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CCdregionValidator Class Reference

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#include <objtools/validator/single_feat_validator.hpp>

+ Inheritance diagram for CCdregionValidator:
+ Collaboration diagram for CCdregionValidator:

Public Member Functions

 CCdregionValidator (const CSeq_feat &feat, CScope &scope, CValidError_imp &imp)
 
void Validate () override
 
- Public Member Functions inherited from CSingleFeatValidator
 CSingleFeatValidator (const CSeq_feat &feat, CScope &scope, CValidError_imp &imp)
 
virtual ~CSingleFeatValidator ()
 

Protected Types

typedef pair< TSeqPos, TSeqPos > TShortIntron
 
- Protected Types inherited from CSingleFeatValidator
enum  ELocationGap {
  eLocationGapNoProblems = 0 , eLocationGapFeatureMatchesGap = 1 , eLocationGapContainedInGap = 4 , eLocationGapContainedInGapOfNs = 8 ,
  eLocationGapInternalIntervalEndpointInGap = 16 , eLocationGapCrossesUnknownGap = 32 , eLocationGapMostlyNs = 64
}
 

Protected Member Functions

void x_ValidateFeatComment () override
 
void x_ValidateExceptText (const string &text) override
 
void x_ValidateQuals ()
 
bool x_ReportOrigProteinId () override
 
void x_ValidateGeneticCode ()
 
void x_ValidateBadMRNAOverlap ()
 
bool x_HasGoodParent ()
 
void x_ValidateSeqFeatLoc () override
 
void x_ValidateFarProducts ()
 
void x_ValidateCDSPeptides ()
 
void x_ValidateCDSPartial ()
 
bool x_BypassCDSPartialTest () const
 
bool x_CDS3primePartialTest () const
 
bool x_CDS5primePartialTest () const
 
bool x_IsProductMisplaced () const
 
void ReportShortIntrons ()
 
void x_ValidateTrans ()
 
void x_ValidateCodebreak ()
 
void x_ReportTranslationProblems (const CCDSTranslationProblems &problems)
 
void x_ReportTranslExceptProblems (const CCDSTranslationProblems::TTranslExceptProblems &problems, bool has_exception)
 
void x_ReportTranslationMismatches (const CCDSTranslationProblems::TTranslationMismatches &mismatches)
 
string MapToNTCoords (TSeqPos pos)
 
void x_ValidateProductId ()
 
void x_ValidateConflict ()
 
void x_ValidateCommonProduct ()
 
void x_ValidateProductPartials ()
 
void x_ValidateParentPartialness (const CSeq_loc &parent_loc, const string &parent_name)
 
void x_ValidateParentPartialness ()
 
bool x_CheckPosNOrGap (TSeqPos pos, const CSeqVector &vec)
 
- Protected Member Functions inherited from CSingleFeatValidator
void PostErr (EDiagSev sv, EErrType et, const string &msg)
 
CBioseq_Handle x_GetBioseqByLocation (const CSeq_loc &loc)
 
void x_ValidateSeqFeatProduct ()
 
void x_ValidateBothStrands ()
 
void x_ValidateGeneId ()
 
void x_ValidateFeatCit ()
 
void x_ValidateGbQual (const CGb_qual &qual)
 
void x_ReportECNumFileStatus ()
 
void x_ValidateExtUserObject ()
 
bool x_HasNamedQual (const string &qual_name)
 
void x_ValidateFeatPartialness ()
 
bool x_AllowFeatureToMatchGapExactly ()
 
void x_ValidateExcept ()
 
void x_ValidateGbquals ()
 
void x_ValidateRptUnitVal (const string &val, const string &key)
 
void x_ValidateRptUnitSeqVal (const string &val, const string &key)
 
void x_ValidateRptUnitRangeVal (const string &val)
 
void x_ValidateLabelVal (const string &val)
 
void x_ValidateCompareVal (const string &val)
 
void x_ValidateReplaceQual (const string &key, const string &qual_str, const string &val)
 
CBioseq_Handle x_GetFeatureProduct (bool look_far, bool &is_far)
 
CBioseq_Handle x_GetFeatureProduct (bool &is_far)
 
void ValidateCharactersInField (string value, string field_name)
 
void ValidateSplice (bool gene_pseudo, bool check_all)
 
