NCBI C++ ToolKit
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CValidError_base Class Reference

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#include <objtools/validator/validerror_base.hpp>

+ Inheritance diagram for CValidError_base:
+ Collaboration diagram for CValidError_base:

Protected Member Functions

 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)
 
CCacheImplGetCache ()
 

Static Protected Member Functions

static CSeq_entry_Handle GetAppropriateXrefParent (CSeq_entry_Handle seh)
 

Protected Attributes

CValidError_impm_Imp
 
CScopem_Scope
 

Detailed Description

Definition at line 48 of file validerror_base.hpp.

Constructor & Destructor Documentation

◆ CValidError_base()

CValidError_base::CValidError_base ( CValidError_imp imp)
protected

Definition at line 3514 of file validatorp.cpp.

◆ ~CValidError_base()

CValidError_base::~CValidError_base ( )
protectedvirtual

Definition at line 3520 of file validatorp.cpp.

Member Function Documentation

◆ GetAppropriateXrefParent()

CSeq_entry_Handle CValidError_base::GetAppropriateXrefParent ( CSeq_entry_Handle  seh)
staticprotected

◆ GetCache()

CCacheImpl & CValidError_base::GetCache ( void  )
protected

◆ PostErr() [1/10]

void CValidError_base::PostErr ( EDiagSev  sv,
EErrType  et,
const string msg,
const CBioseq sq 
)
protected

Definition at line 3555 of file validatorp.cpp.

References m_Imp, and CValidError_imp::PostErr().

◆ PostErr() [2/10]

void CValidError_base::PostErr ( EDiagSev  sv,
EErrType  et,
const string msg,
const CBioseq sq,
const CSeq_graph graph 
)
protected

Definition at line 3605 of file validatorp.cpp.

References m_Imp, and CValidError_imp::PostErr().

◆ PostErr() [3/10]

void CValidError_base::PostErr ( EDiagSev  sv,
EErrType  et,
const string msg,
const CBioseq_set set 
)
protected

Definition at line 3576 of file validatorp.cpp.

References m_Imp, and CValidError_imp::PostErr().

◆ PostErr() [4/10]

void CValidError_base::PostErr ( EDiagSev  sv,
EErrType  et,
const string msg,
const CSeq_align align 
)
protected

Definition at line 3616 of file validatorp.cpp.

References m_Imp, and CValidError_imp::PostErr().

◆ PostErr() [5/10]

void CValidError_base::PostErr ( EDiagSev  sv,
EErrType  et,
const string msg,
const CSeq_annot annot 
)
protected

Definition at line 3586 of file validatorp.cpp.

References m_Imp, and CValidError_imp::PostErr().

◆ PostErr() [6/10]

void CValidError_base::PostErr ( EDiagSev  sv,
EErrType  et,
const string msg,
const CSeq_entry ctx,
const CSeqdesc ds 
)
protected

Definition at line 3565 of file validatorp.cpp.

References ctx, m_Imp, and CValidError_imp::PostErr().

◆ PostErr() [7/10]

void CValidError_base::PostErr ( EDiagSev  sv,
EErrType  et,
const string msg,
const CSeq_entry entry 
)
protected

Definition at line 3626 of file validatorp.cpp.

References m_Imp, and CValidError_imp::PostErr().

◆ PostErr() [8/10]

void CValidError_base::PostErr ( EDiagSev  sv,
EErrType  et,
const string msg,
const CSeq_feat ft 
)
protected

Definition at line 3545 of file validatorp.cpp.

References m_Imp, and CValidError_imp::PostErr().

◆ PostErr() [9/10]

void CValidError_base::PostErr ( EDiagSev  sv,
EErrType  et,
const string msg,
const CSeq_graph graph 
)
protected

Definition at line 3595 of file validatorp.cpp.

References m_Imp, and CValidError_imp::PostErr().

◆ PostErr() [10/10]

void CValidError_base::PostErr ( EDiagSev  sv,
EErrType  et,
const string msg,
const CSerialObject obj 
)
protected

Definition at line 3525 of file validatorp.cpp.

References m_Imp, and CValidError_imp::PostErr().

