Class DomainParsimonyCalculator

Method Details

• executeDolloParsimonyOnBinaryDomainCombintionPresence

  public void executeDolloParsimonyOnBinaryDomainCombintionPresence()

• executeDolloParsimonyOnDomainPresence

  public void executeDolloParsimonyOnDomainPresence()

• executeDolloParsimonyOnDomainPresence

  public void executeDolloParsimonyOnDomainPresence(SortedSet<String> positive_filter)

• executeDolloParsimonyOnSecondaryFeatures

  public void executeDolloParsimonyOnSecondaryFeatures(Map<Species,MappingResults> mapping_results_map)

• executeFitchParsimonyOnBinaryDomainCombintion

  public void executeFitchParsimonyOnBinaryDomainCombintion(boolean use_last)

• executeFitchParsimonyOnBinaryDomainCombintion

  public void executeFitchParsimonyOnBinaryDomainCombintion(long random_number_seed)

• executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures

  public void executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures(boolean use_last)

• executeFitchParsimonyOnDomainPresence

  public void executeFitchParsimonyOnDomainPresence(boolean use_last)

• executeFitchParsimonyOnDomainPresence

  public void executeFitchParsimonyOnDomainPresence(long random_number_seed)

• executeOnGivenBinaryStatesMatrix

  public void executeOnGivenBinaryStatesMatrix(CharacterStateMatrix<CharacterStateMatrix.BinaryStates> binary_states_matrix, String[] character_labels)

• getCost

  public int getCost()

• getGainLossCountsMatrix

  public CharacterStateMatrix<Integer> getGainLossCountsMatrix()

• getGainLossMatrix

  public CharacterStateMatrix<CharacterStateMatrix.GainLossStates> getGainLossMatrix()

• getInternalStatesMatrix

  public CharacterStateMatrix<CharacterStateMatrix.BinaryStates> getInternalStatesMatrix()

• getNetGainsOnNode

  public int getNetGainsOnNode(String node_identifier)

• getSumOfGainsOnNode

  public int getSumOfGainsOnNode(String node_identifier)

• getSumOfLossesOnNode

  public int getSumOfLossesOnNode(String node_identifier)

• getSumOfPresentOnNode

  public int getSumOfPresentOnNode(String node_identifier)

• getTotalGains

  public int getTotalGains()

• getTotalLosses

  public int getTotalLosses()

• getTotalUnchanged

  public int getTotalUnchanged()

• getUnitsGainedOnNode

  public SortedSet<String> getUnitsGainedOnNode(String node_identifier)

• getUnitsLostOnNode

  public SortedSet<String> getUnitsLostOnNode(String node_identifier)

• getUnitsOnNode

  public SortedSet<String> getUnitsOnNode(String node_identifier)

• createInstance

  public static DomainParsimonyCalculator createInstance(Phylogeny phylogeny)

• createInstance

  public static DomainParsimonyCalculator createInstance(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list)

• createInstance

  public static DomainParsimonyCalculator createInstance(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list, Map<String,Set<String>> domain_id_to_secondary_features_map)

• createMatrixOfBinaryDomainCombinationPresenceOrAbsence

  public static CharacterStateMatrix<CharacterStateMatrix.BinaryStates> createMatrixOfBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains> gwcd_list)

• createMatrixOfDomainPresenceOrAbsence

  public static CharacterStateMatrix<CharacterStateMatrix.BinaryStates> createMatrixOfDomainPresenceOrAbsence(List<GenomeWideCombinableDomains> gwcd_list, SortedSet<String> positive_filter)

• createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence

  public static CharacterStateMatrix<CharacterStateMatrix.BinaryStates> createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains> gwcd_list, Map<String,String> domain_id_to_second_features_map)