Uses of Interface
org.forester.evoinference.matrix.character.CharacterStateMatrix
Packages that use CharacterStateMatrix
Package
Description
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Uses of CharacterStateMatrix in org.forester.evoinference.matrix.character
Classes in org.forester.evoinference.matrix.character that implement CharacterStateMatrixMethods in org.forester.evoinference.matrix.character that return CharacterStateMatrix -
Uses of CharacterStateMatrix in org.forester.evoinference.parsimony
Methods in org.forester.evoinference.parsimony that return CharacterStateMatrixModifier and TypeMethodDescriptionDolloParsimony.getGainLossMatrix()
FitchParsimony.getGainLossMatrix()
SankoffParsimony.getGainLossMatrix()
DolloParsimony.getInternalStatesMatrix()
FitchParsimony.getInternalStatesMatrix()
SankoffParsimony.getInternalStatesMatrix()
FitchParsimony.getInternalStatesMatrixPriorToTraceback()
Returns a view of the internal states prior to trace-back.SankoffParsimony.getInternalStatesMatrixPriorToTraceback()
Returns a view of the internal states prior to trace-back.Methods in org.forester.evoinference.parsimony with parameters of type CharacterStateMatrixModifier and TypeMethodDescriptionvoid
DolloParsimony.execute
(Phylogeny p, CharacterStateMatrix<CharacterStateMatrix.BinaryStates> 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) void
SankoffParsimony.execute
(Phylogeny p, CharacterStateMatrix<STATE_TYPE> external_node_states_matrix) -
Uses of CharacterStateMatrix in org.forester.io.parsers.nexus
Methods in org.forester.io.parsers.nexus that return CharacterStateMatrix -
Uses of CharacterStateMatrix in org.forester.surfacing
Methods in org.forester.surfacing that return CharacterStateMatrixModifier and TypeMethodDescriptionDomainParsimonyCalculator.createMatrixOfBinaryDomainCombinationPresenceOrAbsence
(List<GenomeWideCombinableDomains> gwcd_list) DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence
(List<GenomeWideCombinableDomains> gwcd_list, SortedSet<String> positive_filter) DomainParsimonyCalculator.createMatrixOfSecondaryFeatureBinaryDomainCombinationPresenceOrAbsence
(List<GenomeWideCombinableDomains> gwcd_list, Map<String, String> domain_id_to_second_features_map) DomainParsimonyCalculator.getGainLossCountsMatrix()
DomainParsimonyCalculator.getGainLossMatrix()
DomainParsimonyCalculator.getInternalStatesMatrix()
Methods in org.forester.surfacing with parameters of type CharacterStateMatrixModifier and TypeMethodDescriptionstatic 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)