LocARNA::TraceController Class Reference

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

#include <trace_controller.hh>

Inheritance diagram for LocARNA::TraceController:

List of all members.

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.
virtual	~TraceController ()
	Virtual destructor.
void	restrict_by_anchors (const AnchorConstraints &constraints)
	Restrict by anchor constraints.
bool	is_valid (size_type i, size_type j) const
virtual bool	is_valid_match (size_type i, size_type j) const
size_type	get_delta () const
	Read deviation.

---

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

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.

switch between strict and relaxed merging of pairwise trace ranges

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

size_type LocARNA::TraceController::get_delta

(

)

const [inline]

Read deviation.

Returns:

deviation Delta

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

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

bool LocARNA::TraceController::is_valid_match	(	size_type	i,
		size_type	j
	)		const [inline, virtual]

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.

void LocARNA::TraceController::restrict_by_anchors

(

const AnchorConstraints &

constraints

)

Restrict by anchor constraints.

Limits trace ranges due to anchor constraints

Parameters:

constraints

anchor constraints

Note:

surprisingly, this filtering causes no noticable effect in standard alignment

---

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

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