EDiagSev x_SeverityForConsensusSplice ()
 
void x_ReportSpliceProblems (const CSpliceProblems &problems, const string &label)
 
void x_ReportDonorSpliceSiteReadErrors (const CSpliceProblems::TSpliceProblem &problem, const string &label)
 
void x_ReportAcceptorSpliceSiteReadErrors (const CSpliceProblems::TSpliceProblem &problem, const string &label)
 
void x_ValidateNonImpFeat ()
 
void x_ValidateGeneXRef ()
 
void x_ValidateGeneFeaturePair (const CSeq_feat &gene)
 
void x_ValidateNonGene ()
 
void x_ValidateOldLocusTag (const string &old_locus_tag)
 
void x_ValidateImpFeatLoc ()
 
void x_ValidateImpFeatQuals ()
 
void x_ValidateSeqFeatDataType ()
 
void x_ReportPseudogeneConflict (CConstRef< CSeq_feat > gene)
 
void x_ValidateLocusTagGeneralMatch (CConstRef< CSeq_feat > gene)
 
void x_CheckForNonAsciiCharacters ()
 

Static Protected Member Functions

static bool IsPlastid (int genome)
 
static vector< TShortIntron > x_GetShortIntrons (const CSeq_loc &loc, CScope *scope)
 
static void x_AddToIntronList (vector< TShortIntron > &shortlist, TSeqPos last_start, TSeqPos last_stop, TSeqPos this_start, TSeqPos this_stop)
 
static string x_FormatIntronInterval (const TShortIntron &interval)
 
- Static Protected Member Functions inherited from CSingleFeatValidator
static void x_LocHasStrandBoth (const CSeq_loc &feat, bool &both, bool &both_rev)
 
static size_t x_CalculateLocationGaps (CBioseq_Handle bsh, const CSeq_loc &loc, vector< TSeqPos > &gap_starts)
 
static bool x_IsMostlyNs (const CSeq_loc &loc, CBioseq_Handle bsh)
 
static TSeqPos x_FindStartOfGap (CBioseq_Handle bsh, TSeqPos pos, CScope *scope)
 
static bool x_BioseqHasNmAccession (CBioseq_Handle bsh)
 

Protected Attributes

CConstRef< CSeq_feat > m_Gene
 
bool m_GeneIsPseudo
 
- Protected Attributes inherited from CSingleFeatValidator
const CSeq_feat & m_Feat
 
CScope & m_Scope
 
CValidError_imp & m_Imp
 
CBioseq_Handle m_LocationBioseq
 
CBioseq_Handle m_ProductBioseq
 
bool m_ProductIsFar
 

Additional Inherited Members

- Static Public Member Functions inherited from CSingleFeatValidator
static bool x_HasSeqLocBond (const CSeq_feat &feat)
 
static bool s_IsPseudo (const CSeq_feat &feat)
 
static bool s_IsPseudo (const CGene_ref &ref)
 
static bool s_BioseqHasRefSeqThatStartsWithPrefix (CBioseq_Handle bsh, string prefix)
 
static bool s_GeneRefsAreEquivalent (const CGene_ref &g1, const CGene_ref &g2, string &label)
 
static void s_RemoveDuplicateGoTerms (CUser_object::TData &field_list)
 
static void s_RemoveDuplicateGoTerms (CSeq_feat &feat)
 

Detailed Description

Definition at line 198 of file single_feat_validator.hpp.

Member Typedef Documentation

◆ TShortIntron

typedef pair<TSeqPos, TSeqPos> CCdregionValidator::TShortIntron
protected

Definition at line 224 of file single_feat_validator.hpp.

Constructor & Destructor Documentation

◆ CCdregionValidator()

CCdregionValidator::CCdregionValidator ( const CSeq_feat &  feat,
CScope &  scope,
CValidError_imp &  imp 
)

Definition at line 75 of file cdregion_validator.cpp.

References CValidError_imp::GetGeneCache(), CGeneCache::GetGeneFromCache(), m_Gene, m_GeneIsPseudo, CSingleFeatValidator::m_Imp, CSingleFeatValidator::m_Scope, and CSingleFeatValidator::s_IsPseudo().

