NxsCharactersBlock

AddNewCodonPosPartition AddNewExSet AddNewIndexSet AddNewPartition ApplyExset ApplyIncludeset AugmentedSymbolsToMixed CharLabelToNumber CharLabelToNumber codon CodonPosPartitionToPosList Consume continuous DataTypesEnum DebugShowMatrix dna ExcludeCharacter GetAllDatatypeMappers GetAllowAugmentingOfSequenceSymbols GetCharLabel GetContinuousValues GetDataType GetDatatypeMapForMixedType GetDatatypeName GetDefaultCodonPosPartitionName GetDiscreteMatrixRow GetExcludedIndexSet GetGapModeSetting GetGapSymbol GetImpliedBlocks GetIndicesForLabel GetInternalRepresentation GetItems GetMatchcharSymbol GetMaximalStateSetOfColumn GetMaxObsNumStates GetMissingSymbol GetNamedStateSetOfColumn GetNChar GetNCharTotal GetNumActiveChar GetNumChar GetNumEliminated GetNumEquates GetNumIncludedChars GetNumMatrixCols GetNumMatrixRows GetNumObsStates GetNumStates GetNumUserEquates GetNxsTransformationManagerRef GetObsStates GetOriginalDataType GetSimpleContinuousValue GetState GetStateLabel GetStateLabel GetStatesFormat GetSymbols GetTaxonLabel HandleCharlabels HandleCharstatelabels HandleDimensions HandleEliminate HandleFormat HandleLinkCommand HandleMatrix HandleNextTokenState HandleStatelabels HandleStdMatrix HandleTransposedMatrix HasCharLabels IncludeCharacter IsActiveChar IsEliminated IsExcluded IsExcluded IsGapState IsInSymbols IsInterleave IsLabels IsMissingState IsPolymorphic IsRespectCase IsTokens IsTranspose mixed NewProteinCharactersBlock nucleotide NxsCharactersBlock protein Read Report Reset ResetSymbols rna SetAllowAugmentingOfSequenceSymbols SetConvertAugmentedToMixed SetGapModeSetting SetGapSymbol SetNexus SetSupportMixedDatatype ShowStateLabels ShowStates TaxonIndHasData TaxonLabelToNumber WasRestrictionDataype WriteAsNexus WriteLinkCommand WriteStates

std::set<NxsDiscreteStateCell> NxsCharactersBlock::GetObsStates ( unsigned  columnIndex, bool  countMissingStates = true   ) const [inline] Returns the set of "fundamental" states seen in a column (possibly including the gap "state"). If `countMissingStates` is true then missing data is treated as an observation of each state. If it is false then missing codes do not contribute to the count. Partially ambiguous states result in all states in the cell being counted as observed. columnIndex should be in [0, nchar) Warning: {If countMissingStates is true then it a gap as a state, if countMissingStates is false a gap will count as a state if the gapmode is GAP_MODE_NEWSTATE} Definition at line 769 of file nxscharactersblock.h.