This class handles reading and storage for the NEXUS block CHARACTERS. More...
#include <nxscharactersblock.h>
Public Types | |
| enum | DataTypesEnum { , dna, rna, nucleotide, protein, codon, continuous, mixed } |
Public Member Functions | |
| NxsCharactersBlock (NxsTaxaBlockAPI *tb, NxsAssumptionsBlockAPI *ab) | |
| void | SetSupportMixedDatatype (bool v) |
| bool | AugmentedSymbolsToMixed () |
| void | SetConvertAugmentedToMixed (bool v) |
| void | SetAllowAugmentingOfSequenceSymbols (bool v) |
| bool | GetAllowAugmentingOfSequenceSymbols () const |
| std::map< DataTypesEnum, NxsUnsignedSet > | GetDatatypeMapForMixedType () const |
| DataTypesEnum | GetDataType () const |
| bool | TaxonIndHasData (const unsigned ind) const |
| unsigned | GetNCharTotal () const |
| DataTypesEnum | GetOriginalDataType () const |
| unsigned | GetNumActiveChar () NCL_COULD_BE_CONST |
| const NxsUnsignedSet & | GetExcludedIndexSet () const |
| bool | IsActiveChar (unsigned j) const |
| unsigned | ApplyExset (NxsUnsignedSet &exset) |
| unsigned | ApplyIncludeset (NxsUnsignedSet &inset) |
| void | ExcludeCharacter (unsigned i) |
| void | IncludeCharacter (unsigned i) |
| NxsString | GetCharLabel (unsigned i) const |
| bool | HasCharLabels () const |
| GapModeEnum | GetGapModeSetting () const |
| const char * | GetSymbols () NCL_COULD_BE_CONST |
| unsigned | GetNumStates (unsigned i, unsigned j) NCL_COULD_BE_CONST |
| char | GetState (unsigned i, unsigned j, unsigned k=0) const |
| const NxsTransformationManager & | GetNxsTransformationManagerRef () const |
| bool | IsGapState (unsigned taxInd, unsigned charInd) NCL_COULD_BE_CONST |
| bool | IsMissingState (unsigned i, unsigned j) NCL_COULD_BE_CONST |
| bool | IsPolymorphic (unsigned i, unsigned j) NCL_COULD_BE_CONST |
| const NxsDiscreteStateRow & | GetDiscreteMatrixRow (unsigned taxonIndex) const |
| std::vector< const NxsDiscreteDatatypeMapper * > | GetAllDatatypeMappers () const |
| std::vector< double > | GetContinuousValues (unsigned taxIndex, unsigned charIndex, const std::string key) NCL_COULD_BE_CONST |
| std::vector< std::string > | GetItems () const |
| StatesFormatEnum | GetStatesFormat () const |
| void | SetGapModeSetting (GapModeEnum m) |
| NxsDiscreteStateCell | GetInternalRepresentation (unsigned i, unsigned j, unsigned k=0) NCL_COULD_BE_CONST |
| virtual unsigned | GetMaxObsNumStates (bool countMissingStates=true, bool onlyActiveChars=false) NCL_COULD_BE_CONST |
| virtual unsigned | GetNumObsStates (unsigned columnIndex, bool countMissingStates=true) NCL_COULD_BE_CONST |
| std::set< NxsDiscreteStateCell > | GetObsStates (unsigned columnIndex, bool countMissingStates=true) const |
| double | GetSimpleContinuousValue (unsigned i, unsigned j) NCL_COULD_BE_CONST |
| NxsString | GetStateLabel (unsigned charIndex, unsigned charStateIndex) const |
| bool | WasRestrictionDataype () const |
| const char * | GetDatatypeName () const |
| char | GetGapSymbol () const |
| void | SetGapSymbol (char) |
| char | GetMatchcharSymbol () NCL_COULD_BE_CONST |
| char | GetMissingSymbol () const |
| virtual unsigned | CharLabelToNumber (NxsString s) NCL_COULD_BE_CONST |
| virtual unsigned | CharLabelToNumber (const std::string &s) const |
| unsigned | GetIndicesForLabel (const std::string &label, NxsUnsignedSet *inds) const |
| unsigned | GetNumIncludedChars () const |
| unsigned | GetNumEliminated () NCL_COULD_BE_CONST |
| unsigned | GetNChar () const |
| unsigned | GetNumChar () const |
| NxsString | GetStateLabel (unsigned charIndex, unsigned charStateIndex) |
| NxsString | GetTaxonLabel (unsigned i) const |
| bool | IsEliminated (unsigned charIndex) NCL_COULD_BE_CONST |
| bool | IsExcluded (unsigned j) const |
| bool | IsExcluded (unsigned j) |
| virtual unsigned | TaxonLabelToNumber (NxsString s) const |
| virtual bool | AddNewCodonPosPartition (const std::string &label, const NxsPartition &inds, bool isDefault) |
| bool | AddNewIndexSet (const std::string &label, const NxsUnsignedSet &inds) |
| bool | AddNewExSet (const std::string &label, const NxsUnsignedSet &inds) |
| bool | AddNewPartition (const std::string &label, const NxsPartition &inds) |
| void | Consume (NxsCharactersBlock &other) |
| std::set< NxsDiscreteStateCell > | GetNamedStateSetOfColumn (const unsigned colIndex) const |
| std::set< NxsDiscreteStateCell > | GetMaximalStateSetOfColumn (const unsigned colIndex) const |
| virtual void | Report (std::ostream &out) NCL_COULD_BE_CONST |
| void | ShowStateLabels (std::ostream &out, unsigned i, unsigned c, unsigned first_taxon) const |
| void | WriteAsNexus (std::ostream &out) const |
| virtual void | DebugShowMatrix (std::ostream &out, bool use_matchchar, const char *marginText=NULL) const |