Member Function Documentation

◆ IsPlastid()

bool CCdregionValidator::IsPlastid ( int  genome)
staticprotected

Definition at line 877 of file cdregion_validator.cpp.

References CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_chloroplast, CBioSource_Base::eGenome_chromatophore, CBioSource_Base::eGenome_chromoplast, CBioSource_Base::eGenome_cyanelle, CBioSource_Base::eGenome_leucoplast, CBioSource_Base::eGenome_plastid, and CBioSource_Base::eGenome_proplastid.

Referenced by x_ValidateGeneticCode().

◆ MapToNTCoords()

string CCdregionValidator::MapToNTCoords ( TSeqPos  pos)
protected

Definition at line 548 of file cdregion_validator.cpp.

References GetId(), CSeq_feat_Base::GetProduct(), GetStrand(), GetValidatorLocationLabel(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_Scope, ProductToSource(), result, CSeq_point_Base::SetId(), CSeq_point_Base::SetPoint(), CSeq_point_Base::SetStrand(), and tmp.

Referenced by x_ReportTranslationMismatches().

◆ ReportShortIntrons()

void CCdregionValidator::ReportShortIntrons ( )
protected

Definition at line 1632 of file cdregion_validator.cpp.

References eDiag_Warning, eErr_SEQ_FEAT_ShortIntron, CSeq_feat_Base::GetLocation(), CCDSTranslationProblems::GetNonsenseIntrons(), i, CSeq_feat_Base::IsSetExcept(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_Scope, CSingleFeatValidator::PostErr(), x_FormatIntronInterval(), and x_GetShortIntrons().

Referenced by Validate().

◆ Validate()

void CCdregionValidator::Validate ( void  )
overridevirtual

Reimplemented from CSingleFeatValidator.

Definition at line 735 of file cdregion_validator.cpp.

References eDiag_Error, eDiag_Warning, eErr_SEQ_FEAT_CDSproductPackagingProblem, eErr_SEQ_FEAT_OrfCdsHasProduct, eErr_SEQ_FEAT_PseudoCdsHasProduct, eErr_SEQ_FEAT_PseudoCdsViaGeneHasProduct, CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetConflict(), CSeq_feat_Base::GetData(), CCdregion_Base::GetOrf(), CCdregion_Base::IsSetConflict(), CCdregion_Base::IsSetOrf(), CSeq_feat_Base::IsSetProduct(), CValidError_imp::IsSmallGenomeSet(), CSingleFeatValidator::m_Feat, m_Gene, m_GeneIsPseudo, CSingleFeatValidator::m_Imp, CSingleFeatValidator::PostErr(), ReportShortIntrons(), CSingleFeatValidator::s_IsPseudo(), CSingleFeatValidator::Validate(), CSingleFeatValidator::ValidateSplice(), x_IsProductMisplaced(), CSingleFeatValidator::x_ReportPseudogeneConflict(), x_ValidateBadMRNAOverlap(), x_ValidateCDSPartial(), x_ValidateCDSPeptides(), x_ValidateCommonProduct(), x_ValidateConflict(), x_ValidateFarProducts(), x_ValidateGeneticCode(), CSingleFeatValidator::x_ValidateLocusTagGeneralMatch(), x_ValidateParentPartialness(), x_ValidateProductId(), x_ValidateProductPartials(), x_ValidateQuals(), and x_ValidateTrans().

◆ x_AddToIntronList()

void CCdregionValidator::x_AddToIntronList ( vector< TShortIntron > &  shortlist,
TSeqPos  last_start,
TSeqPos  last_stop,
TSeqPos  this_start,
TSeqPos  this_stop 
)
staticprotected

Definition at line 1574 of file cdregion_validator.cpp.

References abs.

Referenced by x_GetShortIntrons().

◆ x_BypassCDSPartialTest()

bool CCdregionValidator::x_BypassCDSPartialTest ( ) const
protected

Definition at line 1454 of file cdregion_validator.cpp.

References CSeq_feat_Base::CanGetExcept(), CSeq_feat_Base::CanGetExcept_text(), NStr::FindNoCase(), CSeq_feat_Base::GetExcept(), CSeq_feat_Base::GetExcept_text(), ITERATE, CSingleFeatValidator::m_Feat, and NPOS.

