true" fork="true">
			<arg value="${file}" />
			<classpath refid="exec.classpath"/>
		</java>
	</target>


	<target name="preCompute" depends="">
		<java classname="main.PreComputation" failonerror="true">
			<jvmarg value="-Xmx4G"/>
			<arg value="-mono" />
			<arg value="${exec.monomers}" />
			<arg value="-rul" />
			<arg value="${exec.rules}" />
			<arg value="-res" />
			<arg value="${exec.residues}" />
			<arg value="-poly" />
			<arg value="${exec.learning}" />
			<arg value="-cha" />
			<arg value="${exec.chains}" />
			<arg value="-markovian" />
			<arg value="${exec.blocSize}" />
			<!--arg value="-v" /-->
			<classpath refid="exec.classpath"/>
		</java>
	</target>

	<target name="s2m" depends="">
		<java classname="main.ProcessPolymers" failonerror="true">
			<arg value="-mono" />
			<arg value="${exec.monomers}" />
			<arg value="-rul" />
			<arg value="${exec.rules}" />
			<arg value="-res" />
			<arg value="${exec.residues}" />
			<arg value="-poly" />
			<arg value="${exec.polymers}" />
			<arg value="-cha" />
			<arg value="${exec.chains}" />
			<arg value="-html" />
			<arg value="-outfolder" />
			<arg value="${exec.outfolder}" />
			<arg value="-v" />
			<classpath refid="exec.classpath"/>
		</java>
	</target>



	<target name="tests_compile" depends="" >
		<javac srcdir="${tests.home}" destdir="${build.home}/tests" includeantruntime="false">
			<classpath>
				<fileset dir="${build.home}/lib">
					<include name="*.jar" />
				</fileset>
				<pathelement path="${build.home}/classes" />
			</classpath>
			<include name="**/*.java"/>
		</javac>
	</target>


	<target name="tests" depends="compile, tests_compile" description="Run JUnits tests to verify program integrity">
		<junit printsummary="true" haltonfailure="false">
			<classpath>
				<fileset dir="${build.home}/lib">
					<include name="*.jar" />
				</fileset>
				<pathelement path="${build.home}/tests" />
				<pathelement path="${build.home}/classes" />
			</classpath>

			<assertions>
				<enable/>
			</assertions>

			<formatter type="xml" usefile="true"/>

			<batchtest>
				<fileset dir="${build.home}/tests">
					<include name="**/*Test*" />
				</fileset>
			</batchtest>
		</junit>

		<move todir="${reports.home}">
			<fileset dir="${basedir}">
				<include name="TEST-*.xml"/>
			</fileset>
		</move>
	</target>


	<target name="create_jar" description="Create executble jar from sourcefiles">
		<jar destfile="${build.home}/s2m.jar"
     basedir="${build.home}/classes"
     includes="**/*.class">
		</jar>
	</target>

</project>