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//////////////////////////////////////////////////////////////////////
// ProbModel.h
//
// Probabilistic model routines
//////////////////////////////////////////////////////////////////////
#ifndef PROBMODEL_H
#define PROBMODEL_H
#include "Assert.h"
#include "Types.h"
#include "AlignedFragment.h"
#include "Score.h"
#include "Sequence.h"
enum STATES {
BEF_X,
BEF_Y,
MATCH,
INS_X,
INS_Y,
AFT_X,
AFT_Y,
NUM_STATES
};
//////////////////////////////////////////////////////////////////////
// Probabilistic model object
//////////////////////////////////////////////////////////////////////
class ProbModel {
double A;
double D;
double E;
double T;
int NUM_TRANS_X;
int NUM_TRANS_Y;
int NUM_TRANS_BOTH;
int TRANSITIONS_EMIT_X[NUM_STATES * NUM_STATES][2];
int TRANSITIONS_EMIT_Y[NUM_STATES * NUM_STATES][2];
int TRANSITIONS_EMIT_BOTH[NUM_STATES * NUM_STATES][2];
SCORE LOG_START[NUM_STATES];
SCORE LOG_FINAL[NUM_STATES];
SCORE LOG_TRANS[NUM_STATES][NUM_STATES];
SCORE LOG_EMIT_2[256][256];
SCORE LOG_EMIT_1[256];
// computing forward/backward recurrences
ScoreMatrix *Forward (const Sequence &sx, const Sequence &sy) const;
ScoreMatrix *Backward (const Sequence &sx, const Sequence &sy) const;
// computing partition coefficient (total probability)
SCORE ComputeTotalProb (const Sequence &sx, const Sequence &sy, const ScoreMatrix &forward, const ScoreMatrix &backward) const;
public:
AlignedFragment * OneAligment(const Sequence &sx, const Sequence &sy, Matrix& trace, ScoreMatrix& m);
ScoreMatrix * Backward (const Sequence &sx, const Sequence &sy, int *map) const;
ScoreMatrix * Forward (const Sequence &sx, const Sequence &sy, int *map) const;
// constructor
ProbModel ();
// posterior probability computation
ScoreMatrix *Posterior (const Sequence &sx, const Sequence &sy, STATES state = NUM_STATES) const;
ScoreMatrix * Posterior (const Sequence &sx, const Sequence &sy, int *map, STATES state = NUM_STATES) const;
//Viterbi decoding
AlignedFragment * Viterbi(const Sequence &sx, const Sequence &sy, int *map);
void ViterbiUpdate(ScoreMatrix *mp, Matrix *pTrace, const Sequence &sx, const Sequence &sy,
int *map, AlignedFragment *frag, int minlength);
SCORE_PAIR * ViterbiInitialize(const Sequence &sx, const Sequence &sy, int *map);
// compute expected sufficient statistics
Matrix *ComputeExpectedCounts (const Sequence &sx, const Sequence &sy) const;
// compute new parameters
void ComputeParams (const Matrix *cts);
};
#endif
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