Referenced by x_ValidateCDSPartial().

◆ x_CDS3primePartialTest()

bool CCdregionValidator::x_CDS3primePartialTest ( ) const
protected

Definition at line 1468 of file cdregion_validator.cpp.

References eNa_strand_minus, CBioseq_Handle::GetInst_Length(), CSeq_feat_Base::GetLocation(), last(), CSingleFeatValidator::m_Feat, and CSingleFeatValidator::m_LocationBioseq.

Referenced by x_ValidateCDSPartial().

◆ x_CDS5primePartialTest()

bool CCdregionValidator::x_CDS5primePartialTest ( ) const
protected

Definition at line 1493 of file cdregion_validator.cpp.

References eNa_strand_minus, first(), CBioseq_Handle::GetInst_Length(), CSeq_feat_Base::GetLocation(), CSingleFeatValidator::m_Feat, and CSingleFeatValidator::m_LocationBioseq.

Referenced by x_ValidateCDSPartial().

◆ x_CheckPosNOrGap()

bool CCdregionValidator::x_CheckPosNOrGap ( TSeqPos  pos,
const CSeqVector &  vec 
)
protected

Definition at line 1794 of file cdregion_validator.cpp.

References CSeqVector::IsInGap().

Referenced by x_ValidateParentPartialness().

◆ x_FormatIntronInterval()

string CCdregionValidator::x_FormatIntronInterval ( const TShortIntron &  interval)
staticprotected

Definition at line 1625 of file cdregion_validator.cpp.

References NStr::NumericToString().

Referenced by ReportShortIntrons().

◆ x_GetShortIntrons()

vector< CCdregionValidator::TShortIntron > CCdregionValidator::x_GetShortIntrons ( const CSeq_loc &  loc,
CScope *  scope 
)
staticprotected

Definition at line 1584 of file cdregion_validator.cpp.

References abs, CSeq_id::Assign(), CScope::GetBioseqHandle(), CBioseq_Handle::GetId(), and x_AddToIntronList().

Referenced by ReportShortIntrons().

◆ x_HasGoodParent()

bool CCdregionValidator::x_HasGoodParent ( )
protected

Definition at line 1125 of file cdregion_validator.cpp.

References Compare(), eContained, eSame, CSeqFeatData::eSubtype_C_region, CSeqFeatData::eSubtype_D_segment, CSeqFeatData::eSubtype_J_segment, CSeqFeatData::eSubtype_V_segment, fCompareOverlapping, CGeneCache::GetFeatTreeFromCache(), CValidError_imp::GetGeneCache(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetLocation(), CScope::GetSeq_featHandle(), CValidError_imp::IsHugeFileMode(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_Imp, CSingleFeatValidator::m_Scope, and Ref().

Referenced by x_ValidateBadMRNAOverlap().

◆ x_IsProductMisplaced()

bool CCdregionValidator::x_IsProductMisplaced ( ) const
protected

Definition at line 1515 of file cdregion_validator.cpp.

References CBioseq_set_Base::eClass_gen_prod_set, CBioseq_set_Base::eClass_nuc_prot, CTextseq_id_Base::GetAccession(), CScope::GetBioseqHandle(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CBioseq_Handle::GetExactComplexityLevel(), CSeq_loc::GetId(), CSeq_feat_Base::GetLocation(), CSeq_id_Base::GetOther(), CSeq_feat_Base::GetProduct(), CSeq_id_Base::IsOther(), CTextseq_id_Base::IsSetAccession(), CCdregion_Base::IsSetOrf(), CSeq_feat_Base::IsSetProduct(), CSingleFeatValidator::m_Feat, m_GeneIsPseudo, CSingleFeatValidator::m_Imp, CSingleFeatValidator::m_ProductBioseq, CSingleFeatValidator::m_ProductIsFar, CSingleFeatValidator::m_Scope, nuc, CValidError_imp::RequireLocalProduct(), CSingleFeatValidator::s_BioseqHasRefSeqThatStartsWithPrefix(), CSingleFeatValidator::s_IsPseudo(), and NStr::StartsWith().

Referenced by Validate().

◆ x_ReportOrigProteinId()

bool CCdregionValidator::x_ReportOrigProteinId ( )
overrideprotectedvirtual

Reimplemented from CSingleFeatValidator.

