ARB
Public Member Functions | Protected Attributes | List of all members
FamilyFinder Class Referenceabstract

#include <awtc_next_neighbours.hxx>

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Public Member Functions

 FamilyFinder (bool rel_matches_, RelativeScoreScaling scaling_)
 
virtual ~FamilyFinder ()
 
void restrict_2_region (const PosRange &range_)
 
void unrestrict ()
 
const PosRangeget_TargetRange () const
 
virtual GB_ERROR searchFamily (const char *sequence, FF_complement compl_mode, int max_results, double min_score)=0
 
const FamilyListgetFamilyList () const
 
void delete_family_list ()
 
bool hits_were_truncated () const
 
bool uses_rel_matches () const
 
RelativeScoreScaling get_scaling () const
 
int getRealHits () const
 

Protected Attributes

FamilyListfamily_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
void FamilyFinder::unrestrict ( )
inline

Definition at line 78 of file awtc_next_neighbours.hxx.

const PosRange& FamilyFinder::get_TargetRange ( ) const
inline

Definition at line 79 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 83 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 86 of file awtc_next_neighbours.hxx.

References hits_truncated.

Referenced by awtc_nn_search().

bool FamilyFinder::uses_rel_matches ( ) const
inline

Definition at line 87 of file awtc_next_neighbours.hxx.

Referenced by alignToNextRelative().

RelativeScoreScaling FamilyFinder::get_scaling ( ) const
inline

Definition at line 88 of file awtc_next_neighbours.hxx.

int FamilyFinder::getRealHits ( ) const
inline

Definition at line 89 of file awtc_next_neighbours.hxx.

References real_hits.

Referenced by awtc_nn_search().

Member Data Documentation

FamilyList* FamilyFinder::family_list
protected
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 63 of file awtc_next_neighbours.hxx.

Referenced by getRealHits().

PosRange FamilyFinder::range
protected

Definition at line 65 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: