LocARNA::Aligner Class Reference

Implements locarna alignment algorithm. More...

#include <aligner.hh>

List of all members.

Public Member Functions
	Aligner (const Aligner &aligner)
	copy constructor
Aligner &	operator= (const Aligner &aligner)
	assignment operator
	Aligner (const AlignerParams &ap)
	Construct from parameters.
	~Aligner ()
	destructor
Alignment const &	get_alignment () const
	return the alignment that was computed by trace()
void	set_alignment (const Alignment &alignment)
	set the alignment
infty_score_t	align ()
	compute the alignment score
void	trace ()
	offer trace as public method. Calls trace(def_scoring_view).
void	set_restriction (const AlignerRestriction &r)
const AlignerRestriction &	get_restriction () const
void	suboptimal (int k, score_t threshold, bool normalized, score_t normalized_L, size_t output_width, bool verbose, bool opt_local_out, bool opt_pos_output, bool opt_write_structure)
	Enumerate suboptimal local alignments.
infty_score_t	normalized_align (score_t L, bool verbose)
	perform normalized local alignment with parameter L
infty_score_t	penalized_align (score_t position_penalty)
score_t	evaluate ()
	evaluate the alignment according to scoring and scoring parameters
RnaStructure	optimize_consensus_structure ()
	find optimum consensus structure
Static Public Member Functions
static AlignerParams	create ()
	create with named parameters

---

Detailed Description

Implements locarna alignment algorithm.

Performs the alignment of two sequences and their associated sets of weighted basepairs

An object always knows about the two sequences and the two weighted base pair sets

usage: construct, align, trace, get_alignment

Note:

Idea "NICE TO HAVE": score matrices should be as small as possible and have offsets. The M-Matrix can be smaller if the maximal arc len is limited. The D-matrix may be smaller if the number of simultaneously needed arc-pairs is limited, due to limit on the local sub-sequence lengths. A special cyclically rotatable matrix would be required for alignment on the top-level. Such matrices are implemented in matrix.hh but currently not used.

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Constructor & Destructor Documentation

LocARNA::Aligner::Aligner

(

const Aligner &

aligner

)

copy constructor

Parameters:

aligner

object to be copied Copies implementation object (not only pointer)

LocARNA::Aligner::Aligner

(

const AlignerParams &

ap

)

Construct from parameters.

Parameters:

ap	parameter for aligner

Note:

ap is copied to new AlignerParams object (by impl class) to allow reference to a temporary

used with implicit type cast (for cleaner syntax)

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Member Function Documentation

static AlignerParams LocARNA::Aligner::create

(

)

[inline, static]

create with named parameters

Returns:

parameter object

score_t LocARNA::Aligner::evaluate

(

)

evaluate the alignment according to scoring and scoring parameters

Returns:

score of the alignment

const AlignerRestriction & LocARNA::Aligner::get_restriction

(

)

const

return the current restriction, mainly used for the k-best algorithm

Aligner& LocARNA::Aligner::operator=

(

const Aligner &

aligner

)

assignment operator

Parameters:

aligner

object to be assigned Assigns implementation object (not only pointer)

RnaStructure LocARNA::Aligner::optimize_consensus_structure

(

)

find optimum consensus structure

Returns:

optimum consensus structure for alignment

infty_score_t LocARNA::Aligner::penalized_align

(

score_t

position_penalty

)

perform local alignment by subtracting a penalty for each alignment position

void LocARNA::Aligner::set_alignment

(

const Alignment &

alignment

)

set the alignment

Parameters:

alignment

the alignment to be stored in the Aligner object

This sets the result of the aligner object / trace; it is useful to evaluate given alignments (where it is used in place of a computation by align()/trace()).

void LocARNA::Aligner::set_restriction

(

const AlignerRestriction &

r

)

set the restriction on the alignment, mainly used for the k-best algorithm

void LocARNA::Aligner::suboptimal	(	int	k,
		score_t	threshold,
		bool	normalized,
		score_t	normalized_L,
		size_t	output_width,
		bool	verbose,
		bool	opt_local_out,
		bool	opt_pos_output,
		bool	opt_write_structure
	)

Enumerate suboptimal local alignments.

special operation mode for computing the k best alignments. Used in place of calls to align() and trace()

Parameters:

k	number of suboptimals to be generated (k==-1 means unlimited)
threshold
normalized
normalized_L
output_width
verbose
opt_local_output
opt_pos_output
opt_write_structure

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

• src/LocARNA/aligner.hh
• src/LocARNA/aligner.cc