Collaboration diagram for SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >:

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Classes
struct	weight
Public Member Functions
void	clearAlignment ()
void	clear ()
	SmithWaterman (Atype A, QualityType qualities, Btype *B, int m, int n, int allowedInsertDelete=INT_MAX, int direction=1, readIndexType MOffset=0, referenceIndexType NOffset=0)
void	setRead (Atype *A)
void	setReadQuality (QualityType *qualities)
void	setReference (Btype *B)
void	setReadLength (int m)
void	setReadOffset (readIndexType MOffset)
void	setReferenceLength (int n)
void	setReferenceOffset (referenceIndexType NOffset)
void	setAllowedInsertDelete (int allowedInsertDelete=INT_MAX)
void	setDirection (int direction)
void	clearH ()
void	populateH ()
void	printH (bool prettyPrint=true)
void	debugPrint (bool doPrintH=true)
void	populateAlignment ()
int	getSumQ ()
int	getSumQForward ()
int	getSumQBackward ()
void	rollCigarForward (CigarRoller &cigar)
void	rollCigarBackward (CigarRoller &cigar)
int	getSoftClipCount ()
void	rollCigar (CigarRoller &cigar)
bool	localAlignment (uint32_t bandSize, Atype &read, readIndexType readLength, QualityType &quality, Btype &reference, referenceIndexType referenceLength, referenceIndexType referenceOffset, CigarRoller &cigarRoller, uint32_t &softClipCount, referenceIndexType &cigarStartingPoint, int &sumQ)
Public Attributes
HCellType	H [maxReadLengthH][maxReferenceLengthH]
Atype *	A
Btype *	B
QualityType *	qualities
int	m
int	n
readIndexType	MOffset
referenceIndexType	NOffset
weight	w
int	allowedInsertDelete
int	direction
int	gapOpenCount
int	gapCloseCount
int	gapExtendCount
vector< pair< int, int > >	alignment
HCellType	maxCostValue
pair< int, int >	maxCostPosition

Detailed Description

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>
class SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >

Definition at line 127 of file SmithWaterman.h.

The documentation for this class was generated from the following file:

general/SmithWaterman.h

Classes

Public Member Functions

Public Attributes

Detailed Description