NxsUnalignedBlock Class Reference

This class handles reading and storage for the NEXUS block UNALIGNED. More...

#include <nxsunalignedblock.h>

List of all members.

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

Detailed Description

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.

The documentation for this class was generated from the following files:
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Generated on Mon Mar 29 16:37:13 2010 for NCL by  doxygen 1.6.3