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

Packages that use CharacterStateMatrix.GainLossStates

Package	Description
org.forester.evoinference.matrix.character
org.forester.evoinference.parsimony
org.forester.surfacing

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

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

Modifier and Type	Method	Description
static CharacterStateMatrix.GainLossStates	CharacterStateMatrix.GainLossStates.valueOf(java.lang.String name)	Returns the enum constant of this type with the specified name.
static CharacterStateMatrix.GainLossStates[]	CharacterStateMatrix.GainLossStates.values()	Returns an array containing the constants of this enum type, 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.GainLossStates

Modifier and Type	Method	Description
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>	DolloParsimony.getGainLossMatrix()
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>	FitchParsimony.getGainLossMatrix()
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>	SankoffParsimony.getGainLossMatrix()

Uses of CharacterStateMatrix.GainLossStates in org.forester.surfacing

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

Modifier and Type	Method	Description
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>	DomainParsimonyCalculator.getGainLossMatrix()

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

Modifier and Type	Method	Description
static void	SurfacingUtil.writeBinaryStatesMatrixAsListToFile(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, java.lang.String filename, java.lang.String indentifier_characters_separator, java.lang.String character_separator, java.util.Map<java.lang.String,java.lang.String> descriptions)
static void	SurfacingUtil.writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis(CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, java.lang.String filename, java.lang.String indentifier_characters_separator, java.lang.String character_separator, BinaryDomainCombination.OutputFormat bc_output_format)
static void	SurfacingUtil.writeBinaryStatesMatrixToList(java.util.Map<java.lang.String,java.util.List<GoId>> domain_id_to_go_ids_map, java.util.Map<GoId,GoTerm> go_id_to_term_map, GoNameSpace go_namespace_limit, boolean domain_combinations, CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix, CharacterStateMatrix.GainLossStates state, java.lang.String filename, java.lang.String indentifier_characters_separator, java.lang.String character_separator, java.lang.String title_for_html, java.lang.String prefix_for_html, java.util.Map<java.lang.String,java.util.Set<java.lang.String>>[] domain_id_to_secondary_features_maps, java.util.SortedSet<java.lang.String> all_pfams_encountered, java.util.SortedSet<java.lang.String> pfams_gained_or_lost, java.lang.String suffix_for_per_node_events_file, java.util.Map<java.lang.String,java.lang.Integer> tax_code_to_id_map)

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

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