Definition at line 843 of file cdregion_validator.cpp.

References CSingleFeatValidator::m_Feat, m_GeneIsPseudo, and CSingleFeatValidator::s_IsPseudo().

◆ x_ReportTranslationMismatches()

void CCdregionValidator::x_ReportTranslationMismatches ( const CCDSTranslationProblems::TTranslationMismatches &  mismatches)
protected

Definition at line 570 of file cdregion_validator.cpp.

References eDiag_Error, eDiag_Warning, eErr_SEQ_FEAT_MisMatchAA, CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode(), CSeq_feat_Base::GetData(), CGenetic_code::GetId(), i, NStr::IntToString(), CSeqFeatData_Base::IsCdregion(), CCdregion_Base::IsSetCode(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_ProductIsFar, MapToNTCoords(), msg(), CSingleFeatValidator::PostErr(), and NStr::SizetToString().

Referenced by x_ReportTranslationProblems().

◆ x_ReportTranslationProblems()

void CCdregionValidator::x_ReportTranslationProblems ( const CCDSTranslationProblems &  problems)
protected

Definition at line 332 of file cdregion_validator.cpp.

References CCDSTranslationProblems::AltStart(), CCDSTranslationProblems::eCDSTranslationProblem_BadStart, CCDSTranslationProblems::eCDSTranslationProblem_ErroneousException, CCDSTranslationProblems::eCDSTranslationProblem_FrameNotConsensus, CCDSTranslationProblems::eCDSTranslationProblem_FrameNotPartial, CCDSTranslationProblems::eCDSTranslationProblem_NoProtein, CCDSTranslationProblems::eCDSTranslationProblem_NoStop, CCDSTranslationProblems::eCDSTranslationProblem_ShouldBePartialButIsnt, CCDSTranslationProblems::eCDSTranslationProblem_ShouldNotBePartialButIs, CCDSTranslationProblems::eCDSTranslationProblem_ShouldStartPartial, CCDSTranslationProblems::eCDSTranslationProblem_StopPartial, CCDSTranslationProblems::eCDSTranslationProblem_TooManyX, CCDSTranslationProblems::eCDSTranslationProblem_UnableToFetch, CCDSTranslationProblems::eCDSTranslationProblem_UnnecessaryException, CCDSTranslationProblems::eCDSTranslationProblem_UnqualifiedException, eDiag_Critical, eDiag_Error, eDiag_Info, eDiag_Warning, eErr_SEQ_FEAT_AltStartCodonException, eErr_SEQ_FEAT_CDShasTooManyXs, eErr_SEQ_FEAT_CdTransFail, eErr_SEQ_FEAT_ErroneousException, eErr_SEQ_FEAT_InternalStop, eErr_SEQ_FEAT_IntronIsStopCodon, eErr_SEQ_FEAT_NoProtein, eErr_SEQ_FEAT_NoStop, eErr_SEQ_FEAT_PartialProblem, eErr_SEQ_FEAT_PartialProblemHasStop, eErr_SEQ_FEAT_ProductFetchFailure, eErr_SEQ_FEAT_ProductLength, eErr_SEQ_FEAT_StartCodon, eErr_SEQ_FEAT_SuspiciousFrame, eErr_SEQ_FEAT_TerminalXDiscrepancy, eErr_SEQ_FEAT_TransLen, eErr_SEQ_FEAT_TranslExcept, eErr_SEQ_FEAT_UnnecessaryException, NStr::EqualNocase(), NStr::Find(), NStr::FindNoCase(), CDbtag_Base::GetDb(), CSeq_feat_Base::GetExcept_text(), CSeq_id_Base::GetGeneral(), GetId(), CCDSTranslationProblems::GetInternalStopCodons(), GetInternalStopErrorMessage(), CSeq_id::GetLabel(), CSeq_feat_Base::GetLocation(), CCDSTranslationProblems::GetNumNonsenseIntrons(), CCDSTranslationProblems::GetProdTerminalX(), CSeq_feat_Base::GetProduct(), CCDSTranslationProblems::GetProtLen(), CCDSTranslationProblems::GetRaggedLength(), GetStartCodonErrorMessage(), CCDSTranslationProblems::GetTranslationMismatches(), CCDSTranslationProblems::GetTranslationProblemFlags(), CCDSTranslationProblems::GetTransLen(), CCDSTranslationProblems::GetTranslExceptProblems(), CCDSTranslationProblems::GetTranslStartCharacter(), CCDSTranslationProblems::GetTranslTerminalX(), CValidError_imp::GetTSE(), CCDSTranslationProblems::HasException(), CCDSTranslationProblems::HasUnparsedTranslExcept(), i, NStr::IntToString(), CValidError_imp::IsDdbj(), IsDeltaOrFarSeg(), CValidError_imp::IsEmbl(), CValidError_imp::IsGED(), CSeq_id_Base::IsGeneral(), CValidError_imp::IsGI(), CValidError_imp::IsGpipe(), CValidError_imp::IsRefSeq(), CDbtag_Base::IsSetDb(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), label, CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_Imp, CSingleFeatValidator::m_LocationBioseq, CSingleFeatValidator::m_ProductIsFar, CSingleFeatValidator::m_Scope, msg(), NPOS, CSingleFeatValidator::PostErr(), s_LocIdType(), NStr::SizetToString(), CCDSTranslationProblems::UnableToTranslate(), CSingleFeatValidator::x_BioseqHasNmAccession(), x_ReportTranslationMismatches(), and x_ReportTranslExceptProblems().

