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variation::CHgvsParser::CContext Class Reference

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#include <misc/hgvs/hgvs_parser2.hpp>

+ Collaboration diagram for variation::CHgvsParser::CContext:

Public Member Functions

 CContext (CRef< CScope > scope, CSeq_id_Resolver::TResolvers &id_resolvers, const string &hgvs)
 CContext (const CContext &other)
void Clear ()
const CBioseq_HandleGetBioseqHandle () const
void SetId (const CSeq_id &id, CVariantPlacement::TMol mol)
const CSeq_idGetId () const
CVariantPlacementSetPlacement ()
const CVariantPlacementGetPlacement () const
bool IsSetPlacement () const
CScopeGetScope () const
const CSeq_featGetCDS () const
CSeq_id_Handle ResolevSeqId (const string &s) const
const stringGetHgvs () const

Private Attributes

CBioseq_Handle m_bsh
CRef< CSeq_featm_cds
CRef< CVariantPlacementm_placement
CRef< CScopem_scope
CSeq_id_Resolver::TResolvers m_seq_id_resolvers
const stringm_hgvs

Detailed Description

CContext encapsulates parsed sequence or location context for an hgvs sub-expression. E.g. given an expression NM_12345.6:c.5_10delinsAT, when creating a variation-ref for delinsAT the context will refer to sequence "NM_12345.6" and location "5_10"

Definition at line 254 of file hgvs_parser2.hpp.

Constructor & Destructor Documentation

◆ CContext() [1/2]

variation::CHgvsParser::CContext::CContext ( CRef< CScope scope,
CSeq_id_Resolver::TResolvers id_resolvers,
const string hgvs 

Definition at line 257 of file hgvs_parser2.hpp.

◆ CContext() [2/2]

variation::CHgvsParser::CContext::CContext ( const CContext other)

Member Function Documentation

◆ Clear()

void variation::CHgvsParser::CContext::Clear ( void  )

Definition at line 267 of file hgvs_parser2.hpp.

◆ GetBioseqHandle()

const CBioseq_Handle& variation::CHgvsParser::CContext::GetBioseqHandle ( void  ) const

Definition at line 274 of file hgvs_parser2.hpp.

◆ GetCDS()

const CSeq_feat & variation::CHgvsParser::CContext::GetCDS ( ) const

Definition at line 379 of file hgvs_parser2.cpp.

References HGVS_THROW.

◆ GetHgvs()

const string& variation::CHgvsParser::CContext::GetHgvs ( ) const

Definition at line 320 of file hgvs_parser2.hpp.

◆ GetId()

const CSeq_id & variation::CHgvsParser::CContext::GetId ( void  ) const

Definition at line 387 of file hgvs_parser2.cpp.

References GetId(), GetLoc(), and NULL.

◆ GetPlacement()

const CVariantPlacement& variation::CHgvsParser::CContext::GetPlacement ( ) const

Definition at line 298 of file hgvs_parser2.hpp.

◆ GetScope()

CScope& variation::CHgvsParser::CContext::GetScope ( void  ) const

Definition at line 308 of file hgvs_parser2.hpp.

◆ IsSetPlacement()

bool variation::CHgvsParser::CContext::IsSetPlacement ( ) const

Definition at line 303 of file hgvs_parser2.hpp.

◆ ResolevSeqId()

CSeq_id_Handle variation::CHgvsParser::CContext::ResolevSeqId ( const string s) const

Definition at line 315 of file hgvs_parser2.hpp.

References CSeq_id_Resolver::s_Get().

◆ SetId()

void variation::CHgvsParser::CContext::SetId ( const CSeq_id id,
CVariantPlacement::TMol  mol 

Clear the context and reset it for the given seq-id. If the sequence is cdna and we're working with "c." coordinates, also find the CDS, as the coordinates are (start|stop)codon-relative.

Definition at line 393 of file hgvs_parser2.cpp.

References CSeqFeatData_Base::e_Cdregion, CVariantPlacement_Base::eMol_cdna, CScope::GetBioseqHandle(), CSeq_feat_Handle::GetData(), CMappedFeat::GetMappedFeature(), HGVS_THROW, SAnnotSelector::IncludeFeatType(), CSeqFeatData_Base::IsCdregion(), variation::CHgvsParser::m_scope, CMappedFeat::Reset(), and SAnnotSelector::SetResolveTSE().

◆ SetPlacement()

CVariantPlacement& variation::CHgvsParser::CContext::SetPlacement ( )

Member Data Documentation

◆ m_bsh

CBioseq_Handle variation::CHgvsParser::CContext::m_bsh

Definition at line 325 of file hgvs_parser2.hpp.

Referenced by CContext().

◆ m_cds

CRef<CSeq_feat> variation::CHgvsParser::CContext::m_cds

Definition at line 326 of file hgvs_parser2.hpp.

Referenced by CContext().

◆ m_hgvs

const string& variation::CHgvsParser::CContext::m_hgvs

Definition at line 330 of file hgvs_parser2.hpp.

◆ m_placement

CRef<CVariantPlacement> variation::CHgvsParser::CContext::m_placement

Definition at line 327 of file hgvs_parser2.hpp.

Referenced by CContext().

◆ m_scope

CRef<CScope> variation::CHgvsParser::CContext::m_scope

Definition at line 328 of file hgvs_parser2.hpp.

Referenced by CContext().

◆ m_seq_id_resolvers

CSeq_id_Resolver::TResolvers variation::CHgvsParser::CContext::m_seq_id_resolvers

Definition at line 329 of file hgvs_parser2.hpp.

Referenced by CContext().

The documentation for this class was generated from the following files:
Modified on Sat Apr 13 11:46:18 2024 by rev. 669887