Referenced by CValidError_bioseqset::CheckForImproperlyNestedSets(), CValidError_bioseqset::CheckForInconsistentBiomols(), CValidError_bioseq::CheckForMissingChromosome(), CValidError_bioseq::CheckForMolinfoOnBioseq(), CValidError_bioseq::CheckForMultipleStructuredComments(), CValidError_bioseq::CheckSourceDescriptor(), CValidError_bioseq::GapByGapInst(), CValidError_bioseq::GetTSAConflictingBiomolTechErrors(), CValidError_bioseq::GetTSANStretchErrors(), CValidError_bioseq::ReportBadAssemblyGap(), CValidError_bioseq::ReportBadGenomeGap(), CValidError_bioseq::ReportBadTSAGap(), CValidError_bioseq::ReportBadWGSGap(), CValidError_annot::ReportLocationGI0(), CValidError_bioseq::ReportModifInconsistentError(), CValidError_bioseqset::SetShouldNotHaveMolInfo(), CValidError_bioseqset::ShouldHaveNoDblink(), CValidError_bioseq::ValidateBioseqContext(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseq::ValidateCDSUTR(), CValidError_bioseq::ValidateCollidingGenes(), CValidError_desc::ValidateComment(), CValidError_bioseq::ValidateCompleteGenome(), CValidError_desc::ValidateDblink(), CValidError_bioseq::ValidateDelta(), CValidError_bioseq::ValidateDeltaLoc(), CValidError_bioseq::ValidateDupOrOverlapFeats(), CValidError_bioseq::ValidateFeatPartialInContext(), CValidError_bioseq::ValidateGBBlock(), CValidError_bioseqset::ValidateGenProdSet(), CValidError_graph::ValidateGraphsOnBioseq(), CValidError_bioseq::ValidateHistory(), CValidError_bioseq::ValidateIDSetAgainstDb(), CValidError_bioseq::ValidateInst(), CValidError_bioseq::ValidateModifDescriptors(), CValidError_desc::ValidateMolInfo(), CValidError_bioseq::ValidateMolInfoContext(), CValidError_bioseq::ValidateMoltypeDescriptors(), CValidError_bioseq::ValidateMultipleGeneOverlap(), CValidError_bioseq::ValidateNsAndGaps(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseq::ValidateOrgContext(), CValidError_bioseqset::ValidatePartsSet(), CValidError_bioseqset::ValidatePopSet(), CValidError_bioseq::ValidateRawConst(), CValidError_bioseq::ValidateRepr(), CValidError_bioseq::ValidateSecondaryAccConflict(), CValidError_bioseq::ValidateSegRef(), CValidError_bioseqset::ValidateSegSet(), CValidError_align::ValidateSeqAlign(), CValidError_annot::ValidateSeqAnnot(), CValidError_desc::ValidateSeqDesc(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_descr::ValidateSeqDescr(), CValidError_bioseq::ValidateSeqFeatContext(), CValidError_bioseq::ValidateSeqGap(), CValidError_graph::ValidateSeqGraphContext(), CValidError_bioseq::ValidateSeqId(), CValidError_bioseq::ValidateSeqIds(), CValidError_bioseq::ValidateSeqLen(), CValidError_bioseq::ValidateSeqParts(), CValidError_bioseqset::ValidateSetElements(), CValidError_bioseqset::ValidateSetTitle(), CValidError_desc::ValidateTitle(), CValidError_bioseq::ValidateTwintrons(), CValidError_bioseq::ValidateUpdateDateContext(), CValidError_desc::ValidateUser(), CValidError_bioseq::ValidateWGSMaster(), CValidError_bioseq::x_CheckForMultipleComments(), CValidError_bioseq::x_CheckForMultiplemRNAs(), CValidError_bioseq::x_CheckGeneralIDs(), CValidError_bioseq::x_CheckMrnaProteinLink(), CValidError_bioseq::x_CheckOrigProteinAndTranscriptIds(), CValidError_bioseq::x_CompareStrings(), CValidError_align::x_ReportAlignErr(), CValidError_bioseq::x_ReportDuplicatePubLabels(), CValidError_bioseq::x_ReportDupOverlapFeaturePair(), CValidError_bioseq::x_ReportGeneOverlapError(), CValidError_bioseq::x_ReportImproperPartial(), CValidError_bioseq::x_ReportInternalPartial(), CValidError_bioseq::x_ReportOverlappingPeptidePair(), CValidError_align::x_ReportSegmentGaps(), CValidError_bioseq::x_ReportStartStopPartialProblem(), CValidError_desc::x_ReportStructuredCommentErrors(), CValidError_bioseq::x_ReportSuspiciousUseOfComplete(), CValidError_bioseq::x_TranscriptIDsMatch(), CValidError_bioseq::x_ValidateAbuttingRNA(), CValidError_bioseq::x_ValidateAbuttingUTR(), CValidError_align::x_ValidateAlignPercentIdentity(), CValidError_bioseq::x_ValidateBarcode(), CValidError_bioseq::x_ValidateCDSagainstVDJC(), CValidError_bioseq::x_ValidateCDSmRNAmatch(), CValidError_bioseq::x_ValidateCompletness(), CValidError_align::x_ValidateDendiag(), CValidError_align::x_ValidateDenseg(), CValidError_align::x_ValidateDim(), CValidError_align::x_ValidateFastaLike(), CValidError_bioseq::x_ValidateGeneCDSmRNACounts(), CValidError_graph::x_ValidateGraphLocation(), CValidError_graph::x_ValidateGraphOnDeltaBioseq(), CValidError_graph::x_ValidateGraphOrderOnBioseq(), CValidError_graph::x_ValidateGraphValues(), CValidError_graph::x_ValidateMaxValues(), CValidError_graph::x_ValidateMinValues(), CValidError_bioseq::x_ValidateMultiplePubs(), CValidError_bioseq::x_ValidateOverlappingRNAFeatures(), CValidError_align::x_ValidatePacked(), CValidError_bioseq::x_ValidatePubFeatures(), CValidError_align::x_ValidateSeqId(), CValidError_align::x_ValidateSeqLength(), CValidError_bioseq::x_ValidateSourceFeatures(), CValidError_align::x_ValidateStd(), CValidError_align::x_ValidateStrand(), CValidError_desc::x_ValidateStructuredComment(), CValidError_desc::x_ValidateStructuredCommentPrefix(), CValidError_desc::x_ValidateStructuredCommentSuffix(), and CValidError_bioseq::x_ValidateTitle().

