Search Toolkit Book for CValidError_imp
#include <objtools/validator/validerror_imp.hpp>
Definition at line 129 of file validerror_imp.hpp.
◆ SLocCheck ◆ TAlign ◆ TAnnot ◆ TBioseq ◆ TCount ◆ TDesc ◆ TEntry ◆ TFeat ◆ TFeatAnnotMap ◆ TGraph ◆ TSet ◆ TSuppressed ◆ CValidError_imp() [1/2] ◆ ~CValidError_imp() CValidError_imp::~CValidError_imp ( ) virtualDefinition at line 191 of file validatorp.cpp.
◆ CValidError_imp() [2/2] ◆ AddBioseqWithNoBiosource() void CValidError_imp::AddBioseqWithNoBiosource ( const CBioseq & seq ) ◆ AddBioseqWithNoPub() void CValidError_imp::AddBioseqWithNoPub ( const CBioseq & seq ) ◆ AddProtWithoutFullRef() ◆ AddToCumulativeInferenceCount() void CValidError_imp::AddToCumulativeInferenceCount ( size_t num ) inline ◆ AddToGeneCount() void CValidError_imp::AddToGeneCount ( size_t num ) inline ◆ AddToGeneXrefCount() void CValidError_imp::AddToGeneXrefCount ( size_t num ) inline ◆ AddToMisplacedFeatureCount() void CValidError_imp::AddToMisplacedFeatureCount ( size_t num ) inline ◆ AddToMisplacedGraphCount() void CValidError_imp::AddToMisplacedGraphCount ( size_t num ) inline ◆ AddToPseudoCount() void CValidError_imp::AddToPseudoCount ( size_t num ) inline ◆ AddToPseudogeneCount() void CValidError_imp::AddToPseudogeneCount ( size_t num ) inline ◆ AddToSmallGenomeSetMisplacedCount() void CValidError_imp::AddToSmallGenomeSetMisplacedCount ( size_t num ) inline ◆ AddToTpaWithHistoryCount() void CValidError_imp::AddToTpaWithHistoryCount ( size_t num ) inline ◆ AddToTpaWithoutHistoryCount() void CValidError_imp::AddToTpaWithoutHistoryCount ( size_t num ) inline ◆ BadMultipleSequenceLocation() ◆ BioSourceKind() ◆ CheckMultipleIds() ◆ DoCompareVDJCtoCDS() bool CValidError_imp::DoCompareVDJCtoCDS ( ) const inline ◆ DoesAnyFeatLocHaveGI() bool CValidError_imp::DoesAnyFeatLocHaveGI ( ) const ◆ DoesAnyGeneHaveLocusTag() bool CValidError_imp::DoesAnyGeneHaveLocusTag ( ) const ◆ DoesAnyProductLocHaveGI() bool CValidError_imp::DoesAnyProductLocHaveGI ( ) const ◆ DoesAnyProteinHaveGeneralID() bool CValidError_imp::DoesAnyProteinHaveGeneralID ( ) const ◆ DoRubiscoTest() bool CValidError_imp::DoRubiscoTest ( ) const inline ◆ DoTaxLookup() bool CValidError_imp::DoTaxLookup ( ) const inline ◆ FindCollidingSerialNumbers() ◆ FindEmbeddedScript() ◆ FindNonAsciiText() ◆ ForceInferences() bool CValidError_imp::ForceInferences ( ) const inline ◆ GatherTentativeName()Definition at line 2746 of file valid_biosource.cpp.
References FOR_EACH_SEQENTRY_ON_SEQSET, CSeq_descr_Base::Get(), CSeq_entry::GetAnnot(), CSeq_entry::GetDescr(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSet(), CSeq_entry::IsSetAnnot(), CSeq_entry::IsSetDescr(), CConstRef< C, Locker >::Reset(), and x_HasTentativeName().
◆ GenerateGoldenFile() bool CValidError_imp::GenerateGoldenFile ( ) const inline ◆ GetAncestor() ◆ GetBioseqHandleFromTSE() ◆ GetCache() ◆ GetCachedGene()Definition at line 276 of file validerror_imp.hpp.
References f, CGeneCache::GetGeneFromCache(), m_GeneCache, and m_Scope.
Referenced by CValidError_bioseq::ValidateBadGeneOverlap(), CValidError_bioseq::ValidateRawConst(), CValidError_bioseq::ValidateSeqFeatContext(), CValidError_bioseq::x_DupFeatSeverity(), x_IsPseudo(), CValidError_bioseq::x_ReportDupOverlapFeaturePair(), CValidError_bioseq::x_ReportUTRPair(), CValidError_bioseq::x_ValidateCDSmRNAmatch(), and CValidError_bioseq::x_ValidateGeneCDSmRNACounts().
◆ GetCDSGivenProduct()Definition at line 2697 of file validatorp.cpp.
References CSeqFeatData_Base::e_Cdregion, CScope::GetBioseqHandle(), CMappedFeat::GetOriginalFeature(), CScope::GetSeq_entryHandle(), IsNT(), m_Scope, m_TSE, CConstRef< C, Locker >::Reset(), SAnnotSelector::SetByProduct(), and SAnnotSelector::SetLimitTSE().
Referenced by CValidError_bioseq::SuppressTrailingXMsg(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::x_ReportOverlappingPeptidePair(), and CProtValidator::x_ValidateMolinfoPartials().
◆ GetContext() ◆ GetCumulativeInferenceCount() size_t CValidError_imp::GetCumulativeInferenceCount ( void ) const inline ◆ GetEntryInfo()Definition at line 1317 of file validatorp.cpp.
References m_pEntryInfo.
Referenced by DoesAnyFeatLocHaveGI(), DoesAnyGeneHaveLocusTag(), DoesAnyProductLocHaveGI(), DoesAnyProteinHaveGeneralID(), HasGiOrAccnVer(), IsDdbj(), IsEmbl(), IsGED(), IsGenbank(), IsGeneious(), IsGenomic(), IsGI(), IsGpipe(), IsGPS(), IsINSDInSep(), IsLocalGeneralOnly(), IsNoBioSource(), IsNoCitSubPubs(), IsNoPubs(), IsPatent(), IsPDB(), IsRefSeq(), IsSeqSubmit(), IsSmallGenomeSet(), IsTPE(), and CValidator::Validate().
◆ GetGeneCache()Definition at line 277 of file validerror_imp.hpp.
References m_GeneCache.
Referenced by CCdregionValidator::CCdregionValidator(), CMRNAValidator::CMRNAValidator(), PostErr(), CRNAValidator::Validate(), CExonValidator::Validate(), CIntronValidator::Validate(), CCdregionValidator::x_HasGoodParent(), CValidError_bioseq::x_MatchesOverlappingFeaturePartial(), CCdregionValidator::x_ValidateFarProducts(), CSingleFeatValidator::x_ValidateGeneId(), CSingleFeatValidator::x_ValidateGeneXRef(), and CSingleFeatValidator::x_ValidateOldLocusTag().
◆ GetGeneCount() size_t CValidError_imp::GetGeneCount ( void ) const inline ◆ GetGeneXrefCount() size_t CValidError_imp::GetGeneXrefCount ( void ) const inline ◆ GetLocalBioseqHandle() ◆ GetmRNAGivenProduct() [1/2] ◆ GetmRNAGivenProduct() [2/2] ◆ GetScope() CScope* CValidError_imp::GetScope ( void ) inline ◆ GetSeqAnnot() ◆ GetTSACDSOnMinusStrandErrors() [1/2] ◆ GetTSACDSOnMinusStrandErrors() [2/2] ◆ GetTSAConflictingBiomolTechErrors() [1/2] ◆ GetTSAConflictingBiomolTechErrors() [2/2] ◆ GetTSANStretchErrors() [1/2] ◆ GetTSANStretchErrors() [2/2] ◆ GetTSE() ◆ GetTSE_Handle() ◆ GetTSEH() ◆ HandleTaxonomyError() [1/3] ◆ HandleTaxonomyError() [2/3]Definition at line 2992 of file valid_biosource.cpp.
References eDiag_Error, eDiag_Warning, eErr_SEQ_DESCR_OrganismNotFound, eErr_SEQ_DESCR_TaxonomyAmbiguousName, eErr_SEQ_DESCR_TaxonomyLookupProblem, NStr::Equal(), NStr::Find(), CBioSource_Base::GetOrg(), CSeqdesc_Base::GetSource(), kInvalidReplyMsg, msg(), and NPOS.
◆ HandleTaxonomyError() [3/3] ◆ HasGiOrAccnVer() bool CValidError_imp::HasGiOrAccnVer ( ) const ◆ HasIsoJTA() ◆ HasName()Definition at line 634 of file valid_pub.cpp.
References CAuth_list_Base::CanGetNames(), CAuth_list_Base::C_Names::e_Ml, CAuth_list_Base::C_Names::e_Std, CAuth_list_Base::C_Names::e_Str, CPerson_id_Base::GetConsortium(), CName_std_Base::GetLast(), CPerson_id_Base::GetMl(), CPerson_id_Base::GetName(), CAuth_list_Base::GetNames(), CPerson_id_Base::GetStr(), NStr::IsBlank(), IsBlankStringList(), CPerson_id_Base::IsConsortium(), CPerson_id_Base::IsMl(), CPerson_id_Base::IsName(), CPerson_id_Base::IsStr(), ITERATE, and names.
◆ HasRefSeq() bool CValidError_imp::HasRefSeq ( void ) const inline ◆ HasTitle()Definition at line 565 of file valid_pub.cpp.
References CTitle_Base::C_E::e_Abr, CTitle_Base::C_E::e_Coden, CTitle_Base::C_E::e_Isbn, CTitle_Base::C_E::e_Iso_jta, CTitle_Base::C_E::e_Issn, CTitle_Base::C_E::e_Jta, CTitle_Base::C_E::e_Ml_jta, CTitle_Base::C_E::e_Name, CTitle_Base::C_E::e_Trans, CTitle_Base::C_E::e_Tsub, CTitle_Base::Get(), NStr::IsBlank(), ITERATE, and str().
◆ IgnoreExceptions() bool CValidError_imp::IgnoreExceptions ( ) const inline ◆ IgnoreInferences() bool CValidError_imp::IgnoreInferences ( ) const inline ◆ IncrementCumulativeInferenceCount() void CValidError_imp::IncrementCumulativeInferenceCount ( ) inline ◆ IncrementGeneCount() void CValidError_imp::IncrementGeneCount ( ) inline ◆ IncrementGeneXrefCount() void CValidError_imp::IncrementGeneXrefCount ( ) inline ◆ IncrementMisplacedFeatureCount() void CValidError_imp::IncrementMisplacedFeatureCount ( ) inline ◆ IncrementMisplacedGraphCount() void CValidError_imp::IncrementMisplacedGraphCount ( ) inline ◆ IncrementPseudoCount() void CValidError_imp::IncrementPseudoCount ( ) inline ◆ IncrementPseudogeneCount() void CValidError_imp::IncrementPseudogeneCount ( ) inline ◆ IncrementSmallGenomeSetMisplacedCount() void CValidError_imp::IncrementSmallGenomeSetMisplacedCount ( ) inline ◆ IncrementTpaWithHistoryCount() void CValidError_imp::IncrementTpaWithHistoryCount ( ) inline ◆ IncrementTpaWithoutHistoryCount() void CValidError_imp::IncrementTpaWithoutHistoryCount ( ) inline ◆ InitializeSourceQualTags() void CValidError_imp::InitializeSourceQualTags ( ) private ◆ IsArtificial() ◆ IsDdbj() bool CValidError_imp::IsDdbj ( void ) const ◆ IsEmbl() bool CValidError_imp::IsEmbl ( void ) const ◆ IsFarFetchCDSproducts() bool CValidError_imp::IsFarFetchCDSproducts ( ) const inline ◆ IsFarFetchMRNAproducts() bool CValidError_imp::IsFarFetchMRNAproducts ( ) const inline ◆ IsFarSequence() ◆ IsGED() bool CValidError_imp::IsGED ( void ) const ◆ IsGenbank() bool CValidError_imp::IsGenbank ( void ) const ◆ IsGeneious() bool CValidError_imp::IsGeneious ( ) const ◆ IsGenomeSubmission() bool CValidError_imp::IsGenomeSubmission ( ) const inline ◆ IsGenomic() bool CValidError_imp::IsGenomic ( ) const ◆ IsGI() bool CValidError_imp::IsGI ( ) const ◆ IsGpipe() bool CValidError_imp::IsGpipe ( void ) constDefinition at line 3600 of file validatorp.cpp.
