LocARNA::AlignerNParams Class Reference

parameters for AlignerN More...

#include <params.hh>

Inheritance diagram for LocARNA::AlignerNParams:

Collaboration diagram for LocARNA::AlignerNParams:

Public Member Functions
AlignerNParams &	sparsification_mapperA (const SparsificationMapper &sparsification_mapperA)
	set parameter sparsification mapper More...
AlignerNParams &	sparsification_mapperB (const SparsificationMapper &sparsification_mapperB)
	set parameter sparsification mapper 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
	AlignerNParams ()
Protected Member Functions inherited from LocARNA::AlignerParams
	AlignerParams ()

Protected Attributes
const SparsificationMapper *	sparsification_mapperA_
	sparsification mapper A
const SparsificationMapper *	sparsification_mapperB_
	sparsification mapper B
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

Friends
class	AlignerN

Detailed Description

parameters for AlignerN

Constructor & Destructor Documentation

LocARNA::AlignerNParams::AlignerNParams ( )

inlineprotected

Construct with default parameters

Member Function Documentation

AlignerNParams& LocARNA::AlignerNParams::sparsification_mapperA ( const SparsificationMapper &  sparsification_mapperA )

inline

set parameter sparsification mapper

Parameters

sparsification_mapperA

scaling sparisification mapper for A

AlignerNParams& LocARNA::AlignerNParams::sparsification_mapperB ( const SparsificationMapper &  sparsification_mapperB )

inline

set parameter sparsification mapper

Parameters

sparsification_mapperB

scaling sparisification mapper for A

---

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

• src/LocARNA/params.hh