Public Member Functions
	VDJRecombinationGenes (const std::string &v_segments_name, const std::string &v_segments_file, const std::string &j_segments_name, const std::string &j_segments_file, bool is_V_ok=nullptr, bool is_J_ok=nullptr)

	VDJRecombinationGenes (const std::string &v_segments_name, const std::string &v_segments_file, const std::string &j_segments_name, const std::string &j_segments_file, const std::string &d_segments_name, const std::string &d_segments_file, bool is_V_ok=nullptr, bool is_J_ok=nullptr, bool *is_D_ok=nullptr)

	VDJRecombinationGenes (const std::string &V_name, const std::vector< std::string > &V_alleles, const std::vector< std::string > &V_sequences, const std::string &J_name, const std::vector< std::string > &J_alleles, const std::vector< std::string > &J_sequences)

	VDJRecombinationGenes (const std::string &V_name, const std::vector< std::string > &V_alleles, const std::vector< std::string > &V_sequences, const std::string &J_name, const std::vector< std::string > &J_alleles, const std::vector< std::string > &J_sequences, const std::string &D_name, const std::vector< std::string > &D_alleles, const std::vector< std::string > &D_sequences)

	VDJRecombinationGenes (const VDJRecombinationGenes &other)

VDJRecombinationGenes &	operator= (const VDJRecombinationGenes &other)

bool	is_vdj () const

void	appendPalindromicNucleotides (GeneSegments gene, seq_len_t from_5_end=4, seq_len_t from_3_end=4)

bool	write (const std::string &v_segments_file="vsegments.txt", const std::string &j_segments_file="jsegments.txt", const std::string &d_segments_file="dsegments.txt") const


const GeneSegmentAlphabet &	V () const

const GeneSegmentAlphabet &	J () const

const GeneSegmentAlphabet &	D () const

Protected Attributes
GSA_ptr	_V

GSA_ptr	_J

GSA_ptr	_D

Member Function Documentation

void ymir::VDJRecombinationGenes::appendPalindromicNucleotides	(	GeneSegments	gene,
		seq_len_t	from_5_end = `4`,
		seq_len_t	from_3_end = `4`
	)

inline

Parameters

segindex 0 for V(ariable), 1 for J(oining), 2 for D(iversity) gene segment.

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

Ymir/src/genesegment.h

Public Member Functions

Protected Attributes

Member Function Documentation