References GetEntryInfo(), and CValidatorEntryInfo::IsGpipe().
Referenced by CSingleFeatValidator::Validate(), CSingleFeatValidator::ValidateCharactersInField(), CValidError_bioseq::ValidateCollidingGenes(), CValidError_bioseq::ValidateFeatPartialInContext(), CValidError_align::ValidateSeqAlign(), CValidError_bioseq::x_ReportInternalPartial(), CCdregionValidator::x_ReportTranslationProblems(), CSingleFeatValidator::x_SeverityForConsensusSplice(), CSingleFeatValidator::x_ValidateFeatPartialness(), CRNAValidator::x_ValidateRnaTrans(), and CCdregionValidator::x_ValidateTrans().
◆ IsGPS() bool CValidError_imp::IsGPS ( ) const ◆ IsHtg() bool CValidError_imp::IsHtg ( ) const ◆ IsHugeFileMode() bool CValidError_imp::IsHugeFileMode ( ) const ◆ IsHugeSet() [1/2] ◆ IsHugeSet() [2/2] ◆ IsIndexerVersion() bool CValidError_imp::IsIndexerVersion ( ) const inline ◆ IsInOrganelleSmallGenomeSet() ◆ IsINSDInSep() bool CValidError_imp::IsINSDInSep ( ) const ◆ IsLatLonCheckState() bool CValidError_imp::IsLatLonCheckState ( ) const inline ◆ IsLatLonIgnoreWater() bool CValidError_imp::IsLatLonIgnoreWater ( ) const inline ◆ IsLocalGeneralOnly() bool CValidError_imp::IsLocalGeneralOnly ( ) const ◆ IsLocusTagGeneralMatch() bool CValidError_imp::IsLocusTagGeneralMatch ( ) const inline ◆ IsMixedStrands() ◆ IsNC() bool CValidError_imp::IsNC ( void ) const ◆ IsNG() bool CValidError_imp::IsNG ( ) const ◆ IsNM() bool CValidError_imp::IsNM ( void ) const ◆ IsNoBioSource() bool CValidError_imp::IsNoBioSource ( ) const ◆ IsNoCitSubPubs() bool CValidError_imp::IsNoCitSubPubs ( ) const ◆ IsNonASCII() bool CValidError_imp::IsNonASCII ( ) const inline ◆ IsNoncuratedRefSeq() ◆ IsNoPubs() bool CValidError_imp::IsNoPubs ( ) const ◆ IsNP() bool CValidError_imp::IsNP ( ) const ◆ IsNR() bool CValidError_imp::IsNR ( void ) const ◆ IsNS() bool CValidError_imp::IsNS ( ) const ◆ IsNT() bool CValidError_imp::IsNT ( ) const ◆ IsNW() bool CValidError_imp::IsNW ( ) const ◆ IsNZ() bool CValidError_imp::IsNZ ( void ) const ◆ IsOtherDNA() ◆ IsOvlPepErr() bool CValidError_imp::IsOvlPepErr ( ) const inline ◆ IsPatent() bool CValidError_imp::IsPatent ( void ) const ◆ IsPDB() bool CValidError_imp::IsPDB ( void ) const ◆ IsRefSeq() bool CValidError_imp::IsRefSeq ( void ) constDefinition at line 3583 of file validatorp.cpp.
References GetContext(), GetEntryInfo(), CValidatorEntryInfo::IsRefSeq(), SValidatorContext::IsRefSeq, and m_RefSeqConventions.
Referenced by RaiseGenomeSeverity(), CSingleFeatValidator::Validate(), CPeptideValidator::Validate(), CImpFeatValidator::Validate(), Validate(), CValidError_bioseqset::ValidateBioseqSet(), ValidateDbxref(), CValidError_bioseq::ValidateDelta(), CValidError_bioseq::ValidateDeltaLoc(), CValidError_bioseqset::ValidatePopSet(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_bioseq::ValidateSeqFeatContext(), CValidError_bioseq::ValidateSeqId(), CValidError_bioseqset::ValidateSetElements(), CValidError_bioseqset::ValidateSetTitle(), CValidError_desc::ValidateTitle(), CValidError_bioseq::x_ReportDuplicatePubLabels(), CValidError_bioseq::x_ReportInternalPartial(), CCdregionValidator::x_ReportTranslationProblems(), CProtValidator::x_ReportUninformativeNames(), CSingleFeatValidator::x_SeverityForConsensusSplice(), CValidError_bioseq::x_SuppressDicistronic(), CValidError_bioseq::x_TranscriptIDsMatch(), CCdregionValidator::x_ValidateFarProducts(), CSingleFeatValidator::x_ValidateGbquals(), CValidError_bioseq::x_ValidateMultiplePubs(), CProtValidator::x_ValidateProteinName(), CRNAValidator::x_ValidateRnaProduct(), CPolyASiteValidator::x_ValidateSeqFeatLoc(), CPolyASignalValidator::x_ValidateSeqFeatLoc(), and CCdregionValidator::x_ValidateTrans().
◆ IsRefSeqConventions() bool CValidError_imp::IsRefSeqConventions ( ) const inline ◆ IsRemoteFetch() bool CValidError_imp::IsRemoteFetch ( ) const inline ◆ IsRequireISOJTA() bool CValidError_imp::IsRequireISOJTA ( ) const inline ◆ IsRequireTaxonID() bool CValidError_imp::IsRequireTaxonID ( ) const inline ◆ IsSeqSubmit() bool CValidError_imp::IsSeqSubmit ( ) const ◆ IsSeqSubmitParent() bool CValidError_imp::IsSeqSubmitParent ( ) const inline ◆ IsSerialNumberInComment() ◆ IsSmallGenomeSet() bool CValidError_imp::IsSmallGenomeSet ( void ) const ◆ IsStandaloneAnnot() bool CValidError_imp::IsStandaloneAnnot ( ) const inline ◆ IsSuppressContext() bool CValidError_imp::IsSuppressContext ( ) const inline ◆ IsSyntheticConstruct()Definition at line 224 of file valid_biosource.cpp.
References NStr::EqualNocase(), NStr::FindNoCase(), COrgName_Base::GetDiv(), COrg_ref::GetLineage(), CBioSource_Base::GetOrg(), COrg_ref_Base::GetOrgname(), COrg_ref_Base::GetTaxname(), COrgName_Base::IsSetDiv(), COrg_ref::IsSetLineage(), CBioSource_Base::IsSetOrg(), COrg_ref_Base::IsSetOrgname(), and COrg_ref_Base::IsSetTaxname().
Referenced by CValidError_bioseq::ValidateMolInfoContext().
◆ IsTPE() bool CValidError_imp::IsTPE ( ) const ◆ IsTransgenic() ◆ IsTSAIntermediate() ◆ IsValidateAlignments() bool CValidError_imp::IsValidateAlignments ( ) const inline ◆ IsValidateExons() bool CValidError_imp::IsValidateExons ( ) const inline ◆ IsValidateIdSet() bool CValidError_imp::IsValidateIdSet ( ) const inline ◆ IsWGSIntermediate() ◆ IsWP() bool CValidError_imp::IsWP ( void ) const ◆ IsXR() bool CValidError_imp::IsXR ( ) const ◆ NewStrainValidation() bool CValidError_imp::NewStrainValidation ( ) const inline ◆ operator=() ◆ PostBadDateError() ◆ PostErr() [1/15] ◆ PostErr() [2/15] ◆ PostErr() [3/15] ◆ PostErr() [4/15] ◆ PostErr() [5/15]Definition at line 377 of file validatorp.cpp.
References ERR_POST_X, CSerialObject::GetThisTypeInfo(), GetTSE(), msg(), Warning(), and x_IsSuppressed().
Referenced by AddProtWithoutFullRef(), CTaxValidationAndCleanup::CheckOneOrg(), FindEmbeddedScript(), FindNonAsciiText(), CSingleFeatValidator::PostErr(), CValidError_base::PostErr(), PostErr(), PostObjErr(), CTaxValidationAndCleanup::ReportIncrementalTaxLookupErrors(), ReportMissingBiosource(), CTaxValidationAndCleanup::ReportSpecificHostErrors(), CTaxValidationAndCleanup::ReportTaxLookupErrors(), Validate(), CValidError_bioseq::ValidateBioseq(), ValidateCitations(), ValidateMultipleTaxIds(), CValidError_annot::ValidateSeqAnnotContext(), ValidateSeqLoc(), ValidateSeqLocIds(), ValidateSubmitBlock(), x_CheckLoc(), CStrainRequest::x_CheckOneStrain(), x_DoBarcodeTests(), x_ReportInvalidFuzz(), CCdregionValidator::x_ValidateFarProducts(), CSingleFeatValidator::x_ValidateFeatComment(), CCdregionValidator::x_ValidateFeatComment(), CSingleFeatValidator::x_ValidateGbQual(), and CMRNAValidator::x_ValidateMrnaGene().
◆ PostErr() [6/15]Definition at line 1007 of file validatorp.cpp.
References IValidError::AddValidErrItem(), eDiag_Error, GenerateGoldenFile(), GetAccessionFromObjects(), CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CSeq_align_Base::GetDim(), GetReportableSeqIdForAlignment(), CSeq_align_Base::GetSegs(), CSeq_align_Base::GetType(), CSeq_align_Base::IsSetSegs(), CSeq_align_Base::IsSetType(), m_ErrRepository, m_genomeSubmission, m_Scope, msg(), NStr::NumericToString(), PostErr(), RaiseGenomeSeverity(), CSeq_align_Base::C_Segs::SelectionName(), dtl::version, CSeq_align_Base::C_Segs::Which(), x_AddValidErrItem(), and x_IsSuppressed().
◆ PostErr() [7/15]Definition at line 901 of file validatorp.cpp.
References IValidError::AddValidErrItem(), eDiag_Error, GenerateGoldenFile(), GetAccessionFromObjects(), m_ErrRepository, m_genomeSubmission, m_Scope, msg(), RaiseGenomeSeverity(), dtl::version, x_AddValidErrItem(), and x_IsSuppressed().
◆ PostErr() [8/15]Definition at line 745 of file validatorp.cpp.
References IValidError::AddValidErrItem(), AppendBioseqLabel(), eDiag_Error, GenerateGoldenFile(), GetAccessionFromBioseq(), m_ErrRepository, m_genomeSubmission, m_SuppressContext, msg(), RaiseGenomeSeverity(), dtl::version, x_AddValidErrItem(), and x_IsSuppressed().
◆ PostErr() [9/15]Definition at line 969 of file validatorp.cpp.
References IValidError::AddValidErrItem(), AppendBioseqLabel(), eDiag_Error, GenerateGoldenFile(), GetAccessionFromObjects(), CSeq_loc::GetLabel(), CSeq_graph_Base::GetLoc(), CSeq_graph_Base::GetTitle(), CSeq_graph_Base::IsSetTitle(), m_ErrRepository, m_genomeSubmission, m_Scope, m_SuppressContext, msg(), RaiseGenomeSeverity(), dtl::version, x_AddValidErrItem(), and x_IsSuppressed().
◆ PostErr() [10/15] ◆ PostErr() [11/15]Definition at line 818 of file validatorp.cpp.
