Uses of Interface
org.forester.evoinference.matrix.character.CharacterStateMatrix

Packages that use CharacterStateMatrix

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

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

Classes in org.forester.evoinference.matrix.character that implement CharacterStateMatrix

Modifier and Type	Class and Description
class	BasicCharacterStateMatrix<S>

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

Modifier and Type	Method and Description
CharacterStateMatrix<S>	BasicCharacterStateMatrix.copy()
CharacterStateMatrix<S>	CharacterStateMatrix.copy()
CharacterStateMatrix<S>	BasicCharacterStateMatrix.pivot()
CharacterStateMatrix<S>	CharacterStateMatrix.pivot()

Uses of CharacterStateMatrix in org.forester.evoinference.parsimony

Methods in org.forester.evoinference.parsimony that return CharacterStateMatrix

Modifier and Type	Method and Description
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>	SankoffParsimony.getGainLossMatrix()
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>	DolloParsimony.getGainLossMatrix()
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>	FitchParsimony.getGainLossMatrix()
CharacterStateMatrix<STATE_TYPE>	SankoffParsimony.getInternalStatesMatrix()
CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	DolloParsimony.getInternalStatesMatrix()
CharacterStateMatrix<STATE_TYPE>	FitchParsimony.getInternalStatesMatrix()
CharacterStateMatrix<List<STATE_TYPE>>	SankoffParsimony.getInternalStatesMatrixPriorToTraceback() Returns a view of the internal states prior to trace-back.
CharacterStateMatrix<List<STATE_TYPE>>	FitchParsimony.getInternalStatesMatrixPriorToTraceback() Returns a view of the internal states prior to trace-back.

Methods in org.forester.evoinference.parsimony with parameters of type CharacterStateMatrix

Modifier and Type	Method and Description
void	DolloParsimony.execute(Phylogeny p, CharacterStateMatrix<CharacterStateMatrix.BinaryStates> external_node_states_matrix)
void	SankoffParsimony.execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix)
void	FitchParsimony.execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix)
void	FitchParsimony.execute(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix, boolean verbose)

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

Methods in org.forester.io.parsers.nexus that return CharacterStateMatrix

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

Uses of CharacterStateMatrix in org.forester.surfacing

Methods in org.forester.surfacing that return CharacterStateMatrix

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<Integer>	DomainParsimonyCalculator.getGainLossCountsMatrix()
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>	DomainParsimonyCalculator.getGainLossMatrix()
CharacterStateMatrix<CharacterStateMatrix.BinaryStates>	DomainParsimonyCalculator.getInternalStatesMatrix()

Methods in org.forester.surfacing with parameters of type CharacterStateMatrix

Modifier and Type	Method and Description
static void	SurfacingUtil.collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, BinaryDomainCombination.DomainCombinationType dc_type, List<BinaryDomainCombination> all_binary_domains_combination_gained, boolean get_gains)
void	DomainParsimonyCalculator.executeOnGivenBinaryStatesMatrix(CharacterStateMatrix<CharacterStateMatrix.BinaryStates> binary_states_matrix, String[] character_labels)
static void	SurfacingUtil.writeBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, String filename, String indentifier_characters_separator, String character_separator, Map<String,String> descriptions)
static void	SurfacingUtil.writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, String filename, String indentifier_characters_separator, String character_separator, BinaryDomainCombination.OutputFormat bc_output_format)
static void	SurfacingUtil.writeBinaryStatesMatrixToList(Map<String,List<GoId>> domain_id_to_go_ids_map, Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, boolean domain_combinations, CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, String filename, String indentifier_characters_separator, String character_separator, String title_for_html, String prefix_for_html, Map<String,Set<String>>[] domain_id_to_secondary_features_maps, SortedSet<String> all_pfams_encountered, SortedSet<String> pfams_gained_or_lost, String suffix_for_per_node_events_file, Map<String,Integer> tax_code_to_id_map)
static void	SurfacingUtil.writeMatrixToFile(CharacterStateMatrix<?> matrix, String filename, CharacterStateMatrix.Format format)