Inheritance diagram for ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >:

Public Member Functions
	VDJAlignerBase (const VDJRecombinationGenes &genes, VDJAlignerParameters params)

void	set_genes (const VDJRecombinationGenes &genes)

void	set_parameters (VDJAlignerParameters params)


AlignmentType	alignVar (seg_index_t id, const sequence_t &sequence) const
	General methods for alignment.

AlignmentType	alignDiv (seg_index_t id, const sequence_t &sequence) const

AlignmentType	alignJoi (seg_index_t id, const sequence_t &sequence) const


bool	alignVar ()
	Align the given sequence to all gene segments of the specific gene. More...

bool	alignDiv ()

bool	alignJoi ()

Public Member Functions inherited from ymir::ClonotypeBuilder
Clonotype	buildClonotype ()
	Build clone alignment structure with stored information. More...

ClonotypeBuilder &	setSequence (const std::string &seq)

ClonotypeBuilder &	setSequenceType (SequenceType seq_type)

ClonotypeBuilder &	setNucleotideSeq ()

ClonotypeBuilder &	setAminoAcidSeq ()

ClonotypeBuilder &	setRecombination (Recombination recomb)

Public Member Functions inherited from ymir::VDJAlignmentBuilder
	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 Member Functions

void	_alignVar (seg_index_t id, const sequence_t &sequence, AlignmentType *vec) const
	Internal alignment functions. More...

void	_alignDiv (seg_index_t id, const sequence_t &sequence, AlignmentType *vec) const

void	_alignJoi (seg_index_t id, const sequence_t &sequence, AlignmentType *vec) const

	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

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

Protected Member Functions inherited from ymir::VDJAlignmentBuilder
	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
VDJAlignerParameters	_params

VDJRecombinationGenes	_genes

V_Aligner	_V_Aligner

D_Aligner	_D_Aligner

J_Aligner	_J_Aligner

Protected Attributes inherited from ymir::Clonotype
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.

Protected Attributes inherited from ymir::VDJAlignmentBuilder
NoGapAlignmentVector	_Valign

NoGapAlignmentVector	_Jalign

NoGapAlignmentVector	_Dalign

std::vector< seg_index_t >	_n_Dalign

std::vector< seg_index_t >	_Dseg

Member Function Documentation

template<typename AlignmentType , typename V_Aligner , typename D_Aligner , typename J_Aligner >

void ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >::_alignVar	(	seg_index_t	id,
		const sequence_t &	sequence,
		AlignmentType *	vec
	)		const

inlineprotected

Internal alignment functions.

Parameters

id
sequence
vec

template<typename AlignmentType , typename V_Aligner , typename D_Aligner , typename J_Aligner >

bool ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >::alignVar ( )

inline

Align the given sequence to all gene segments of the specific gene.

Parameters

sequence sequence sequence.

Returns: True if has been aligned at least one gene segment, False if no gene segments have been aligned.

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

Ymir/src/aligner.h

Public Member Functions

Protected Member Functions

Protected Attributes

Member Function Documentation