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