post_process.cpp File Reference

#include <ncbi_pch.hpp>
#include <objmgr/seq_vector.hpp>
#include <objects/seqfeat/Delta_item.hpp>
#include <objtools/readers/hgvs/post_process.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objtools/readers/hgvs/irep_to_seqfeat_errors.hpp>
#include <corelib/ncbidiag.hpp>

Include dependency graph for post_process.cpp:

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Functions
CRef< CSeq_feat >	g_NormalizeVariationSeqfeat (const CSeq_feat &feat, CScope *scope)
void	s_ValidateSeqLiteral (const CSeq_literal &literal, const CSeq_loc &location, CScope *scope, bool IsCDS=false)
void	g_ValidateVariationSeqfeat (const CSeq_feat &feat, CScope *scope, bool IsCDS)

Function Documentation

g_NormalizeVariationSeqfeat()

CRef<CSeq_feat> g_NormalizeVariationSeqfeat	(	const CSeq_feat &	feat,
		CScope *	scope
	)

Definition at line 127 of file post_process.cpp.

References CNormalizeVariant::GetNormalizedIdentity().

Referenced by CHgvsNaIrepReader::CreateSeqfeat(), and CHgvsProtIrepReader::CreateSeqfeat().

g_ValidateVariationSeqfeat()

void g_ValidateVariationSeqfeat	(	const CSeq_feat &	feat,
		CScope *	scope,
		bool	IsCDS
	)

Definition at line 262 of file post_process.cpp.

References CVariation_ref_Base::C_Data::C_Set::eData_set_type_package, CVariation_inst_Base::eType_del, CVariation_inst_Base::eType_delins, CVariation_inst_Base::eType_ins, CVariation_inst_Base::eType_inv, CSeq_feat_Base::GetData(), CVariation_ref_Base::GetData(), CVariation_ref_Base::C_Data::GetInstance(), CSeq_feat_Base::GetLocation(), CVariation_ref_Base::C_Data::GetSet(), CSeqFeatData_Base::GetVariation(), CVariation_ref_Base::C_Data::C_Set::GetVariations(), CVariation_ref_Base::C_Data::IsInstance(), CVariation_ref_Base::C_Data::IsSet(), CSeq_feat_Base::IsSetData(), CVariation_ref_Base::IsSetData(), CSeqFeatData_Base::IsVariation(), NCBI_THROW, NStr::NumericToString(), CValidateVariant::ValidateIdentityInst(), and CValidateVariant::ValidateMicrosatelliteInst().

Referenced by CHgvsToSeqfeatConverter::Run().

s_ValidateSeqLiteral()

void s_ValidateSeqLiteral	(	const CSeq_literal &	literal,
		const CSeq_loc &	location,
		CScope *	scope,
		bool	IsCDS = false
	)

Definition at line 136 of file post_process.cpp.

References ERR_POST, GetLength(), NStr::IntToString(), literal(), location, NCBI_THROW, and Warning().

Referenced by CValidateVariant::ValidateIdentityInst(), and CValidateVariant::ValidateMicrosatelliteInst().