ymir::Clonotype Struct Reference

Inheritance diagram for ymir::Clonotype:

Public Member Functions
	Clonotype (const sequence_t &sequence, SequenceType seq_type, Recombination recomb, const segments_storage_t &segments, const NoGapAlignmentVector &alignments, const n_D_alignments_storage_t &n_D_alignments)
	Clonotype (const sequence_t &sequence, SequenceType seq_type, Recombination recomb, VDJAlignment alignment)
sequence_t::const_iterator	seq_iterator (seq_len_t pos) const
Recombination	recombination () const
SequenceType	sequence_type () const
std::string	toString () const
	Return the string representation of the clonotype.
bool	is_good () const
const sequence_t &	sequence () const
	Get the sequence of this Clonotype. More...
const sequence_t &	nuc_sequence () const
sequence_t	aa_sequence () const
bool	isCoding () const
	Check if clonotype's sequence is coding, noncoding or out-of-frame.
bool	isNoncoding () const
bool	isOutOfFrame () const
Public Member Functions inherited from ymir::VDJAlignment
	VDJAlignment (const segments_storage_t &segments, const NoGapAlignmentVector &alignments, const n_D_alignments_storage_t &n_D_alignments)
virtual	~VDJAlignment ()
	Move constructor for _segments, _alignments and _n_D_alignments.
bool	operator== (const VDJAlignment &other)
bool	operator!= (const VDJAlignment &other)
seq_len_t	numDivAlignments (seg_index_t index) const
	Get the number of D gene alignments for the given D gene.
seg_index_t	nVar () const
	Get the number of alignments for the specific gene.
seg_index_t	nJoi () const
seg_index_t	nDiv () const
seg_index_t	getVar (size_t index) const
	Get the index of the aligned gene segment for the specific gene.
seg_index_t	getJoi (size_t index) const
seg_index_t	getDiv (size_t index) const
seq_len_t	getVarGeneStart (seg_index_t vgene) const
	Get alignments for the specific gene.
seq_len_t	getVarGeneEnd (seg_index_t vgene) const
seq_len_t	getVarSeqStart (seg_index_t vgene) const
seq_len_t	getVarSeqEnd (seg_index_t vgene) const
seq_len_t	getVarLen (seg_index_t vgene) const
bool	isVarMismatch (seg_index_t vgene, seq_len_t pos) const
seq_len_t	getJoiGeneStart (seg_index_t jgene) const
seq_len_t	getJoiGeneEnd (seg_index_t jgene) const
seq_len_t	getJoiSeqStart (seg_index_t jgene) const
seq_len_t	getJoiSeqEnd (seg_index_t jgene) const
seq_len_t	getJoiLen (seg_index_t jgene) const
bool	isJoiMismatch (seg_index_t jgene, seq_len_t pos) const
seq_len_t	getDivGeneStart (seg_index_t dgene, seg_index_t align_i) const
seq_len_t	getDivGeneEnd (seg_index_t dgene, seg_index_t align_i) const
seq_len_t	getDivSeqStart (seg_index_t dgene, seg_index_t align_i) const
seq_len_t	getDivSeqEnd (seg_index_t dgene, seg_index_t align_i) const
seq_len_t	getDivLen (seg_index_t dgene, seg_index_t align_i) const
bool	isDivMismatch (seg_index_t dgene, seg_index_t align_i, seq_len_t pos) const
error_num_t	numDivMismatches (seg_index_t dgene, seg_index_t align_i, seq_len_t start, seq_len_t end) const

Protected Attributes
Recombination	_recomb
SequenceType	_seq_type
sequence_t	_sequence
bool	_good
Protected Attributes inherited from ymir::VDJAlignment
segments_storage_t	_segments
NoGapAlignmentVector	_alignments
	vector of indices of segments, aligned on this clone: V1–V2–V3–J1–J2–D1–D2–... More...
n_D_alignments_storage_t	_n_D_alignments
	Vector of alignments for segments.

Additional Inherited Members
Public Types inherited from ymir::VDJAlignment
typedef std::array< seg_index_t, 3 >	segments_storage_t
typedef std::vector< seg_index_t >	n_D_alignments_storage_t
Protected Member Functions inherited from ymir::VDJAlignment
	VDJAlignment ()

Member Function Documentation

const sequence_t& ymir::Clonotype::sequence ( ) const

inline

Get the sequence of this Clonotype.

Function sequence() returns just stored sequence; nuc_sequence() tries to return the nucleotide sequence and fails in debug mode if the stored sequence is the amino acid one; aa_sequence() always returns amino acid sequence.

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

• Ymir/src/clonotype.h