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_Handle &	GetBioseqHandle () const
void	SetId (const CSeq_id &id, CVariantPlacement::TMol mol)
const CSeq_id &	GetId () const
CVariantPlacement &	SetPlacement ()
const CVariantPlacement &	GetPlacement () const
bool	IsSetPlacement () const
CScope &	GetScope () const
const CSeq_feat &	GetCDS () const
CSeq_id_Handle	ResolevSeqId (const string &s) const
const string &	GetHgvs () const

Private Attributes
CBioseq_Handle	m_bsh
CRef< CSeq_feat >	m_cds
CRef< CVariantPlacement >	m_placement
CRef< CScope >	m_scope
CSeq_id_Resolver::TResolvers	m_seq_id_resolvers
const string &	m_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  )

inline

Definition at line 257 of file hgvs_parser2.hpp.

CContext() [2/2]

variation::CHgvsParser::CContext::CContext

(

const CContext &

other

)

Definition at line 358 of file hgvs_parser2.cpp.

References CSerialObject::Assign(), m_bsh, m_cds, m_placement, m_scope, m_seq_id_resolvers, and CRef< C, Locker >::Reset().

Member Function Documentation

Clear()

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

inline

Definition at line 267 of file hgvs_parser2.hpp.

GetBioseqHandle()

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

inline

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

inline

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

inline

Definition at line 298 of file hgvs_parser2.hpp.

GetScope()

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

inline

Definition at line 308 of file hgvs_parser2.hpp.

IsSetPlacement()

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

inline

Definition at line 303 of file hgvs_parser2.hpp.

ResolevSeqId()

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

inline

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 ( )

inline

Definition at line 288 of file hgvs_parser2.hpp.

References CVariantPlacement_Base::eMol_unknown, and CVariantPlacement_Base::Reset().

Referenced by variation::CHgvsParser::x_expr2().

Member Data Documentation

m_bsh

CBioseq_Handle variation::CHgvsParser::CContext::m_bsh

private

Definition at line 325 of file hgvs_parser2.hpp.

Referenced by CContext().

m_cds

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

private

Definition at line 326 of file hgvs_parser2.hpp.

Referenced by CContext().

m_hgvs

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

private

Definition at line 330 of file hgvs_parser2.hpp.

m_placement

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

private

Definition at line 327 of file hgvs_parser2.hpp.

Referenced by CContext().

m_scope

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

mutableprivate

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

mutableprivate

Definition at line 329 of file hgvs_parser2.hpp.

Referenced by CContext().

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

• include/misc/hgvs/hgvs_parser2.hpp
• src/misc/hgvs/hgvs_parser2.cpp