MSAReader_a3m Class Reference

#include <msaReader.h>

Inheritance diagram for MSAReader_a3m:

Public Member Functions
	MSAReader (std::string _file, Alphabet _alphabet, bool _checkValidation, bool _omitGaps=false)
	Constructor.
Public Member Functions inherited from MSAReader
	MSAReader (std::string _file, Alphabet _alphabet, bool _checkValidation, bool _omitGaps=false)
	Constructor.
std::vector< Sequence >	read ()
	Read the MSA file.

Private Member Functions
void	readFile (std::ifstream &file) override

Additional Inherited Members
Protected Member Functions inherited from MSAReader
int	isUnaligned ()
	Check if the MSA sequences are aligned.
std::string	containsInvalidLetters (Alphabet alphabet)
	Check if the sequences contain any invalid characters.
void	makeUppercase ()
	Convert all lowercase letters to uppercase in the sequences.
void	validateSequences (Alphabet alphabet)
	Validate the sequences for any invalid characters or unaligned sequences.
Protected Attributes inherited from MSAReader
std::string	file
Alphabet	alphabet
bool	checkValidation
bool	omitGaps
std::vector< Sequence >	Sequences

Member Function Documentation

MSAReader()

MSAReader::MSAReader	(	std::string	_file,
		Alphabet	_alphabet,
		bool	_checkValidation,
		bool	_omitGaps = false )

Constructor.

Parameters

_file
_alphabet
_checkValidation
_omitGaps

readFile()

void MSAReader_a3m::readFile ( std::ifstream & file )

overrideprivatevirtual

Implements MSAReader.

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The documentation for this class was generated from the following files:

• code/msaReader.h
• code/msaReader.cpp