Uses of Class
org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates

Packages that use CharacterStateMatrix.BinaryStates

Package	Description
org.forester.evoinference.matrix.character
org.forester.evoinference.parsimony
org.forester.io.parsers.nexus
org.forester.surfacing

Uses of CharacterStateMatrix.BinaryStates in org.forester.evoinference.matrix.character

Methods in org.forester.evoinference.matrix.character that return CharacterStateMatrix.BinaryStates

Modifier and Type	Method and Description
static CharacterStateMatrix.BinaryStates	CharacterStateMatrix.BinaryStates.valueOf(String name) Returns the enum constant of this type with the specified name.
static CharacterStateMatrix.BinaryStates[]	CharacterStateMatrix.BinaryStates.values() Returns an array containing the constants of this enum type, in the order they are declared.

Uses of CharacterStateMatrix.BinaryStates in org.forester.evoinference.parsimony

Methods in org.forester.evoinference.parsimony that return types with arguments of type CharacterStateMatrix.BinaryStates

Modifier and Type	Method and Description
CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	DolloParsimony.getInternalStatesMatrix()

Method parameters in org.forester.evoinference.parsimony with type arguments of type CharacterStateMatrix.BinaryStates

Modifier and Type	Method and Description
void	DolloParsimony.execute(Phylogeny p, CharacterStateMatrix<CharacterStateMatrix.BinaryStates> external_node_states_matrix)

Uses of CharacterStateMatrix.BinaryStates in org.forester.io.parsers.nexus

Methods in org.forester.io.parsers.nexus that return types with arguments of type CharacterStateMatrix.BinaryStates

Modifier and Type	Method and Description
CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	NexusBinaryStatesMatrixParser.getMatrix()
CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	PaupLogParser.parse()

Uses of CharacterStateMatrix.BinaryStates in org.forester.surfacing

Methods in org.forester.surfacing that return types with arguments of type CharacterStateMatrix.BinaryStates

Modifier and Type	Method and Description
static CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	DomainParsimonyCalculator.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains> gwcd_list)
static CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence(List<GenomeWideCombinableDomains> gwcd_list, SortedSet<String> positive_filter)
static CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	DomainParsimonyCalculator.createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence(List<GenomeWideCombinableDomains> gwcd_list, Map<String,String> domain_id_to_second_features_map)
CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	DomainParsimonyCalculator.getInternalStatesMatrix()

Method parameters in org.forester.surfacing with type arguments of type CharacterStateMatrix.BinaryStates

Modifier and Type	Method and Description
void	DomainParsimonyCalculator.executeOnGivenBinaryStatesMatrix(CharacterStateMatrix<CharacterStateMatrix.BinaryStates> binary_states_matrix, String[] character_labels)