Uses of Interface
org.forester.evoinference.matrix.character.CharacterStateMatrix
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Packages that use CharacterStateMatrix Package Description org.forester.evoinference.matrix.character org.forester.evoinference.parsimony org.forester.io.parsers.nexus org.forester.surfacing -
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Uses of CharacterStateMatrix in org.forester.evoinference.matrix.character
Classes in org.forester.evoinference.matrix.character that implement CharacterStateMatrix Modifier and Type Class Description class
BasicCharacterStateMatrix<S>
Methods in org.forester.evoinference.matrix.character that return CharacterStateMatrix Modifier and Type Method Description CharacterStateMatrix<S>
BasicCharacterStateMatrix. copy()
CharacterStateMatrix<S>
CharacterStateMatrix. copy()
CharacterStateMatrix<S>
BasicCharacterStateMatrix. pivot()
CharacterStateMatrix<S>
CharacterStateMatrix. pivot()
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Uses of CharacterStateMatrix in org.forester.evoinference.parsimony
Methods in org.forester.evoinference.parsimony that return CharacterStateMatrix Modifier and Type Method Description CharacterStateMatrix<CharacterStateMatrix.GainLossStates>
DolloParsimony. getGainLossMatrix()
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>
FitchParsimony. getGainLossMatrix()
CharacterStateMatrix<CharacterStateMatrix.GainLossStates>
SankoffParsimony. getGainLossMatrix()
CharacterStateMatrix<CharacterStateMatrix.BinaryStates>
DolloParsimony. getInternalStatesMatrix()
CharacterStateMatrix<STATE_TYPE>
FitchParsimony. getInternalStatesMatrix()
CharacterStateMatrix<STATE_TYPE>
SankoffParsimony. getInternalStatesMatrix()
CharacterStateMatrix<java.util.List<STATE_TYPE>>
FitchParsimony. getInternalStatesMatrixPriorToTraceback()
Returns a view of the internal states prior to trace-back.CharacterStateMatrix<java.util.List<STATE_TYPE>>
SankoffParsimony. 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 Description void
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)
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Uses of CharacterStateMatrix in org.forester.io.parsers.nexus
Methods in org.forester.io.parsers.nexus that return CharacterStateMatrix Modifier and Type Method Description CharacterStateMatrix<CharacterStateMatrix.BinaryStates>
NexusBinaryStatesMatrixParser. getMatrix()
CharacterStateMatrix<CharacterStateMatrix.BinaryStates>
PaupLogParser. parse()
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Uses of CharacterStateMatrix in org.forester.surfacing
Methods in org.forester.surfacing with parameters of type CharacterStateMatrix 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)
void
DomainParsimonyCalculator. executeOnGivenBinaryStatesMatrix(CharacterStateMatrix<CharacterStateMatrix.BinaryStates> binary_states_matrix, java.lang.String[] character_labels)
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)
static void
SurfacingUtil. writeMatrixToFile(CharacterStateMatrix<?> matrix, java.lang.String filename, CharacterStateMatrix.Format format)
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