SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType > Member List

This is the complete list of members for SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >, including all inherited members.

A (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
alignment (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
allowedInsertDelete (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
B (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
clear() (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
clearAlignment() (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
clearH() (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
debugPrint(bool doPrintH=true) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
direction (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
gapCloseCount (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
gapExtendCount (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
gapOpenCount (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
getSoftClipCount() (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
getSumQ() (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
getSumQBackward() (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
getSumQForward() (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
H (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
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) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
m (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
maxCostPosition (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
maxCostValue (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
MOffset (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
n (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
NOffset (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
populateAlignment() (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
populateH() (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
printH(bool prettyPrint=true) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
qualities (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
rollCigar(CigarRoller &cigar) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
rollCigarBackward(CigarRoller &cigar) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
rollCigarForward(CigarRoller &cigar) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
setAllowedInsertDelete(int allowedInsertDelete=INT_MAX) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
setDirection(int direction) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
setRead(Atype *A) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
setReadLength(int m) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
setReadOffset(readIndexType MOffset) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
setReadQuality(QualityType *qualities) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
setReference(Btype *B) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
setReferenceLength(int n) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
setReferenceOffset(referenceIndexType NOffset) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
SmithWaterman() (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
SmithWaterman(Atype *A, QualityType *qualities, Btype *B, int m, int n, int allowedInsertDelete=INT_MAX, int direction=1, readIndexType MOffset=0, referenceIndexType NOffset=0) (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >	[inline]
w (defined in SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >)	SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >