MSAReader Class Reference

#include <msaReader.h>

Inheritance diagram for MSAReader:

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

Protected Member Functions
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.
virtual void	readFile (std::ifstream &file)=0

Protected Attributes
std::string	file
Alphabet	alphabet
bool	checkValidation
bool	omitGaps
std::vector< Sequence >	Sequences

Constructor & Destructor Documentation

MSAReader()

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

Constructor.

Parameters

_file
_alphabet
_checkValidation
_omitGaps

Member Function Documentation

containsInvalidLetters()

string MSAReader::containsInvalidLetters ( Alphabet alphabet )

protected

Check if the sequences contain any invalid characters.

Returns

The sequence number and position of the first invalid character, or an empty string if valid

isUnaligned()

int MSAReader::isUnaligned ( )

protected

Check if the MSA sequences are aligned.

Returns

-1 if aligned, otherwise return the index of the unaligned sequence

makeUppercase()

void MSAReader::makeUppercase ( )

protected

Convert all lowercase letters to uppercase in the sequences.

read()

vector< Sequence > MSAReader::read

(

)

Read the MSA file.

Returns

The processed sequences in the file

readFile()

virtual void MSAReader::readFile ( std::ifstream & file )

protectedpure virtual

Implemented in MSAReader_a2m, MSAReader_a3m, MSAReader_aln, MSAReader_clustal, MSAReader_fasta, MSAReader_pfam, and MSAReader_sto.

validateSequences()

void MSAReader::validateSequences ( Alphabet alphabet )

protected

Validate the sequences for any invalid characters or unaligned sequences.

Parameters

alphabet

Member Data Documentation

alphabet

Alphabet MSAReader::alphabet

protected

checkValidation

bool MSAReader::checkValidation

protected

file

std::string MSAReader::file

protected

omitGaps

bool MSAReader::omitGaps

protected

Sequences

std::vector<Sequence> MSAReader::Sequences

protected

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

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