References IValidError::AddValidErrItem(), ctx, CBioseq_set_Base::eClass_genbank, eDiag_Error, GenerateGoldenFile(), GetAccessionFromObjects(), GetContext(), CValidErrorFormat::GetDescriptorContent(), CValidErrorFormat::GetDescriptorLabel(), SValidatorContext::HugeSetId, IsHugeSet(), m_ErrRepository, m_genomeSubmission, m_Scope, m_SuppressContext, msg(), RaiseGenomeSeverity(), dtl::version, and x_IsSuppressed().
◆ PostErr() [12/15]Definition at line 1060 of file validatorp.cpp.
References IValidError::AddValidErrItem(), CSeq_entry::eContent, eDiag_Error, GenerateGoldenFile(), GetAccessionFromObjects(), CSeq_entry::GetLabel(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), m_ErrRepository, m_genomeSubmission, m_Scope, msg(), PostErr(), RaiseGenomeSeverity(), dtl::version, x_AddValidErrItem(), and x_IsSuppressed().
◆ PostErr() [13/15]Definition at line 650 of file validatorp.cpp.
References IValidError::AddValidErrItem(), eDiag_Error, eExtreme_Positional, GenerateGoldenFile(), GetAccessionFromObjects(), CSeq_feat_Base::GetData(), CValidErrorFormat::GetFeatureBioseqLabel(), CValidErrorFormat::GetFeatureContentLabel(), CValidErrorFormat::GetFeatureIdLabel(), CValidErrorFormat::GetFeatureLocationLabel(), CValidErrorFormat::GetFeatureProductLocLabel(), CSeqFeatData_Base::GetGene(), GetGeneCache(), CGeneCache::GetGeneFromCache(), CSeq_feat_Base::GetLocation(), CGene_ref_Base::GetLocus_tag(), CSeq_loc::GetStart(), NStr::IntToString(), NStr::IsBlank(), CSeqFeatData_Base::IsGene(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetLocation(), CGene_ref_Base::IsSetLocus_tag(), location, m_CollectLocusTags, m_ErrRepository, m_genomeSubmission, m_Scope, m_SuppressContext, msg(), offset, RaiseGenomeSeverity(), dtl::version, and x_IsSuppressed().
◆ PostErr() [14/15]Definition at line 932 of file validatorp.cpp.
References IValidError::AddValidErrItem(), eDiag_Error, GenerateGoldenFile(), GetAccessionFromObjects(), CSeq_loc::GetLabel(), CSeq_graph_Base::GetLoc(), CSeq_graph_Base::GetTitle(), CSeq_graph_Base::IsSetTitle(), m_ErrRepository, m_genomeSubmission, m_Scope, msg(), RaiseGenomeSeverity(), dtl::version, x_AddValidErrItem(), and x_IsSuppressed().
◆ PostErr() [15/15]Definition at line 775 of file validatorp.cpp.
References IValidError::AddValidErrItem(), CBioseq_set_Base::eClass_not_set, eDiag_Error, GenerateGoldenFile(), GetAccessionFromBioseqSet(), CValidErrorFormat::GetBioseqSetLabel(), GetContext(), IsHugeSet(), m_ErrRepository, m_genomeSubmission, m_SuppressContext, msg(), RaiseGenomeSeverity(), st(), dtl::version, x_AddValidErrItem(), and x_IsSuppressed().
◆ PostObjErr()Definition at line 1214 of file validatorp.cpp.
References ctx, CSerialObject::GetThisTypeInfo(), msg(), and PostErr().
Referenced by CTaxValidationAndCleanup::CheckOneOrg(), PostBadDateError(), CQualifierRequest::PostErrors(), CTaxValidationAndCleanup::ReportIncrementalTaxLookupErrors(), CTaxValidationAndCleanup::ReportTaxLookupErrors(), ValidateDbxref(), ValidateOrgModVoucher(), CStrainRequest::x_CheckOneStrain(), CValidError_bioseq::x_CheckSingleStrandedRNAViruses(), and CValidError_bioseq::x_ReportLineageConflictWithMol().
◆ RaiseGenomeSeverity() ◆ ReportMissingBiosource()Definition at line 2671 of file validatorp.cpp.
References eDiag_Error, eDiag_Fatal, eErr_SEQ_DESCR_NoOrgFound, eErr_SEQ_DESCR_NoSourceDescriptor, GetContext(), i, IsPatent(), IsPDB(), m_BioseqWithNoSource, m_pEntryInfo, and PostErr().
Referenced by Validate().
◆ ReportMissingPubs()Definition at line 1343 of file valid_pub.cpp.
References eDiag_Error, eDiag_Info, eDiag_Warning, eErr_GENERIC_MissingPubRequirement, eErr_SEQ_DESCR_NoPubFound, CBioseq_Handle::GetCompleteBioseq(), GetContext(), CScope::GetSeq_entryHandle(), CValidError_bioseq::IsTSAAccession(), CValidError_bioseq::IsWGSAccession(), CValidError_bioseq::IsWGSMaster(), m_Scope, s_CuratedRefSeqLowerToWarning(), s_IsGpipe(), s_IsNoncuratedRefSeq(), s_IsTSA_Contig(), and s_IsWgs_Contig().
Referenced by Validate().
◆ ReportSpliceAsError() bool CValidError_imp::ReportSpliceAsError ( ) const inline ◆ RequireLocalProduct() ◆ Reset() void CValidError_imp::Reset ( size_t initialInferenceCount, bool notJustLocalOrGeneral, bool hasRefSeq )Definition at line 321 of file validatorp.cpp.
References set< Key, Compare >::clear(), m_CumulativeInferenceCount, m_FarFetchFailure, m_HasRefSeq, m_IsNC, m_IsNG, m_IsNM, m_IsNP, m_IsNR, m_IsNS, m_IsNT, m_IsNW, m_IsNZ, m_IsStandaloneAnnot, m_IsTbl2Asn, m_IsWP, m_IsXR, m_NotJustLocalOrGeneral, m_NumAlign, m_NumAnnot, m_NumBioseq, m_NumBioseq_set, m_NumDesc, m_NumDescr, m_NumFeat, m_NumGenes, m_NumGeneXrefs, m_NumGraph, m_NumMisplacedFeatures, m_NumMisplacedGraphs, m_NumPseudo, m_NumPseudogene, m_NumSmallGenomeSetMisplaced, m_NumTopSetSiblings, m_NumTpaWithHistory, m_NumTpaWithoutHistory, m_pEntryInfo, m_PrgCallback, m_Scope, m_SeqAnnot, m_TSE, CConstRef< C, Locker >::Reset(), and SetSuppressed().
Referenced by x_Init().
◆ ResetCumulativeInferenceCount() void CValidError_imp::ResetCumulativeInferenceCount ( ) inline ◆ ResetGeneCount() void CValidError_imp::ResetGeneCount ( ) inline ◆ ResetGeneXrefCount() void CValidError_imp::ResetGeneXrefCount ( ) inline ◆ ResetMisplacedFeatureCount() void CValidError_imp::ResetMisplacedFeatureCount ( ) inline ◆ ResetMisplacedGraphCount() void CValidError_imp::ResetMisplacedGraphCount ( ) inline ◆ ResetPseudoCount() void CValidError_imp::ResetPseudoCount ( ) inline ◆ ResetPseudogeneCount() void CValidError_imp::ResetPseudogeneCount ( ) inline ◆ ResetSmallGenomeSetMisplacedCount() void CValidError_imp::ResetSmallGenomeSetMisplacedCount ( ) inline ◆ ResetTpaWithHistoryCount() void CValidError_imp::ResetTpaWithHistoryCount ( ) inline ◆ ResetTpaWithoutHistoryCount() void CValidError_imp::ResetTpaWithoutHistoryCount ( ) inline ◆ s_IsSalmonellaGenus() ◆ SetContext() ◆ SetErrorRepository() void CValidError_imp::SetErrorRepository ( IValidError * errors ) ◆ SetFarFetchFailure() void CValidError_imp::SetFarFetchFailure ( ) inline ◆ SetOptions() void CValidError_imp::SetOptions ( Uint4 options )Definition at line 277 of file validatorp.cpp.
References CValidator::eVal_collect_locus_tags, CValidator::eVal_compare_vdjc_to_cds, CValidator::eVal_do_barcode_tests, CValidator::eVal_do_rubisco_test, CValidator::eVal_do_tax_lookup, CValidator::eVal_far_fetch_cds_products, CValidator::eVal_far_fetch_mrna_products, CValidator::eVal_force_inferences, CValidator::eVal_generate_golden_file, CValidator::eVal_genome_submission, CValidator::eVal_ignore_exceptions, CValidator::eVal_ignore_inferences, CValidator::eVal_indexer_version, CValidator::eVal_inference_accns, CValidator::eVal_latlon_check_state, CValidator::eVal_latlon_ignore_water, CValidator::eVal_locus_tag_general_match, CValidator::eVal_need_isojta, CValidator::eVal_new_strain_validation, CValidator::eVal_no_context, CValidator::eVal_non_ascii, CValidator::eVal_ovl_pep_err, CValidator::eVal_refseq_conventions, CValidator::eVal_remote_fetch, CValidator::eVal_report_splice_as_error, CValidator::eVal_seqsubmit_parent, CValidator::eVal_use_entrez, CValidator::eVal_val_align, CValidator::eVal_val_exons, CValidator::eVal_validate_id_set, m_CollectLocusTags, m_CompareVDJCtoCDS, m_DoBarcodeTests, m_DoRubiscoText, m_DoTaxLookup, m_FarFetchCDSproducts, m_FarFetchMRNAproducts, m_ForceInferences, m_GenerateGoldenFile, m_genomeSubmission, m_IgnoreExceptions, m_IgnoreInferences, m_IndexerVersion, m_LatLonCheckState, m_LatLonIgnoreWater, m_LocusTagGeneralMatch, m_NewStrainValidation, m_NonASCII, m_OvlPepErr, m_RefSeqConventions, m_RemoteFetch, m_ReportSpliceAsError, m_RequireISOJTA, m_SeqSubmitParent, m_SuppressContext, m_UseEntrez, m_ValidateAlignments, m_ValidateExons, m_ValidateIdSet, and m_ValidateInferenceAccessions.
Referenced by x_Init().
◆ SetProgressCallback() ◆ SetScope() ◆ SetSuppressed() ◆ SetTSE() ◆ Setup() [1/3]Definition at line 3372 of file validatorp.cpp.
References CScope::AddTopLevelSeqEntry(), CSerialObject::Assign(), m_ObjMgr, m_Scope, m_TSE, m_TSEH, CRef< C, Locker >::Reset(), CConstRef< C, Locker >::Reset(), CSeq_entry_Base::SetSeq(), and Setup().
◆ Setup() [2/3]Definition at line 3360 of file validatorp.cpp.
References CScope::AddTopLevelSeqEntry(), CSeq_annot_Handle::GetCompleteSeq_annot(), CSeq_annot_Handle::GetScope(), m_IsStandaloneAnnot, m_Scope, m_SeqAnnot, m_TSE, m_TSEH, CRef< C, Locker >::Reset(), and CConstRef< C, Locker >::Reset().
◆ Setup() [3/3]Definition at line 3112 of file validatorp.cpp.
