Inheritance diagram for ymir::MAAGBuilder:

Public Member Functions
	MAAGBuilder (const ModelParameterVector &param_vec, const VDJRecombinationGenes &genes)
	Constructor for the builder from given vector with event probabilities and gene segments.

void	updateModelParameterVector (const ModelParameterVector &param_vec)


MAAG	build (const Clonotype &clonotype, MetadataMode metadata_mode, ErrorMode error_mode, SequenceType seq_type=NUCLEOTIDE) const
	Build MAAGs from the given clonotypes. More...

MAAGRepertoire	build (const ClonesetView &cloneset, MetadataMode metadata_mode, ErrorMode error_mode, SequenceType seq_type=NUCLEOTIDE, bool verbose=true) const


prob_t	buildAndCompute (const Clonotype &clonotype, ErrorMode error_mode, SequenceType seq_type=NUCLEOTIDE, MAAGComputeProbAction action=SUM_PROBABILITY) const
	Compute generation probabilities without building the full information about MAAGs. More...

vector< prob_t >	buildAndCompute (const ClonesetView &cloneset, ErrorMode error_mode, SequenceType seq_type=NUCLEOTIDE, MAAGComputeProbAction action=SUM_PROBABILITY, bool verbose=true) const


void	updateEventProbabilities (MAAG *maag) const
	Replace event probabilities in the given MAAGs if they have stored event indices. More...

void	updateEventProbabilities (MAAGRepertoire *repertoire, bool verbose=true) const

Protected Member Functions
	MAAGBuilder ()
	Private default constructor.

void	buildVariable (const Clonotype &clonotype, ProbMMC &probs, EventIndMMC &events, ErrMMC &errors, vector< seq_len_t > &seq_poses, MetadataMode metadata_mode, ErrorMode error_mode) const
	Build probability and events matrices for Variable gene segments. More...

void	buildJoining (const Clonotype &clonotype, ProbMMC &probs, EventIndMMC &events, ErrMMC &errors, vector< seq_len_t > &seq_poses, MetadataMode metadata_mode, ErrorMode error_mode) const
	Build probability and events matrices for Joining gene segments. More...

void	buildDiversity (const Clonotype &clonotype, ProbMMC &probs, EventIndMMC &events, ErrMMC &errors, vector< seq_len_t > &seq_poses, MetadataMode metadata_mode, ErrorMode error_mode) const
	Build probability and events matrices for Diversity gene segments. More...

void	buildVJinsertions (const Clonotype &clonotype, ProbMMC &probs, EventIndMMC &events, const vector< seq_len_t > &seq_poses, MetadataMode metadata_mode, ErrorMode error_mode) const
	Build probability and events matrices for Variable-Joining gene segments insertions. More...

void	buildVDinsertions (const Clonotype &clonotype, ProbMMC &probs, EventIndMMC &events, const vector< seq_len_t > &seq_poses, MetadataMode metadata_mode, ErrorMode error_mode) const
	Build probability and events matrices for Variable-Diversity gene segments insertions. More...

void	buildDJinsertions (const Clonotype &clonotype, ProbMMC &probs, EventIndMMC &events, const vector< seq_len_t > &seq_poses, MetadataMode metadata_mode, ErrorMode error_mode) const
	Build probability and events matrices for Diversity-Joining gene segments insertions. More...

void	buildInsertions (const string &sequence, ProbMMC &probs, EventIndMMC &events, const vector< seq_len_t > &seq_poses, ProbMMC::node_ind_t ins_node_index, event_ind_t null_insertion, seq_len_t max_size, MetadataMode metadata_mode, bool error_mode, seq_len_t left_vertices_start, seq_len_t left_vertices_end, seq_len_t right_vertices_start, seq_len_t right_vertices_end, const AbstractInsertionModel &mc, bool reversed=false) const
	General function for building insertions. More...

Protected Member Functions inherited from ymir::MAAG
	MAAG ()
	Default constructor.

	MAAG (const MAAG &other)

	MAAG (MAAG &&other)

virtual	~MAAG ()
	Special swap constructor for MAAGs that will be used only for computation of the full probability. More...