Member Data Documentation

◆ m_Imp

CValidError_imp& CValidError_base::m_Imp
protected

Definition at line 73 of file validerror_base.hpp.

Referenced by CValidError_bioseqset::CheckForInconsistentBiomols(), CValidError_bioseq::CheckForPubOnBioseq(), CValidError_bioseq::CheckSourceDescriptor(), CValidError_bioseq::CheckTpaHistory(), GetCache(), CValidError_annot::IsLocationUnindexed(), CValidError_bioseqset::IsMrnaProductInGPS(), CValidError_bioseq::NumOfIntervals(), PostErr(), CValidError_bioseq::SuppressTrailingXMsg(), CValidError_bioseq::ValidateBadGeneOverlap(), CValidError_bioseq::ValidateBioseq(), CValidError_bioseq::ValidateBioseqContext(), CValidError_bioseqset::ValidateBioseqSet(), CValidError_bioseq::ValidateCollidingGenes(), CValidError_desc::ValidateComment(), CValidError_bioseq::ValidateDelta(), CValidError_bioseq::ValidateDeltaLoc(), CValidError_bioseq::ValidateFeatPartialInContext(), CValidError_bioseq::ValidateInst(), CValidError_bioseq::ValidateMolInfoContext(), CValidError_bioseq::ValidateNsAndGaps(), CValidError_bioseqset::ValidatePopSet(), CValidError_bioseq::ValidateRawConst(), CValidError_bioseq::ValidateSegRef(), CValidError_align::ValidateSeqAlign(), CValidError_annot::ValidateSeqAnnot(), CValidError_annot::ValidateSeqAnnotContext(), CValidError_desc::ValidateSeqDesc(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqFeatContext(), CValidError_graph::ValidateSeqGraphContext(), CValidError_bioseq::ValidateSeqId(), CValidError_bioseq::ValidateSeqIds(), CValidError_bioseqset::ValidateSetElements(), CValidError_bioseqset::ValidateSetTitle(), CValidError_desc::ValidateTitle(), CValidError_bioseq::ValidateTwintrons(), CValidError_bioseq::ValidateUpdateDateContext(), CValidError_bioseq::ValidateWGSMaster(), CValidError_bioseq::x_CheckSingleStrandedRNAViruses(), CValidError_bioseq::x_CompareStrings(), CValidError_bioseq::x_DupFeatSeverity(), CValidError_bioseq::x_IsPartialAtSpliceSiteOrGap(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CValidError_bioseq::x_ReportDuplicatePubLabels(), CValidError_bioseq::x_ReportDupOverlapFeaturePair(), CValidError_bioseq::x_ReportImproperPartial(), CValidError_bioseq::x_ReportInternalPartial(), CValidError_bioseq::x_ReportLineageConflictWithMol(), CValidError_bioseq::x_ReportOverlappingPeptidePair(), CValidError_bioseq::x_ReportStartStopPartialProblem(), CValidError_bioseq::x_ReportUTRPair(), CValidError_bioseq::x_ShowBioProjectWarning(), CValidError_bioseq::x_SuppressDicistronic(), CValidError_bioseq::x_TranscriptIDsMatch(), CValidError_bioseq::x_ValidateCDSagainstVDJC(), CValidError_bioseq::x_ValidateCDSmRNAmatch(), CValidError_align::x_ValidateDendiag(), CValidError_align::x_ValidateDenseg(), CValidError_bioseq::x_ValidateGeneCDSmRNACounts(), CValidError_graph::x_ValidateGraphLocation(), CValidError_bioseq::x_ValidateMultiplePubs(), CValidError_align::x_ValidatePacked(), CValidError_align::x_ValidateStd(), and CValidError_bioseq::x_ValidateTitle().

