<commit_before><commit_msg>test file for sequence generator dr.app.SequenceSimulator<commit_after><?xml version="1.0" standalone="yes"?>
<!-- $Id:  $ -->
<!-- Tests the sequence simulator -->

<beast>

	<!-- The list of taxa analyse (can also include dates/ages).                 -->
	<!-- ntax=6                                                                  -->
	<taxa id="taxa1">
		<taxon id="human"/>
		<taxon id="chimp"/>
		<taxon id="bonobo"/>
		<taxon id="gorilla"/>
		<taxon id="orangutan"/>
		<taxon id="siamang"/>
	</taxa>

	<tree id="treeML" units="years" usingDates="false">
		<node height="0.099582">
			<node height="0.069125">
				<node height="0.036038">
					<node height="0.024003">
						<node height="0.000000">
							<taxon idref="human"/>
						</node>
						<node height="0.010772">
							<node height="0.000000">
								<taxon idref="chimp"/>
							</node>
							<node height="0.000000">
								<taxon idref="bonobo"/>
							</node>
						</node>
					</node>
					<node height="0.000000">
						<taxon idref="gorilla"/>
					</node>
				</node>
				<node height="0.000000">
					<taxon idref="orangutan"/>
				</node>
			</node>
			<node height="0.000000">
				<taxon idref="siamang"/>
			</node>
		</node>
	</tree>

    <!-- JC -->

	<hkyModel id="jc69">
		<frequencies>
			<frequencyModel dataType="nucleotide">
				<frequencies>
					<parameter dimension="4" value="0.25 0.25 0.25 0.25"/>
				</frequencies>
			</frequencyModel>
		</frequencies>
		<kappa>
			<parameter id="jc69.kappa" value="1.0" lower="0.0" upper="100.0"/>
		</kappa>
	</hkyModel>

	<siteModel id="siteModel1">
		<substitutionModel>
			<hkyModel idref="jc69"/>
		</substitutionModel>
		<mutationRate>
			<parameter id="siteModel1.mu" value="1.0" lower="0.0"/>
		</mutationRate>
	</siteModel>

	<report>
		<sequenceSimulator id="myAlignment" replications='10000'>
			<tree idref="treeML"/>
			<siteModel idref="siteModel1"/>
		</sequenceSimulator>
	</report>
	
	<patterns id="myPatterns">
		<sequenceSimulator idref="myAlignment"/>
	</patterns>
	
	<treeModel id="treeModel1">
		<tree idref="treeML"/>
		<rootHeight>
			<parameter id="treeModel1.rootHeight"/>
		</rootHeight>
		<nodeHeights internalNodes="true">
			<parameter id="treeModel1.internalNodeHeights"/>
		</nodeHeights>
		<nodeHeights internalNodes="true" rootNode="true">
			<parameter id="treeModel1.allInternalNodeHeights"/>
		</nodeHeights>
	</treeModel>
	
	<treeLikelihood id="treeLikelihood1">
		<patterns idref="myPatterns"/>
		<treeModel idref="treeModel1"/>
		<siteModel idref="siteModel1"/>
	</treeLikelihood>


	<operators id="operators">
		<scaleOperator scaleFactor="0.5" weight="1">
			<parameter idref="jc69.kappa"/>
		</scaleOperator>
	</operators>
	
		<mcmc id="mcmc" chainLength="500000" autoOptimize="true">
		<posterior>
			<likelihood id="likelihood">
			<treeLikelihood idref="treeLikelihood1"/>
			</likelihood>
			<!--<prior>
			
			</prior>-->
		</posterior>
		<operators idref="operators"/>
		<log logEvery="50000">
			<column label="Likelihood" dp="4" width="12">
				<compoundLikelihood idref="likelihood"/>
			</column>
			<column label="Kappa" sf="6" width="12">
				<parameter idref="jc69.kappa"/>
			</column>
		</log>
		<log logEvery="1000" fileName="testSimulation.log">
			<compoundLikelihood idref="likelihood"/>			
			<parameter idref="jc69.kappa"/>
		</log>
	</mcmc>

	<report>
		<property name="timer">
			<object idref="mcmc"/>
		</property>
	</report>

	<traceAnalysis fileName="testSimulation.log"/>
		
</beast>
	
{'fraction_non_alphanumeric': 0.18943481965350753, 'fraction_numerical': 0.0448736154501562, 'mean_word_length': 3.2484921592279856, 'pattern_counts': {'":': 0, '<': 129, '<?xml version=': 1, '>': 129, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 1}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6418997', 'n_tokens_mistral': 1589, 'n_tokens_neox': 1248, 'n_words': 230}