BitMagic-C++
Data Structures | Functions | Variables
xsample04a.cpp File Reference

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 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 ()
 
static int parse_args (int argc, char *argv[])
 
static int load_FASTA (const std::string &fname, std::vector< char > &seq_vect)
 
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[])
 

Variables

std::string ifa_name
 
bool is_timing = false
 
unsigned parallel_jobs = 4
 
bm::chrono_taker::duration_map_type timing_map
 

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[] 
)

◆ 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().

Variable Documentation

◆ ifa_name

std::string ifa_name
Examples
xsample04a.cpp.

Definition at line 66 of file xsample04a.cpp.

Referenced by main(), and parse_args().

◆ is_timing

bool is_timing = false
Examples
xsample04a.cpp.

Definition at line 67 of file xsample04a.cpp.

Referenced by main(), and parse_args().

◆ parallel_jobs

unsigned parallel_jobs = 4
Examples
xsample04a.cpp.

Definition at line 68 of file xsample04a.cpp.

Referenced by main(), and parse_args().

◆ timing_map

Examples
xsample04a.cpp.

Definition at line 119 of file xsample04a.cpp.

Referenced by load_FASTA(), and main().