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cbrc::Centroid Class Reference

#include <Centroid.hh>

List of all members.


Detailed Description

(1) Forward and backward algorithm on the DP region given by Xdrop algorithm (2) -centroid decoding

Definition at line 30 of file Centroid.hh.


Public Types

enum  { MAT = 64 }
typedef unsigned char uchar

Public Member Functions

double backward (const uchar *seq1, const uchar *seq2, size_t start1, size_t start2, XdropAligner::direction dir, const GeneralizedAffineGapCosts &gap)
 Centroid (const XdropAligner &xa_, const int sm[MAT][MAT], double T_=1.0)
void chunkProbabilities (std::vector< double > &probs, const std::vector< SegmentPair > &chunks)
void computeExpectedCounts (const uchar *seq1, const uchar *seq2, size_t start1, size_t start2, XdropAligner::direction dir, const GeneralizedAffineGapCosts &gap, ExpectedCount &count) const
double dp (double gamma)
double forward (const uchar *seq1, const uchar *seq2, size_t start1, size_t start2, XdropAligner::direction dir, const GeneralizedAffineGapCosts &gap)
void reset ()
void traceback (std::vector< SegmentPair > &chunks, double gamma) const

Private Types

typedef std::vector
< std::vector< double > > 
dmatrix_t
typedef std::vector< double > dvec_t

Private Member Functions

double cell (const dmatrix_t &matrix, size_t antiDiagonal, size_t seq1pos) const
double diag (const dmatrix_t &matrix, size_t antiDiagonal, size_t seq1pos) const
void initBackwardMatrix ()
void initDecodingMatrix ()
void initForwardMatrix ()
void updateScore (double score, size_t antiDiagonal, size_t cur)

Private Attributes

dmatrix_t bD
size_t bestAntiDiagonal
size_t bestPos1
double bestScore
dmatrix_t bI
dmatrix_t bM
dmatrix_t bP
dmatrix_t fD
dmatrix_t fI
dmatrix_t fM
dmatrix_t fP
size_t lastAntiDiagonal
double match_score [MAT][MAT]
dmatrix_t pp
dvec_t scale
double T
dmatrix_t X
const XdropAligner & xa
double Z

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

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