NCBI C++ ToolKit
Functions
compartments.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/general/general__.hpp>
#include <objects/seqloc/seqloc__.hpp>
#include <objects/seq/seq__.hpp>
#include <algo/align/prosplign/compartments.hpp>
#include <algo/align/prosplign/prosplign_exception.hpp>
#include <algo/align/util/hit_comparator.hpp>
#include <algo/align/util/compartment_finder.hpp>
+ Include dependency graph for compartments.cpp:

Go to the source code of this file.

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Functions

 USING_SCOPE (ncbi::objects)
 
int CountQueryCoverage (THitRefs &hitrefs)
 
void RestoreOriginalHits (THitRefs &hitrefs, const THitRefs &orig_hitrefs, bool is_protein_subject)
 
void RemoveOverlaps (THitRefs &hitrefs)
 
double TotalScore (THitRefs &hitrefs)
 
int TotalRawScore (THitRefs &hitrefs)
 
CRef< CScoreIntScore (const string &id, int value)
 
CRef< CScoreRealScore (const string &id, double value)
 
CRef< CSeq_annotMakeCompartment (THitRefs &hitrefs)
 
unique_ptr< CCompartmentAccessor< THit > > CreateCompartmentAccessor (const THitRefs &orig_hitrefs, CCompartOptions compart_options, const vector< pair< THit::TCoord, THit::TCoord > > *gaps)
 Selects compartments. More...
 
TCompartments SelectCompartmentsHits (const THitRefs &orig_hitrefs, CCompartOptions compart_options, const vector< pair< THit::TCoord, THit::TCoord > > *gaps)
 Composition of first two functions. More...
 
TCompartments FormatAsAsn (CCompartmentAccessor< THit > *comps_ptr, CCompartOptions compart_options, const vector< pair< THit::TCoord, THit::TCoord > > *gaps)
 
TCompartmentStructs MakeCompartments (const TCompartments &compartments, CCompartOptions compart_options)
 
TCompartmentStructs MakeCompartments (const CSplign::THitRefs &hitrefs, CCompartOptions compart_options)
 Composition of all three functions. More...
 

Function Documentation

◆ CountQueryCoverage()

int CountQueryCoverage ( THitRefs hitrefs)

Definition at line 49 of file compartments.cpp.

References _ASSERT, ITERATE, len, and max().

Referenced by CreateCompartmentAccessor(), and MakeCompartment().

◆ 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 > *  comps_ptr,
CCompartOptions  compart_options,
const vector< pair< THit::TCoord, THit::TCoord > > *  gaps 
)

◆ IntScore()

CRef<CScore> IntScore ( const string id,
int  value 
)

Definition at line 139 of file compartments.cpp.

References result, and rapidjson::value.

Referenced by MakeCompartment().

◆ MakeCompartment()

CRef<CSeq_annot> MakeCompartment ( THitRefs hitrefs)

◆ MakeCompartments() [1/2]

TCompartmentStructs MakeCompartments ( const CSplign::THitRefs hitrefs,
CCompartOptions  compart_options 
)

Composition of all three functions.

Definition at line 427 of file compartments.cpp.

References MakeCompartments(), and SelectCompartmentsHits().

◆ MakeCompartments() [2/2]

TCompartmentStructs MakeCompartments ( const TCompartments compartments,
CCompartOptions  compart_options 
)

◆ RealScore()

CRef<CScore> RealScore ( const string id,
double  value 
)

Definition at line 147 of file compartments.cpp.

References result, and rapidjson::value.

Referenced by MakeCompartment().

◆ RemoveOverlaps()

void RemoveOverlaps ( THitRefs hitrefs)

Definition at line 111 of file compartments.cpp.

References copy(), remove_if(), and CHitFilter< THit >::s_RunGreedy().

Referenced by CreateCompartmentAccessor().

◆ RestoreOriginalHits()

void RestoreOriginalHits ( THitRefs hitrefs,
const THitRefs orig_hitrefs,
bool  is_protein_subject 
)

Definition at line 75 of file compartments.cpp.

References ITERATE, and NON_CONST_ITERATE.

Referenced by CreateCompartmentAccessor().

◆ SelectCompartmentsHits()

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

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().

◆ TotalRawScore()

int TotalRawScore ( THitRefs hitrefs)

Definition at line 130 of file compartments.cpp.

References i, ITERATE, and result.

Referenced by MakeCompartment().

◆ TotalScore()

double TotalScore ( THitRefs hitrefs)

Definition at line 121 of file compartments.cpp.

References i, ITERATE, and result.

Referenced by MakeCompartment().

◆ USING_SCOPE()

USING_SCOPE ( ncbi::objects  )
Modified on Wed Jul 17 13:19:56 2024 by modify_doxy.py rev. 669887