#include <params.hh>

Inheritance diagram for LocARNA::AlignerPParams:

Collaboration diagram for LocARNA::AlignerPParams:

[legend]

Public Member Functions
AlignerPParams &	pf_scale (pf_score_t pf_scale)
	set parameter pf_scale More...

Public Member Functions inherited from LocARNA::AlignerParams
AlignerParams &	seqA (const Sequence &seqA)
	set parameter seqeunce A More...

AlignerParams &	seqB (const Sequence &seqB)
	set parameter seqeunce A More...

AlignerParams &	arc_matches (const ArcMatches &arc_matches)
	set parameter arc matches More...

AlignerParams &	scoring (const Scoring &scoring)
	set parameter scoring More...

AlignerParams &	no_lonely_pairs (bool no_lonely_pairs)
	set parameter no_lonely_pairs More...

AlignerParams &	struct_local (bool struct_local)
	set parameter struct_local More...

AlignerParams &	sequ_local (bool sequ_local)
	set parameter sequ_local More...

AlignerParams &	free_endgaps (const std::string &free_endgaps)
	set parameter free_endgaps More...

AlignerParams &	DO_TRACE (bool DO_TRACE)
	set parameter DO_TRACE More...

AlignerParams &	trace_controller (const TraceController &trace_controller)
	set parameter trace_controller More...

AlignerParams &	max_diff_am (int max_diff_am)
	set parameter max_diff_am More...

AlignerParams &	max_diff_at_am (int max_diff_at_am)
	set parameter max_diff_at_am More...

AlignerParams &	min_am_prob (double min_am_prob)
	set parameter min_am_prob More...

AlignerParams &	min_bm_prob (double min_bm_prob)
	set parameter min_bm_prob More...

AlignerParams &	stacking (bool stacking)
	set parameter stacking More...

AlignerParams &	constraints (const AnchorConstraints &constraints)
	set parameter constraints More...

Protected Member Functions
	AlignerPParams ()

Protected Member Functions inherited from LocARNA::AlignerParams
	AlignerParams ()

Protected Attributes
pf_score_t	pf_scale_
	scaling factor for partition function

Protected Attributes inherited from LocARNA::AlignerParams
const Sequence *	seqA_
	sequence A

const Sequence *	seqB_
	sequence B

const ArcMatches *	arc_matches_
	arc matches

const Scoring *	scoring_
	scoring object

bool	no_lonely_pairs_
	no lonely pairs option

bool	struct_local_
	allow exclusions for maximizing alignment of connected substructures

bool	sequ_local_
	sequence local alignment / maximize alignment of subsequences

std::string	free_endgaps_
	description of potentially allowed free end gaps

bool	DO_TRACE_
	whether do perfom trace back

const TraceController *	trace_controller_
	trace controller controlling allowed trace cells

int	max_diff_am_
	maximal difference of arc lengths in arc match

int	max_diff_at_am_
	maximal difference of positions at ends of an arc match

double	min_am_prob_
	minimal probability of an arc match

double	min_bm_prob_
	minimal probability of a base match

bool	stacking_
	whether to use stacking

const AnchorConstraints *	constraints_
	anchor constraints

Detailed Description

parameters for AlignerP

Constructor & Destructor Documentation

LocARNA::AlignerPParams::AlignerPParams ( )

inlineprotected

Construct with default parameters

AlignerPParams& LocARNA::AlignerPParams::pf_scale ( pf_score_t pf_scale )

inline

set parameter pf_scale

Parameters

pf_scale scaling factor for partition function

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