combines the TraceController with the Mapper for both sequences More...

#include <exact_matcher.hh>

Inheritance diagram for LocARNA::SparseTraceController:

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Collaboration diagram for LocARNA::SparseTraceController:

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Public Types
typedef std::pair< matidx_t, matidx_t >	matpos_t
	a type for a position in a sparsified matrix

typedef std::pair< seqpos_t, seqpos_t >	pair_seqpos_t
	a type for a pair of positions in the sequences

Public Types inherited from LocARNA::TraceRange
typedef MultipleAlignment::SeqEntry	SeqEntry
	alias for MultipleAlignment::SeqEntry

typedef std::pair< SeqEntry, SeqEntry >	seqentry_pair_t
	pair of sequence entries

Public Member Functions
	SparseTraceController (const SparsificationMapper &sparse_mapperA_, const SparsificationMapper &sparse_mapperB_, const TraceController &trace_controller_)
	constructor More...

const SparsificationMapper &	get_sparse_mapperA () const
	destructor More...

const SparsificationMapper &	get_sparse_mapperB () const
	returns reference to sparsification mapper for sequence B

matidx_t	min_col_idx (index_t indexA, index_t indexB, matidx_t idx_i, index_t left_endB=std::numeric_limits< index_t >::max()) const
	minimal column of trace in a row in the sparsified matrix More...

matidx_t	idx_after_max_col_idx (index_t indexA, index_t indexB, matidx_t idx_i, index_t left_endB=std::numeric_limits< index_t >::max()) const
	index after maximal column of trace in a row in the sparsified matrix More...

matpos_t	diag_pos_bef (index_t indexA, index_t indexB, pair_seqpos_t cur_pos_seq, index_t left_endA=std::numeric_limits< index_t >::max(), index_t left_endB=std::numeric_limits< index_t >::max()) const
	computes the first valid matrix position before a sequence position considering the trace controller More...

pair_seqpos_t	pos_in_seq (index_t idxA, index_t idxB, const matpos_t &cur_pos) const
	maps the matrix position cur_pos to the corresponding pair of positions in sequence A and B More...

bool	matching_wo_gap (index_t idxA, index_t idxB, const matpos_t &idx_pos_diag, pair_seqpos_t seq_pos_to_be_matched) const
	is a EPM without a gap in between possible More...

bool	pos_unpaired (index_t idxA, index_t idxB, matpos_t pos) const
	checks whether the matrix position pos can be unpaired in both sequences More...

bool	is_valid_idx_pos (index_t idxA, index_t idxB, matpos_t mat_pos) const
	checks whether a matrix position is valid More...

Public Member Functions inherited from LocARNA::TraceController
	TraceController (const Sequence &seqA, const Sequence &seqB, const MultipleAlignment *ma, int delta, bool relaxed_merging=false)
	Constructs for the general case of alignment of alignments. More...

virtual	~TraceController ()
	Virtual destructor.

void	restrict_by_anchors (const AnchorConstraints &constraints)
	Restrict by anchor constraints. More...

void	restrict_by_trace_probabilities (const TraceProbs &trace_probs, double min_prob)
	Restrict by anchor constraints. More...

TraceController	reverse () const
	Controller for the reversed sequences. More...

bool	is_valid (size_type i, size_type j) const
	Is (i,j) a valid cell of the DP matrices (i.e. on some possible trace)? More...

virtual bool	is_valid_match (size_type i, size_type j) const

size_type	get_delta () const
	Read deviation. More...

Public Member Functions inherited from LocARNA::TraceRange
	TraceRange (const SeqEntry &pseqA, const SeqEntry &pseqB, const SeqEntry &aliA, const SeqEntry &aliB, size_type delta)
	Construct from pair of alignment strings. More...

	TraceRange (size_type lenA, size_type lenB, const std::vector< TraceRange > &trs, size_type delta)
	Construct as consensus trace range from a set of traces. More...

size_type	consensus_cost (size_type i, size_type j, const std::vector< TraceRange > &trs) const
	Computes cost of a cut in the consensus trace of a trace range set. More...

size_t	rows () const
	Read number of rows. More...

size_t	min_col (size_t i) const
	Minimal column of trace in a row. More...

size_t	max_col (size_t i) const
	Maximal column of trace in a row. More...

TraceRange	reverse () const
	Ranges for reversed sequences. More...

void	print_debug (std::ostream &out=std::cerr) const

Additional Inherited Members
Static Public Member Functions inherited from LocARNA::TraceRange
static seqentry_pair_t	remove_common_gaps (const SeqEntry &aliA, const SeqEntry &aliB)

Protected Types inherited from LocARNA::TraceRange
using	idx_vec_t = std::vector< size_t >

Protected Member Functions inherited from LocARNA::TraceRange
	TraceRange (size_t lenA, size_t lenB)
	Construct "empty". More...