Referenced by x_ValidateTrans().

◆ x_ReportTranslExceptProblems()

void CCdregionValidator::x_ReportTranslExceptProblems ( const CCDSTranslationProblems::TTranslExceptProblems &  problems,
bool  has_exception 
)
protected

Definition at line 644 of file cdregion_validator.cpp.

References eDiag_Warning, eErr_SEQ_FEAT_TranslExcept, eErr_SEQ_FEAT_TranslExceptPhase, eErr_SEQ_FEAT_UnnecessaryTranslExcept, CCDSTranslationProblems::eTranslExceptPhase, CCDSTranslationProblems::eTranslExceptSuspicious, CCDSTranslationProblems::eTranslExceptUnexpected, CCDSTranslationProblems::eTranslExceptUnnecessary, msg(), CSingleFeatValidator::PostErr(), and NStr::SizetToString().

Referenced by x_ReportTranslationProblems().

◆ x_ValidateBadMRNAOverlap()

void CCdregionValidator::x_ValidateBadMRNAOverlap ( )
protected

Definition at line 1049 of file cdregion_validator.cpp.

References CSeq_feat_Base::CanGetExcept_text(), eDiag_Info, eDiag_Warning, eErr_SEQ_FEAT_CDSmRNArange, eErr_SEQ_FEAT_PseudoCDSmRNArange, eOverlap_CheckIntRev, eOverlap_Interval, eOverlap_Simple, eOverlap_SubsetRev, CSeqFeatData::eSubtype_mRNA, NStr::FindNoCase(), GetBestOverlappingFeat(), CSeq_feat_Base::GetExcept_text(), CSeq_feat_Base::GetLocation(), CSingleFeatValidator::m_Feat, m_GeneIsPseudo, CSingleFeatValidator::m_Scope, NPOS, CSingleFeatValidator::PostErr(), CSingleFeatValidator::s_IsPseudo(), text(), and x_HasGoodParent().

Referenced by Validate().

◆ x_ValidateCDSPartial()

void CCdregionValidator::x_ValidateCDSPartial ( )
protected

Definition at line 1338 of file cdregion_validator.cpp.

References CMolInfo_Base::CanGetCompleteness(), CSeqdesc_Base::e_Molinfo, CMolInfo_Base::eCompleteness_complete, CMolInfo_Base::eCompleteness_has_left, CMolInfo_Base::eCompleteness_has_right, CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_no_right, CMolInfo_Base::eCompleteness_other, CMolInfo_Base::eCompleteness_partial, CMolInfo_Base::eCompleteness_unknown, eDiag_Error, eDiag_Warning, eErr_SEQ_FEAT_PartialProblem, eExtreme_Biological, CMolInfo_Base::GetCompleteness(), CSeq_feat_Base::GetLocation(), CSeqdesc_Base::GetMolinfo(), CSeq_loc::IsPartialStart(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_ProductBioseq, CSingleFeatValidator::PostErr(), x_BypassCDSPartialTest(), x_CDS3primePartialTest(), and x_CDS5primePartialTest().

