LocARNA::TraceRange Class Reference

Represents a range of traces. More...

#include <trace_controller.hh>

Inheritance diagram for LocARNA::TraceRange:

Collaboration diagram for LocARNA::TraceRange:

Public Types
typedef MultipleAlignment::SeqEntry	SeqEntry
	alias for MultipleAlignment::SeqEntry
typedef std::pair< SeqEntry, SeqEntry >	seqentry_pair_t
	pair of sequence entries

Public Member Functions
	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

Static Public Member Functions
static seqentry_pair_t	remove_common_gaps (const SeqEntry &aliA, const SeqEntry &aliB)

Protected Types
using	idx_vec_t = std::vector< size_t >

Protected Member Functions
	TraceRange (size_t lenA, size_t lenB)
	Construct "empty". More...

Protected Attributes
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

Represents a range of traces.

Represents a range of possible traces in a dynamic programming matrix for aligning two sequences

See also

TraceController

Constructor & Destructor Documentation

TraceRange() [1/3]

LocARNA::TraceRange::TraceRange	(	const SeqEntry &	pseqA,
		const SeqEntry &	pseqB,
		const SeqEntry &	aliA,
		const SeqEntry &	aliB,
		size_type	delta
	)

Construct from pair of alignment strings.

construct trace range of two sequences given two alignment strings of the sequences and the allowed deviation delta the sequences can contain gaps themselves (which happens, when sequences orignate from a sequence profile).

Parameters

pseqA	SeqEntry of sequence A
pseqB	SeqEntry of sequence B
aliA	alignment SeqEntry for sequence A
aliB	alignment SeqEntry for sequence B
delta	the allowed deviation

side conditions: remove_gaps(seqA) == remove_gaps(aliA) && remove_gaps(seqB) == remove_gaps(aliB) where remove_gaps is a function that removes all gap symbols length(aliA)==length(aliB)

TraceRange() [2/3]

LocARNA::TraceRange::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.

Constructs object as consensus trace ranges of the traces trs. The construction follows an idea of relaxing the deviation constraints by computing a trace with minimal accumulated distance to all traces and then determining its delta environment.

Parameters

lenA	length of sequence A
lenB	length of sequence B
trs	set of traces
delta	deviation

TraceRange() [3/3]

LocARNA::TraceRange::TraceRange ( size_t  lenA, size_t  lenB  )

inlineprotected

Construct "empty".

only sets lengths

Member Function Documentation

consensus_cost()

size_type LocARNA::TraceRange::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.

Parameters

i	cut.first
j	cut.second
trs	set of trace ranges

Returns

cost of cut (i,j) in consensus of trs

max_col()

size_t LocARNA::TraceRange::max_col ( size_t  i ) const

inline

Maximal column of trace in a row.

Parameters

i	row of matrix, 0<=i<=rows()

Returns

maximal valid trace cell in the row i

min_col()

size_t LocARNA::TraceRange::min_col ( size_t  i ) const

inline

Minimal column of trace in a row.

Parameters

i	row of matrix, 0<=i<=rows()

Returns

minimal valid trace cell in the row i

print_debug()

void LocARNA::TraceRange::print_debug

(

std::ostream &

out = std::cerr

)

const

Print object to ouptut stream for debugging

Parameters

out	output stream

remove_common_gaps()

TraceRange::seqentry_pair_t LocARNA::TraceRange::remove_common_gaps ( const SeqEntry &  aliA, const SeqEntry &  aliB  )

static

Remove common gaps in pairwise alignment

Parameters

aliA	alignment string A with name (SeqEntry)
aliB	alignment string B with name (SeqEntry)

Returns

pair of "sequence entries" that represent the pairwise alignment given by aliA and aliB where gap-only columns are removed

reverse()

TraceRange LocARNA::TraceRange::reverse

(

)

const

Ranges for reversed sequences.

Returns

the "reversed" ranges

rows()

size_t LocARNA::TraceRange::rows ( ) const

inline

Read number of rows.

Returns

length of seqA, i.e. the maximal row of the trace

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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