MDA
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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) |
The forward and backward algorithms.