◆ m_Scope

CScope* CValidError_base::m_Scope
protected

Definition at line 74 of file validerror_base.hpp.

Referenced by CValidError_bioseq::CheckForMultipleStructuredComments(), CValidError_bioseq::GapByGapInst(), CValidError_bioseq::GetTSANStretchErrors(), CValidError_graph::GetUngappedSeqLen(), CValidError_bioseqset::IsCDSProductInGPS(), CValidError_bioseq::IsHistAssemblyMissing(), CValidError_annot::IsLocationUnindexed(), CValidError_bioseqset::IsMrnaProductInGPS(), CValidError_bioseq::SuppressTrailingXMsg(), CValidError_bioseq::ValidateBadGeneOverlap(), CValidError_bioseq::ValidateBioseq(), CValidError_bioseq::ValidateBioseqContext(), CValidError_bioseq::ValidateCollidingGenes(), CValidError_bioseq::ValidateCompleteGenome(), CValidError_bioseq::ValidateDelta(), CValidError_bioseq::ValidateDeltaLoc(), CValidError_bioseq::ValidateFeatPartialInContext(), CValidError_bioseqset::ValidateGenProdSet(), CValidError_bioseq::ValidateMultipleGeneOverlap(), CValidError_bioseq::ValidateNsAndGaps(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePopSet(), CValidError_bioseq::ValidateRawConst(), CValidError_bioseq::ValidateSecondaryAccConflict(), CValidError_bioseq::ValidateSegRef(), CValidError_annot::ValidateSeqAnnot(), CValidError_annot::ValidateSeqAnnotContext(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqFeatContext(), CValidError_graph::ValidateSeqGraphContext(), CValidError_bioseq::ValidateSeqId(), CValidError_bioseq::ValidateSeqLen(), CValidError_bioseq::ValidateSeqParts(), CValidError_bioseqset::ValidateSetElements(), CValidError_bioseq::ValidateTwintrons(), CValidError_bioseq::x_CompareStrings(), CValidError_align::x_GetIds(), CValidError_bioseq::x_IdXrefsNotReciprocal(), CValidError_bioseq::x_IsPartialAtSpliceSiteOrGap(), CValidError_bioseq::x_IsRangeGap(), CValidError_bioseq::x_IsSameAsCDS(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CValidError_bioseq::x_PartialAdjacentToIntron(), CValidError_bioseq::x_ReportGeneOverlapError(), CValidError_bioseq::x_ReportOverlappingPeptidePair(), CValidError_bioseq::x_ShowBioProjectWarning(), CValidError_bioseq::x_TranscriptIDsMatch(), CValidError_align::x_ValidateAlignPercentIdentity(), CValidError_bioseq::x_ValidateBarcode(), CValidError_bioseq::x_ValidateCDSagainstVDJC(), CValidError_bioseq::x_ValidateCDSmRNAmatch(), CValidError_bioseq::x_ValidateCompletness(), CValidError_align::x_ValidateDim(), CValidError_align::x_ValidateFastaLike(), CValidError_graph::x_ValidateGraphLocation(), CValidError_graph::x_ValidateGraphOnDeltaBioseq(), CValidError_graph::x_ValidateGraphValues(), CValidError_bioseq::x_ValidateOverlappingRNAFeatures(), CValidError_align::x_ValidateSegmentGap(), CValidError_align::x_ValidateSeqId(), CValidError_align::x_ValidateSeqLength(), CValidError_bioseqset::x_ValidateSetDescriptors(), CValidError_bioseq::x_ValidateSourceFeatures(), CValidError_align::x_ValidateStrand(), and CValidError_bioseq::x_ValidateTitle().


The documentation for this class was generated from the following files:
Modified on Sat Apr 13 11:43:04 2024 by modify_doxy.py rev. 669887