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NCBI C++ ToolKit: include/algo/align/prosplign/compartments.hpp File Reference

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  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...
  ◆ TCompartments ◆ TCompartmentStructs ◆ THit ◆ THitRef ◆ THitRefs ◆ CreateCompartmentAccessor()

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()

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]

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] ◆ SelectCompartmentsHits() ◆ USING_SCOPE()

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