LocARNA::ScoringParams Class Reference

Parameters for scoring. More...

#include <scoring.hh>

List of all members.

Public Member Functions
	ScoringParams (score_t basematch_, score_t basemismatch_, score_t indel_, score_t indel_loop_, score_t indel_opening_, score_t indel_opening_loop_, RibosumFreq *ribosum_, Ribofit *ribofit_, score_t unpaired_penalty_, score_t struct_weight_, score_t tau_factor_, score_t exclusion_, double exp_probA_, double exp_probB_, double temp_, bool stacking_, bool new_stacking_, bool mea_scoring_, score_t alpha_factor_, score_t beta_factor_, score_t gamma_factor_, score_t probability_scale_)
Public Attributes
const score_t	basematch
const score_t	basemismatch
	constant cost of a base mismatch
const score_t	indel
	cost per indel (for linear or affine gap cost).
const score_t	indel_loop
	cost per indel for loops (for linear or affine gap cost).
const score_t	indel_opening
	cost per gap (for affine gap-cost). Use affine gap cost if non-zero.
const score_t	indel_opening_loop
const RibosumFreq *	ribosum
const Ribofit *	ribofit
const score_t	unpaired_penalty
	penalty/cost for unpaired bases matched/mismatched/gapped
const score_t	struct_weight
const score_t	tau_factor
const score_t	exclusion
	cost of one exclusion.
const double	exp_probA
const double	exp_probB
const double	temperature_alipf
const bool	stacking
	turn on/off stacking terms
const bool	new_stacking
	turn on/off new stacking terms
const bool	mea_scoring
	turn on/off mea scoring
const score_t	alpha_factor
	weight for mea contribution "unstructured"
const score_t	beta_factor
	weight for mea contribution "structure"
const score_t	gamma_factor
	weight for mea contribution "consensus"
const score_t	probability_scale

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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

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Constructor & Destructor Documentation

LocARNA::ScoringParams::ScoringParams	(	score_t	basematch_,
		score_t	basemismatch_,
		score_t	indel_,
		score_t	indel_loop_,
		score_t	indel_opening_,
		score_t	indel_opening_loop_,
		RibosumFreq *	ribosum_,
		Ribofit *	ribofit_,
		score_t	unpaired_penalty_,
		score_t	struct_weight_,
		score_t	tau_factor_,
		score_t	exclusion_,
		double	exp_probA_,
		double	exp_probB_,
		double	temp_,
		bool	stacking_,
		bool	new_stacking_,
		bool	mea_scoring_,
		score_t	alpha_factor_,
		score_t	beta_factor_,
		score_t	gamma_factor_,
		score_t	probability_scale_
	)		[inline]

Construct with all scoring parameters

Parameters:

basematch_
basemismatch_
indel_
indel_loop_
indel_opening_
indel_opening_loop_
ribosum_
ribofit_
unpaired_penalty_
struct_weight_
tau_factor_
exclusion_
exp_probA_
exp_probB_
temp_
stacking_
new_stacking_
mea_scoring_
alpha_factor_
beta_factor_
gamma_factor_
probability_scale_

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Member Data Documentation

const score_t LocARNA::ScoringParams::basematch

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

const score_t LocARNA::ScoringParams::indel_opening_loop

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

const score_t LocARNA::ScoringParams::probability_scale

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.

const Ribofit* LocARNA::ScoringParams::ribofit

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

const RibosumFreq* LocARNA::ScoringParams::ribosum

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)

const score_t LocARNA::ScoringParams::struct_weight

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

const score_t LocARNA::ScoringParams::tau_factor

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

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

• src/LocARNA/scoring.hh