MAAG &	operator= (const MAAG &other)

MAAG &	operator= (MAAG &&other)

seq_len_t	position (seq_len_t i) const

bool	has_events () const

bool	has_errors () const

prob_t	error_prob () const

const std::string &	sequence () const

seq_len_t	n_poses () const

SequenceType	sequence_type () const

dim_t	rows (node_ind_t node_i) const

dim_t	cols (node_ind_t node_i) const

prob_t	fullProbability (event_ind_t v_index, event_ind_t j_index) const
	Compute and return the full assembling probability of this sequence (i.e., with all gene segments alignments). More...

prob_t	fullProbability (event_ind_t v_index, event_ind_t d_index, event_ind_t j_index) const

prob_t	fullProbability (MAAGComputeProbAction action=SUM_PROBABILITY) const

event_ind_t	nVar () const
	Get the number of aligned gene segments. More...

event_ind_t	nJoi () const

event_ind_t	nDiv () const

prob_t	event_probability (node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col) const
	Access to event indices, event probabilities and mismatches in the underlying matrices of the MAAG. More...

event_ind_t	event_index (node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col) const

error_num_t	errors (node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col) const

bool	save (const std::string &filepath) const
	Save the graph to the harddrive and load a previously saved graph. More...

bool	save (std::ostream &stream) const

bool	load (const std::string &filepath)

bool	load (std::istream &stream)

Recombination	recombination () const

bool	is_vj () const

bool	is_vdj () const

Protected Member Functions inherited from ymir::MultiMatrixChain< _Scalar >
void	resize (node_ind_t n_nodes)

node_ind_t	chainSize () const

void	initNode (node_ind_t node_i, matrix_ind_t n_matrices, dim_t rows, dim_t cols)

void	swap (MultiMatrixChain &other)

void	finish ()

void	fill (node_ind_t node, matrix_ind_t mat, _Scalar val=0)

matrix_t	matrix (node_ind_t node, matrix_ind_t mat) const

_Scalar	operator[] (size_t index) const

size_t	values_size () const

matrix_ind_t	nodeSize (node_ind_t node_i) const

dim_t	nodeRows (node_ind_t node_i) const

dim_t	nodeColumns (node_ind_t node_i) const

_Scalar &	operator() (node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col)
	Access element with specified indices at specified matrix. More...

_Scalar	operator() (node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col) const

_Scalar &	at (node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col)

_Scalar	at (node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col) const

node_ind_t	addNode ()
	Add new node with pattern matrix.

node_ind_t	addNode (matrix_ind_t n_matrices, dim_t rows, dim_t cols)

Protected Attributes
unique_ptr< ModelParameterVector >	_param_vec

unique_ptr< VDJRecombinationGenes >	_genes

Protected Attributes inherited from ymir::MAAG
prob_t	_err_prob

pEventIndMMC	_events

pErrMMC	_errors

unique_ptr< seq_len_t[]>	_seq_poses

unique_ptr< sequence_t >	_sequence

SequenceType	_seq_type

Recombination	_recomb

seq_len_t	_n_poses

Protected Attributes inherited from ymir::MultiMatrixChain< _Scalar >
std::vector< Node >	_chain

std::vector< _Scalar >	_values

Additional Inherited Members
Protected Types inherited from ymir::MultiMatrixChain< _Scalar >
typedef uint8_t	node_ind_t
	Node index type.

typedef uint8_t	matrix_ind_t
	Matrix index type.

typedef seq_len_t	dim_t
	Type of dimensions of matrices (rows and columns).

typedef Matrix< _Scalar, dim_t >	matrix_t
	Type of matrices in the chain.

Member Function Documentation

MAAG ymir::MAAGBuilder::build	(	const Clonotype &	clonotype,
		MetadataMode	metadata_mode,
		ErrorMode	error_mode,
		SequenceType	seq_type = `NUCLEOTIDE`
	)		const

inline

Build MAAGs from the given clonotypes.

Parameters

clonotype	Clonotype from which build the MAAG.
cloneset	Set of clonotypes from which build the repertoires of MAAGs.
metadata_mode	If true than make MAAG with stored event indices.
aminoacid	If true than build MAAGs from the aminoacid sequences.

Returns: Newly constructed MAAG.

prob_t ymir::MAAGBuilder::buildAndCompute	(	const Clonotype &	clonotype,
		ErrorMode	error_mode,
		SequenceType	seq_type = `NUCLEOTIDE`,
		MAAGComputeProbAction	action = `SUM_PROBABILITY`
	)		const

inline

Compute generation probabilities without building the full information about MAAGs.

Parameters

clonotype
cloneset
aminoacid	If true then compute amino acid generation probabilities.
action	What action to perform for computing generation probabilties - either sum all probabilities or choose the max one.

void ymir::MAAGBuilder::buildDiversity	(	const Clonotype &	clonotype,
		ProbMMC &	probs,
		EventIndMMC &	events,
		ErrMMC &	errors,
		vector< seq_len_t > &	seq_poses,
		MetadataMode	metadata_mode,
		ErrorMode	error_mode
	)		const

inlineprotected

Build probability and events matrices for Diversity gene segments.

Parameters

clonotype	Clonotype that used for building the graph.
probs	Multi-Matrix Chain with event probabilities.
events	Multi-Matrix Chain with event indices.
seq_poses	Vector of positions.
metadata_mode	Boolean if build should be full.

void ymir::MAAGBuilder::buildDJinsertions	(	const Clonotype &	clonotype,
		ProbMMC &	probs,
		EventIndMMC &	events,
		const vector< seq_len_t > &	seq_poses,
		MetadataMode	metadata_mode,
		ErrorMode	error_mode
	)		const

inlineprotected

Build probability and events matrices for Diversity-Joining gene segments insertions.

