Package org.forester.surfacing
Class DomainParsimonyCalculator
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- org.forester.surfacing.DomainParsimonyCalculator
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public final class DomainParsimonyCalculator extends java.lang.Object
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Method Summary
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Method Detail
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executeDolloParsimonyOnBinaryDomainCombintionPresence
public void executeDolloParsimonyOnBinaryDomainCombintionPresence()
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executeDolloParsimonyOnDomainPresence
public void executeDolloParsimonyOnDomainPresence()
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executeDolloParsimonyOnDomainPresence
public void executeDolloParsimonyOnDomainPresence(java.util.SortedSet<java.lang.String> positive_filter)
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executeDolloParsimonyOnSecondaryFeatures
public void executeDolloParsimonyOnSecondaryFeatures(java.util.Map<Species,MappingResults> mapping_results_map)
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executeFitchParsimonyOnBinaryDomainCombintion
public void executeFitchParsimonyOnBinaryDomainCombintion(boolean use_last)
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executeFitchParsimonyOnBinaryDomainCombintion
public void executeFitchParsimonyOnBinaryDomainCombintion(long random_number_seed)
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executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures
public void executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures(boolean use_last)
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executeFitchParsimonyOnDomainPresence
public void executeFitchParsimonyOnDomainPresence(boolean use_last)
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executeFitchParsimonyOnDomainPresence
public void executeFitchParsimonyOnDomainPresence(long random_number_seed)
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executeOnGivenBinaryStatesMatrix
public void executeOnGivenBinaryStatesMatrix(CharacterStateMatrix<CharacterStateMatrix.BinaryStates> binary_states_matrix, java.lang.String[] character_labels)
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getCost
public int getCost()
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getGainLossCountsMatrix
public CharacterStateMatrix<java.lang.Integer> getGainLossCountsMatrix()
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getGainLossMatrix
public CharacterStateMatrix<CharacterStateMatrix.GainLossStates> getGainLossMatrix()
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getInternalStatesMatrix
public CharacterStateMatrix<CharacterStateMatrix.BinaryStates> getInternalStatesMatrix()
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getNetGainsOnNode
public int getNetGainsOnNode(java.lang.String node_identifier)
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getSumOfGainsOnNode
public int getSumOfGainsOnNode(java.lang.String node_identifier)
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getSumOfLossesOnNode
public int getSumOfLossesOnNode(java.lang.String node_identifier)
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getSumOfPresentOnNode
public int getSumOfPresentOnNode(java.lang.String node_identifier)
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getTotalGains
public int getTotalGains()
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getTotalLosses
public int getTotalLosses()
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getTotalUnchanged
public int getTotalUnchanged()
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getUnitsGainedOnNode
public java.util.SortedSet<java.lang.String> getUnitsGainedOnNode(java.lang.String node_identifier)
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getUnitsLostOnNode
public java.util.SortedSet<java.lang.String> getUnitsLostOnNode(java.lang.String node_identifier)
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getUnitsOnNode
public java.util.SortedSet<java.lang.String> getUnitsOnNode(java.lang.String node_identifier)
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createInstance
public static DomainParsimonyCalculator createInstance(Phylogeny phylogeny)
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createInstance
public static DomainParsimonyCalculator createInstance(Phylogeny phylogeny, java.util.List<GenomeWideCombinableDomains> gwcd_list)
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createInstance
public static DomainParsimonyCalculator createInstance(Phylogeny phylogeny, java.util.List<GenomeWideCombinableDomains> gwcd_list, java.util.Map<java.lang.String,java.util.Set<java.lang.String>> domain_id_to_secondary_features_map)
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createMatrixOfBinaryDomainCombinationPresenceOrAbsence
public static CharacterStateMatrix<CharacterStateMatrix.BinaryStates> createMatrixOfBinaryDomainCombinationPresenceOrAbsence(java.util.List<GenomeWideCombinableDomains> gwcd_list)
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createMatrixOfDomainPresenceOrAbsence
public static CharacterStateMatrix<CharacterStateMatrix.BinaryStates> createMatrixOfDomainPresenceOrAbsence(java.util.List<GenomeWideCombinableDomains> gwcd_list, java.util.SortedSet<java.lang.String> positive_filter)
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createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence
public static CharacterStateMatrix<CharacterStateMatrix.BinaryStates> createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence(java.util.List<GenomeWideCombinableDomains> gwcd_list, java.util.Map<java.lang.String,java.lang.String> domain_id_to_second_features_map)
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