This class handles reading and storage for the NEXUS block UNALIGNED. More...
#include <nxsunalignedblock.h>
Public Member Functions | |
| NxsUnalignedBlock (NxsTaxaBlockAPI *tb) | |
| virtual | ~NxsUnalignedBlock () |
| NxsCharactersBlock::DataTypesEnum | GetDataType () const |
| NxsCharactersBlock::DataTypesEnum | GetOriginalDataType () const |
| NxsDiscreteStateRow | GetInternalRepresentation (unsigned i, unsigned j) |
| unsigned | GetNTaxWithData () |
| unsigned | GetNTaxTotal () |
| unsigned | GetNTaxTotal () const |
| unsigned | GetNumEquates () |
| unsigned | GetNumMatrixRows () |
| unsigned | GetNumStates (unsigned i, unsigned j) |
| unsigned | NumCharsForTaxon (unsigned i) |
| char | GetMissingSymbol () |
| bool | IsLabels () |
| bool | IsMissingState (unsigned i, unsigned j) |
| bool | IsPolymorphic (unsigned i, unsigned j) |
| bool | IsRespectCase () |
| const char * | GetSymbols () |
| virtual void | DebugShowMatrix (std::ostream &out, const char *marginText=NULL) NCL_COULD_BE_CONST |
| virtual void | Report (std::ostream &out) NCL_COULD_BE_CONST |
| virtual void | Reset () |
| void | SetNexus (NxsReader *nxsptr) |
| void | WriteAsNexus (std::ostream &out) const |
| void | WriteFormatCommand (std::ostream &out) const |
| void | WriteMatrixCommand (std::ostream &out) const |
| virtual VecBlockPtr | GetImpliedBlocks () |
| virtual void | HandleLinkCommand (NxsToken &token) |
| virtual void | WriteLinkCommand (std::ostream &out) const |
Protected Member Functions | |
| bool | IsInSymbols (char ch) |
| void | HandleDimensions (NxsToken &token) |
| void | HandleEndblock (NxsToken &token) |
| virtual void | HandleFormat (NxsToken &token) |
| virtual void | HandleMatrix (NxsToken &token) |
| virtual bool | HandleNextState (NxsToken &token, unsigned taxInd, unsigned charInd, NxsDiscreteStateRow &new_row, const NxsString &) |
| virtual void | Read (NxsToken &token) |
| void | ResetSymbols () |
| std::string | FormatState (NxsDiscreteDatum x) const |
This class handles reading and storage for the NEXUS block UNALIGNED.
It overrides the member functions Read and Reset, which are abstract virtual functions in the base class NxsBlock. > Below is a table showing the correspondence between the elements of an UNALIGNED block in a NEXUS file and the variables and member functions of the NxsUnalignedBlock 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
NTAX ntax GetNTax
FORMAT DATATYPE datatype GetDataType
RESPECTCASE respectingCase IsRespectCase
MISSING missing GetMissingSymbol
SYMBOLS symbols GetSymbols
EQUATE equates GetEquateKey GetEquateValue GetNumEquates
(NO)LABELS labels IsLabels
TAXLABELS taxonLabels GetTaxonLabels
MATRIX matrix GetState GetInternalRepresentation GetNumStates GetNumMatrixRows IsPolymorphic >
Definition at line 68 of file nxsunalignedblock.h.
1.6.3