| virtual void | WriteLinkCommand (std::ostream &out) const |
| bool | IsInterleave () NCL_COULD_BE_CONST |
| bool | IsLabels () NCL_COULD_BE_CONST |
| bool | IsRespectCase () const |
| bool | IsTokens () NCL_COULD_BE_CONST |
| bool | IsTranspose () NCL_COULD_BE_CONST |
| virtual VecBlockPtr | GetImpliedBlocks () |
| unsigned | GetNumEquates () NCL_COULD_BE_CONST |
| unsigned | GetNumUserEquates () const |
| unsigned | GetNumMatrixCols () NCL_COULD_BE_CONST |
| unsigned | GetNumMatrixRows () NCL_COULD_BE_CONST |
| virtual void | Reset () |
| void | SetNexus (NxsReader *nxsptr) |
| virtual void | HandleLinkCommand (NxsToken &token) |
| virtual std::string | GetDefaultCodonPosPartitionName () const |
Static Public Member Functions | |
| static void | CodonPosPartitionToPosList (const NxsPartition &codonPos, std::list< int > *charIndices) |
| static NxsCharactersBlock * | NewProteinCharactersBlock (const NxsCharactersBlock *codonBlock, bool mapPartialAmbigToUnknown, bool gapToUnknown, const std::vector< NxsDiscreteStateCell > &aaIndices) |
Protected Member Functions | |
| bool | IsInSymbols (char ch) NCL_COULD_BE_CONST |
| void | ShowStates (std::ostream &out, unsigned i, unsigned j) NCL_COULD_BE_CONST |
| void | HandleCharlabels (NxsToken &token) |
| void | HandleCharstatelabels (NxsToken &token) |
| void | HandleDimensions (NxsToken &token, NxsString newtaxaLabel, NxsString ntaxLabel, NxsString ncharLabel) |
| void | HandleEliminate (NxsToken &token) |
| virtual void | HandleFormat (NxsToken &token) |
| virtual void | HandleMatrix (NxsToken &token) |
| bool | HandleNextTokenState (NxsToken &token, unsigned taxNum, unsigned charNum, NxsDiscreteStateRow &row, NxsDiscreteDatatypeMapper &, const NxsDiscreteStateRow *firstTaxonRow, const NxsString &nameStr) |
| void | HandleStatelabels (NxsToken &token) |
| virtual void | HandleStdMatrix (NxsToken &token) |
| virtual void | HandleTransposedMatrix (NxsToken &token) |
| virtual void | Read (NxsToken &token) |
| void | ResetSymbols () |
| void | WriteStates (NxsDiscreteDatum &d, char *s, unsigned slen) NCL_COULD_BE_CONST |
This class handles reading and storage for the NEXUS block CHARACTERS.
It overrides the member functions Read and Reset, which are abstract virtual functions in the base class NxsBlock.
Important change in starting in version 2.1: The ELIMINATE command is now dealt with as if it were an automatic exclude statment. Previous versions of NCL were more in keeping with the NEXUS specification, in that NCL did not store eliminate characters. This resulted in a confusing situation in which the Characters block maintained an original index for a character and a current index. Some public functions of NxsCharactersBlock took arguments that needed the original character index, while the vast majority of methods interpretted a character index as the current index of a character. ELIMINATE commands are *very* rare in modern NEXUS files (Mesquite does not even recognize the command), thus the increased complexity of the API that was caused by not storing ELIMINATED character was deemed a counterproductive. In NCL 2.1 (and later), the characters block stores every character, and the user of NCL can query the NxsCharactersBlock about whether a character has been excluded or not (you can also ask for the set of eliminated chararcters). Optimizations for avoiding excluded characters are no longer the responsibility of NxsCharactersBlock.
Thus, a normal loop through all characters in the data matrix should look something like this: > for(unsigned j = 0; j < nchar; j++) { if (IsExcluded(j)) continue; }
Below is a table showing the correspondence between the elements of a CHARACTERS block in a NEXUS file and the variables and member functions of the NxsCharactersBlock class that can be used to access each piece of information stored. Items in parenthesis should be viewed as "see also" items. > NEXUS Command Data Member Command Atribute Member Functions --------------------------------------------------------------------- DIMENSIONS NEWTAXA newtaxa
NCHAR nChar GetNChar
FORMAT DATATYPE datatype GetDataType
RESPECTCASE respectingCase IsRespectCase
MISSING missing GetMissingSymbol
GAP gap GetGapSymbol
SYMBOLS symbols GetSymbols
EQUATE userEquates GetEquateKey GetEquateValue GetNumEquates
MATCHCHAR matchchar GetMatchcharSymbol
(NO)LABELS labels IsLabels
TRANSPOSE transposing IsTranspose
INTERLEAVE interleaving IsInterleave
ITEMS GetItems
STATESFORMAT GetStatesPresent
(NO)TOKENS tokens IsTokens
ELIMINATE eliminated GetNumEliminated IsExcluded MATRIX matrix GetState GetInternalRepresentation GetNumStates GetNumMatrixRows GetNumMatrixCols IsPolymorphic >
Definition at line 470 of file nxscharactersblock.h.
1.6.3
