LocARNA::AlignerParams Class Reference

Parameter for alignment by Aligner. More...

#include <params.hh>

Inheritance diagram for LocARNA::AlignerParams:

Collaboration diagram for LocARNA::AlignerParams:

Public Member Functions
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
	AlignerParams ()

Protected Attributes
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	Aligner
class	AlignerImpl

Detailed Description

Parameter for alignment by Aligner.

Collects the parameters for the aligner object. These parameters controll the kind of alignment (local/global), restrictions/constraints on the alignment and certain heuristics. Parameters for the score are collected in a different class.

Class supports the named arguments idiom for setting parameters

See also

Aligner

ScoringParams

Constructor & Destructor Documentation

LocARNA::AlignerParams::AlignerParams ( )

inlineprotected

Construct with default parameters

Member Function Documentation

AlignerParams& LocARNA::AlignerParams::arc_matches ( const ArcMatches &  arc_matches )

inline

set parameter arc matches

Parameters

seqB	arc matches

AlignerParams& LocARNA::AlignerParams::constraints ( const AnchorConstraints &  constraints )

inline

set parameter constraints

Parameters

constraints

anchor constraints

AlignerParams& LocARNA::AlignerParams::DO_TRACE ( bool  DO_TRACE )

inline

set parameter DO_TRACE

Parameters

DO_TRACE

perform backtrace

AlignerParams& LocARNA::AlignerParams::free_endgaps ( const std::string &  free_endgaps )

inline

set parameter free_endgaps

Parameters

free_endgaps

description of potentially allowed free end gaps

AlignerParams& LocARNA::AlignerParams::max_diff_am ( int  max_diff_am )

inline

set parameter max_diff_am

Parameters

max_diff_am

maximal difference of arc lengths in arc match

AlignerParams& LocARNA::AlignerParams::max_diff_at_am ( int  max_diff_at_am )

inline

set parameter max_diff_at_am

Parameters

max_diff_at_am

maximal difference at arc match positions

AlignerParams& LocARNA::AlignerParams::min_am_prob ( double  min_am_prob )

inline

set parameter min_am_prob

Parameters

min_am_prob

minimal probability of an arc match

AlignerParams& LocARNA::AlignerParams::min_bm_prob ( double  min_bm_prob )

inline

set parameter min_bm_prob

Parameters

min_bm_prob

minimal probability of a base match

AlignerParams& LocARNA::AlignerParams::no_lonely_pairs ( bool  no_lonely_pairs )

inline

set parameter no_lonely_pairs

Parameters

no_lonely_pairs

no lonely pairs option

AlignerParams& LocARNA::AlignerParams::scoring ( const Scoring &  scoring )

inline

set parameter scoring

Parameters

scoring

scoring object

AlignerParams& LocARNA::AlignerParams::seqA ( const Sequence &  seqA )

inline

set parameter seqeunce A

Parameters

seqA	sequence A

AlignerParams& LocARNA::AlignerParams::seqB ( const Sequence &  seqB )

inline

set parameter seqeunce A

Parameters

seqB	sequence B

AlignerParams& LocARNA::AlignerParams::sequ_local ( bool  sequ_local )

inline

set parameter sequ_local

Parameters

sequ_local

sequence local alignment / maximize alignment of subsequences

AlignerParams& LocARNA::AlignerParams::stacking ( bool  stacking )

inline

set parameter stacking

Parameters

stacking

whether to use stacking

AlignerParams& LocARNA::AlignerParams::struct_local ( bool  struct_local )

inline

set parameter struct_local

Parameters

struct_local

allow exclusions for maximizing alignment of connected substructures

AlignerParams& LocARNA::AlignerParams::trace_controller ( const TraceController &  trace_controller )

inline

set parameter trace_controller

Parameters

trace_controller

trace controller controlling allowed trace cells

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

• src/LocARNA/params.hh
• src/LocARNA/params.cc