References NStr::CompareNocase(), ConstBegin(), DoesAnyFeatLocHaveGI(), DoesAnyGeneHaveLocusTag(), DoesAnyProductLocHaveGI(), CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Other, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeqdesc_Base::e_Source, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, CSeqdesc_Base::e_User, CBioseq_set_Base::eClass_gen_prod_set, CBioseq_set_Base::eClass_small_genome_set, CBioSource_Base::eGenome_genomic, NStr::EqualNocase(), FOR_EACH_SEQID_ON_BIOSEQ, CTextseq_id_Base::GetAccession(), CSeq_entry_Handle::GetCompleteSeq_entry(), GetContext(), CUser_object_Base::GetData(), CSeq_id_Base::GetGeneral(), CSeq_id_Base::GetOther(), CSeq_entry_Handle::GetScope(), CObject_id_Base::GetStr(), CSeq_id::GetTextseq_Id(), CUser_object_Base::GetType(), CTextseq_id_Base::GetVersion(), i, CNcbiApplication::Instance(), NStr::IsBlank(), CTextseq_id_Base::IsSetAccession(), CTextseq_id_Base::IsSetVersion(), CDbtag::IsSkippable(), CObject_id_Base::IsStr(), ITERATE, m_IsNC, m_IsNG, m_IsNM, m_IsNP, m_IsNR, m_IsNS, m_IsNT, m_IsNW, m_IsNZ, m_IsTbl2Asn, m_IsWP, m_IsXR, m_NumAlign, m_NumAnnot, m_NumBioseq, m_NumBioseq_set, m_NumDesc, m_NumDescr, m_NumFeat, m_NumGraph, m_NumTopSetSiblings, m_pEntryInfo, m_PrgCallback, m_PrgInfo, m_Scope, CValidator::CProgressInfo::m_Total, m_TSE, m_TSEH, CRef< C, Locker >::Reset(), s_CountTopSetSiblings(), s_SeqLocHasGI(), CValidatorEntryInfo::SetDdbj(), CValidatorEntryInfo::SetEmbl(), CValidatorEntryInfo::SetFeatLocHasGI(), CValidatorEntryInfo::SetGED(), CValidatorEntryInfo::SetGenbank(), CValidatorEntryInfo::SetGeneHasLocusTag(), CValidatorEntryInfo::SetGenomic(), CValidatorEntryInfo::SetGI(), CValidatorEntryInfo::SetGiOrAccnVer(), CValidatorEntryInfo::SetGpipe(), CValidatorEntryInfo::SetGPS(), CValidatorEntryInfo::SetINSDInSep(), CValidatorEntryInfo::SetLocalGeneralOnly(), CValidatorEntryInfo::SetNoBioSource(), CValidatorEntryInfo::SetNoCitSubPubs(), CValidatorEntryInfo::SetNoPubs(), CValidatorEntryInfo::SetPatent(), CValidatorEntryInfo::SetPDB(), CValidatorEntryInfo::SetProductLocHasGI(), CValidatorEntryInfo::SetProteinHasGeneralID(), CValidatorEntryInfo::SetRefSeq(), CValidatorEntryInfo::SetSmallGenomeSet(), CValidatorEntryInfo::SetTPE(), SetTSE(), si, CSeq_id_Base::Which(), and x_SetEntryInfo().
Referenced by GetTSACDSOnMinusStrandErrors(), GetTSAConflictingBiomolTechErrors(), GetTSANStretchErrors(), Setup(), and Validate().
◆ ShouldSubdivide() bool CValidError_imp::ShouldSubdivide ( ) const inline ◆ UseEntrez() bool CValidError_imp::UseEntrez ( ) const inline ◆ Validate() [1/8]Definition at line 1922 of file validatorp.cpp.
References CBioSource_Base::eGenome_unknown, FindCollidingSerialNumbers(), FindEmbeddedScript(), FindNonAsciiText(), CBioSource_Base::GetGenome(), CBioSource_Base::GetOrg(), CBioSource_Base::IsSetGenome(), CBioSource_Base::IsSetOrg(), m_ObjMgr, m_Scope, CRef< C, Locker >::Reset(), ValidateBioSource(), and ValidateTaxonomy().
◆ Validate() [2/8] ◆ Validate() [3/8]Definition at line 1838 of file validatorp.cpp.
References CSeq_annot_Base::C_Data::e_Align, CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, FindCollidingSerialNumbers(), FindEmbeddedScript(), FindNonAsciiText(), CSeq_annot_Handle::GetCompleteSeq_annot(), IsValidateAlignments(), Setup(), CValidError_align::ValidateSeqAlign(), CValidError_annot::ValidateSeqAnnot(), CValidError_feat::ValidateSeqFeat(), CValidError_graph::ValidateSeqGraph(), and CSeq_annot_Handle::Which().
◆ Validate() [4/8] ◆ Validate() [5/8]Definition at line 1333 of file validatorp.cpp.
References _ASSERT, ConstBegin(), DoesAnyProteinHaveGeneralID(), CSeqFeatData_Base::e_not_set, CSeq_entry_Base::e_not_set, CBioseq_set_Base::eClass_eco_set, CBioseq_set_Base::eClass_gen_prod_set, CBioseq_set_Base::eClass_mut_set, CBioseq_set_Base::eClass_phy_set, CBioseq_set_Base::eClass_pop_set, CBioseq_set_Base::eClass_small_genome_set, CBioseq_set_Base::eClass_wgs_set, eDiag_Critical, eDiag_Error, eDiag_Fatal, eDiag_Info, eDiag_Warning, eErr_GENERIC_NonAsciiAsn, eErr_INTERNAL_Exception, eErr_SEQ_FEAT_CollidingFeatureIDs, eErr_SEQ_FEAT_OnlyGeneXrefs, eErr_SEQ_FEAT_TooManyInferenceAccessions, eErr_SEQ_INST_BadSeqIdFormat, eErr_SEQ_INST_FarFetchFailure, eErr_SEQ_INST_ProteinsHaveGeneralID, eErr_SEQ_INST_TpaAssemblyProblem, eErr_SEQ_PKG_FeaturePackagingProblem, eErr_SEQ_PKG_GPSnonGPSPackaging, eErr_SEQ_PKG_GraphPackagingProblem, eErr_SEQ_PKG_INSDRefSeqPackaging, eErr_SEQ_PKG_NoBioseqFound, CBioseq_CI::eLevel_All, CSeq_inst_Base::eMol_not_set, NStr::Equal(), ERR_POST_X, CValidator::CProgressInfo::eState_Initializing, FindCollidingSerialNumbers(), FindEmbeddedScript(), FindNonAsciiText(), FOR_EACH_GBQUAL_ON_FEATURE, FOR_EACH_SEQID_ON_BIOSEQ, CValidError_feat::GetAccessionsFromInferenceString(), CScope::GetBioseqHandle(), CBioseq_Handle::GetCompleteBioseq(), CSeq_entry_Handle::GetCompleteSeq_entry(), GetContext(), CTSE_Handle::GetFeaturesWithId(), CObject_id_Base::GetId(), CSeq_feat_Base::GetId(), CFeat_id_Base::GetLocal(), CValidError_feat::GetPrefixAndAccessionFromInferenceAccession(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CSeq_entry_Handle::GetTSE_Handle(), GetTSEH(), i, InferenceAccessionCutoff, IsHugeFileMode(), CObject_id_Base::IsId(), IsIndexerVersion(), IsINSDInSep(), CFeat_id_Base::IsLocal(), IsRefSeq(), CSeq_entry_Handle::IsSeq(), CSeq_entry_Handle::IsSet(), CSeq_feat_Base::IsSetId(), IsWP(), ITERATE, label, m_CumulativeInferenceCount, m_DoBarcodeTests, m_DoTaxLookup, m_FarFetchFailure, m_ForceInferences, m_IgnoreInferences, m_NonASCII, m_NumGenes, m_NumGeneXrefs, m_NumMisplacedFeatures, m_NumMisplacedGraphs, m_NumSmallGenomeSetMisplaced, m_NumTpaWithHistory, m_NumTpaWithoutHistory, m_PrgCallback, m_PrgInfo, m_Scope, CValidator::CProgressInfo::m_State, m_TSE, m_ValidateInferenceAccessions, NStr::NumericToString(), PostErr(), ReportMissingBiosource(), ReportMissingPubs(), SetContext(), CValidatorEntryInfo::SetNoPubs(), CValidatorEntryInfo::SetSeqSubmit(), Setup(), si, NStr::SizetToString(), NStr::StartsWith(), NStr::TruncateSpacesInPlace(), CValidError_bioseq::ValidateBioseq(), CValidError_bioseqset::ValidateBioseqSet(), ValidateCitations(), ValidateCitSub(), ValidateMultipleTaxIds(), ValidateTaxonomy(), Warning(), CSeq_entry_Handle::Which(), x_DoBarcodeTests(), and x_SetEntryInfo().
◆ Validate() [6/8]Definition at line 1891 of file validatorp.cpp.
References CBioSource_Base::eGenome_unknown, ctll::empty(), FindCollidingSerialNumbers(), FindEmbeddedScript(), FindNonAsciiText(), CSeqFeatData_Base::GetBiosrc(), CSeq_feat_Base::GetData(), CBioSource_Base::GetGenome(), CBioSource_Base::GetOrg(), CSeqFeatData_Base::IsBiosrc(), CSeq_feat_Base::IsSetData(), CBioSource_Base::IsSetGenome(), CBioSource_Base::IsSetOrg(), m_ObjMgr, m_Scope, CRef< C, Locker >::Reset(), CValidError_feat::SetScope(), CValidError_feat::SetTSE(), CValidError_feat::ValidateSeqFeat(), and ValidateTaxonomy().
◆ Validate() [7/8]Definition at line 1778 of file validatorp.cpp.
References CSeq_submit_Base::C_Data::e_Entrys, CBioseq_set_Base::eClass_wgs_set, eDiag_Warning, eErr_SEQ_PKG_SeqSubmitWithWgsSet, FOR_EACH_SEQENTRY_ON_SEQSUBMIT, CSubmit_block_Base::GetCit(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_submit_Base::GetData(), CScope::GetSeq_entryHandle(), CSeq_entry_Base::GetSet(), CSeq_submit_Base::GetSub(), CSubmit_block_Base::GetTool(), IsHugeFileMode(), IsHugeSet(), CSeq_entry_Base::IsSet(), CSeq_submit_Base::IsSetSub(), CSubmit_block_Base::IsSetTool(), PostErr(), SetContext(), CValidatorEntryInfo::SetGeneious(), CValidatorEntryInfo::SetSeqSubmit(), Setup(), NStr::StartsWith(), Validate(), ValidateSubmitBlock(), CSeq_submit_Base::C_Data::Which(), and x_SetEntryInfo().
◆ Validate() [8/8] ◆ ValidateAffil()Definition at line 988 of file valid_pub.cpp.
References ctx, eDiag_Warning, eErr_GENERIC_MissingPubRequirement, NStr::Equal(), CAffil_Base::C_Std::GetAffil(), CAffil_Base::C_Std::GetCity(), CAffil_Base::C_Std::GetCountry(), CAffil_Base::C_Std::GetDiv(), CAffil_Base::C_Std::GetEmail(), CAffil_Base::C_Std::GetFax(), CAffil_Base::C_Std::GetPhone(), CAffil_Base::C_Std::GetPostal_code(), CAffil_Base::C_Std::GetStreet(), CAffil_Base::C_Std::GetSub(), NStr::IsBlank(), CAffil_Base::C_Std::IsSetAffil(), CAffil_Base::C_Std::IsSetCity(), CAffil_Base::C_Std::IsSetCountry(), CAffil_Base::C_Std::IsSetDiv(), CAffil_Base::C_Std::IsSetEmail(), CAffil_Base::C_Std::IsSetFax(), CAffil_Base::C_Std::IsSetPhone(), CAffil_Base::C_Std::IsSetPostal_code(), CAffil_Base::C_Std::IsSetStreet(), and CAffil_Base::C_Std::IsSetSub().
Referenced by ValidateSubmitBlock().
◆ ValidateAuthorList()Definition at line 730 of file valid_pub.cpp.
References CValidator::BadCharsInAuthor(), CValidator::BadCharsInAuthorName(), NStr::CompareNocase(), ctx, eDiag_Warning, eErr_GENERIC_AuthorListHasEtAl, eErr_GENERIC_PublicationInconsistency, eErr_SEQ_FEAT_BadAuthorSuffix, eErr_SEQ_FEAT_BadCharInAuthorLastName, eErr_SEQ_FEAT_BadCharInAuthorName, NStr::EqualNocase(), CName_std_Base::GetFirst(), CName_std_Base::GetInitials(), CName_std_Base::GetLast(), CName_std::GetStandardSuffixes(), CName_std_Base::GetSuffix(), NStr::IsBlank(), CName_std_Base::IsSetFirst(), CName_std_Base::IsSetInitials(), CName_std_Base::IsSetLast(), CName_std_Base::IsSetSuffix(), ITERATE, last(), names, NStr::ReplaceInPlace(), str(), and NStr::TruncateSpacesInPlace().
