Inheritance diagram for ymir::VDJAlignment:

Public Types
typedef std::array< seg_index_t, 3 >	segments_storage_t

typedef std::vector< seg_index_t >	n_D_alignments_storage_t

Public Member Functions
	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 Member Functions
	VDJAlignment ()

Protected Attributes
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.

Constructor & Destructor Documentation

ymir::VDJAlignment::VDJAlignment ( )

inlineprotected

Accumulated number of alignments for each D gene segment; vector's length == _segments[2] + 1. Number of alignments for i-th gene is equal to v[i+1] - v[i].

Member Data Documentation

NoGapAlignmentVector ymir::VDJAlignment::_alignments

protected

vector of indices of segments, aligned on this clone: V1–V2–V3–J1–J2–D1–D2–...

Two concatenated vectors: vector of length 3 w/ numbers of aligned segments (V-J-D) and

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

Ymir/src/vdj_alignment.h

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Data Documentation