NCBI C++ ToolKit
Classes | Typedefs | Functions
compartments.hpp File Reference
#include <corelib/ncbistl.hpp>
#include <corelib/ncbiargs.hpp>
#include <algo/align/splign/splign.hpp>
#include <objects/seqalign/seqalign__.hpp>
#include <algo/align/util/compartment_finder.hpp>
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Classes

class  CCompartOptions
 
struct  SCompartment
 

Typedefs

typedef CSplign::THit THit
 
typedef CSplign::THitRef THitRef
 
typedef CSplign::THitRefs THitRefs
 
typedef list< CRef< CSeq_annot > > TCompartments
 
typedef vector< SCompartmentTCompartmentStructs
 

Functions

 USING_SCOPE (objects)
 
unique_ptr< CCompartmentAccessor< THit > > CreateCompartmentAccessor (const THitRefs &orig_hitrefs, CCompartOptions compart_options, const vector< pair< THit::TCoord, THit::TCoord > > *gaps=NULL)
 Selects compartments. More...
 
TCompartments FormatAsAsn (CCompartmentAccessor< THit > *comparts_ptr, CCompartOptions compart_options, const vector< pair< THit::TCoord, THit::TCoord > > *gaps=NULL)
 
TCompartmentStructs MakeCompartments (const TCompartments &asn_representation, CCompartOptions compart_options)
 
TCompartments SelectCompartmentsHits (const THitRefs &hitrefs, CCompartOptions compart_options, const vector< pair< THit::TCoord, THit::TCoord > > *gaps=NULL)
 Composition of first two functions. More...
 
TCompartmentStructs MakeCompartments (const THitRefs &hitrefs, CCompartOptions compart_options)
 Composition of all three functions. More...
 

Typedef Documentation

◆ TCompartments

typedef list<CRef<CSeq_annot> > TCompartments

Definition at line 111 of file compartments.hpp.

◆ TCompartmentStructs

Definition at line 112 of file compartments.hpp.

◆ THit

Definition at line 107 of file compartments.hpp.

◆ THitRef

Definition at line 108 of file compartments.hpp.

◆ THitRefs

Definition at line 109 of file compartments.hpp.

Function Documentation

◆ CreateCompartmentAccessor()

unique_ptr<CCompartmentAccessor<THit> > CreateCompartmentAccessor ( const THitRefs orig_hitrefs,
CCompartOptions  compart_options,
const vector< pair< THit::TCoord, THit::TCoord > > *  gaps = NULL 
)

◆ FormatAsAsn()

TCompartments FormatAsAsn ( CCompartmentAccessor< THit > *  comparts_ptr,
CCompartOptions  compart_options,
const vector< pair< THit::TCoord, THit::TCoord > > *  gaps = NULL 
)

◆ MakeCompartments() [1/2]

TCompartmentStructs MakeCompartments ( const TCompartments asn_representation,
CCompartOptions  compart_options 
)

◆ MakeCompartments() [2/2]

TCompartmentStructs MakeCompartments ( const THitRefs hitrefs,
CCompartOptions  compart_options 
)

Composition of all three functions.

Definition at line 427 of file compartments.cpp.

References MakeCompartments(), and SelectCompartmentsHits().

◆ SelectCompartmentsHits()

TCompartments SelectCompartmentsHits ( const THitRefs hitrefs,
CCompartOptions  compart_options,
const vector< pair< THit::TCoord, THit::TCoord > > *  gaps = NULL 
)

Composition of first two functions.

Definition at line 303 of file compartments.cpp.

References CreateCompartmentAccessor(), and FormatAsAsn().

Referenced by CAdvancedAlignCleanup::GetProsplignCompartments(), MakeCompartments(), and CProSplignJob::x_GenerateCompartments().

◆ USING_SCOPE()

USING_SCOPE ( objects  )
Modified on Fri Jan 05 07:25:47 2024 by modify_doxy.py rev. 669887