Multi-Alignment Assembly Graph - basic class for representing all possible generation scenarios of a nucleotide or amino acid sequence of an immune receptor. More...

#include <maag.h>

Inheritance diagram for ymir::MAAG:

Public Member Functions
	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 Attributes
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

Friends
class	MAAGForwardBackwardAlgorithm

class	MAAGBuilder

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.

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)

Detailed Description

Multi-Alignment Assembly Graph - basic class for representing all possible generation scenarios of a nucleotide or amino acid sequence of an immune receptor.

Constructor & Destructor Documentation

virtual ymir::MAAG::~MAAG ( )

inlinevirtual

Special swap constructor for MAAGs that will be used only for computation of the full probability.

Special swap constructor for MAAGs that will be used for statistical inference.

Member Function Documentation

prob_t ymir::MAAG::event_probability	(	node_ind_t	node_i,
		matrix_ind_t	mat_i,
		dim_t	row,
		dim_t	col
	)		const

inline

Access to event indices, event probabilities and mismatches in the underlying matrices of the MAAG.

Parameters

node_i	Index of the node.
mat_i	Index of the matrix in the node.
row	Which row to choose.
col	Which column to choose.

Returns: Event probability, event index or is mismatch. In the second case zero will be returned if no event chain matrix is stored in this MAAG.

prob_t ymir::MAAG::fullProbability	(	event_ind_t	v_index,
		event_ind_t	j_index
	)		const

inline

Compute and return the full assembling probability of this sequence (i.e., with all gene segments alignments).

Parameters

v_index	Which aligned Variable gene segment to choose.
d_index	Which aligned Diversity gene segment to choose.
j_index	Which aligned Joining gene segment to choose.
action

Returns: Full assembling probability. Returns 0 if wrong recombination function is used.

event_ind_t ymir::MAAG::nVar ( ) const

inline

Get the number of aligned gene segments.

Returns: Number of the aligned specific gene segments.

bool ymir::MAAG::save ( const std::string & filepath ) const

inline

Save the graph to the harddrive and load a previously saved graph.

Parameters

filepath	Path to the file with a saved graph for loading and new file for saving.
stream	An output / input stream, from that read the graph or save the graph.

Member Data Documentation

pErrMMC ymir::MAAG::_errors

protected

Matrix of indices of events for each edge.

pEventIndMMC ymir::MAAG::_events

protected

Probability of a error.

unique_ptr<seq_len_t[]> ymir::MAAG::_seq_poses

protected

Matrix of number of errors for each scenario event position.

SequenceType ymir::MAAG::_seq_type

protected

Nucleotide or amino acid CDR3 sequence.

unique_ptr<sequence_t> ymir::MAAG::_sequence

protected

Vector of the initial clonotype sequence's positions for each vertex.

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

Ymir/src/maag.h

Public Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation