Uses of Enum Class
org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates
Packages that use CharacterStateMatrix.GainLossStates
Package
Description
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Uses of CharacterStateMatrix.GainLossStates in org.forester.evoinference.matrix.character
Methods in org.forester.evoinference.matrix.character that return CharacterStateMatrix.GainLossStatesModifier and TypeMethodDescriptionReturns the enum constant of this class with the specified name.static CharacterStateMatrix.GainLossStates[]
CharacterStateMatrix.GainLossStates.values()
Returns an array containing the constants of this enum class, in the order they are declared. -
Uses of CharacterStateMatrix.GainLossStates in org.forester.evoinference.parsimony
Methods in org.forester.evoinference.parsimony that return types with arguments of type CharacterStateMatrix.GainLossStatesModifier and TypeMethodDescriptionDolloParsimony.getGainLossMatrix()
FitchParsimony.getGainLossMatrix()
SankoffParsimony.getGainLossMatrix()
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Uses of CharacterStateMatrix.GainLossStates in org.forester.surfacing
Methods in org.forester.surfacing that return types with arguments of type CharacterStateMatrix.GainLossStatesMethods in org.forester.surfacing with parameters of type CharacterStateMatrix.GainLossStatesModifier and TypeMethodDescriptionstatic 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) Method parameters in org.forester.surfacing with type arguments of type CharacterStateMatrix.GainLossStatesModifier and TypeMethodDescriptionstatic void
SurfacingUtil.collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile
(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, BinaryDomainCombination.DomainCombinationType dc_type, List<BinaryDomainCombination> all_binary_domains_combination_gained, boolean get_gains) 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)