Inheritance diagram for ymir::VDJAlignmentBuilder:

Public Member Functions
	VDJAlignmentBuilder ()
	Move constructor for _segments, _alignments and _n_D_alignments.

VDJAlignment	buildAlignment ()

VDJAlignmentBuilder &	addAlignment (GeneSegments gene, seg_index_t seg_index, seq_len_t genestart, seq_len_t seqstart, seq_len_t alignment_len)


VDJAlignmentBuilder &	addVarAlignment (seg_index_t vseg, seq_len_t vstart, seq_len_t seqstart, seq_len_t alignment_len)
	Add singular alignments to the builder.

VDJAlignmentBuilder &	addJoiAlignment (seg_index_t jseg, seq_len_t jstart, seq_len_t seqstart, seq_len_t alignment_len)

VDJAlignmentBuilder &	addDivAlignment (seg_index_t dseg, seq_len_t dstart, seq_len_t seqstart, seq_len_t alignment_len)


VDJAlignmentBuilder &	addVarAlignment (const NoGapAlignmentVector &vec)
	Add vectors of alignments to the builder. More...

VDJAlignmentBuilder &	addJoiAlignment (const NoGapAlignmentVector &vec)

VDJAlignmentBuilder &	addDivAlignment (const NoGapAlignmentVector &vec)

Protected Attributes
NoGapAlignmentVector	_Valign

NoGapAlignmentVector	_Jalign

NoGapAlignmentVector	_Dalign

std::vector< seg_index_t >	_n_Dalign

std::vector< seg_index_t >	_Dseg

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
Protected 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 ()

	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

Member Function Documentation

VDJAlignmentBuilder& ymir::VDJAlignmentBuilder::addVarAlignment ( const NoGapAlignmentVector & vec )

inline

Add vectors of alignments to the builder.

Add alignments to the builder. IMPORTANT NOTE: for V / J alignments each input vectors counts as a set of various V or J gene segments. For D alignments input vec counts as a set of alignments for a specific D gene segment (i.e., only one!).

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

Ymir/src/vdj_alignment_builder.h

Public Member Functions

Protected Attributes

Additional Inherited Members

Member Function Documentation