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

bool NxsCharactersBlock::AugmentedSymbolsToMixed (  )  If you say FORMAT DATATYPE=DNA SYMBOLS="01" ; then the valid symbols become "ACGT01". Returns: true if a sequence type will be converted to standard (default block would return false). the "setter" function is NxsCharactersBlock::SetConvertAugmentedToMixed() Dealing with Datatype=Mixed AugmentedSymbolsToMixed tries to split such a matrix into a datatype=mixed(dna:charset_dna,standard:charset_std) by inferring the charpartition (charset_dna,charset_std). It does this by using GetNamedStateSetOfColumn to detect which states were listed in a column. Returns true if the translation to mixed was performed. This will only occur if GetOriginalDataType() != GetDataType() because this is the symptom that there was symbol augmentation of a built in datatype. Note that in the GetNamedStateSetOfColumn then ? will not expand the states present in a symbol. Thus when parsing: Matrix 1: Matrix 2: s ACGT10{ACGT01-} s ACGT10? t ACGT100 t ACGT100 The last character of the first taxon would be parsed as having the potential to have states {ACGT01-}. But when interperted with GetNamedStateSetOfColumn, Matrix 2 can be "explained" by four DNA columns, and three Standard (01) columns. Matrix 1, on the other hand would be found to have four DNA columns, and two Standard (01) columns, and one standard ("ACGT01") column. Note: this function ignores the gap mode setting and treats gaps as newstates for the purposes of the conversion. Temporary: Will return false if userDefinedEquatesBeforeConversion is true Definition at line 1606 of file nxscharactersblock.cpp.