src/algo/align/prosplign/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:

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Typedefs
typedef CSplign::THit	THit
typedef CSplign::THitRef	THitRef
typedef CSplign::THitRefs	THitRefs
Functions
	USING_SCOPE (ncbi::objects)
int	CountQueryCoverage (THitRefs &hitrefs)
void	RemoveOverlaps (THitRefs &hitrefs)
double	TotalScore (THitRefs &hitrefs)
CRef< CScore >	IntScore (const string &id, int value)
CRef< CScore >	RealScore (const string &id, double value)
CRef< CSeq_annot >	MakeCompartment (THitRefs &hitrefs, const THitRefs &orig_hitrefs)
TCompartments	SelectCompartmentsHits (const THitRefs &orig_hitrefs, CCompartOptions compart_options)
TCompartmentStructs	MakeCompartments (const TCompartments &compartments, CCompartOptions compart_options)
TCompartmentStructs	MakeCompartments (const CSplign::THitRefs &hitrefs, CCompartOptions compart_options)
	Composition of above two functions.

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Typedef Documentation

typedef CSplign::THit THit

Definition at line 48 of file compartments.cpp.

typedef CSplign::THitRef THitRef

Definition at line 49 of file compartments.cpp.

typedef CSplign::THitRefs THitRefs

Definition at line 50 of file compartments.cpp.

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Function Documentation

int CountQueryCoverage (  THitRefs &  hitrefs  )

Definition at line 52 of file compartments.cpp. References ITERATE, and len. Referenced by SelectCompartmentsHits().

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

Definition at line 96 of file compartments.cpp.

CRef<CSeq_annot> MakeCompartment (  THitRefs &  hitrefs, const THitRefs &  orig_hitrefs )

Definition at line 112 of file compartments.cpp. References _ASSERT, eNa_strand_minus, eNa_strand_plus, CSeq_align_Base::eType_partial, ITERATE, RealScore(), CSeq_align_Base::SetSegs(), and CSeq_align_Base::SetType(). Referenced by SelectCompartmentsHits().

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

Composition of above two functions. Definition at line 282 of file compartments.cpp. References MakeCompartments(), and SelectCompartmentsHits().

TCompartmentStructs MakeCompartments (  const TCompartments &  compartments, CCompartOptions  compart_options )

Definition at line 236 of file compartments.cpp. References CSeq_annot_Base::GetDesc(), CSeq_loc_Base::GetInt(), and ITERATE.

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

Definition at line 104 of file compartments.cpp. Referenced by MakeCompartment().

void RemoveOverlaps (  THitRefs &  hitrefs  )

Definition at line 77 of file compartments.cpp. References remove_if(), and CHitFilter< THit >::s_RunGreedy(). Referenced by SelectCompartmentsHits().

TCompartments SelectCompartmentsHits (  const THitRefs &  orig_hitrefs, CCompartOptions  compart_options )

Definition at line 167 of file compartments.cpp. References align, CountQueryCoverage(), CAlign_def_Base::eAlign_type_ref, eNa_strand_minus, eNa_strand_plus, CCompartmentAccessor< THit >::GetBox(), CCompartmentAccessor< THit >::GetFirst(), CCompartmentAccessor< THit >::GetNext(), CCompartmentAccessor< THit >::GetStrand(), ITERATE, len, CCompartOptions::m_ByCoverage, CCompartOptions::m_CompartmentPenalty, CCompartOptions::m_MaxIntron, CCompartOptions::m_MinCompartmentIdty, CCompartOptions::m_MinSingleCompartmentIdty, MakeCompartment(), NCBI_THROW, RemoveOverlaps(), CCompartmentAccessor< THit >::Run(), CCompartmentAccessor< THit >::SetMaxIntron(), and TotalScore().

double TotalScore (  THitRefs &  hitrefs  )

Definition at line 87 of file compartments.cpp. References ITERATE. Referenced by SelectCompartmentsHits().

USING_SCOPE (  ncbi::objects   )

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