BitMagic-C++: xsample04a.cpp File Reference

BitMagic-C++

Example: DNA index construction. More...

#include <iostream>
#include <sstream>
#include <regex>
#include <time.h>
#include <stdio.h>
#include <stdexcept>
#include <memory>
#include <vector>
#include <future>
#include <thread>
#include <mutex>
#include "bm.h"
#include "bmdbg.h"
#include "bmtimer.h"
#include "bmundef.h"

Include dependency graph for xsample04a.cpp:

Go to the source code of this file.

Data Structures
class	DNA_FingerprintScanner
	Utility for keeping all DNA finger print vectors and search using various techniques. More...

Functions
static void	show_help ()
	More...

static int	parse_args (int argc, char *argv[])
	More...

static int	load_FASTA (const std::string &fname, std::vector< char > &seq_vect)
	More...

static void	fingerprint_compare (const DNA_FingerprintScanner &idx1, const DNA_FingerprintScanner &idx2)
	Check correctness of indexes constructed using different methods. More...

int	main (int argc, char *argv[])
	More...

Variables
std::string	ifa_name
	More...

bool	is_timing = false
	More...

unsigned	parallel_jobs = 4
	More...

bm::chrono_taker ::duration_map_type	timing_map
	More...

Detailed Description

Example: DNA index construction.

Definition in file xsample04a.cpp.

Function Documentation

◆ fingerprint_compare()

static void fingerprint_compare	(	const DNA_FingerprintScanner &	idx1,
		const DNA_FingerprintScanner &	idx2
	)

static

Check correctness of indexes constructed using different methods.

Examples: xsample04a.cpp.

Definition at line 398 of file xsample04a.cpp.

References bm::bvector< Alloc >::compare(), and DNA_FingerprintScanner::GetVector().

Referenced by main().

◆ load_FASTA()

static int load_FASTA	(	const std::string &	fname,
		std::vector< char > &	seq_vect
	)

static

Examples: xsample04a.cpp.

Definition at line 123 of file xsample04a.cpp.

References timing_map.

Referenced by main().

◆ main()

int main	(	int	argc,
		char *	argv[]
	)

Examples: xsample04a.cpp.

Definition at line 417 of file xsample04a.cpp.

References DNA_FingerprintScanner::Build(), DNA_FingerprintScanner::BuildParallel(), fingerprint_compare(), ifa_name, is_timing, load_FASTA(), parallel_jobs, parse_args(), bm::chrono_taker< TOut >::print_duration_map(), show_help(), and timing_map.

◆ parse_args()

static int parse_args	(	int	argc,
		char *	argv[]
	)

static

Examples: xsample04a.cpp.

Definition at line 71 of file xsample04a.cpp.

References ifa_name, is_timing, parallel_jobs, and show_help().

Referenced by main().

◆ show_help()

static void show_help ( )

static

Examples: xsample04a.cpp.

Definition at line 51 of file xsample04a.cpp.

Referenced by main(), and parse_args().