LocARNA::TraceController Class Reference

Controls the matrix cells valid for traces. More...

#include <trace_controller.hh>

Inheritance diagram for LocARNA::TraceController:

Collaboration diagram for LocARNA::TraceController:

Public Member Functions
	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
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
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

Controls the matrix cells valid for traces.

Controls the matrix cells that need to be filled in a dynamic programming algorithm because they occur on valid traces due to the max-diff heuristic

The valid traces can be defined either unrestricted, or by a maximal difference of i and j for matrix cells (i,j) or due to a maximal difference to a given alignment (trace).

Constructor & Destructor Documentation

TraceController()

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.

Parameters

seqA	sequence A
seqB	sequence B
ma	multiple reference alignment
delta	the allowed difference
relaxed_merging	whether to use relaxed merging of trace ranges

Note

If delta == -1 then min_col is 1 and max_col is lenB

If delta != -1 and ma==NULL, then define min j, max j by deviation |i-(lenA/lenB)*j|<=delta

These values are chosen such that for all j between min and max, the delta constraint holds for all pairs of sequences in seqA and seqB.

Member Function Documentation

get_delta()

size_type LocARNA::TraceController::get_delta ( ) const

inline

Read deviation.

Returns

deviation Delta

is_valid()

bool LocARNA::TraceController::is_valid ( size_type  i, size_type  j  ) const

inline

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

test for matrix entries on valid trace

Parameters

i	position in sequence A in 1..lenA or 0
j	position in sequence B in 1..lenB or 0

Returns

whether matrix cell (i.j) is valid

Parameters

i	index
j	index

Returns

flag, whether (i,j) is valid

Note

(i,j) must be matrix entry, i.e. in correct range

is_valid_match()

bool LocARNA::TraceController::is_valid_match ( size_type  i, size_type  j  ) const

inlinevirtual

test for allowed matches due to valid traces

Parameters

i	position in sequence A in 1..lenA
j	position in sequence B in 1..lenB

Returns

whether i~j is an allowed match due to valid traces

Implements LocARNA::MatchController.

restrict_by_anchors()

void LocARNA::TraceController::restrict_by_anchors

(

const AnchorConstraints &

constraints

)

Restrict by anchor constraints.

Limits trace ranges due to anchor constraints

Parameters

constraints

anchor constraints

restrict_by_trace_probabilities()

void LocARNA::TraceController::restrict_by_trace_probabilities	(	const TraceProbs &	trace_probs,
		double	min_prob
	)

Restrict by anchor constraints.

Limits trace ranges due to anchor constraints

Parameters

trace_probs	trace probabilities
min_prob	minimum trace probability

Limit trace to the ranges that contain all trace cells (i,j) that have at least the threshold probability min_prob

reverse()

TraceController LocARNA::TraceController::reverse

(

)

const

Controller for the reversed sequences.

Note

useful for backward alignment e.g. for computing edge probabilities; for an example

See also

PFGotoh::PFGotoh()

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

• src/LocARNA/trace_controller.hh
• src/LocARNA/trace_controller.cc