ARB: FamilyFinder Class Reference

ARB

#include <awtc_next_neighbours.hxx>

Inheritance diagram for FamilyFinder:

Inheritance graph

Collaboration diagram for FamilyFinder:

Collaboration graph

Public Member Functions
	FamilyFinder (bool rel_matches_, RelativeScoreScaling scaling_)

virtual	~FamilyFinder ()

void	restrict_2_region (const PosRange &range_)

void	unrestrict ()

const PosRange &	get_TargetRange () const

virtual GB_ERROR	searchFamily (const char *sequence, FF_complement compl_mode, int max_results, double min_score)=0

const FamilyList *	getFamilyList () const

void	delete_family_list ()

bool	hits_were_truncated () const

bool	uses_rel_matches () const

RelativeScoreScaling	get_scaling () const

int	getRealHits () const

Protected Attributes
FamilyList *	family_list

bool	hits_truncated

long	real_hits

PosRange	range

Detailed Description

Definition at line 51 of file awtc_next_neighbours.hxx.

Constructor & Destructor Documentation

FamilyFinder::FamilyFinder	(	bool	rel_matches_,
		RelativeScoreScaling	scaling_
	)

Definition at line 90 of file AWTC_next_neighbours.cxx.

FamilyFinder::~FamilyFinder ( )

virtual

Definition at line 99 of file AWTC_next_neighbours.cxx.

References delete_family_list().

Member Function Documentation

void FamilyFinder::restrict_2_region ( const PosRange & range_ )

inline

Definition at line 69 of file awtc_next_neighbours.hxx.

Referenced by awtc_nn_search(), awtc_nn_search_all_listed(), and FastAligner_start().

void FamilyFinder::unrestrict ( )

inline

Definition at line 76 of file awtc_next_neighbours.hxx.

const PosRange& FamilyFinder::get_TargetRange ( ) const

inline

Definition at line 77 of file awtc_next_neighbours.hxx.

References range.

Referenced by alignToNextRelative().

virtual GB_ERROR FamilyFinder::searchFamily	(	const char *	sequence,
		FF_complement	compl_mode,
		int	max_results,
		double	min_score
	)

pure virtual

Implemented in PT_FamilyFinder.

Referenced by alignToNextRelative().

const FamilyList* FamilyFinder::getFamilyList ( ) const

inline

Definition at line 81 of file awtc_next_neighbours.hxx.

References family_list.

Referenced by alignToNextRelative(), awtc_nn_search(), and awtc_nn_search_all_listed().

void FamilyFinder::delete_family_list ( )

Definition at line 103 of file AWTC_next_neighbours.cxx.

References family_list, and NULp.

Referenced by ~FamilyFinder(), and PT_FamilyFinder::~PT_FamilyFinder().

bool FamilyFinder::hits_were_truncated ( ) const

inline

Definition at line 84 of file awtc_next_neighbours.hxx.

References hits_truncated.

Referenced by awtc_nn_search().

bool FamilyFinder::uses_rel_matches ( ) const

inline

Definition at line 85 of file awtc_next_neighbours.hxx.

Referenced by alignToNextRelative().

RelativeScoreScaling FamilyFinder::get_scaling ( ) const

inline

Definition at line 86 of file awtc_next_neighbours.hxx.

int FamilyFinder::getRealHits ( ) const

inline

Definition at line 87 of file awtc_next_neighbours.hxx.

References real_hits.

Referenced by awtc_nn_search().

Member Data Documentation

FamilyList* FamilyFinder::family_list

protected

Definition at line 56 of file awtc_next_neighbours.hxx.

Referenced by delete_family_list(), getFamilyList(), and PT_FamilyFinder::results2string().

bool FamilyFinder::hits_truncated

protected

Definition at line 58 of file awtc_next_neighbours.hxx.

Referenced by hits_were_truncated().

long FamilyFinder::real_hits

protected

Definition at line 61 of file awtc_next_neighbours.hxx.

Referenced by getRealHits().

PosRange FamilyFinder::range

protected

Definition at line 63 of file awtc_next_neighbours.hxx.

Referenced by get_TargetRange(), and PT_FamilyFinder::searchFamily().

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

AWTC/awtc_next_neighbours.hxx
AWTC/AWTC_next_neighbours.cxx