<commit_before><!-- Build BEAST MCMC. It is also used by Hudson BEAST_MCMC project. JUnit test is available for this build. -->
<project basedir="." default="build_all_BEAST" name="BUILD_BEAST_MCMC">
	<description>
		Build BEAST MCMC. It is also used by Hudson BEAST_MCMC project. JUnit test is available for this build.
	    $Id: build_BEAST_MCMC.xml,v 1.5 2009/04/15 <NAME> Exp $
	</description>

	<!-- set global properties for this build -->
	<property name="src" location="src" />
	<property name="build" location="build" />
	<property name="lib" location="lib" />
	<property name="dist" location="build/dist" />

	<property name="main_class_BEAST" value="dr.app.beast.BeastMain" />
	<property name="main_class_BEAUTI" value="dr.app.beauti.BeautiApp" />
	<property name="main_class_TRACER" value="dr.app.tracer.application.TracerApp" />
	<property name="main_class_Annotator" value="dr.app.tools.TreeAnnotator" />
	<property name="main_class_LogCombiner" value="dr.app.tools.LogCombiner" />
	<property name="report"  value="${build}/junitreport"/>

	<path id="classpath">
		<fileset dir="${lib}" includes="**/*.jar"/>
	</path>

	<!-- start -->
	<target name="init">
		<echo message="${ant.project.name}: ${ant.file}" />
	</target>

	<target name="clean">
		<delete dir="bin" />
	</target>

	<!-- clean previous build, and then compile Java source code, and Juint test -->
	<target name="build_all_BEAST" depends="clean,compile-all,junit"
        description="Clean and Build all run-time stuff">
	</target>

	<!-- clean previous build, compile Java source code, and Juint test, and make the beast.jar and beauti.jar -->
	<target name="build_jar_all_BEAST" depends="clean,compile-all,junit,dist_all_BEAST"
        description="Clean and Build all run-time stuff">
	</target>

	<!-- No JUnit Test, clean previous build, compile Java source code, and make the beast.jar and beauti.jar -->
	<target name="build_jar_all_BEAST_NoJUnitTest" depends="clean,compile-all,dist_all_BEAST"
        description="Clean and Build all run-time stuff">
	</target>

	<!-- compile Java source code -->
	<target name="compile-all" depends="init">
		<mkdir dir="${build}" />

		<!-- Compile the java code from ${src} into ${build} /bin -->
		<javac source="1.5" srcdir="${src}" destdir="${build}" classpathref="classpath" 
		       fork="true"
		       memoryinitialsize="256m"
		       memorymaximumsize="256m">
			<include name="dr/app/beast/**" />
			<include name="dr/app/beauti/**" />
			<include name="dr/app/tracer/**"/>
			<include name="dr/app/oldbeauti/**" />
			<include name="dr/app/beagle/**" />
			<include name="dr/app/seqgen/**" />
			<include name="dr/app/tools/**" />
			<include name="dr/app/util/**" />
			<include name="dr/evolution/**" />
			<include name="dr/evomodel/**" />
			<include name="dr/evomodelxml/**" />
			<include name="dr/evoxml/**" />
			<include name="dr/exporters/**" />
			<include name="dr/gui/chart/**" />
			<include name="dr/gui/tree/**" />
			<include name="dr/inference/**" />
			<include name="dr/inferencexml/**"/>
			<include name="dr/math/**" />
			<include name="dr/matrix/**" />
			<include name="dr/stats/**" />
			<include name="dr/util/**" /><commit_msg>Issue 202: Add explicit target of JDK 1.5 to javac to allow building using JDK 1.6 but run on JDK 1.5 machines<commit_after><!-- Build BEAST MCMC. It is also used by Hudson BEAST_MCMC project. JUnit test is available for this build. -->
<project basedir="." default="build_all_BEAST" name="BUILD_BEAST_MCMC">
	<description>
		Build BEAST MCMC. It is also used by Hudson BEAST_MCMC project. JUnit test is available for this build.
	    $Id: build_BEAST_MCMC.xml,v 1.5 2009/04/15 <NAME> Exp $
	</description>

	<!-- set global properties for this build -->
	<property name="src" location="src" />
	<property name="build" location="build" />
	<property name="lib" location="lib" />
	<property name="dist" location="build/dist" />

	<property name="main_class_BEAST" value="dr.app.beast.BeastMain" />
	<property name="main_class_BEAUTI" value="dr.app.beauti.BeautiApp" />
	<property name="main_class_TRACER" value="dr.app.tracer.application.TracerApp" />
	<property name="main_class_Annotator" value="dr.app.tools.TreeAnnotator" />
	<property name="main_class_LogCombiner" value="dr.app.tools.LogCombiner" />
	<property name="report"  value="${build}/junitreport"/>

	<path id="classpath">
		<fileset dir="${lib}" includes="**/*.jar"/>
	</path>

	<!-- start -->
	<target name="init">
		<echo message="${ant.project.name}: ${ant.file}" />
	</target>

	<target name="clean">
		<delete dir="bin" />
	</target>

	<!-- clean previous build, and then compile Java source code, and Juint test -->
	<target name="build_all_BEAST" depends="clean,compile-all,junit"
        description="Clean and Build all run-time stuff">
	</target>

	<!-- clean previous build, compile Java source code, and Junit test, and make the beast.jar and beauti.jar -->
	<target name="build_jar_all_BEAST" depends="clean,compile-all,junit,dist_all_BEAST"
        description="Clean and Build all run-time stuff">
	</target>

	<!-- No JUnit Test, clean previous build, compile Java source code, and make the beast.jar and beauti.jar -->
	<target name="build_jar_all_BEAST_NoJUnitTest" depends="clean,compile-all,dist_all_BEAST"
        description="Clean and Build all run-time stuff">
	</target>

	<!-- compile Java source code -->
	<target name="compile-all" depends="init">
		<mkdir dir="${build}" />

		<!-- Compile the java code from ${src} into ${build} /bin -->
		<javac source="1.5" target="1.5" srcdir="${src}" destdir="${build}" classpathref="classpath" 
		       fork="true"
		       memoryinitialsize="256m"
		       memorymaximumsize="256m">
			<include name="dr/app/beast/**" />
			<include name="dr/app/beauti/**" />
			<include name="dr/app/tracer/**"/>
			<include name="dr/app/oldbeauti/**" />
			<include name="dr/app/beagle/**" />
			<include name="dr/app/seqgen/**" />
			<include name="dr/app/tools/**" />
			<include name="dr/app/util/**" />
			<include name="dr/evolution/**" />
			<include name="dr/evomodel/**" />
			<include name="dr/evomodelxml/**" />
			<include name="dr/evoxml/**" />
			<include name="dr/exporters/**" />
			<include name="dr/gui/chart/**" />
			<include name="dr/gui/tree/**" />
			<include name="dr/inference/**" />
			<include name="dr/inferencexml/**"/>
			<include name="dr/math/**" />
			<include name="dr/matrix/**" />
			<include name="dr/stats/**" />
			<include name="dr/util/**" />
{'fraction_non_alphanumeric': 0.18842364532019704, 'fraction_numerical': 0.007235221674876847, 'mean_word_length': 3.9709257842387147, 'pattern_counts': {'":': 0, '<': 125, '<?xml version=': 0, '>': 125, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 8}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2807120', 'n_tokens_mistral': 2330, 'n_tokens_neox': 2157, 'n_words': 512}