◆ ValidateAuthorsInPubequiv()Definition at line 834 of file valid_pub.cpp.
References ctx, CPub_Base::e_Article, CPub_Base::e_Book, CPub_Base::e_Equiv, CPub_Base::e_Gen, CPub_Base::e_Man, CPub_Base::e_Patent, CPub_Base::e_Proc, CPub_Base::e_Sub, eDiag_Error, eErr_GENERIC_BadSubmissionAuthorName, NStr::EqualNocase(), first(), FOR_EACH_PUB_ON_PUBEQUIV, CPub_Base::GetArticle(), CCit_art_Base::GetAuthors(), CCit_book_Base::GetAuthors(), CCit_gen_Base::GetAuthors(), CCit_pat_Base::GetAuthors(), CCit_sub_Base::GetAuthors(), CCit_proc_Base::GetBook(), CPub_Base::GetBook(), CCit_let_Base::GetCit(), CPub_Base::GetEquiv(), CName_std_Base::GetFirst(), CPub_Base::GetGen(), CName_std_Base::GetLast(), CPub_Base::GetMan(), CAuth_list_Base::GetNames(), CPub_Base::GetPatent(), CPub_Base::GetPmid(), CPub_Base::GetProc(), CPub_Base::GetSub(), IsBadSubmissionFirstName(), IsBadSubmissionLastName(), CPub_Base::IsPmid(), CCit_art_Base::IsSetAuthors(), CCit_gen_Base::IsSetAuthors(), CName_std_Base::IsSetFirst(), CName_std_Base::IsSetLast(), ITERATE, last(), names, CPub_Base::Which(), and ZERO_ENTREZ_ID.
◆ ValidateBadAffil() ◆ ValidateBadNameStd()Definition at line 1079 of file valid_pub.cpp.
References NStr::CompareNocase(), ctx, eDiag_Error, eErr_GENERIC_BadFirstName, eErr_GENERIC_BadLastName, first(), CName_std_Base::GetFirst(), CName_std_Base::GetLast(), CName_std_Base::IsSetFirst(), CName_std_Base::IsSetLast(), and last().
◆ ValidateBioSource()Definition at line 515 of file valid_biosource.cpp.
References CPCRSetList::AddFwdName(), CPCRSetList::AddFwdSeq(), CPCRSetList::AddRevName(), CPCRSetList::AddRevSeq(), CPCRSetList::AreSetsUnique(), CBioSource_Base::CanGetOrg(), CSubSource::CheckCellLine(), NStr::CompareNocase(), count, ctx, CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, NStr::eCase, eDiag_Critical, eDiag_Error, eDiag_Info, eDiag_Warning, eErr_SEQ_DESCR_BadAltitude, eErr_SEQ_DESCR_BadOrganelleLocation, eErr_SEQ_DESCR_BadPCRPrimerSequence, eErr_SEQ_DESCR_BadPlastidName, eErr_SEQ_DESCR_BioSourceInconsistency, eErr_SEQ_DESCR_ChromosomeLocation, eErr_SEQ_DESCR_ChromosomeWithoutLocation, eErr_SEQ_DESCR_DuplicatePCRPrimerSequence, eErr_SEQ_DESCR_EnvironSampleMissingQualifier, eErr_SEQ_DESCR_InvalidMatingType, eErr_SEQ_DESCR_InvalidSexQualifier, eErr_SEQ_DESCR_InvalidTissueType, eErr_SEQ_DESCR_MissingEnvironmentalSample, eErr_SEQ_DESCR_MissingLineage, eErr_SEQ_DESCR_MissingMetagenomicQualifier, eErr_SEQ_DESCR_MissingPlasmidLocation, eErr_SEQ_DESCR_MissingPlasmidName, eErr_SEQ_DESCR_MultipleSourceQualifiers, eErr_SEQ_DESCR_NoOrgFound, eErr_SEQ_DESCR_ObsoleteSourceLocation, eErr_SEQ_DESCR_StrainWithEnvironSample, eErr_SEQ_DESCR_SuspectedContaminatedCellLine, eErr_SEQ_DESCR_TaxonomyBlankSample, eErr_SEQ_DESCR_TaxonomyIsMetagenome, eErr_SEQ_DESCR_UnculturedNeedsEnvSample, CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_chloroplast, CBioSource_Base::eGenome_chromatophore, CBioSource_Base::eGenome_chromoplast, CBioSource_Base::eGenome_chromosome, CBioSource_Base::eGenome_extrachrom, CBioSource_Base::eGenome_genomic, CBioSource_Base::eGenome_insertion_seq, CBioSource_Base::eGenome_kinetoplast, CBioSource_Base::eGenome_leucoplast, CBioSource_Base::eGenome_macronuclear, CBioSource_Base::eGenome_nucleomorph, CBioSource_Base::eGenome_plasmid, CBioSource_Base::eGenome_plastid, CBioSource_Base::eGenome_proplastid, CBioSource_Base::eGenome_proviral, CBioSource_Base::eGenome_transposon, CBioSource_Base::eGenome_unknown, NStr::eNocase, NStr::Equal(), NStr::EqualCase(), NStr::EqualNocase(), CSubSource_Base::eSubtype_altitude, CSubSource_Base::eSubtype_cell_line, CSubSource_Base::eSubtype_chromosome, CSubSource_Base::eSubtype_collected_by, CSubSource_Base::eSubtype_collection_date, CSubSource_Base::eSubtype_country, CSubSource_Base::eSubtype_environmental_sample, CSubSource_Base::eSubtype_fwd_primer_name, CSubSource_Base::eSubtype_fwd_primer_seq, CSubSource_Base::eSubtype_germline, CSubSource_Base::eSubtype_identified_by, CSubSource_Base::eSubtype_isolation_source, CSubSource_Base::eSubtype_lat_lon, CSubSource_Base::eSubtype_linkage_group, CSubSource_Base::eSubtype_map, CSubSource_Base::eSubtype_mating_type, COrgMod_Base::eSubtype_metagenome_source, CSubSource_Base::eSubtype_metagenomic, COrgMod_Base::eSubtype_nat_host, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_plastid_name, CSubSource_Base::eSubtype_rearranged, CSubSource_Base::eSubtype_rev_primer_name, CSubSource_Base::eSubtype_rev_primer_seq, CSubSource_Base::eSubtype_segment, CSubSource_Base::eSubtype_sex, COrgMod_Base::eSubtype_strain, CSubSource_Base::eSubtype_tissue_type, CSubSource_Base::eSubtype_transgenic, NStr::Find(), NStr::FindNoCase(), FOR_EACH_DBXREF_ON_ORGREF, FOR_EACH_SEQID_ON_BIOSEQ, FOR_EACH_SUBSOURCE_ON_BIOSOURCE, CTextseq_id_Base::GetAccession(), COrgName_Base::GetDiv(), CBioSource_Base::GetGenome(), CBioSource::GetGenomeByOrganelle(), CBioSource::GetLineage(), COrgName_Base::GetLineage(), COrgName_Base::GetMod(), CSubSource_Base::GetName(), CBioSource_Base::GetOrg(), CBioSource::GetOrganelleByGenome(), COrg_ref_Base::GetOrgname(), CBioSource_Base::GetPcr_primers(), CSeq_entry_Base::GetSeq(), CBioSource_Base::GetSubtype(), CSubSource::GetSubtypeName(), COrgMod::GetSubtypeName(), COrg_ref_Base::GetTaxname(), CSeq_id::GetTextseq_Id(), CSubSource::IsAltitudeValid(), NStr::IsBlank(), CSubSource::IsCorrectLatLonFormat(), CSubSource::IsMultipleValuesAllowed(), CSeq_entry_Base::IsSeq(), CTextseq_id_Base::IsSetAccession(), COrgName_Base::IsSetDiv(), CBioSource_Base::IsSetGenome(), CBioSource::IsSetLineage(), COrgName_Base::IsSetLineage(), CSubSource_Base::IsSetName(), COrg_ref::IsSetOrgMod(), COrg_ref_Base::IsSetOrgname(), CBioSource_Base::IsSetPcr_primers(), COrg_ref_Base::IsSetTaxname(), IsUnexpectedViralOrgModQualifier(), IsUnexpectedViralSubSourceQualifier(), CSubSource::IsValidSexQualifierValue(), CValidError_bioseq::IsWGS(), ITERATE, msg(), CSubSource::NCBI_UseGeoLocNameForCountry(), NPOS, s_GetJustNucSeqEntry(), s_GetNucSeqFromContext(), s_HasWGSTech(), s_IsAllDigitsOrSpaces(), s_IsChromosome(), s_IsEukaryoteOrProkaryote(), s_ReportUndefinedSpeciesId(), NStr::StartsWith(), str(), subname, toupper(), val, and CSeq_id_Base::Which().
Referenced by CSrcFeatValidator::Validate(), Validate(), and CValidError_desc::ValidateSeqDesc().
◆ ValidateBioSourceForSeq()Definition at line 2270 of file valid_biosource.cpp.
References ctx, CSeqFeatData_Base::e_Biosrc, CSeqdesc_Base::e_Molinfo, CSeqdesc_Base::e_Title, CMolInfo_Base::eBiomol_cRNA, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::eBiomol_other_genetic, CBioseq_set_Base::eClass_parts, CMolInfo_Base::eCompleteness_complete, eDiag_Error, eDiag_Info, eDiag_Warning, eErr_SEQ_DESCR_BacteriaMissingSourceQualifier, eErr_SEQ_DESCR_BioSourceNeedsChromosome, eErr_SEQ_DESCR_InconsistentVirusMoltype, eErr_SEQ_DESCR_InvalidForType, eErr_SEQ_DESCR_SyntheticConstructNeedsArtificial, eErr_SEQ_DESCR_SyntheticConstructWrongMolType, eErr_SEQ_DESCR_UnnecessaryBioSourceFocus, CBioSource_Base::eGenome_proviral, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_rna, NStr::eNocase, CBioSource_Base::eOrigin_synthetic, NStr::EqualNocase(), CSeq_inst_Base::eRepr_seg, CSubSource_Base::eSubtype_environmental_sample, COrgMod_Base::eSubtype_isolate, COrgMod_Base::eSubtype_other, CSubSource_Base::eSubtype_other, COrgMod_Base::eSubtype_strain, NStr::Find(), NStr::FindNoCase(), FOR_EACH_SUBSOURCE_ON_BIOSOURCE, CMolInfo_Base::GetBiomol(), CBioseq_Handle::GetCompleteBioseq(), CMolInfo_Base::GetCompleteness(), CBioseq_Handle::GetInst(), COrgName_Base::GetLineage(), COrgName_Base::GetMod(), CSeq_inst_Base::GetMol(), CSeqdesc_Base::GetMolinfo(), COrg_ref_Base::GetOrgname(), CSeqdesc_Base::GetTitle(), CBioseq_Handle::IsAa(), NStr::IsBlank(), CSeqdesc_Base::IsMolinfo(), CMolInfo_Base::IsSetBiomol(), CMolInfo_Base::IsSetCompleteness(), CBioseq_Handle::IsSetInst(), COrg_ref::IsSetLineage(), COrgName_Base::IsSetMod(), CSeq_inst_Base::IsSetMol(), COrg_ref_Base::IsSetOrgname(), ITERATE, om, s_CompleteGenomeNeedsChromosome(), s_IsArchaea(), s_IsBacteria(), s_IsBioSample(), rapidjson::source, and NStr::StartsWith().
Referenced by CValidError_bioseq::ValidateSeqDescContext().
◆ ValidateCitations()Definition at line 2858 of file validatorp.cpp.
References CSeqFeatData_Base::e_Pub, CPub::eContent, eDiag_Warning, eErr_SEQ_FEAT_FeatureCitationProblem, NStr::EndsWith(), NStr::EqualNocase(), f, IAbstractCitation::fLabel_Unique, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_feat_Handle::GetData(), CSeqFeatData_Base::GetPub(), CCleanup::GetPubdescLabels(), ITERATE, label, len, NStr::NumericToString(), PostErr(), and s_CollectPubDescriptorLabels().