Protected Attributes inherited from LocARNA::TraceRange
size_t	lenA_
	length of sequence A

size_t	lenB_
	length of sequence B

idx_vec_t	min_col_
	minimal column in row

idx_vec_t	max_col_
	maximal column in row

Detailed Description

combines the TraceController with the Mapper for both sequences

Constructor & Destructor Documentation

◆ SparseTraceController()

LocARNA::SparseTraceController::SparseTraceController	(	const SparsificationMapper &	sparse_mapperA_,
		const SparsificationMapper &	sparse_mapperB_,
		const TraceController &	trace_controller_
	)

inline

constructor

Parameters

sparse_mapperA_	sparsification mapper for sequence A
sparse_mapperB_	sparsification mapper for sequence B
trace_controller_	trace controller

Member Function Documentation

◆ diag_pos_bef()

matpos_t LocARNA::SparseTraceController::diag_pos_bef	(	index_t	indexA,
		index_t	indexB,
		pair_seqpos_t	cur_pos_seq,
		index_t	left_endA = `std::numeric_limits<index_t>::max()`,
		index_t	left_endB = `std::numeric_limits<index_t>::max()`
	)		const

inline

computes the first valid matrix position before a sequence position considering the trace controller

Parameters

indexA	index that is used for sequence A
indexB	index that is used for sequence B
cur_pos_seq	the pair of positions in sequence A and B, respectively
left_endA	set to left end of the arc in sequence A if indexing by the arcs is used default setting is the index for sequence A if indexing by the left ends is used
left_endB	set to left end of the arc in sequence B if indexing by the arcs is used default setting is the index for sequence B if indexing by the left ends is used

Returns: the first valid matrix position before the sequence position cur_pos_seq

◆ get_sparse_mapperA()

const SparsificationMapper& LocARNA::SparseTraceController::get_sparse_mapperA ( ) const

inline

destructor

returns reference to sparsification mapper for sequence A

◆ idx_after_max_col_idx()

matidx_t LocARNA::SparseTraceController::idx_after_max_col_idx	(	index_t	indexA,
		index_t	indexB,
		matidx_t	idx_i,
		index_t	left_endB = `std::numeric_limits<index_t>::max()`
	)		const

inline

index after maximal column of trace in a row in the sparsified matrix

Parameters

indexA	index that is used for sequence A
indexB	index that is used for sequence B
idx_i	row index in the sparsified matrix
left_endB	set to left end of the arc in sequence B if indexing by the arcs is used default setting is the index for sequence B if indexing by the left ends is used

◆ is_valid_idx_pos()

bool LocARNA::SparseTraceController::is_valid_idx_pos	(	index_t	idxA,
		index_t	idxB,
		matpos_t	mat_pos
	)		const

inline

checks whether a matrix position is valid

Parameters

idxA	index that is used for sequence A
idxB	index that is used for sequence B
mat_pos	a position in the condensed matrix

◆ matching_wo_gap()

bool LocARNA::SparseTraceController::matching_wo_gap	(	index_t	idxA,
		index_t	idxB,
		const matpos_t &	idx_pos_diag,
		pair_seqpos_t	seq_pos_to_be_matched
	)		const

inline

is a EPM without a gap in between possible

returns true iff the corresponding sequence position of the position idx_pos_diag is directly left adjacent to the sequence position pair seq_pos_to_be_matched, i.e. a continuative matching in matrix LR is possible without switching to a gap matrix

Parameters

idxA	index that is used for sequence A
idxB	index that is used for sequence B
idx_pos_diag	a position in the condensed matrix
seq_pos_to_be_matched	a pair of positions in sequence A and B

◆ min_col_idx()

matidx_t LocARNA::SparseTraceController::min_col_idx	(	index_t	indexA,
		index_t	indexB,
		matidx_t	idx_i,
		index_t	left_endB = `std::numeric_limits<index_t>::max()`
	)		const

inline

minimal column of trace in a row in the sparsified matrix

Parameters

indexA	index that is used for sequence A
indexB	index that is used for sequence B
idx_i	row index in the sparsified matrix
left_endB	set to left end of the arc in sequence B if indexing by the arcs is used default setting is the index for sequence B if indexing by the left ends is used

◆ pos_in_seq()

pair_seqpos_t LocARNA::SparseTraceController::pos_in_seq	(	index_t	idxA,
		index_t	idxB,
		const matpos_t &	cur_pos
	)		const

inline

maps the matrix position cur_pos to the corresponding pair of positions in sequence A and B

Parameters

idxA	index that is used for sequence A
idxB	index that is used for sequence B
cur_pos	a pair of positions in sequence A and B

◆ pos_unpaired()

bool LocARNA::SparseTraceController::pos_unpaired	(	index_t	idxA,
		index_t	idxB,
		matpos_t	pos
	)		const

inline

checks whether the matrix position pos can be unpaired in both sequences

Parameters

idxA	index that is used for sequence A
idxB	index that is used for sequence B
pos	position in the condensed matrix

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

src/LocARNA/exact_matcher.hh

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SparseTraceController()

Member Function Documentation

◆ diag_pos_bef()

◆ get_sparse_mapperA()

◆ idx_after_max_col_idx()

◆ is_valid_idx_pos()

◆ matching_wo_gap()

◆ min_col_idx()

◆ pos_in_seq()

◆ pos_unpaired()