variation::CVariationUtil::CCdregionIndex Class Reference

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Cache seq-data in the CDS regions and the cds features by location. More...

Collaboration diagram for variation::CVariationUtil::CCdregionIndex:

Classes
struct	SCdregion
struct	SSeqData

Public Types
typedef vector< SCdregion >	TCdregions

Public Member Functions
	CCdregionIndex (CScope &scope, TOptions options)
void	Get (const CSeq_loc &loc, TCdregions &cdregions)
CRef< CSeq_literal >	GetCachedLiteralAtLoc (const CSeq_loc &loc)
void	Clear ()

Private Types
typedef map< CSeq_id_Handle, SSeqData >	TSeqDataMap
typedef CRangeMap< TCdregions, TSeqPos >	TRangeMap
typedef map< CSeq_id_Handle, TRangeMap >	TIdRangeMap

Private Member Functions
void	x_Index (const CSeq_id_Handle &idh)
void	x_CacheSeqData (const CSeq_loc &loc, const CSeq_id_Handle &idh)

Private Attributes
CRef< CScope >	m_scope
TIdRangeMap	m_data
TSeqDataMap	m_seq_data_map
TOptions	m_options

Detailed Description

Cache seq-data in the CDS regions and the cds features by location.

Definition at line 399 of file variation_util2.hpp.

Member Typedef Documentation

TCdregions

typedef vector<SCdregion> variation::CVariationUtil::CCdregionIndex::TCdregions

Definition at line 412 of file variation_util2.hpp.

TIdRangeMap

typedef map<CSeq_id_Handle, TRangeMap> variation::CVariationUtil::CCdregionIndex::TIdRangeMap

private

Definition at line 438 of file variation_util2.hpp.

TRangeMap

typedef CRangeMap<TCdregions, TSeqPos> variation::CVariationUtil::CCdregionIndex::TRangeMap

private

Definition at line 437 of file variation_util2.hpp.

TSeqDataMap

typedef map<CSeq_id_Handle, SSeqData> variation::CVariationUtil::CCdregionIndex::TSeqDataMap

private

Definition at line 436 of file variation_util2.hpp.

Constructor & Destructor Documentation

CCdregionIndex()

variation::CVariationUtil::CCdregionIndex::CCdregionIndex ( CScope &  scope, TOptions  options  )

inline

Definition at line 414 of file variation_util2.hpp.

Member Function Documentation

Clear()

void variation::CVariationUtil::CCdregionIndex::Clear ( void  )

inline

Definition at line 424 of file variation_util2.hpp.

References map_checker< Container >::clear(), m_data, and m_seq_data_map.

Referenced by variation::CVariationUtil::ClearCache().

Get()

void variation::CVariationUtil::CCdregionIndex::Get	(	const CSeq_loc &	loc,
		TCdregions &	cdregions
	)

Definition at line 4128 of file variation_util2.cpp.

References CSeq_loc::Assign(), CRangeMapBase< Traits >::begin(), variation::ChangeIdsInPlace(), eGetId_Canonical, ITERATE, variation::CVariationUtil::m_scope, results, and CRangeMapIterator< Traits >::Valid().

Referenced by variation::CVariationUtil::AttachProteinConsequences().

GetCachedLiteralAtLoc()

CRef< CSeq_literal > variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc

(

const CSeq_loc &

loc

)

Definition at line 4090 of file variation_util2.cpp.

References CSeq_loc::Assign(), variation::ChangeIdsInPlace(), eExtreme_Positional, eGetId_Canonical, eNa_strand_plus, CSeq_loc::GetLabel(), COpenRange< Position >::GetLength(), CSeq_loc::GetStart(), CSeq_loc::GetStrand(), CSeq_loc::GetTotalRange(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsPnt(), literal(), variation::CVariationUtil::m_scope, CSeq_loc_Mapper_Base::Map(), variation::CVariationUtil::CCdregionIndex::SSeqData::mapper, NULL, variation::CVariationUtil::CCdregionIndex::SSeqData::seq_data, and CTempString::size().

Referenced by variation::CVariationUtil::x_GetLiteralAtLoc().

x_CacheSeqData()

void variation::CVariationUtil::CCdregionIndex::x_CacheSeqData ( const CSeq_loc &  loc, const CSeq_id_Handle &  idh  )

private

Definition at line 4050 of file variation_util2.cpp.

References CSeq_loc::Assign(), CSeqVector::begin(), CBioseq_Handle::eCoding_Iupac, eGetId_Canonical, eNa_strand_plus, CSeqVector::end(), CScope::GetBioseqHandle(), GetId(), CBioseq_Handle::GetInst_Length(), GetLength(), CBioseq_Handle::GetRangeSeq_loc(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_loc_Base::IsEmpty(), CSeq_loc_Base::IsNull(), CSeq_loc_Base::IsWhole(), variation::CVariationUtil::m_scope, variation::CVariationUtil::CCdregionIndex::SSeqData::mapper, NULL, CRef< C, Locker >::Reset(), variation::CVariationUtil::CCdregionIndex::SSeqData::seq_data, and CSeq_loc::SetInt().

x_Index()

void variation::CVariationUtil::CCdregionIndex::x_Index ( const CSeq_id_Handle &  idh )

private

Definition at line 4003 of file variation_util2.cpp.

References CSeq_loc::Add(), variation::CVariationUtil::CCdregionIndex::SCdregion::cdregion_feat, CSeqFeatData_Base::e_Cdregion, CSeq_loc_Base::e_Null, CSeqFeatData_Base::e_Rna, variation::CVariationUtil::fOpt_cache_exon_sequence, CSeq_loc::fSortAndMerge_All, CScope::GetBioseqHandle(), CSeq_feat_Handle::GetData(), CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), CMappedFeat::GetLocation(), CMappedFeat::GetProduct(), CMappedFeat::GetSeq_feat(), SAnnotSelector::IncludeFeatType(), CSeqFeatData_Base::IsRna(), CSeq_feat_Handle::IsSetProduct(), variation::CVariationUtil::m_scope, NULL, CConstRef< C, Locker >::Reset(), CBioseq_Handle::Reset(), Seq_loc_Merge(), SAnnotSelector::SetAdaptiveDepth(), and SAnnotSelector::SetResolveAll().

Member Data Documentation

m_data

TIdRangeMap variation::CVariationUtil::CCdregionIndex::m_data

private

Definition at line 444 of file variation_util2.hpp.

Referenced by Clear().

m_options

TOptions variation::CVariationUtil::CCdregionIndex::m_options

private

Definition at line 446 of file variation_util2.hpp.

m_scope

CRef<CScope> variation::CVariationUtil::CCdregionIndex::m_scope

private

Definition at line 443 of file variation_util2.hpp.

m_seq_data_map

TSeqDataMap variation::CVariationUtil::CCdregionIndex::m_seq_data_map

private

Definition at line 445 of file variation_util2.hpp.

Referenced by Clear().

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The documentation for this class was generated from the following files:

• include/misc/hgvs/variation_util2.hpp
• src/misc/hgvs/variation_util2.cpp