CValidError_annot Class Reference

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#include <objtools/validator/validerror_annot.hpp>

Inheritance diagram for CValidError_annot:

Collaboration diagram for CValidError_annot:

Public Member Functions
	CValidError_annot (CValidError_imp &imp)
	~CValidError_annot () override
void	ValidateSeqAnnot (const CSeq_annot_Handle &annot)
void	ValidateSeqAnnot (const CSeq_annot &annot)
void	ValidateSeqAnnotContext (const CSeq_annot &annot, const CBioseq &seq)
void	ValidateSeqAnnotContext (const CSeq_annot &annot, const CBioseq_set &set)
bool	IsLocationUnindexed (const CSeq_loc &loc)
void	ReportLocationGI0 (const CSeq_feat &f, const string &label)

Private Attributes
CValidError_graph	m_GraphValidator
CValidError_align	m_AlignValidator
CValidError_feat	m_FeatValidator
Private Attributes inherited from CValidError_base
CValidError_imp &	m_Imp
CScope *	m_Scope

Additional Inherited Members
Private Member Functions inherited from CValidError_base
	CValidError_base (CValidError_imp &imp)
virtual	~CValidError_base ()
void	PostErr (EDiagSev sv, EErrType et, const string &msg, const CSerialObject &obj)
void	PostErr (EDiagSev sv, EErrType et, const string &msg, const CSeq_feat &ft)
void	PostErr (EDiagSev sv, EErrType et, const string &msg, const CBioseq &sq)
void	PostErr (EDiagSev sv, EErrType et, const string &msg, const CSeq_entry &ctx, const CSeqdesc &ds)
void	PostErr (EDiagSev sv, EErrType et, const string &msg, const CBioseq_set &set)
void	PostErr (EDiagSev sv, EErrType et, const string &msg, const CSeq_annot &annot)
void	PostErr (EDiagSev sv, EErrType et, const string &msg, const CSeq_graph &graph)
void	PostErr (EDiagSev sv, EErrType et, const string &msg, const CBioseq &sq, const CSeq_graph &graph)
void	PostErr (EDiagSev sv, EErrType et, const string &msg, const CSeq_align &align)
void	PostErr (EDiagSev sv, EErrType et, const string &msg, const CSeq_entry &entry)
CCacheImpl &	GetCache ()
Static Private Member Functions inherited from CValidError_base
static CSeq_entry_Handle	GetAppropriateXrefParent (CSeq_entry_Handle seh)

Detailed Description

Definition at line 63 of file validerror_annot.hpp.

Constructor & Destructor Documentation

CValidError_annot()

CValidError_annot::CValidError_annot

(

CValidError_imp &

imp

)

Definition at line 54 of file validerror_annot.cpp.

~CValidError_annot()

CValidError_annot::~CValidError_annot ( )

override

Definition at line 63 of file validerror_annot.cpp.

Member Function Documentation

IsLocationUnindexed()

bool CValidError_annot::IsLocationUnindexed

(

const CSeq_loc &

loc

)

Definition at line 309 of file validerror_annot.cpp.

References CScope::fDoNotRecalculate, CScope::GetBioseqHandleFromTSE(), CBioseq_Handle::GetBioseqLength(), CScope::GetSequenceLength(), CValidError_imp::GetTSE(), kInvalidSeqPos, CValidError_base::m_Imp, and CValidError_base::m_Scope.

Referenced by ValidateSeqAnnotContext().

ReportLocationGI0()

void CValidError_annot::ReportLocationGI0	(	const CSeq_feat &	f,
		const string &	label
	)

Definition at line 337 of file validerror_annot.cpp.

References eDiag_Critical, eErr_SEQ_FEAT_FeatureLocationIsGi0, f, label, CValidError_base::PostErr(), NStr::UIntToString(), and ZERO_GI.

Referenced by ValidateSeqAnnotContext().

ValidateSeqAnnot() [1/2]

void CValidError_annot::ValidateSeqAnnot

(

const CSeq_annot &

annot

)

Definition at line 74 of file validerror_annot.cpp.

References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), eDiag_Error, eErr_SEQ_ALIGN_BlastAligns, eErr_SEQ_ANNOT_AnnotIDs, eErr_SEQ_ANNOT_AnnotLOCs, CAnnot_descr_Base::Get(), CSeq_annot_Base::C_Data::GetAlign(), CValidError_base::GetAppropriateXrefParent(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_annot_Base::GetData(), CSeq_annot_Base::GetDesc(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_annot_Base::C_Data::GetGraph(), CObjectManager::GetInstance(), CSeq_annot_Handle::GetParentEntry(), CScope::GetSeq_annotHandle(), CObject_id_Base::GetStr(), CValidError_imp::GetTSEH(), CSeq_annot::IsAlign(), CSeq_annot::IsFtable(), CSeq_annot::IsGraph(), CSeq_annot::IsIds(), CSeq_annot::IsLocs(), CSeq_annot_Base::IsSetDesc(), CObject_id_Base::IsStr(), CValidError_imp::IsValidateAlignments(), m_AlignValidator, m_FeatValidator, m_GraphValidator, CValidError_base::m_Imp, CValidError_base::m_Scope, CValidError_base::PostErr(), CValidError_feat::SetScope(), CValidError_feat::SetTSE(), CValidError_imp::ShouldSubdivide(), CValidError_align::ValidateSeqAlign(), CValidError_feat::ValidateSeqFeat(), and CValidError_graph::ValidateSeqGraph().

