Example: Use of sparse vector for compressed DNA strings. More...

#include <assert.h>
#include <stdlib.h>
#include <iostream>
#include <vector>
#include <algorithm>
#include <utility>
#include "bm.h"
#include "bmsparsevec.h"
#include "bmsparsevec_algo.h"
#include "bmsparsevec_serial.h"
#include "bmdbg.h"
#include "bmtimer.h"
#include "bmundef.h"

Include dependency graph for xsample06.cpp:

Go to the source code of this file.

Typedefs
typedef bm::sparse_vector< unsigned, bm::bvector<> >	svector_u32
typedef std::vector< char >	vector_char_type
typedef std::vector< std::pair< unsigned, unsigned > >	vector_pairs_type

Functions
unsigned	DNA2int (char DNA_bp)
	Translate DNA letter to integer code Please note this function uses extended alphabet ATGC plus 'N' and '$' Ns are used to indicate ambiguity and $ is part of Burrows-Wheeler transform.
char	int2DNA (unsigned code)
	Translate integer code to DNA letter.
template<typename SV>
void	PrintSV (const SV &sv)
	Print sparse vector.
template<typename SV, typename VECT>
void	TestSV (const SV &sv, const VECT &vect)
	Test sparse vector against reference vector (for QA purposes).
static int	compare_sv (const svector_u32 &sv1, const svector_u32 &sv2)
static int	compare_sv_it (const svector_u32 &sv1, const svector_u32 &sv2)
static void	generate_DNA_vector (svector_u32 &sv, vector_char_type &vect, unsigned sz)
static void	add_centromer_Ns (svector_u32 &sv, vector_char_type &vect, unsigned csz)
static void	generate_big_case (svector_u32 &sv, vector_char_type &vect)
static void	generate_mismatches (vector_pairs_type &vect_m, const vector_char_type &vect, unsigned m_count)
static void	test_mismatch_search (const svector_u32 &sv, const vector_pairs_type &vect_m)
static void	test_vect_mismatch_search (const vector_char_type &vect, const vector_pairs_type &vect_m)
static void	test_strcmp (const vector_char_type &vect, const vector_pairs_type &vect_m)
static void	test_sv_cmp (const svector_u32 &sv, const vector_pairs_type &vect_m)
void	test_sv_cmp_it (const svector_u32 &sv, const vector_pairs_type &vect_m)
int	main (void)

Variables
const unsigned	rep = 20000
bm::chrono_taker ::duration_map_type	timing_map

Detailed Description

Example: Use of sparse vector for compressed DNA strings.

Definition in file xsample06.cpp.

Typedef Documentation

◆ svector_u32

typedef bm::sparse_vector<unsigned, bm::bvector<> > svector_u32

Examples: svsample08.cpp, svsample09.cpp, svsample10.cpp, and xsample06.cpp.

Definition at line 132 of file xsample06.cpp.

◆ vector_char_type

typedef std::vector<char> vector_char_type

Examples: xsample06.cpp, xsample07.cpp, and xsample07a.cpp.

Definition at line 133 of file xsample06.cpp.

◆ vector_pairs_type

typedef std::vector<std::pair<unsigned, unsigned> > vector_pairs_type

Examples: xsample06.cpp.

Definition at line 134 of file xsample06.cpp.

Function Documentation

◆ add_centromer_Ns()

void add_centromer_Ns	(	svector_u32 &	sv,
		vector_char_type &	vect,
		unsigned	csz )

static

Examples: xsample06.cpp.

Definition at line 201 of file xsample06.cpp.

References DNA2int(), and bm::sparse_vector< Val, BV >::size().

Referenced by generate_big_case().

◆ compare_sv()

int compare_sv	(	const svector_u32 &	sv1,
		const svector_u32 &	sv2 )

static

Examples: xsample06.cpp.

Definition at line 141 of file xsample06.cpp.

References bm::sparse_vector_find_first_mismatch().

Referenced by test_sv_cmp().

◆ compare_sv_it()

int compare_sv_it	(	const svector_u32 &	sv1,
		const svector_u32 &	sv2 )

static

Examples: xsample06.cpp.

Definition at line 162 of file xsample06.cpp.

References bm::sparse_vector< Val, BV >::begin(), and bm::sparse_vector< Val, BV >::size().

Referenced by test_sv_cmp_it().

◆ DNA2int()

unsigned DNA2int ( char DNA_bp )

inline

Translate DNA letter to integer code Please note this function uses extended alphabet ATGC plus 'N' and '$' Ns are used to indicate ambiguity and $ is part of Burrows-Wheeler transform.