common.cpp File Reference

This file contains common utility functions used in the MSA project. More...

#include <algorithm>
#include <vector>
#include <string>
#include <functional>
#include <stdexcept>
#include "common.h"

Functions
string	getFormat (const string &file, const string &format, const string &name)
	Get format of the given file.
void	keepNonGapPositionsOfQuerySequence (vector< Sequence > &sequences)
	Remove gap positions of the query sequence from all sequences.
string	getAllowedLetters (Alphabet alphabet)
	Return all standard + non-standard + gap letters for the given alphabet.
string	getStandardLetters (Alphabet alphabet)
	Return standard letters of the given alphabet.
string	getNonStandardLetters (Alphabet alphabet)
	Return non-standard letters of the given alphabet.

Detailed Description

This file contains common utility functions used in the MSA project.

Function Documentation

getAllowedLetters()

string getAllowedLetters

(

Alphabet

alphabet

)

Return all standard + non-standard + gap letters for the given alphabet.

gets the list of allowed letters for the provided input alphabet

Parameters

alphabet

Returns

getFormat()

string getFormat	(	const string &	file,
		const string &	format,
		const string &	name )

Get format of the given file.

Parameters

file
format
name

Returns

finalFormat

getNonStandardLetters()

string getNonStandardLetters

(

Alphabet

alphabet

)

Return non-standard letters of the given alphabet.

gets the list of non-standard letters for the provided input alphabet

Parameters

alphabet

Returns

getStandardLetters()

string getStandardLetters

(

Alphabet

alphabet

)

Return standard letters of the given alphabet.

gets the list of standard letters for the provided input alphabet

Parameters

alphabet

Returns

keepNonGapPositionsOfQuerySequence()

void keepNonGapPositionsOfQuerySequence

(

vector< Sequence > &

sequences

)

Remove gap positions of the query sequence from all sequences.

Parameters

sequences