Uses of Class
org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates
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Packages that use CharacterStateMatrix.BinaryStates Package Description org.forester.evoinference.matrix.character org.forester.evoinference.parsimony org.forester.io.parsers.nexus org.forester.surfacing -
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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 Description static CharacterStateMatrix.BinaryStates
CharacterStateMatrix.BinaryStates. valueOf(java.lang.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 Description CharacterStateMatrix<CharacterStateMatrix.BinaryStates>
DolloParsimony. getInternalStatesMatrix()
Method parameters in org.forester.evoinference.parsimony with type arguments of type CharacterStateMatrix.BinaryStates Modifier and Type Method Description void
DolloParsimony. execute(Phylogeny p, CharacterStateMatrix<CharacterStateMatrix.BinaryStates> external_node_states_matrix)
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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 Description CharacterStateMatrix<CharacterStateMatrix.BinaryStates>
NexusBinaryStatesMatrixParser. getMatrix()
CharacterStateMatrix<CharacterStateMatrix.BinaryStates>
PaupLogParser. parse()
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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 Description static CharacterStateMatrix<CharacterStateMatrix.BinaryStates>
DomainParsimonyCalculator. createMatrixOfBinaryDomainCombinationPresenceOrAbsence(java.util.List<GenomeWideCombinableDomains> gwcd_list)
static CharacterStateMatrix<CharacterStateMatrix.BinaryStates>
DomainParsimonyCalculator. createMatrixOfDomainPresenceOrAbsence(java.util.List<GenomeWideCombinableDomains> gwcd_list, java.util.SortedSet<java.lang.String> positive_filter)
static CharacterStateMatrix<CharacterStateMatrix.BinaryStates>
DomainParsimonyCalculator. createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence(java.util.List<GenomeWideCombinableDomains> gwcd_list, java.util.Map<java.lang.String,java.lang.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 Description void
DomainParsimonyCalculator. executeOnGivenBinaryStatesMatrix(CharacterStateMatrix<CharacterStateMatrix.BinaryStates> binary_states_matrix, java.lang.String[] character_labels)
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