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consistency_aln.hpp File Reference

Alignment functions to be used in the consistency approach. More...

#include <string>
#include <algorithm>
#include <utility>
#include "Library.hpp"
#include "../utils/MatrixStack.hpp"
#include "../clustering/Tree.hpp"

Go to the source code of this file.

Namespaces

namespace  MDAT
 The general namespace of this project.
 

Functions

void MDAT::nw_dyn_consistency (size_t dim1, size_t dim2, Matrix< std::pair< int, char > > &matrix)
 This is a special version of the Needleman-Wunsch algorithm for consistency chaining. More...
 
void MDAT::nw_dyn_consistency_traceback (size_t i, size_t j, const Matrix< std::pair< int, char > > &matrix, std::string &edit_string1, std::string &edit_string2)
 Traceback for the nw_dyn_consistency algorithm. More...
 
void MDAT::gotoh_dyn_consistency (int dim1, int dim2, MatrixStack< 3, std::pair< int, char > > &matrices, int gop, int gep)
 Calculation of pairwise alignment. More...
 
void MDAT::gotoh_dyn_consistency_traceback (size_t i, size_t j, MatrixStack< 3, std::pair< int, char > > &matrices, std::string &edit_string1, std::string &edit_string2)
 Traceback for the gotoh_dyn_consistency algorithm. More...
 
template<typename DataType >
void MDAT::enterDataIntoMatrix (Matrix< std::pair< DataType, char > > &matrix, size_t dim1, size_t dim2, const std::map< Match, DataType > &match_points)
 
template<typename DataType , typename GapFunction >
void MDAT::progressive_consistency_align (const Library< DataType > &lib, Tree &guide_tree, DataType &set, GapFunction gap_func)
 Produces a progressive alignment of a dataset. More...
 

Detailed Description

Alignment functions to be used in the consistency approach.