org.forester.surfacing

Class DomainParsimonyCalculator

java.lang.Object

org.forester.surfacing.DomainParsimonyCalculator

public final class DomainParsimonyCalculator
extends Object

Method Summary

Modifier and Type	Method and Description
static DomainParsimonyCalculator	createInstance(Phylogeny phylogeny)
static DomainParsimonyCalculator	createInstance(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list)
static DomainParsimonyCalculator	createInstance(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list, Map<String,Set<String>> domain_id_to_secondary_features_map)
static CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	createMatrixOfBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains> gwcd_list)
static CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	createMatrixOfDomainPresenceOrAbsence(List<GenomeWideCombinableDomains> gwcd_list, SortedSet<String> positive_filter)
static CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains> gwcd_list, Map<String,String> domain_id_to_second_features_map)
void	executeDolloParsimonyOnBinaryDomainCombintionPresence()
void	executeDolloParsimonyOnDomainPresence()
void	executeDolloParsimonyOnDomainPresence(SortedSet<String> positive_filter)
void	executeDolloParsimonyOnSecondaryFeatures(Map<Species,MappingResults> mapping_results_map)
void	executeFitchParsimonyOnBinaryDomainCombintion(boolean use_last)
void	executeFitchParsimonyOnBinaryDomainCombintion(long random_number_seed)
void	executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures(boolean use_last)
void	executeFitchParsimonyOnDomainPresence(boolean use_last)
void	executeFitchParsimonyOnDomainPresence(long random_number_seed)
void	executeOnGivenBinaryStatesMatrix(CharacterStateMatrix<CharacterStateMatrix.BinaryStates> binary_states_matrix, String[] character_labels)
int	getCost()
CharacterStateMatrix<Integer>	getGainLossCountsMatrix()
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>	getGainLossMatrix()
CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	getInternalStatesMatrix()
int	getNetGainsOnNode(String node_identifier)
int	getSumOfGainsOnNode(String node_identifier)
int	getSumOfLossesOnNode(String node_identifier)
int	getSumOfPresentOnNode(String node_identifier)
int	getTotalGains()
int	getTotalLosses()
int	getTotalUnchanged()
SortedSet<String>	getUnitsGainedOnNode(String node_identifier)
SortedSet<String>	getUnitsLostOnNode(String node_identifier)
SortedSet<String>	getUnitsOnNode(String node_identifier)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

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)