LocARNA::Scoring Class Reference

Provides methods for the scoring of alignments. More...

#include <scoring.hh>

List of all members.

Public Types
typedef BasePairs__Arc	Arc
	arc
Public Member Functions
	Scoring (const Sequence &seqA, const Sequence &seqB, const RnaData &rna_dataA, const RnaData &rna_dataB, const ArcMatches &arc_matches, const MatchProbs *match_probs, const ScoringParams &params, bool exp_scores=false)
	construct scoring object
void	modify_by_parameter (score_t lambda)
void	apply_unpaired_penalty ()
score_t	lambda () const
	Get factor lambda for normalized alignment.
score_t	basematch (size_type i, size_type j) const
	Score of a match of bases (without structure)
pf_score_t	exp_basematch (size_type i, size_type j) const
	Boltzmann weight of score of a base match (without structure)
score_t	arcmatch (const ArcMatch &am, bool stacked=false) const
	Score of arc match, support explicit arc match scores.
score_t	arcmatch (const BasePairs__Arc &arcA, const BasePairs__Arc &arcB, bool stacked=false) const
	Score of arc match, given two arcs.
template<bool gapAorB>
score_t	arcDel (const BasePairs__Arc &arc, bool stacked=false) const
	Very basic interface, score of aligning a basepair to gap.
pf_score_t	exp_arcmatch (const ArcMatch &am) const
	Boltzmann weight of score of arc match.
score_t	arcmatch_stacked (const ArcMatch &am) const
	Score of stacked arc match.
template<bool gapInA>
score_t	gapX (size_type alignedToGap) const
score_t	gapA (size_type posA) const
pf_score_t	exp_gapA (size_type posA) const
	Boltzmann weight of score of deletion.
score_t	gapB (size_type posB) const
pf_score_t	exp_gapB (size_type posB) const
	Boltzmann weight of score of insertion.
score_t	exclusion () const
	cost of an exclusion
score_t	indel_opening () const
	cost to begin a new indel
score_t	loop_indel_score (const score_t score) const
	multiply an score by the ratio of indel_loop/indel
score_t	indel_opening_loop () const
	cost to begin a new indel
pf_score_t	exp_indel_opening () const
	exp of cost to begin a new indel
pf_score_t	exp_indel_opening_loop () const
	exp of cost to begin a new indel in loops
double	prob_exp (size_type len) const
	Expected base pair probability.
bool	stacking () const
	Query stacking flag.
bool	is_stackable_arcA (const Arc &a) const
	Is arc of A stackable.
bool	is_stackable_arcB (const Arc &a) const
	Is arc of B stackable.
bool	is_stackable_am (const ArcMatch &am) const
	Is arc match stackable.

---

Detailed Description

Provides methods for the scoring of alignments.

Maintains and provides the scores for the alignment of two specific Rnas. Configurable via class ScoringParams, supports the classic LocARNA-score as well as the LocARNA MEA-Score. for "Classic Score" it supports * match/mismatch cost or RIBOSUM for bases * linear or affine gap cost * arc match scores build of arc probabilitiesmatch_probs and optionally base match contribution or RIBOSUM for the "MEA Score" it supports * base match/mismatch scores derived from base match probabilities * RIBOSUM for base and arc match contribution * arc match score contributions from arc probabilities * weighting of single score contributions

The scoring class supports only characters ACGU, gap -, and N for ribosum scoring. ALL other characters are treated as unknown characters and are basically ignored. In consequence, IUPAC codes are handled badly. Even more important, for ribosum scoring, sequences have to be upper case and Ts should be converted to Us!!!

Note:

The class implements two versions of the stacking score (controlled by ScoringParams flags stacking and new_stacking. The first flag lets the class derive the arc weights for stacked arcs from the conditional probability of the base pair (i,j) if (i+1,j-1) exists. The new_stacking flag adds a log odd contribution derived from the joint probability of (i,j) and (i+1,j-1) to the weight of (i,j).

Todo:

check proper use of unpaired penalty; e.g. is correction needed for arc match (like for lambda)??

---

Constructor & Destructor Documentation

LocARNA::Scoring::Scoring	(	const Sequence &	seqA,
		const Sequence &	seqB,
		const RnaData &	rna_dataA,
		const RnaData &	rna_dataB,
		const ArcMatches &	arc_matches,
		const MatchProbs *	match_probs,
		const ScoringParams &	params,
		bool	exp_scores = false
	)

construct scoring object

Parameters:

seqA	first sequence
seqB	second sequence
rna_dataA	probability data of first sequence
rna_dataB	probability data of second sequence
arc_matches	the (significant) arc matches between the sequences
match_probs	pointer to base match probabilities (can be 0L for non-mea scores)
params	a collection of parameters for scoring
exp_scores	only if true, the results of the exp_* scoring functions are defined, otherwise precomputations can be ommitted.

---

Member Function Documentation

void LocARNA::Scoring::apply_unpaired_penalty

(

)

subtract the fixed unpaired_penalty from base match and base indel scores it is similar to method Please note that the base match and gap scores of ALL bases including the paired ones will be modified!

template<bool isA>

score_t LocARNA::Scoring::arcDel	(	const BasePairs__Arc &	arc,
		bool	stacked = false
	)		const

Very basic interface, score of aligning a basepair to gap.

