common.h File Reference

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

#include <vector>
#include <string>

Go to the source code of this file.

Classes
struct	Sequence

Enumerations
enum	Normalization { Sqrt_L = 0 , L , None }
enum	Alphabet { protein = 0 , RNA , DNA }
enum	NonStandardHandler { AsStandard = 0 , ConsiderGapInCutoff , ConsiderGap }

Functions
std::string	getFormat (const std::string &file, const std::string &format, const std::string &name)
	Get the format from a file path.
void	keepNonGapPositionsOfQuerySequence (std::vector< Sequence > &sequences)
	Keep only the positions of non-gap residues of the query sequence for all sequences.
std::string	getAllowedLetters (Alphabet alphabet)
	gets the list of allowed letters for the provided input alphabet
std::string	getStandardLetters (Alphabet alphabet)
	gets the list of standard letters for the provided input alphabet
std::string	getNonStandardLetters (Alphabet alphabet)
	gets the list of non-standard letters for the provided input alphabet

Variables
const std::vector< std::string >	VALID_FORMATS = {"fasta", "afa", "fas", "fst", "fsa", "a2m", "a3m", "sto", "clustal", "aln", "pfam"}
const std::vector< std::string >	FASTA_FORMATS = {"fasta", "afa", "fas", "fst", "fsa"}
const std::string	STANDARD_AMINO_ACIDS = "ACDEFGHIKLMNPQRSTVWY"
const std::string	NON_STANDARD_AMINO_ACIDS = "XOUBJZ"
const std::string	STANDARD_RNA_NUCLEOTIDES = "AUCG"
const std::string	STANDARD_DNA_NUCLEOTIDES = "ATCG"
const std::string	NON_STANDARD_NUCLEOTIDES = "N"
const std::string	GAP = "-."

Detailed Description

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

Enumeration Type Documentation

Alphabet

enum Alphabet

Enumerator
protein
RNA
DNA

NonStandardHandler

enum NonStandardHandler

Enumerator
AsStandard
ConsiderGapInCutoff
ConsiderGap

Normalization

enum Normalization

Enumerator
Sqrt_L
L
None

Function Documentation

getAllowedLetters()

std::string getAllowedLetters

(

Alphabet

alphabet

)

gets the list of allowed letters for the provided input alphabet

Parameters

alphabet

Returns

list of allowed letters

gets the list of allowed letters for the provided input alphabet

Parameters

alphabet

Returns

getFormat()

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

Get the format from a file path.

Parameters

file	file path.
format	file format if given by user.
name	name of the file (for error messages).

Returns

The format string.

getNonStandardLetters()

std::string getNonStandardLetters

(

Alphabet

alphabet

)

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

Parameters

alphabet

Returns

list of non-standard letters

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

Parameters

alphabet

Returns

getStandardLetters()

std::string getStandardLetters

(

Alphabet

alphabet

)

gets the list of standard letters for the provided input alphabet

Parameters

alphabet

Returns

list of standard letters

gets the list of standard letters for the provided input alphabet

Parameters

alphabet

Returns

keepNonGapPositionsOfQuerySequence()

void keepNonGapPositionsOfQuerySequence

(

std::vector< Sequence > &

sequences

)

Keep only the positions of non-gap residues of the query sequence for all sequences.

Parameters

sequences

The vector of sequences to process.

Variable Documentation

FASTA_FORMATS

const std::vector<std::string> FASTA_FORMATS = {"fasta", "afa", "fas", "fst", "fsa"}

inline

GAP

const std::string GAP = "-."

NON_STANDARD_AMINO_ACIDS

const std::string NON_STANDARD_AMINO_ACIDS = "XOUBJZ"

NON_STANDARD_NUCLEOTIDES

const std::string NON_STANDARD_NUCLEOTIDES = "N"

STANDARD_AMINO_ACIDS

const std::string STANDARD_AMINO_ACIDS = "ACDEFGHIKLMNPQRSTVWY"

STANDARD_DNA_NUCLEOTIDES

const std::string STANDARD_DNA_NUCLEOTIDES = "ATCG"

STANDARD_RNA_NUCLEOTIDES

const std::string STANDARD_RNA_NUCLEOTIDES = "AUCG"

VALID_FORMATS

const std::vector<std::string> VALID_FORMATS = {"fasta", "afa", "fas", "fst", "fsa", "a2m", "a3m", "sto", "clustal", "aln", "pfam"}