Uses of Class
org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates
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Packages that use CharacterStateMatrix.GainLossStates Package Description org.forester.evoinference.matrix.character org.forester.evoinference.parsimony org.forester.surfacing -
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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()
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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.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)
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