LocARNA::SparseTraceController Class Reference

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

#include <exact_matcher.hh>

Inheritance diagram for LocARNA::SparseTraceController:

List of all members.

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 Member Functions
	SparseTraceController (const SparsificationMapper &sparse_mapperA_, const SparsificationMapper &sparse_mapperB_, const TraceController &trace_controller_)
	constructor
const SparsificationMapper &	get_sparse_mapperA () const
	destructor
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
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
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
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
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
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
bool	is_valid_idx_pos (index_t idxA, index_t idxB, matpos_t mat_pos) const
	checks whether a matrix position is valid

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Detailed Description

combines the TraceController with the Mapper for both sequences

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Constructor & Destructor Documentation

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

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Member Function Documentation

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

const SparsificationMapper& LocARNA::SparseTraceController::get_sparse_mapperA

(

)

const [inline]

destructor

returns reference to sparsification mapper for sequence A

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

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

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

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

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

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

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

• src/LocARNA/exact_matcher.hh