ValidateSeqAnnot() [2/2]

void CValidError_annot::ValidateSeqAnnot

(

const CSeq_annot_Handle &

annot

)

Definition at line 68 of file validerror_annot.cpp.

References CSeq_annot_Handle::GetCompleteSeq_annot().

Referenced by CValidError_imp::Validate(), CValidError_bioseq::ValidateBioseq(), and CValidError_bioseqset::ValidateBioseqSet().

ValidateSeqAnnotContext() [1/2]

void CValidError_annot::ValidateSeqAnnotContext	(	const CSeq_annot &	annot,
		const CBioseq &	seq
	)

Definition at line 140 of file validerror_annot.cpp.

References Compare(), CSeq_id::e_YES, CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_segset, eDiag_Error, eErr_SEQ_FEAT_UnindexedFeature, CSerialObject::Equals(), CSeq_inst_Base::eRepr_raw, CSeq_inst_Base::eRepr_seg, CScope::GetBioseqHandle(), CValidator::CCacheImpl::GetBioseqHandleFromLocation(), CValidError_base::GetCache(), CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetCompleteBioseq(), CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_annot_Base::C_Data::GetGraph(), CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CBioseq_Handle::GetParentEntry(), CSeq_entry_Handle::GetParentEntry(), CSeq_inst_Base::GetRepr(), CSeq_entry_Handle::GetSet(), CValidError_imp::GetTSE_Handle(), CValidError_imp::IncrementMisplacedFeatureCount(), CValidError_imp::IncrementSmallGenomeSetMisplacedCount(), CSeq_annot::IsFtable(), CSeq_annot::IsGraph(), IsLocationUnindexed(), CSeq_entry_Handle::IsSeq(), CSeq_entry_Handle::IsSet(), CBioseq_Base::IsSetId(), CValidError_imp::IsSmallGenomeSet(), label, m_GraphValidator, CValidError_base::m_Imp, CValidError_base::m_Scope, CValidError_imp::PostErr(), ReportLocationGI0(), and CValidError_graph::ValidateSeqGraphContext().

Referenced by CValidError_bioseq::ValidateBioseq(), and CValidError_bioseqset::ValidateBioseqSet().

ValidateSeqAnnotContext() [2/2]

void CValidError_annot::ValidateSeqAnnotContext	(	const CSeq_annot &	annot,
		const CBioseq_set &	set
	)

Definition at line 273 of file validerror_annot.cpp.

References CBioseq_set_Base::eClass_gen_prod_set, CBioseq_set_Base::eClass_nuc_prot, eDiag_Error, eErr_SEQ_FEAT_UnindexedFeature, CScope::GetBioseq_setHandle(), CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_annot_Base::C_Data::GetGraph(), CValidError_imp::GetTSE(), CValidError_imp::IncrementMisplacedFeatureCount(), CValidError_imp::IncrementSmallGenomeSetMisplacedCount(), CSeq_annot::IsFtable(), CSeq_annot::IsGraph(), IsLocationUnindexed(), CValidError_imp::IsSmallGenomeSet(), m_GraphValidator, CValidError_base::m_Imp, CValidError_base::m_Scope, CValidError_imp::PostErr(), ReportLocationGI0(), s_HasOneIntervalInSet(), CValidError_graph::ValidateSeqGraphContext(), and x_IsEmblOrDdbjOnSet().

Member Data Documentation

m_AlignValidator

CValidError_align CValidError_annot::m_AlignValidator

private

Definition at line 79 of file validerror_annot.hpp.

Referenced by ValidateSeqAnnot().

m_FeatValidator

CValidError_feat CValidError_annot::m_FeatValidator

private

Definition at line 80 of file validerror_annot.hpp.

Referenced by ValidateSeqAnnot().

m_GraphValidator

CValidError_graph CValidError_annot::m_GraphValidator

private

Definition at line 78 of file validerror_annot.hpp.

Referenced by ValidateSeqAnnot(), and ValidateSeqAnnotContext().

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

• include/objtools/validator/validerror_annot.hpp
• src/objtools/validator/validerror_annot.cpp