Referenced by Validate().
◆ ValidateCitSub()Definition at line 1129 of file valid_pub.cpp.
References CAuth_list_Base::CanGetAffil(), CCit_sub_Base::CanGetAuthors(), CAuth_list_Base::CanGetNames(), CheckDate(), ctx, CAffil_Base::e_Std, CAuth_list_Base::C_Names::e_Std, CAffil_Base::e_Str, eDateValid_valid, eDiag_Critical, eDiag_Error, eDiag_Warning, eErr_GENERIC_BadDate, eErr_GENERIC_MissingPubRequirement, CAuth_list_Base::GetAffil(), CCit_sub_Base::GetAuthors(), CCit_sub_Base::GetDate(), CPerson_id_Base::GetName(), CAuth_list_Base::GetNames(), CAffil_Base::GetStd(), CAffil_Base::GetStr(), HAS_VALUE, NStr::IsBlank(), CSubSource::IsCollectionDateAfterTime(), CPerson_id_Base::IsName(), CCit_sub_Base::IsSetDate(), ITERATE, names, NULL, and CAffil_Base::Which().
Referenced by Validate().
◆ ValidateDbxref() [1/2]Definition at line 1984 of file validatorp.cpp.
References ctx, CValidator::eBadCapitalization, CValidator::eContainsSpace, CValidator::eDbHasSgml, eDiag_Error, eDiag_Warning, eErr_GENERIC_SgmlPresentInText, eErr_SEQ_FEAT_IllegalDbXref, CValidator::eNotForSource, CValidator::eOnlyForRefSeq, CValidator::eOnlyForSource, CValidator::eRefSeqNotForSource, CValidator::eTagHasSgml, CValidator::eUnrecognized, flags, CDbtag_Base::GetDb(), CDbtag::GetDBFlags(), CObject_id_Base::GetId(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), IsGPS(), CObject_id_Base::IsId(), IsRefSeq(), CDbtag_Base::IsSetDb(), CDbtag_Base::IsSetTag(), CObject_id_Base::IsStr(), CValidator::IsValidDbxref(), kEmptyStr, NStr::NumericToString(), and PostObjErr().
Referenced by CProtValidator::Validate(), and ValidateDbxref().
◆ ValidateDbxref() [2/2] ◆ ValidateInferenceAccessions() bool CValidError_imp::ValidateInferenceAccessions ( ) const inline ◆ ValidateLatLonCountry() ◆ ValidateMultipleTaxIds()Definition at line 1277 of file validatorp.cpp.
References CSeqdesc_Base::e_Source, eDiag_Error, eDiag_Warning, eErr_SEQ_DESCR_MultipleTaxonIDs, NStr::EqualNocase(), COrg_ref_Base::GetDb(), COrg_ref_Base::IsSetDb(), ITERATE, m_TSE, PostErr(), and s_IsPhage().
Referenced by Validate().
◆ ValidateOrgModVoucher()Definition at line 3502 of file valid_biosource.cpp.
References ctx, eDiag_Error, eDiag_Info, eDiag_Warning, eErr_SEQ_DESCR_BadCollectionCode, eErr_SEQ_DESCR_BadInstitutionCode, eErr_SEQ_DESCR_BadInstitutionCountry, eErr_SEQ_DESCR_BadInstitutionGeoLocName, eErr_SEQ_DESCR_IncorrectlyFormattedVoucherID, eErr_SEQ_DESCR_MissingPersonalCollectionName, eErr_SEQ_DESCR_UnstructuredVoucher, eErr_SEQ_DESCR_WrongVoucherType, COrgMod_Base::eSubtype_bio_material, COrgMod_Base::eSubtype_culture_collection, COrgMod_Base::eSubtype_specimen_voucher, NStr::FindNoCase(), COrgMod_Base::GetSubname(), COrgMod_Base::GetSubtype(), COrgMod::IsBiomaterialValid(), NStr::IsBlank(), COrgMod::IsCultureCollectionValid(), COrgMod_Base::IsSetSubname(), COrgMod_Base::IsSetSubtype(), COrgMod::IsSpecimenVoucherValid(), ITERATE, CSubSource::NCBI_UseGeoLocNameForCountry(), PostObjErr(), NStr::Split(), NStr::StartsWith(), and val.
◆ ValidateOrgName()Definition at line 1947 of file valid_biosource.cpp.
References COrgMod::CheckMultipleVouchers(), ContainsSgml(), ctx, COrgName_Base::C_Name::e_Binomial, eDiag_Critical, eDiag_Error, eDiag_Info, eDiag_Warning, eErr_GENERIC_SgmlPresentInText, eErr_SEQ_DESCR_BadOrgMod, eErr_SEQ_DESCR_BadTypeMaterial, eErr_SEQ_DESCR_BadVariety, eErr_SEQ_DESCR_BioSourceInconsistency, eErr_SEQ_DESCR_HasStrainAndIsolate, eErr_SEQ_DESCR_IdenticalInstitutionCode, eErr_SEQ_DESCR_MultipleIsolates, eErr_SEQ_DESCR_MultipleStrains, eErr_SEQ_DESCR_OrgModValueInvalid, eErr_SEQ_DESCR_UnbalancedParentheses, NStr::eNocase, NStr::Equal(), NStr::EqualNocase(), COrgMod_Base::eSubtype_bio_material, COrgMod_Base::eSubtype_culture_collection, COrgMod_Base::eSubtype_gb_synonym, COrgMod_Base::eSubtype_isolate, COrgMod_Base::eSubtype_old_name, COrgMod_Base::eSubtype_other, COrgMod_Base::eSubtype_serovar, COrgMod_Base::eSubtype_specimen_voucher, COrgMod_Base::eSubtype_strain, COrgMod_Base::eSubtype_sub_species, COrgMod_Base::eSubtype_synonym, COrgMod_Base::eSubtype_type_material, COrgMod_Base::eSubtype_variety, NStr::Find(), NStr::FindNoCase(), FOR_EACH_ORGMOD_ON_ORGNAME, COrgName_Base::C_Name::GetBinomial(), COrgName_Base::GetDiv(), CBinomialOrgName_Base::GetGenus(), COrgName_Base::GetLineage(), COrgName_Base::GetName(), CBinomialOrgName_Base::GetSpecies(), COrgMod_Base::GetSubname(), COrgMod_Base::GetSubtype(), NStr::IntToString(), NStr::IsBlank(), COrgMod::IsIsolateValid(), COrgName_Base::IsSetDiv(), CBinomialOrgName_Base::IsSetGenus(), COrgName_Base::IsSetLineage(), COrgName_Base::IsSetMod(), COrgName_Base::IsSetName(), CBinomialOrgName_Base::IsSetSpecies(), COrgMod_Base::IsSetSubname(), COrgMod::IsStrainValid(), COrgMod::IsValidTypeMaterial(), COrgMod::NCBI_ValidateForMultipleIsolates(), s_UnbalancedParentheses(), NStr::StartsWith(), str(), subname, val, and COrgName_Base::C_Name::Which().
◆ ValidateOrgRef()Definition at line 1714 of file valid_biosource.cpp.
References NStr::CompareNocase(), ContainsSgml(), ctx, eDiag_Error, eDiag_Fatal, eDiag_Warning, eErr_GENERIC_SgmlPresentInText, eErr_SEQ_DESCR_BadOrgMod, eErr_SEQ_DESCR_HostIdenticalToOrganism, eErr_SEQ_DESCR_NoOrgFound, eErr_SEQ_DESCR_NoTaxonID, eErr_SEQ_DESCR_OrganismIsUndefinedSpecies, eErr_SEQ_DESCR_OrgModMissingValue, eErr_SEQ_DESCR_UnbalancedParentheses, NStr::eNocase, NStr::Equal(), NStr::EqualNocase(), COrgMod_Base::eSubtype_forma, COrgMod_Base::eSubtype_forma_specialis, COrgMod_Base::eSubtype_nat_host, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_serovar, COrgMod_Base::eSubtype_sub_species, COrgMod_Base::eSubtype_variety, NStr::Find(), NStr::FindNoCase(), FOR_EACH_DBXREF_ON_ORGREF, FOR_EACH_ORGMOD_ON_ORGNAME, COrg_ref_Base::GetCommon(), COrg_ref_Base::GetDb(), COrgName_Base::GetLineage(), COrg_ref_Base::GetOrgname(), COrgMod::GetSubtypeName(), COrg_ref_Base::GetTaxname(), COrg_ref_Base::IsSetCommon(), COrg_ref_Base::IsSetDb(), COrgName_Base::IsSetLineage(), COrgName_Base::IsSetName(), COrg_ref_Base::IsSetOrgname(), COrg_ref_Base::IsSetTaxname(), COrg_ref::IsSubspeciesValid(), COrg_ref::IsVarietyValid(), NPOS, NStr::ReplaceInPlace(), s_FindWholeName(), s_HasMetagenomeSource(), s_IsUndefinedSpecies(), s_UnbalancedParentheses(), NStr::StartsWith(), subname, toupper(), and NStr::TruncateSpacesInPlace().
◆ ValidateOrgRefs() ◆ ValidatePCRReactionSet() ◆ ValidatePubArticle()Definition at line 321 of file valid_pub.cpp.
References ctx, eDiag_Error, eDiag_Warning, eErr_GENERIC_MissingISOJTA, eErr_GENERIC_MissingPubRequirement, CCit_art_Base::GetFrom(), CCit_art_Base::C_From::GetJournal(), CCit_art_Base::GetTitle(), CCit_jour_Base::GetTitle(), IsElectronicJournal(), IsInpress(), CCit_art_Base::C_From::IsJournal(), CCit_art_Base::IsSetTitle(), and ZERO_ENTREZ_ID.
◆ ValidatePubArticleNoPMID()Definition at line 356 of file valid_pub.cpp.
References CImprint_Base::CanGetPrepub(), CImprint_Base::CanGetPubstatus(), CheckDate(), ctx, CDate_Base::e_not_set, eDateValid_valid, eDiag_Error, eDiag_Info, eDiag_Warning, eErr_GENERIC_MissingPages, eErr_GENERIC_MissingPagesEpub, eErr_GENERIC_MissingPubRequirement, eErr_GENERIC_MissingVolume, eErr_GENERIC_MissingVolumeEpub, eErr_GENERIC_PublicationInconsistency, CImprint_Base::ePrepub_in_press, ePubStatus_aheadofprint, ePubStatus_epublish, NStr::Equal(), CImprint_Base::GetDate(), CCit_art_Base::GetFrom(), CCit_jour_Base::GetImp(), CCit_art_Base::C_From::GetJournal(), CImprint_Base::GetPages(), CImprint_Base::GetPrepub(), CImprint_Base::GetPubstatus(), CDate_Base::GetStd(), CDate_Base::GetStr(), CImprint_Base::GetVolume(), CDate_std_Base::GetYear(), NStr::IsBlank(), IsElectronicJournal(), CCit_art_Base::C_From::IsJournal(), CImprint_Base::IsSetDate(), CCit_jour_Base::IsSetImp(), CImprint_Base::IsSetPages(), CImprint_Base::IsSetPrepub(), CImprint_Base::IsSetPubstatus(), CImprint_Base::IsSetVolume(), CDate_std_Base::IsSetYear(), CDate_Base::IsStd(), CDate_Base::IsStr(), and CDate_Base::Which().
◆ ValidatePubdesc()Definition at line 77 of file valid_pub.cpp.