Parameters

clonotype	Clonotype that used for building the graph.
probs	Multi-Matrix Chain with event probabilities.
events	Multi-Matrix Chain with event indices.
seq_poses	Vector of positions.
metadata_mode	Boolean if build should be full.

void ymir::MAAGBuilder::buildInsertions	(	const string &	sequence,
		ProbMMC &	probs,
		EventIndMMC &	events,
		const vector< seq_len_t > &	seq_poses,
		ProbMMC::node_ind_t	ins_node_index,
		event_ind_t	null_insertion,
		seq_len_t	max_size,
		MetadataMode	metadata_mode,
		bool	error_mode,
		seq_len_t	left_vertices_start,
		seq_len_t	left_vertices_end,
		seq_len_t	right_vertices_start,
		seq_len_t	right_vertices_end,
		const AbstractInsertionModel &	mc,
		bool	reversed = `false`
	)		const

inlineprotected

General function for building insertions.

Parameters

clonotype	Clonotype that used for building the graph.
probs	Multi-Matrix Chain with event probabilities.
events	Multi-Matrix Chain with event indices.
seq_poses	Vector of positions.
ins_node_index	Node of the event / prob matrix with insertions.
null_insertion	Event index of insertions of length zero.
max_size	Maximum size of the length of insertions.
metadata_mode	Boolean if build should be full.
left_vertices_start	Starting index in seq_poses for the vertices in the left matrix.
left_vertices_end	Ending index in seq_poses for the vertices in the left matrix.
right_vertices_start	Starting index in seq_poses for the vertices in the right matrix.
right_vertices_end	Ending index in seq_poses for the vertices in the right matrix.
mc	Insertion model that uses for generation of N nucleotides.

void ymir::MAAGBuilder::buildJoining	(	const Clonotype &	clonotype,
		ProbMMC &	probs,
		EventIndMMC &	events,
		ErrMMC &	errors,
		vector< seq_len_t > &	seq_poses,
		MetadataMode	metadata_mode,
		ErrorMode	error_mode
	)		const

inlineprotected

Build probability and events matrices for Joining gene segments.

Parameters

clonotype	Clonotype that used for building the graph.
probs	Multi-Matrix Chain with event probabilities.
events	Multi-Matrix Chain with event indices.
seq_poses	Vector of positions.
metadata_mode	Boolean if build should be full.

void ymir::MAAGBuilder::buildVariable	(	const Clonotype &	clonotype,
		ProbMMC &	probs,
		EventIndMMC &	events,
		ErrMMC &	errors,
		vector< seq_len_t > &	seq_poses,
		MetadataMode	metadata_mode,
		ErrorMode	error_mode
	)		const

inlineprotected

Build probability and events matrices for Variable gene segments.

Parameters

clonotype	Clonotype that used for building the graph.
probs	Multi-Matrix Chain with event probabilities.
events	Multi-Matrix Chain with event indices.
seq_poses	Vector of positions.
metadata_mode	Boolean if build should be full.

void ymir::MAAGBuilder::buildVDinsertions	(	const Clonotype &	clonotype,
		ProbMMC &	probs,
		EventIndMMC &	events,
		const vector< seq_len_t > &	seq_poses,
		MetadataMode	metadata_mode,
		ErrorMode	error_mode
	)		const

inlineprotected

Build probability and events matrices for Variable-Diversity gene segments insertions.

Parameters

clonotype	Clonotype that used for building the graph.
probs	Multi-Matrix Chain with event probabilities.
events	Multi-Matrix Chain with event indices.
seq_poses	Vector of positions.
metadata_mode	Boolean if build should be full.

void ymir::MAAGBuilder::buildVJinsertions	(	const Clonotype &	clonotype,
		ProbMMC &	probs,
		EventIndMMC &	events,
		const vector< seq_len_t > &	seq_poses,
		MetadataMode	metadata_mode,
		ErrorMode	error_mode
	)		const

inlineprotected

Build probability and events matrices for Variable-Joining gene segments insertions.

Parameters

clonotype	Clonotype that used for building the graph.
probs	Multi-Matrix Chain with event probabilities.
events	Multi-Matrix Chain with event indices.
seq_poses	Vector of positions.
metadata_mode	Boolean if build should be full.

void ymir::MAAGBuilder::updateEventProbabilities ( MAAG * maag ) const

inline

Replace event probabilities in the given MAAGs if they have stored event indices.

Parameters

maag	MAAG with an event indices matrix.
repertoire	Repertoire with MAAGs with event indices matrices.

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

Ymir/src/maagbuilder.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Member Function Documentation