solutions.h File Reference

#include <map>
#include <iostream>
#include <array>
#include <string>
#include <limits>
#include <fstream>
#include <iomanip>
#include <complex>
#include <set>

Go to the source code of this file.

Namespaces
	SolutionUtils
	SolutionUtils::Profile

Functions
template<int ALPHABET_SIZE>
float	SolutionUtils::Profile::score_mult (const std::array< int, ALPHABET_SIZE > &query, const std::array< int, ALPHABET_SIZE > &reference, const std::array< std::array< float, ALPHABET_SIZE >, ALPHABET_SIZE > &A)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>
void	profile_alignment_solution (std::vector< std::array< int, 5 >> query, std::vector< std::array< int, 5 >> reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, std::vector< char > &alignments)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>
void	global_linear_solution (std::string query, std::string reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, map< string, string > &alignments)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS, int SOL_BANDWIDTH>
void	fixed_banding_global_linear_solution (std::string query, std::string reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, map< string, string > &alignments)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>
void	global_affine_solution (std::string query, std::string reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< string, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, map< string, string > &alignments)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>
void	local_linear_solution (std::string query, std::string reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, map< string, string > &alignments)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>
void	local_affine_solution (std::string query, std::string reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< string, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, map< string, string > &alignments)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>
void	semi_global_linear_long_short_solution (std::string query, std::string reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, map< string, string > &alignments)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>
void	semi_global_linear_short_long_solution (std::string query, std::string reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, map< string, string > &alignments)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>
void	overlap_linear_prefix_suffix_solution (std::string query, std::string reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, map< string, string > &alignments)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>
void	overlap_linear_suffix_prefix_solution (std::string query, std::string reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, map< string, string > &alignments)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>
void	local_two_piece_affine_solution (std::string query, std::string reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< string, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, map< string, string > &alignments)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>
void	global_dtw_solution (std::vector< std::complex< float >> query, std::vector< std::complex< float >> reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< string, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, map< string, string > &alignments)
template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>
void	global_two_piece_affine_solution (std::string query, std::string reference, PENALTY_T &penalties, array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &score_mat, array< array< string, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &tb_mat, map< string, string > &alignments)
template<typename T , int M, int N>
void	print_matrix (array< array< T, N >, M > &mat, string name, std::set< std::tuple< int, int, int >> incorrect_coordinates, int layer_k)
template<typename T , int M, int N>
void	fprint_matrix (ofstream &file, array< array< T, N >, M > &mat, string name)
template<typename T , int M, int N>
void	fprint_matrix (ofstream &file, array< array< T, N >, M > &mat, string query, string reference, string name)
template<typename T , int N>
void	print_vector (array< T, N > &vec, string name)

Function Documentation

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS, int SOL_BANDWIDTH>

void fixed_banding_global_linear_solution	(	std::string	query,
		std::string	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		map< string, string > &	alignments
	)

template<typename T , int M, int N>

void fprint_matrix	(	ofstream &	file,
		array< array< T, N >, M > &	mat,
		string	name
	)

template<typename T , int M, int N>

void fprint_matrix	(	ofstream &	file,
		array< array< T, N >, M > &	mat,
		string	query,
		string	reference,
		string	name
	)

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>

void global_affine_solution	(	std::string	query,
		std::string	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< string, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		map< string, string > &	alignments
	)

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>

void global_dtw_solution	(	std::vector< std::complex< float >>	query,
		std::vector< std::complex< float >>	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< string, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		map< string, string > &	alignments
	)

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>

void global_linear_solution	(	std::string	query,
		std::string	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		map< string, string > &	alignments
	)

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>

void global_two_piece_affine_solution	(	std::string	query,
		std::string	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< string, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		map< string, string > &	alignments
	)

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>

void local_affine_solution	(	std::string	query,
		std::string	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< string, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		map< string, string > &	alignments
	)

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>

void local_linear_solution	(	std::string	query,
		std::string	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		map< string, string > &	alignments
	)

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>

void local_two_piece_affine_solution	(	std::string	query,
		std::string	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< string, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		map< string, string > &	alignments
	)

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>

void overlap_linear_prefix_suffix_solution	(	std::string	query,
		std::string	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		map< string, string > &	alignments
	)

Overlap case 1: query and ref are reads, align prefix of ref with suffix of query

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>

void overlap_linear_suffix_prefix_solution	(	std::string	query,
		std::string	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		map< string, string > &	alignments
	)

Overlap case 2: query and ref are reads, align suffix of ref with prefix of query

template<typename T , int M, int N>

void print_matrix	(	array< array< T, N >, M > &	mat,
		string	name,
		std::set< std::tuple< int, int, int >>	incorrect_coordinates,
		int	layer_k
	)

template<typename T , int N>

void print_vector	(	array< T, N > &	vec,
		string	name
	)

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>

void profile_alignment_solution	(	std::vector< std::array< int, 5 >>	query,
		std::vector< std::array< int, 5 >>	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		std::vector< char > &	alignments
	)

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>

void semi_global_linear_long_short_solution	(	std::string	query,
		std::string	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		map< string, string > &	alignments
	)

Semi-global case 1: aligning a long query sequence with a short reference sequence

template<typename PENALTY_T , int SOL_MAX_QUERY_LENGTH, int SOL_MAX_REFERENCE_LENGTH, int SOL_N_LAYERS>

void semi_global_linear_short_long_solution	(	std::string	query,
		std::string	reference,
		PENALTY_T &	penalties,
		array< array< array< float, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH >, SOL_N_LAYERS > &	score_mat,
		array< array< char, SOL_MAX_REFERENCE_LENGTH >, SOL_MAX_QUERY_LENGTH > &	tb_mat,
		map< string, string > &	alignments
	)

Semi-global case 2: aligning a short query sequence with a long query sequence