References ctx, CPub_Base::e_Article, CPub_Base::e_Equiv, CPub_Base::e_Gen, CPub_Base::e_Medline, CPub_Base::e_Muid, CPub_Base::e_Pmid, CPub_Base::e_Sub, eDiag_Error, eDiag_Fatal, eDiag_Warning, eErr_GENERIC_MedlineEntryPub, eErr_GENERIC_UnexpectedPubStatusComment, eErr_GENERIC_UnnecessaryPubEquiv, eErr_SEQ_DESCR_CollidingPublications, eErr_SEQ_DESCR_NoPubFound, ePubStatus_aheadofprint, ePubStatus_epublish, ePubStatus_ppublish, NStr::Find(), FOR_EACH_PUB_ON_PUBDESC, CPub_equiv_Base::Get(), CPub_Base::GetArticle(), CPubdesc_Base::GetComment(), CCit_art_Base::GetFrom(), CPub_Base::GetGen(), CCit_jour_Base::GetImp(), CCit_art_Base::C_From::GetJournal(), CPub_Base::GetMuid(), CPub_Base::GetPmid(), CPubdesc_Base::GetPub(), CImprint_Base::GetPubstatus(), CPub_Base::GetSub(), NStr::IsBlank(), CCit_art_Base::C_From::IsJournal(), CPubdesc_Base::IsSetComment(), CCit_art_Base::IsSetFrom(), CCit_jour_Base::IsSetImp(), CPubdesc_Base::IsSetPub(), CImprint_Base::IsSetPubstatus(), NStr::NumericToString(), CPub_Base::Which(), and ZERO_ENTREZ_ID.
Referenced by CPubFeatValidator::Validate(), Validate(), and CValidError_desc::ValidateSeqDesc().
◆ ValidatePubGen()Definition at line 227 of file valid_pub.cpp.
References CheckDate(), ctx, eDateValid_valid, eDiag_Error, eDiag_Warning, eErr_GENERIC_MissingPubRequirement, eErr_GENERIC_StructuredCitGenCit, NStr::eNocase, NStr::Equal(), NStr::FindCase(), gen, s_CitGenIsJustBackBoneIDNumber(), and NStr::StartsWith().
◆ ValidatePubHasAuthor()Definition at line 679 of file valid_pub.cpp.
References ctx, CPub_Base::e_Article, CPub_Base::e_Gen, eDiag_Error, eDiag_Warning, eErr_GENERIC_MissingPubRequirement, FOR_EACH_PUB_ON_PUBDESC, CPub_Base::GetArticle(), CCit_art_Base::GetAuthors(), CCit_gen_Base::GetAuthors(), CPub_Base::GetGen(), CCit_gen_Base::GetSerial_number(), CCit_art_Base::IsSetAuthors(), CCit_gen_Base::IsSetAuthors(), CCit_gen_Base::IsSetCit(), CCit_gen_Base::IsSetDate(), CCit_gen_Base::IsSetJournal(), CCit_gen_Base::IsSetSerial_number(), s_CitGenIsJustBackBoneIDNumber(), and CPub_Base::Which().
◆ ValidateSeqLoc()Definition at line 2409 of file validatorp.cpp.
References CSeqFeatData::AllowAdjacentIntervals(), BadSeqLocSortOrder(), CSeq_feat_Base::CanGetExcept_text(), CValidator::DoesSeqLocContainAdjacentIntervals(), CValidator::DoesSeqLocContainDuplicateIntervals(), eDiag_Error, eDiag_Warning, eErr_INTERNAL_Exception, eErr_SEQ_FEAT_AbuttingIntervals, eErr_SEQ_FEAT_BadTranssplicedInterval, eErr_SEQ_FEAT_DuplicateExonInterval, eErr_SEQ_FEAT_GenomeSetMixedStrand, eErr_SEQ_FEAT_MixedStrand, eErr_SEQ_FEAT_NestedSeqLocMix, eErr_SEQ_FEAT_SeqLocOrder, eErr_SEQ_FEAT_StrandOther, NStr::Equal(), CSeq_inst_Base::eRepr_seg, CSeqFeatData::eSubtype_primer_bind, CSeq_inst_Base::eTopology_circular, NStr::FindNoCase(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetExcept_text(), CBioseq_Handle::GetInst(), CBioseq_Handle::GetInst_Repr(), CSeqFeatData::GetSubtype(), CSerialObject::GetThisTypeInfo(), CSeq_inst_Base::GetTopology(), GetValidatorLocationLabel(), IsGeneious(), IsMixedStrands(), IsPseudo(), CValidator::IsSeqLocCorrectlyOrdered(), CSeq_feat_Base::IsSetExcept(), CBioseq_Handle::IsSetInst(), CBioseq_Handle::IsSetInst_Repr(), CSeq_inst_Base::IsSetTopology(), IsSmallGenomeSet(), label, lc, m_Scope, NPOS, PostErr(), CSeqFeatData::RequireLocationIntervalsInBiologicalOrder(), s_CountMix(), ValidateSeqLocIds(), CException::what(), x_CheckLoc(), x_InitLocCheck(), and x_ReportInvalidFuzz().
Referenced by CSingleFeatValidator::Validate(), CValidError_bioseq::ValidateSegRef(), and CSingleFeatValidator::x_ValidateSeqFeatProduct().
◆ ValidateSeqLocIds()Definition at line 3384 of file validatorp.cpp.
References BadMultipleSequenceLocation(), eDiag_Critical, eDiag_Error, eDiag_Warning, eErr_SEQ_FEAT_BadLocation, eErr_SEQ_FEAT_DifferntIdTypesInSeqLoc, eErr_SEQ_INST_BadSeqIdFormat, IsSameBioseq(), IsTemporary(), m_Scope, CSeq_id::Match(), and PostErr().
Referenced by ValidateSeqLoc().
◆ ValidateSourceQualTags()Definition at line 2648 of file valid_biosource.cpp.
References ctx, eDiag_Warning, eErr_SEQ_DESCR_StructuredSourceNote, NStr::FindNoCase(), i, NStr::IsBlank(), isspace(), m_SourceQualTags, match(), sm_SourceQualPrefixes, and str().
◆ ValidateSpecificHost() [1/2] ◆ ValidateSpecificHost() [2/2]Definition at line 2821 of file valid_biosource.cpp.
References chunk_size, eDiag_Error, eErr_SEQ_DESCR_TaxonomyLookupProblem, CTaxValidationAndCleanup::GetSpecificHostLookupRequest(), CTaxValidationAndCleanup::GetTopReportObject(), i, CTaxValidationAndCleanup::IncrementalSpecificHostMapUpdate(), NStr::IsBlank(), kDefaultChunkSize, len, min(), and CTaxValidationAndCleanup::ReportSpecificHostErrors().
◆ ValidateStrain()Definition at line 2853 of file valid_biosource.cpp.
References chunk_size, eDiag_Error, eErr_SEQ_DESCR_TaxonomyLookupProblem, CTaxValidationAndCleanup::GetStrainLookupRequest(), CTaxValidationAndCleanup::GetTopReportObject(), i, CTaxValidationAndCleanup::IncrementalStrainMapUpdate(), NStr::IsBlank(), kDefaultChunkSize, len, min(), and CTaxValidationAndCleanup::ReportStrainErrors().
◆ ValidateSubAffil()Definition at line 1017 of file valid_pub.cpp.
References ctx, eDiag_Critical, eDiag_Warning, eErr_GENERIC_MissingPubRequirement, NStr::EqualCase(), CAffil_Base::C_Std::GetAffil(), CAffil_Base::C_Std::GetCountry(), CAffil_Base::C_Std::GetDiv(), CAffil_Base::C_Std::GetSub(), NStr::IsBlank(), CAffil_Base::C_Std::IsSetAffil(), CAffil_Base::C_Std::IsSetCountry(), CAffil_Base::C_Std::IsSetDiv(), and CAffil_Base::C_Std::IsSetSub().
◆ ValidateSubmitBlock()Definition at line 1703 of file validatorp.cpp.
References eDiag_Error, eDiag_Warning, eErr_GENERIC_BadSubmissionAuthorName, eErr_GENERIC_PastReleaseDate, NStr::EqualNocase(), first(), CAuthor_Base::GetAffil(), CCit_sub_Base::GetAuthors(), CSubmit_block_Base::GetCit(), CContact_info_Base::GetContact(), CSubmit_block_Base::GetContact(), CName_std_Base::GetFirst(), CSubmit_block_Base::GetHup(), CName_std_Base::GetLast(), CAuthor_Base::GetName(), CPerson_id_Base::GetName(), CAuth_list_Base::GetNames(), CSubmit_block_Base::GetReldate(), CAffil_Base::GetStd(), IsBadSubmissionFirstName(), IsBadSubmissionLastName(), IsDateInPast(), CPerson_id_Base::IsName(), CAuthor_Base::IsSetAffil(), CCit_sub_Base::IsSetAuthors(), CSubmit_block_Base::IsSetCit(), CContact_info_Base::IsSetContact(), CSubmit_block_Base::IsSetContact(), CName_std_Base::IsSetFirst(), CSubmit_block_Base::IsSetHup(), CName_std_Base::IsSetLast(), CSubmit_block_Base::IsSetReldate(), CAffil_Base::IsStd(), ITERATE, last(), names, PostErr(), and ValidateAffil().
Referenced by Validate().
◆ ValidateSubSource()Definition at line 1267 of file valid_biosource.cpp.
References ContainsSgml(), ctx, eDiag_Critical, eDiag_Error, eDiag_Info, eDiag_Warning, eErr_GENERIC_SgmlPresentInText, eErr_SEQ_DESCR_BadBioSourceFrequencyValue, eErr_SEQ_DESCR_BadCollectionDate, eErr_SEQ_DESCR_BadContigOrScaffoldChromosome, eErr_SEQ_DESCR_BadCountryCapitalization, eErr_SEQ_DESCR_BadCountryCode, eErr_SEQ_DESCR_BadGeoLocNameCapitalization, eErr_SEQ_DESCR_BadGeoLocNameCode, eErr_SEQ_DESCR_BadNullCollectionDate, eErr_SEQ_DESCR_BadNullCountry, eErr_SEQ_DESCR_BadNullGeoLocName, eErr_SEQ_DESCR_BadPCRPrimerName, eErr_SEQ_DESCR_BadPlasmidChromosomeLinkageName, eErr_SEQ_DESCR_BadSubSource, eErr_SEQ_DESCR_BadTextInSourceQualifier, eErr_SEQ_DESCR_LatLonFormat, eErr_SEQ_DESCR_LatLonRange, eErr_SEQ_DESCR_NonViralSegment, eErr_SEQ_DESCR_ObsoleteSourceQual, eErr_SEQ_DESCR_ReplacedCountryCode, eErr_SEQ_DESCR_ReplacedGeoLocNameCode, eErr_SEQ_DESCR_UnbalancedParentheses, NStr::EndsWith(), NStr::eNocase, NStr::Equal(), CSubSource_Base::eSubtype_cell_line, CSubSource_Base::eSubtype_cell_type, CSubSource_Base::eSubtype_chromosome, CSubSource_Base::eSubtype_collection_date, CSubSource_Base::eSubtype_country, CSubSource_Base::eSubtype_endogenous_virus_name, CSubSource_Base::eSubtype_environmental_sample, CSubSource_Base::eSubtype_frequency, CSubSource_Base::eSubtype_fwd_primer_name, CSubSource_Base::eSubtype_fwd_primer_seq, CSubSource_Base::eSubtype_germline, CSubSource_Base::eSubtype_insertion_seq_name, CSubSource_Base::eSubtype_isolation_source, CSubSource_Base::eSubtype_lat_lon, CSubSource_Base::eSubtype_linkage_group, CSubSource_Base::eSubtype_mating_type, CSubSource_Base::eSubtype_metagenomic, CSubSource_Base::eSubtype_other, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_rearranged, CSubSource_Base::eSubtype_rev_primer_name, CSubSource_Base::eSubtype_rev_primer_seq, CSubSource_Base::eSubtype_segment, CSubSource_Base::eSubtype_sex, CSubSource_Base::eSubtype_tissue_type, CSubSource_Base::eSubtype_transgenic, CSubSource_Base::eSubtype_transposon_name, NStr::Find(), NStr::FindNoCase(), CSeqFeatData_Base::GetBiosrc(), CSubSource::GetCollectionDateProblem(), CSeq_feat_Base::GetData(), CSubSource_Base::GetName(), CBioSource_Base::GetOrg(), CSeqdesc_Base::GetSource(), CSubSource_Base::GetSubtype(), CSubSource::GetSubtypeName(), COrg_ref_Base::GetTaxname(), CSerialObject::GetThisTypeInfo(), NStr::IsBlank(), CSubSource::IsChromosomeNameValid(), CSubSource::IsCorrectLatLonFormat(), isdigit(), CSubSource::IsEndogenousVirusNameValid(), CSubSource::IsLinkageGroupNameValid(), CSubSource::IsPlasmidNameValid(), CSubSource::IsSegmentValid(), CSeq_feat_Base::IsSetData(), CSubSource_Base::IsSetName(), CSubSource_Base::IsSetSubtype(), CBioSource::IsSetTaxname(), CSeqdesc_Base::IsSource(), CCountries::IsValid(), CPCRPrimerSeq::IsValid(), CSubSource::NCBI_UseGeoLocNameForCountry(), CSubSource::NeedsNoText(), NStr::ReplaceInPlace(), s_UnbalancedParentheses(), NStr::StartsWith(), subname, toupper(), and CCountries::WasValid().
