Inheritance diagram for ymir::ClonotypeBuilder:

Public Member Functions
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)

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

	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 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

Clonotype ymir::ClonotypeBuilder::buildClonotype ( )

inline

Build clone alignment structure with stored information.

Returns: Pointer to the newly created ClonotypeAlignment object.

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

Ymir/src/clonotype_builder.h

Public Member Functions

Additional Inherited Members

Member Function Documentation