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fw_bw.hpp File Reference

The forward and backward algorithms. More...

#include <cstdlib>
#include <cfloat>
#include <cmath>
#include <algorithm>
#include <utility>
#include <stack>
#include <vector>
#include "HMM.hpp"
#include "Library.hpp"
#include "../utils/fast_math.hpp"
#include "../utils/Matrix.hpp"

Go to the source code of this file.

Classes

struct  MDAT::hmm_match
 

Namespaces

namespace  MDAT
 The general namespace of this project.
 

Functions

template<typename DataType >
float MDAT::hmm_forward (const DataType &seq1, const DataType &seq2, const HMM &hmm, Matrix< float > &dp_mat, float **insert_matrices)
 
float MDAT::hmm_forward (const HMM &hmm, std::vector< float > &ins_probs1, std::vector< float > &ins_probs2, Matrix< float > &match_probs, Matrix< float > &dp_mat, float **insert_matrices)
 
template<typename DataType >
float MDAT::hmm_backward (const DataType &seq1, const DataType &seq2, const HMM &hmm, Matrix< float > &dp_mat, float **insert_matrices)
 
float MDAT::hmm_backward (const HMM &hmm, std::vector< float > &ins_probs1, std::vector< float > &ins_probs2, Matrix< float > &match_probs, Matrix< float > &dp_mat, float **insert_matrices)
 
template<typename DataType , typename LibraryDataType >
void MDAT::hmm2lib (const DataType &seq1, const DataType &seq2, const Matrix< float > &forward_mat, const Matrix< float > &backward_mat, Library< LibraryDataType > &lib, float total_probability)
 
template<typename LibraryType >
void MDAT::hmm2lib (const Sequence &seq1, int id1, const Sequence &seq2, int id2, const Matrix< float > &forward_mat, const Matrix< float > &backward_mat, Library< LibraryType > &lib, float total_probability)
 
template<typename DataType >
void MDAT::all_hmm_pairs (const std::vector< DataType > &set, Library< std::vector< DataType > > &lib, Matrix< float > &dist_mat, size_t start, size_t end)
 Calculates all hmm pairs inside the given limit. More...
 
template<typename DataType >
void MDAT::all_hmm_pairs (const std::vector< DataType > &set, Library< std::vector< DataType > > &lib, Matrix< float > &dist_mat)
 
template<typename DataType >
void MDAT::all_hmm_pairs (const DataType &set, Library< DataType > &lib, Matrix< float > &dist_mat)
 
template<typename DataType , typename LibraryType >
void MDAT::all_hmm_pairs (const DataType &set, Library< LibraryType > &lib, Matrix< float > &dist_mat, size_t start, size_t end)
 

Detailed Description

The forward and backward algorithms.