NEFFy
NEFF Calculator and MSA File Converter
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MSAReader_a2m Class Reference

#include <msaReader.h>

Inheritance diagram for MSAReader_a2m:
MSAReader

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< Sequenceread ()
 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< SequenceSequences
 

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_a2m::readFile ( std::ifstream & file)
overrideprivatevirtual

Implements MSAReader.


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