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< SCompartment >	TCompartmentStructs

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

typedef vector<SCompartment> TCompartmentStructs

Definition at line 112 of file compartments.hpp.

THit

typedef CSplign::THit THit

Definition at line 107 of file compartments.hpp.

THitRef

typedef CSplign::THitRef THitRef

Definition at line 108 of file compartments.hpp.

THitRefs

typedef CSplign::THitRefs 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
	)

Selects compartments.

Hits should be for a single query-subject pair. Pass precalculated non-bridgeable gaps to prohibit compartment to go over it

Definition at line 237 of file compartments.cpp.

References CountQueryCoverage(), CCompartOptions::eAminoAcid, CCompartOptions::eCoverage, CCompartOptions::eGuess, CCompartOptions::eScore, CCompartmentAccessor< THit >::GetFirst(), CCompartmentAccessor< THit >::GetNext(), CAlignShadow::GetQuerySpan(), CAlignShadow::GetSubjSpan(), ITERATE, len, CCompartOptions::m_CompartmentPenalty, CCompartOptions::m_Maximizing, CCompartOptions::m_MaxIntron, CCompartOptions::m_MaxOverlap, CCompartOptions::m_MinCompartmentIdty, CCompartOptions::m_MinSingleCompartmentIdty, CCompartOptions::m_SubjectMol, max(), NCBI_THROW, NULL, RemoveOverlaps(), RestoreOriginalHits(), CCompartmentAccessor< THit >::Run(), CCompartmentAccessor< THit >::SetMaxIntron(), and CCompartmentAccessor< THit >::SetMaxOverlap().

Referenced by DoCompartments(), and SelectCompartmentsHits().

FormatAsAsn()

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

Definition at line 313 of file compartments.cpp.

References _ASSERT, eExtreme_Positional, CCompartmentAccessor< THit >::GetBox(), CCompartmentAccessor< THit >::GetFirst(), CSeq_loc::GetId(), CCompartmentAccessor< THit >::GetNext(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), i, CCompartOptions::m_MaxExtent, MakeCompartment(), CSeq_id::Match(), CRef< C, Locker >::NotEmpty(), NULL, results, CSeq_annot_Base::SetDesc(), and CSeq_loc::SetInt().

Referenced by DoCompartments(), and SelectCompartmentsHits().

MakeCompartments() [1/2]

TCompartmentStructs MakeCompartments	(	const TCompartments &	asn_representation,
		CCompartOptions	compart_options
	)

Definition at line 392 of file compartments.cpp.

References eExtreme_Positional, eNa_strand_minus, CAnnot_descr_Base::Get(), CUser_field_Base::GetData(), CSeq_annot_Base::GetDesc(), CUser_object::GetField(), CUser_field_Base::C_Data::GetInt(), CUser_field_Base::C_Data::GetReal(), CAnnotdesc_Base::GetRegion(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CObject_id_Base::GetStr(), CSeq_loc::GetStrand(), CUser_object_Base::GetType(), CAnnotdesc_Base::GetUser(), i, int, CAnnotdesc_Base::IsRegion(), CObject_id_Base::IsStr(), CAnnotdesc_Base::IsUser(), ITERATE, NULL, results, and ct::sort().

Referenced by DoCompartments(), and MakeCompartments().

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(), FormatAsAsn(), and results.

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

USING_SCOPE()

USING_SCOPE

(

objects

)