◆ ValidateTaxNameOrgname() ◆ ValidateTaxonomy() [1/2] ◆ ValidateTaxonomy() [2/2] ◆ ValidateTentativeName() ◆ x_AddValidErrItem() ◆ x_CheckForStrandChange() void CValidError_imp::x_CheckForStrandChange ( SLocCheck & lc ) private ◆ x_CheckLoc()Definition at line 2322 of file validatorp.cpp.
References CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, eDiag_Critical, eDiag_Error, eErr_INTERNAL_Exception, eErr_SEQ_FEAT_Range, eNa_strand_other, eNa_strand_unknown, GetLength(), GetValidatorLocationLabel(), IsValid(), l(), label, lc, m_Scope, PostErr(), x_CheckForStrandChange(), x_CheckPackedInt(), and x_CheckSeqInt().
Referenced by ValidateSeqLoc().
◆ x_CheckPackedInt() ◆ x_CheckPCRPrimer() ◆ x_CheckSeqInt() ◆ x_CreateTaxValidator() ◆ x_DoBarcodeTests()Definition at line 3527 of file validatorp.cpp.
References ADD_BARCODE_ERR, BarcodeTestFails(), eDiag_Info, eDiag_Warning, eErr_GENERIC_BarcodeTestFails, eErr_GENERIC_BarcodeTestPasses, eErr_GENERIC_BarcodeTooManyNs, GetBarcodeValues(), kTooManyNs, msg(), PostErr(), r(), and results.
Referenced by Validate().
◆ x_DowngradeForMissingAffil()Definition at line 1046 of file valid_pub.cpp.
References CSeqdesc_Base::e_Embl, CSeq_inst_Base::eMol_na, NStr::EqualNocase(), CCit_sub_Base::GetDate(), CSeqdesc_Base::GetEmbl(), CEMBL_block_Base::GetKeywords(), CDate_Base::GetStd(), CDate_std_Base::GetYear(), CCit_sub_Base::IsSetDate(), CEMBL_block_Base::IsSetKeywords(), CDate_std_Base::IsSetYear(), CDate_Base::IsStd(), m_Scope, and s_IsRefSeqInSep().
◆ x_Init() void CValidError_imp::x_Init ( Uint4 options, size_t initialInferenceCount, bool notJustLocalOrGeneral, bool hasRefSeq ) private ◆ x_InitLocCheck() ◆ x_IsFarFetchFailure() ◆ x_IsSuppressed() ◆ x_ReportInvalidFuzz() [1/4] ◆ x_ReportInvalidFuzz() [2/4]Definition at line 2142 of file validatorp.cpp.
References CSeq_feat_Base::CanGetExcept_text(), eDiag_Error, eErr_SEQ_FEAT_InvalidFuzz, CInt_fuzz_Base::eLim_circle, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, CInt_fuzz_Base::eLim_unk, CSeq_inst_Base::eTopology_circular, CSeq_inst_Base::eTopology_not_set, NStr::FindNoCase(), CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_feat_Base::GetExcept_text(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CSeq_interval_Base::GetId(), CBioseq_Handle::GetInst_Topology(), CInt_fuzz_Base::GetLim(), CSerialObject::GetThisTypeInfo(), CSeq_interval_Base::GetTo(), CInt_fuzz_Base::IsLim(), CSeq_feat_Base::IsSetExcept(), CSeq_interval_Base::IsSetFrom(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CBioseq_Handle::IsSetInst_Topology(), CSeq_interval_Base::IsSetTo(), kSpaceLeftCircle, kSpaceLeftFirst, kSpaceRightCircle, kSpaceRightLast, m_Scope, NPOS, and PostErr().
◆ x_ReportInvalidFuzz() [3/4] ◆ x_ReportInvalidFuzz() [4/4]Definition at line 2221 of file validatorp.cpp.
References eDiag_Error, eErr_SEQ_FEAT_InvalidFuzz, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, CSeq_inst_Base::eTopology_circular, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_point_Base::GetFuzz(), CSeq_point_Base::GetId(), CBioseq_Handle::GetInst_Topology(), CInt_fuzz_Base::GetLim(), CSeq_point_Base::GetPoint(), CInt_fuzz_Base::IsLim(), CSeq_point_Base::IsSetFuzz(), CSeq_point_Base::IsSetId(), CBioseq_Handle::IsSetInst_Topology(), CSeq_point_Base::IsSetPoint(), kSpaceLeftFirst, kSpaceRightLast, m_Scope, and PostErr().
◆ x_ReportPCRSeqProblem() ◆ x_SalmonellaErrorLevel() EDiagSev CValidError_imp::x_SalmonellaErrorLevel ( ) private ◆ x_SetEntryInfo() ◆ x_ValidatePages() ◆ m_BioseqWithNoSource ◆ m_biosource_kind ◆ m_cache ◆ m_CollectLocusTags bool CValidError_imp::m_CollectLocusTags private ◆ m_CompareVDJCtoCDS bool CValidError_imp::m_CompareVDJCtoCDS private ◆ m_CumulativeInferenceCount size_t CValidError_imp::m_CumulativeInferenceCount private ◆ m_DoBarcodeTests bool CValidError_imp::m_DoBarcodeTests private ◆ m_DoRubiscoText bool CValidError_imp::m_DoRubiscoText private ◆ m_DoTaxLookup bool CValidError_imp::m_DoTaxLookup private ◆ m_ErrRepository ◆ m_FarFetchCDSproducts bool CValidError_imp::m_FarFetchCDSproducts private ◆ m_FarFetchFailure bool CValidError_imp::m_FarFetchFailure private ◆ m_FarFetchMRNAproducts bool CValidError_imp::m_FarFetchMRNAproducts private ◆ m_ForceInferences bool CValidError_imp::m_ForceInferences private ◆ m_GeneCache ◆ m_GenerateGoldenFile bool CValidError_imp::m_GenerateGoldenFile private ◆ m_genomeSubmission bool CValidError_imp::m_genomeSubmission private ◆ m_HasRefSeq bool CValidError_imp::m_HasRefSeq private ◆ m_IgnoreExceptions bool CValidError_imp::m_IgnoreExceptions private ◆ m_IgnoreInferences bool CValidError_imp::m_IgnoreInferences private ◆ m_IndexerVersion bool CValidError_imp::m_IndexerVersion private ◆ m_InitialSeqIds ◆ m_IsNC ◆ m_IsNG ◆ m_IsNM ◆ m_IsNP ◆ m_IsNR ◆ m_IsNS ◆ m_IsNT ◆ m_IsNW ◆ m_IsNZ ◆ m_IsStandaloneAnnot bool CValidError_imp::m_IsStandaloneAnnot private ◆ m_IsTbl2Asn bool CValidError_imp::m_IsTbl2Asn private ◆ m_IsWP ◆ m_IsXR ◆ m_LatLonCheckState bool CValidError_imp::m_LatLonCheckState private ◆ m_LatLonIgnoreWater bool CValidError_imp::m_LatLonIgnoreWater private ◆ m_LocusTagGeneralMatch bool CValidError_imp::m_LocusTagGeneralMatch private ◆ m_NewStrainValidation bool CValidError_imp::m_NewStrainValidation private ◆ m_NonASCII bool CValidError_imp::m_NonASCII private ◆ m_NotJustLocalOrGeneral bool CValidError_imp::m_NotJustLocalOrGeneral private ◆ m_NumAlign size_t CValidError_imp::m_NumAlign private ◆ m_NumAnnot size_t CValidError_imp::m_NumAnnot private ◆ m_NumBioseq size_t CValidError_imp::m_NumBioseq private ◆ m_NumBioseq_set size_t CValidError_imp::m_NumBioseq_set private ◆ m_NumDesc size_t CValidError_imp::m_NumDesc private ◆ m_NumDescr size_t CValidError_imp::m_NumDescr private ◆ m_NumFeat size_t CValidError_imp::m_NumFeat private ◆ m_NumGenes size_t CValidError_imp::m_NumGenes private ◆ m_NumGeneXrefs size_t CValidError_imp::m_NumGeneXrefs private ◆ m_NumGraph size_t CValidError_imp::m_NumGraph private ◆ m_NumMisplacedFeatures size_t CValidError_imp::m_NumMisplacedFeatures private ◆ m_NumMisplacedGraphs size_t CValidError_imp::m_NumMisplacedGraphs private ◆ m_NumPseudo size_t CValidError_imp::m_NumPseudo private ◆ m_NumPseudogene size_t CValidError_imp::m_NumPseudogene private ◆ m_NumSmallGenomeSetMisplaced size_t CValidError_imp::m_NumSmallGenomeSetMisplaced private ◆ m_NumTopSetSiblings size_t CValidError_imp::m_NumTopSetSiblings private ◆ m_NumTpaWithHistory size_t CValidError_imp::m_NumTpaWithHistory private ◆ m_NumTpaWithoutHistory size_t CValidError_imp::m_NumTpaWithoutHistory private ◆ m_ObjMgr ◆ m_OvlPepErr bool CValidError_imp::m_OvlPepErr private ◆ m_pContext ◆ m_pEntryInfo ◆ m_PrgCallback ◆ m_PrgInfo ◆ m_PubSerialNumbers ◆ m_RefSeqConventions bool CValidError_imp::m_RefSeqConventions private ◆ m_RemoteFetch bool CValidError_imp::m_RemoteFetch private ◆ m_ReportSpliceAsError bool CValidError_imp::m_ReportSpliceAsError private ◆ m_RequireISOJTA bool CValidError_imp::m_RequireISOJTA private ◆ m_ScopeDefinition at line 547 of file validerror_imp.hpp.
Referenced by GetBioseqHandleFromTSE(), GetCachedGene(), GetCDSGivenProduct(), GetLocalBioseqHandle(), GetmRNAGivenProduct(), GetScope(), IsFarSequence(), IsMixedStrands(), PostErr(), Reset(), SetScope(), Setup(), Validate(), ValidateSeqLoc(), ValidateSeqLocIds(), x_CheckForStrandChange(), x_CheckLoc(), x_CheckSeqInt(), and x_ReportInvalidFuzz().
◆ m_SeqAnnot ◆ m_SeqSubmitParent bool CValidError_imp::m_SeqSubmitParent private ◆ m_SuppressContext bool CValidError_imp::m_SuppressContext private ◆ m_SuppressedErrors ◆ m_TSE ◆ m_TSEH ◆ m_UseEntrez bool CValidError_imp::m_UseEntrez private ◆ m_ValidateAlignments bool CValidError_imp::m_ValidateAlignments private ◆ m_ValidateExons bool CValidError_imp::m_ValidateExons private ◆ m_ValidateIdSet bool CValidError_imp::m_ValidateIdSet private ◆ m_ValidateInferenceAccessions bool CValidError_imp::m_ValidateInferenceAccessions privateThe documentation for this class was generated from the following files:
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