Note:

gapAorB whether deleting element in A or B (true for A)

Parameters:

arc	the base pair
stacked	whether the base pair is stacked

Returns:

score_t LocARNA::Scoring::arcmatch	(	const ArcMatch &	am,
		bool	stacked = false
	)		const

Score of arc match, support explicit arc match scores.

Parameters:

am	arc match
stacked	is stacked? (optional parameter)

Returns:

Score of arc match am (potentially stacked)

Note:

This method supports explicit arc match scores. Such scores are required for the probabilistic mode of (m)locarna.

This method should be prefered over arcmatch(const Arc &arcA, const Arc &arcB, bool stacked=false) unless explicit arc match scores are not needed and the use of this method would be too inefficient.

score_t LocARNA::Scoring::arcmatch	(	const BasePairs__Arc &	arcA,
		const BasePairs__Arc &	arcB,
		bool	stacked = false
	)		const

Score of arc match, given two arcs.

Parameters:

arcA	base pair in A
arcB	base pair in B
stacked	is stacked? (optional parameter)

Returns:

Score of arc match am (potentially stacked)

Note:

This method does not support explicit arc match scores, since this would require to know the arcmatch object.

Using this method is disallowed if arc_matches->explicit_scores()==true (This results in a run-time error if !NDEBUG).

score_t LocARNA::Scoring::arcmatch_stacked

(

const ArcMatch &

am

)

const [inline]

Score of stacked arc match.

Parameters:

am

arc match

Returns:

Score of arc match am when stacked

score_t LocARNA::Scoring::basematch	(	size_type	i,
		size_type	j
	)		const [inline]

Score of a match of bases (without structure)

Parameters:

i	position in A
j	position in B

Returns:

score of base match i~j

pf_score_t LocARNA::Scoring::exp_arcmatch

(

const ArcMatch &

am

)

const [inline]

Boltzmann weight of score of arc match.

Parameters:

am

arc match

Returns:

Boltzmann weight of score of arc match am

pf_score_t LocARNA::Scoring::exp_basematch	(	size_type	i,
		size_type	j
	)		const [inline]

Boltzmann weight of score of a base match (without structure)

Parameters:

i	position in A
j	position in B

Returns:

Boltzmann weight of score of base match i~j

pf_score_t LocARNA::Scoring::exp_gapA

(

size_type

posA

)

const [inline]

Boltzmann weight of score of deletion.

Parameters:

posA	position in A

Returns:

Boltzmann weight of score of deletion of posA after posB

pf_score_t LocARNA::Scoring::exp_gapB

(

size_type

posB

)

const [inline]

Boltzmann weight of score of insertion.

Parameters:

posB	position in B

Returns:

Boltzmann weight of score of insertion of posB after posA

score_t LocARNA::Scoring::gapA

(

size_type

posA

)

const [inline]

Score of deletion

Parameters:

posA	position in A

Returns:

score of deletion of posA after posB

score_t LocARNA::Scoring::gapB

(

size_type

posB

)

const [inline]

Score of insertion

Parameters:

posB	position in B

Returns:

score of insertion of posB after posA

score_t LocARNA::Scoring::gapX< false >

(

size_type

alignedToGap

)

const [inline]

Score of deletion

Parameters:

alignedToGap	position in A or B
gapInA	whether symbol in A (true) or B (false) is aligned to gap

Returns:

score of deletion : posA <--> posB

bool LocARNA::Scoring::is_stackable_am

(

const ArcMatch &

am

)

const

Is arc match stackable.

Parameters:

am

Arc match

Returns:

whether stackable

bool LocARNA::Scoring::is_stackable_arcA

(

const Arc &

a

)

const

Is arc of A stackable.

Parameters:

a

Arc

Returns:

whether stackable

bool LocARNA::Scoring::is_stackable_arcB

(

const Arc &

a

)

const

Is arc of B stackable.

Parameters:

a

Arc

Returns:

whether stackable

score_t LocARNA::Scoring::lambda

(

)

const [inline]

Get factor lambda for normalized alignment.

Returns:

lambda

void LocARNA::Scoring::modify_by_parameter

(

score_t

lambda

)

modify scoring by a parameter lambda. Used in the computational of normalized local alignment by fractional programming in the form of the Dinkelbach algorithm. The modification is destructive. modify_by_parameter(0) results in unmodified scoring. Repeated modifications are valid. The Outcome is *undefined* when the Scoring object is used to obtain exponentiated scores (methods exp_...) as in partition function alignment.

Parameters:

lambda

the parameter

double LocARNA::Scoring::prob_exp

(

size_type

len

)

const

Expected base pair probability.

Parameters:

len	length of RNA sequence

Returns:

expected base pair probability for sequence length

Note:

influences computation of weights for base pairs

bool LocARNA::Scoring::stacking

(

)

const [inline]

Query stacking flag.

Returns:

flag, whether stacking is used (old or new stacking terms)

---

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

• src/LocARNA/scoring.hh
• src/LocARNA/scoring.cc