LocARNA::AlignerParams Class Reference

Parameter for alignment by Aligner. More...

#include <params.hh>

Inheritance diagram for LocARNA::AlignerParams:

List of all members.

Public Member Functions
AlignerParams &	seqA (const Sequence &seqA)
	set parameter seqeunce A
AlignerParams &	seqB (const Sequence &seqB)
	set parameter seqeunce A
AlignerParams &	arc_matches (const ArcMatches &arc_matches)
	set parameter arc matches
AlignerParams &	scoring (const Scoring &scoring)
	set parameter scoring
AlignerParams &	no_lonely_pairs (bool no_lonely_pairs)
	set parameter no_lonely_pairs
AlignerParams &	struct_local (bool struct_local)
	set parameter struct_local
AlignerParams &	sequ_local (bool sequ_local)
	set parameter sequ_local
AlignerParams &	free_endgaps (const std::string &free_endgaps)
	set parameter free_endgaps
AlignerParams &	DO_TRACE (bool DO_TRACE)
	set parameter DO_TRACE
AlignerParams &	trace_controller (const TraceController &trace_controller)
	set parameter trace_controller
AlignerParams &	max_diff_am (int max_diff_am)
	set parameter max_diff_am
AlignerParams &	max_diff_at_am (int max_diff_at_am)
	set parameter max_diff_at_am
AlignerParams &	stacking (bool stacking)
	set parameter stacking
AlignerParams &	constraints (const AnchorConstraints &constraints)
	set parameter constraints
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_
bool	sequ_local_
std::string	free_endgaps_
	description of potentially allowed free end gaps
bool	DO_TRACE_
	whether do perfom trace back
const TraceController *	trace_controller_
int	max_diff_am_
	maximal difference of arc lengths in arc match
int	max_diff_at_am_
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

(

)

[inline, protected]

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::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

---

Member Data Documentation

int LocARNA::AlignerParams::max_diff_at_am_ [protected]

maximal difference of positions at ends of an arc match

bool LocARNA::AlignerParams::sequ_local_ [protected]

sequence local alignment / maximize alignment of subsequences

bool LocARNA::AlignerParams::struct_local_ [protected]

allow exclusions for maximizing alignment of connected substructures

const TraceController* LocARNA::AlignerParams::trace_controller_ [protected]

trace controller controlling allowed trace cells

---

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

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