org.forester.surfacing
Class DomainParsimonyCalculator
java.lang.Object
org.forester.surfacing.DomainParsimonyCalculator
public final class DomainParsimonyCalculator
- extends Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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)