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