org.forester.surfacing
Class DomainParsimonyCalculator

java.lang.Object
  extended by org.forester.surfacing.DomainParsimonyCalculator

public final class DomainParsimonyCalculator
extends Object


Method Summary
static DomainParsimonyCalculator createInstance(Phylogeny phylogeny)
           
static DomainParsimonyCalculator createInstance(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list)
           
static DomainParsimonyCalculator createInstance(Phylogeny phylogeny, List<GenomeWideCombinableDomains> gwcd_list, Map<DomainId,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<DomainId> positive_filter)
           
 void executeDolloParsimonyOnBinaryDomainCombintionPresence()
           
 void executeDolloParsimonyOnDomainPresence()
           
 void executeDolloParsimonyOnDomainPresence(SortedSet<DomainId> positive_filter)
           
 void executeDolloParsimonyOnSecondaryFeatures(Map<Species,MappingResults> mapping_results_map)
           
 void executeFitchParsimonyOnBinaryDomainCombintion(boolean use_last)
           
 void executeFitchParsimonyOnBinaryDomainCombintion(long random_number_seed)
           
 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<DomainId> 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)

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<DomainId,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<DomainId> positive_filter)