converter.cpp File Reference

MSA File Converter. More...

#include <iostream>
#include <vector>
#include <string>
#include <unordered_map>
#include <algorithm>
#include "flagHandler.h"
#include "msaReader.h"
#include "msaWriter.h"

Functions
int	convert (string inFile, string outFile, string inFormat, string outFormat, bool checkValidation, Alphabet alphabet)
	Convert the format of the input MSA file to the format of the output MSA file.
Alphabet	getAlphabet (FlagHandler &flagHandler)
	Get given alphabet by user.
int	main (int argc, char **argv)

Variables
const char *	docstr
unordered_map< string, FlagInfo >	Flags

Detailed Description

MSA File Converter.

This program converts the format of an input Multiple Sequence Alignment (MSA) file to the format of an output MSA file.

Usage: ./converter –in_file=<input_file> –out_file=<output_file> [options]

Options: –in_file=<input_file> Path to the input MSA file –out_file=<output_file> Path to the output MSA file –alphabet=

Valid alphabet of MSA; alphabet option (0: Protein, 1: RNA, 2: DNA) (default: 0) –check_validation=<true/false> Perform validation on sequences (default: true)

For more comprehensive instructions, please refer to the documentation at https://maryam-haghani.github.io/NEFFy.

Function Documentation

convert()

int convert	(	string	inFile,
		string	outFile,
		string	inFormat,
		string	outFormat,
		bool	checkValidation,
		Alphabet	alphabet )

Convert the format of the input MSA file to the format of the output MSA file.

Parameters

inFile
outFile
inFormat
outFormat
checkValidation
alphabet

Returns

size

getAlphabet()

Alphabet getAlphabet

(

FlagHandler &

flagHandler

)

Get given alphabet by user.

Parameters

flagHandler

Returns

main()

int main	(	int	argc,
		char **	argv )

Variable Documentation

docstr

const char* docstr

Flags

unordered_map<string, FlagInfo> Flags

Initial value:

=
{
    {"in_file", {true, ""}},                
    {"out_file", {true, ""}},               
    {"in_format", {false, ""}},             
    {"out_format", {false, ""}},            
    {"alphabet", {false, "0"}},             
    {"check_validation", {false, "true"}},  
}