Parameters for scoring. More...

#include <scoring.hh>

Public Types
using	valid_args = std::tuple< match, mismatch, indel, indel_loop, indel_opening, indel_opening_loop, ribosum, ribofit, unpaired_penalty, struct_weight, tau_factor, exclusion, exp_probA, exp_probB, temperature_alipf, stacking, new_stacking, mea_scoring, mea_alpha, mea_beta, mea_gamma, probability_scale >

Public Member Functions
	DEFINE_NAMED_ARG_DEFAULT_FEATURE (match, score_t, 50)

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (mismatch, score_t, 0)
	constant cost of a base mismatch

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (indel, score_t, -150)
	cost per indel (for linear or affine gap cost).

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (indel_opening, score_t, -750)
	cost per gap (for affine gap-cost). Use affine gap cost if non-zero.

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (indel_loop, score_t, -200)
	cost per indel for loops (for linear or affine gap cost).

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (indel_opening_loop, score_t, -800)

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (ribosum, const RibosumFreq *, nullptr)

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (ribofit, const Ribofit *, nullptr)

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (unpaired_penalty, score_t, 0)
	penalty/cost for unpaired bases matched/mismatched/gapped

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (struct_weight, score_t, 200)

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (tau_factor, score_t, 50)

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (exclusion, score_t, 0)
	cost of one exclusion.

	DEFINE_NAMED_ARG_FEATURE (exp_probA, double)

	DEFINE_NAMED_ARG_FEATURE (exp_probB, double)

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (temperature_alipf, double, 150)

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (stacking, bool, false)
	turn on/off stacking terms

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (new_stacking, bool, false)
	turn on/off new stacking terms

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (mea_scoring, bool, false)
	turn on/off mea scoring

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (mea_alpha, score_t, 0)
	weight for mea contribution "unstructured"

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (mea_beta, score_t, 200)
	weight for mea contribution "structure"

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (mea_gamma, score_t, 100)
	weight for mea contribution "consensus"

	DEFINE_NAMED_ARG_DEFAULT_FEATURE (probability_scale, score_t, 10000)

template<typename... Args>
	ScoringParams (Args... argpack)

Detailed Description

Parameters for scoring.

Contains all parameters for doing the scoring of alignments in class Scoring. The class encapsulates the configuration of the score.

See also: Scoring

Constructor & Destructor Documentation

◆ ScoringParams()

template<typename... Args>

LocARNA::ScoringParams::ScoringParams ( Args... argpack )

inline

Construct with scoring parameters

Note: Store only pointers to objects passed by pointer; the objects must be kept alive by the caller

Member Function Documentation

◆ DEFINE_NAMED_ARG_DEFAULT_FEATURE() [1/7]

LocARNA::ScoringParams::DEFINE_NAMED_ARG_DEFAULT_FEATURE	(	indel_opening_loop	,
		score_t	,
		-	800
	)

cost per gap for loops(for affine gap-cost). Use affine gap cost if non-zero.

◆ DEFINE_NAMED_ARG_DEFAULT_FEATURE() [2/7]

LocARNA::ScoringParams::DEFINE_NAMED_ARG_DEFAULT_FEATURE	(	match	,
		score_t	,
		50
	)

constant bonus for a base match. together with basemismatch yields the simplest form of base match/mismatch scoring. Can be replaced by RIBOSUM scores.

◆ DEFINE_NAMED_ARG_DEFAULT_FEATURE() [3/7]

LocARNA::ScoringParams::DEFINE_NAMED_ARG_DEFAULT_FEATURE	(	probability_scale	,
		score_t	,
		10000
	)

resolution of the mea score. Since the mea score is composed from probabilities and scores are integral there must be some factor to scale the probabilities in order to get scores.

◆ DEFINE_NAMED_ARG_DEFAULT_FEATURE() [4/7]

LocARNA::ScoringParams::DEFINE_NAMED_ARG_DEFAULT_FEATURE	(	ribofit	,
		const Ribofit *	,
		nullptr
	)

the ribofit matrix, if non-null it is used for base match/mismatch instead of constant values and as contribution for arc-matchs (tau_factor). Overrides ribosum

◆ DEFINE_NAMED_ARG_DEFAULT_FEATURE() [5/7]

LocARNA::ScoringParams::DEFINE_NAMED_ARG_DEFAULT_FEATURE	(	ribosum	,
		const RibosumFreq *	,
		nullptr
	)

the ribosum matrix, if non-null (and ribofit==null) it is used for base match/mismatch instead of constant values and as contribution for arc-matchs (tau_factor)

◆ DEFINE_NAMED_ARG_DEFAULT_FEATURE() [6/7]

LocARNA::ScoringParams::DEFINE_NAMED_ARG_DEFAULT_FEATURE	(	struct_weight	,
		score_t	,
		200
	)

Factor for structure contribution in the classic score. Maximal contribution of 1/2 arc match

◆ DEFINE_NAMED_ARG_DEFAULT_FEATURE() [7/7]

LocARNA::ScoringParams::DEFINE_NAMED_ARG_DEFAULT_FEATURE	(	tau_factor	,
		score_t	,
		50
	)

Factor for the contribution of sequence score or ribosum score to arc matchs

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

src/LocARNA/scoring.hh

Public Types

Public Member Functions