Public Member Functions
	GeneSegmentAlphabet (GeneSegments gene_segment, const std::string &name, const std::string &filepath, bool *is_ok=nullptr)

	GeneSegmentAlphabet (GeneSegments gene_segment, const std::string &name, const std::vector< std::string > &alleles, const std::vector< std::string > &sequences)

const std::string &	name () const

const GeneSegment &	operator[] (seg_index_t index) const

const GeneSegment &	operator[] (const std::string &name) const

seg_index_t	size () const

seg_index_t	max () const

void	appendPalindromicNucleotides (seq_len_t from_5_end, seq_len_t from_3_end)
	Append P(alindromic)-nucleotides to all gene segment sequences from 3'end, 5'end or both. More...

bool	write (const std::string &filepath) const
	Save segment alphabet to the given file as a tab-separated table with 3 columns.

bool	read (const std::string &filepath)

seq_len_t	maxLength () const

GeneSegments	gene_segment () const

Protected Member Functions
void	addGeneSegment (const std::string &name, const std::string &seq, seg_index_t index)

Protected Attributes
std::string	_name

std::unordered_map< std::string, seg_index_t >	_map

std::vector< GeneSegment >	_vec

GeneSegments	_gene_segment

Member Function Documentation

void ymir::GeneSegmentAlphabet::appendPalindromicNucleotides	(	seq_len_t	from_5_end,
		seq_len_t	from_3_end
	)

inline

Append P(alindromic)-nucleotides to all gene segment sequences from 3'end, 5'end or both.

Parameters

from_5_end	Number of P nucleotides to append from the 3' end (i.e., sequences' start).
from_3_end	Number of P nucleotides to append from the 3' end (i.e., sequences' end).

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

Classes