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

NxsDiscreteStateCell NxsCharactersBlock::GetInternalRepresentation ( unsigned  i, unsigned  j, unsigned  k = 0   ) [inline] This function is no longer the most efficient way to access parsed data (see notes on NxsCharacterBlock and GetMatrix() and GetMatrixDecoder() methods. Returns internal representation of the state for taxon `i', character `j'. In the normal situation, `k' is 0 meaning there is only one state with no uncertainty or polymorphism. If there are multiple states, specify a number in the range [0..n) where n is the number of states returned by the GetNumStates function. Use the IsPolymorphic function to determine whether the multiple states correspond to uncertainty in state assignment or polymorphism in the taxon. The value returned from this function is one of the following: ~ o -3 means gap state (see note below) o -2 means missing state (see note below) o an integer 0 or greater is internal representation of a state ~ Note: gap and missing states are actually represented internally in a different way; for a description of the actual internal representation of states, see the documentation for NxsDiscreteDatum. Definition at line 1579 of file nxscharactersblock.h.