variation_ref::CHgvsParser::CContext Class Reference

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#include <misc/hgvs/hgvs_parser.hpp>

Collaboration diagram for variation_ref::CHgvsParser::CContext:

Public Types
enum	EMolType {   eMol_not_set , eMol_g , eMol_c , eMol_r ,   eMol_p , eMol_mt }

Public Member Functions
	CContext (CRef< CScope > scope)
	CContext (const CContext &other)
void	Clear ()
TSeqPos	GetLength () const
void	SetId (const CSeq_id &id, EMolType mol_type)
void	Validate (const CSeq_literal &literal) const
void	Validate (const CSeq_literal &literal, const CSeq_loc &loc) const
void	SetLoc (const SOffsetLoc &loc)
bool	IsSetLoc () const
CScope &	GetScope () const
const CSeq_loc &	GetLoc () const
const SOffsetLoc &	GetOffsetLoc () const
const CSeq_id &	GetId () const
const CSeq_feat &	GetCDS () const
EMolType	GetMolType (bool check=true) const

Private Attributes
CBioseq_Handle	m_bsh
EMolType	m_mol_type
CRef< CSeq_feat >	m_cds
CRef< CSeq_id >	m_seq_id
SOffsetLoc	m_loc
CRef< CScope >	m_scope

Detailed Description

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

Definition at line 247 of file hgvs_parser.hpp.

Member Enumeration Documentation

EMolType

enum variation_ref::CHgvsParser::CContext::EMolType

Enumerator
eMol_not_set
eMol_g
eMol_c
eMol_r
eMol_p
eMol_mt

Definition at line 261 of file hgvs_parser.hpp.

Constructor & Destructor Documentation

CContext() [1/2]

variation_ref::CHgvsParser::CContext::CContext ( CRef< CScope >  scope )

inline

Definition at line 250 of file hgvs_parser.hpp.

CContext() [2/2]

variation_ref::CHgvsParser::CContext::CContext ( const CContext &  other )

inline

Definition at line 256 of file hgvs_parser.hpp.

Member Function Documentation

Clear()

void variation_ref::CHgvsParser::CContext::Clear ( void  )

inline

Definition at line 270 of file hgvs_parser.hpp.

GetCDS()

const CSeq_feat & variation_ref::CHgvsParser::CContext::GetCDS

(

)

const

Definition at line 196 of file hgvs_parser.cpp.

References HGVS_THROW.

GetId()

const CSeq_id & variation_ref::CHgvsParser::CContext::GetId

(

void

)

const

Definition at line 188 of file hgvs_parser.cpp.

References HGVS_THROW.

GetLength()

TSeqPos variation_ref::CHgvsParser::CContext::GetLength ( void  ) const

inline

Definition at line 279 of file hgvs_parser.hpp.

GetLoc()

const CSeq_loc & variation_ref::CHgvsParser::CContext::GetLoc

(

void

)

const

Definition at line 175 of file hgvs_parser.cpp.

References HGVS_THROW.

GetMolType()

CHgvsParser::CContext::EMolType variation_ref::CHgvsParser::CContext::GetMolType

(

bool

check = true

)

const

Definition at line 204 of file hgvs_parser.cpp.

References check, and HGVS_THROW.

GetOffsetLoc()

const CHgvsParser::SOffsetLoc & variation_ref::CHgvsParser::CContext::GetOffsetLoc

(

)

const

Definition at line 183 of file hgvs_parser.cpp.

GetScope()

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

inline

Definition at line 314 of file hgvs_parser.hpp.

IsSetLoc()

bool variation_ref::CHgvsParser::CContext::IsSetLoc ( ) const

inline

Definition at line 309 of file hgvs_parser.hpp.

SetId()

void variation_ref::CHgvsParser::CContext::SetId	(	const CSeq_id &	id,
		EMolType	mol_type
	)

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 212 of file hgvs_parser.cpp.

References CScope::GetBioseqHandle(), CSeq_feat_Handle::GetData(), CMappedFeat::GetMappedFeature(), HGVS_THROW, CSeqFeatData_Base::IsCdregion(), variation_ref::CHgvsParser::m_scope, and CMappedFeat::Reset().

SetLoc()

void variation_ref::CHgvsParser::CContext::SetLoc ( const SOffsetLoc &  loc )

inline

Definition at line 304 of file hgvs_parser.hpp.

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

Validate() [1/2]

void variation_ref::CHgvsParser::CContext::Validate ( const CSeq_literal &  literal ) const

inline

Definition at line 291 of file hgvs_parser.hpp.

References GetLoc(), and literal().

Validate() [2/2]

void variation_ref::CHgvsParser::CContext::Validate	(	const CSeq_literal &	literal,
		const CSeq_loc &	loc
	)		const

Definition at line 246 of file hgvs_parser.cpp.

References CSeqVector::begin(), CBioseq_Handle::eCoding_Iupac, CSeqVector::end(), CSeqVector::GetSeqData(), HGVS_THROW, literal(), and variation_ref::CHgvsParser::m_scope.

Member Data Documentation

m_bsh

CBioseq_Handle variation_ref::CHgvsParser::CContext::m_bsh

private

Definition at line 331 of file hgvs_parser.hpp.

m_cds

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

private

Definition at line 333 of file hgvs_parser.hpp.

m_loc

SOffsetLoc variation_ref::CHgvsParser::CContext::m_loc

private

Definition at line 335 of file hgvs_parser.hpp.

m_mol_type

EMolType variation_ref::CHgvsParser::CContext::m_mol_type

private

Definition at line 332 of file hgvs_parser.hpp.

m_scope

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

mutableprivate

Definition at line 336 of file hgvs_parser.hpp.

m_seq_id

CRef<CSeq_id> variation_ref::CHgvsParser::CContext::m_seq_id

private

Definition at line 334 of file hgvs_parser.hpp.

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

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