Referenced by Validate().

◆ x_ValidateCDSPeptides()

void CCdregionValidator::x_ValidateCDSPeptides ( )
protected

Definition at line 1238 of file cdregion_validator.cpp.

References CSeq_feat_Base::CanGetData(), CSeq_feat_Base::CanGetProduct(), Compare(), CSeqFeatData_Base::e_Prot, eDiag_Warning, eDiagFilter_All, eDiagFilter_Post, eErr_SEQ_FEAT_GeneOnNucPositionOfPeptide, eOverlap_SubsetRev, CSeq_loc_Mapper_Base::eProductToLocation, eSame, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mat_peptide_aa, CSeqFeatData::eSubtype_preprotein, CSeqFeatData::eSubtype_propeptide_aa, CSeqFeatData::eSubtype_sig_peptide_aa, CSeqFeatData::eSubtype_transit_peptide_aa, fCompareOverlapping, GetBestOverlappingFeat(), CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), GetDiagFilter(), CSeq_feat_Handle::GetFeatSubtype(), CSeqFeatData_Base::GetGene(), CSeq_feat_Handle::GetGeneXref(), CSeq_feat_Base::GetLocation(), CSeq_feat_Handle::GetLocation(), CGene_ref_Base::GetLocus(), CGene_ref_Base::GetLocus_tag(), CSeq_feat_Base::GetProduct(), CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsGene(), CGene_ref_Base::IsSetLocus(), CGene_ref_Base::IsSetLocus_tag(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_Scope, CSeq_loc_Mapper_Base::Map(), nuc, CSingleFeatValidator::PostErr(), prev(), prot, and SetDiagFilter().

Referenced by Validate().

◆ x_ValidateCodebreak()

void CCdregionValidator::x_ValidateCodebreak ( )
protected

Definition at line 683 of file cdregion_validator.cpp.

References Compare(), eContained, eDiag_Critical, eDiag_Error, eErr_SEQ_FEAT_CDSrange, eErr_SEQ_FEAT_DuplicateTranslExcept, eErr_SEQ_FEAT_TranslExceptIsPartial, eExtreme_Biological, eSame, eSeqLocCheck_error, fCompareOverlapping, FOR_EACH_CODEBREAK_ON_CDREGION, fS2P_AllowTer, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCode_break_Base::GetLoc(), CSeq_feat_Base::GetLocation(), GetValidatorLocationLabel(), CSeq_loc_Base::IsNull(), CSeq_feat_Base::IsSetProduct(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_Scope, msg(), CSingleFeatValidator::PostErr(), SeqLocCheck(), SourceToProduct(), and str().

Referenced by x_ValidateTrans().

◆ x_ValidateCommonProduct()

void CCdregionValidator::x_ValidateCommonProduct ( )
protected

Definition at line 1730 of file cdregion_validator.cpp.

References CCdregion_Base::CanGetOrf(), eDiag_Critical, eDiag_Warning, eErr_SEQ_FEAT_MissingCDSproduct, eErr_SEQ_FEAT_MultipleCDSproducts, CScope::GetBioseqHandle(), CSeqFeatData_Base::GetCdregion(), GetCDSForProduct(), CSeq_feat_Base::GetData(), GetId(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), CValidError_imp::IsGPS(), CSeq_feat_Base::IsSetProduct(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_Imp, CSingleFeatValidator::m_LocationBioseq, CSingleFeatValidator::m_ProductBioseq, CSingleFeatValidator::m_ProductIsFar, CSingleFeatValidator::m_Scope, CSingleFeatValidator::PostErr(), and CValidError_imp::RequireLocalProduct().

Referenced by Validate().

◆ x_ValidateConflict()

void CCdregionValidator::x_ValidateConflict ( )
protected

Definition at line 1699 of file cdregion_validator.cpp.

References CSeq_data_Base::e_Ncbieaa, CBioseq_Handle::eCoding_Iupac, eDiag_Error, eDiag_Warning, eErr_SEQ_FEAT_BadConflictFlag, eErr_SEQ_FEAT_ConflictFlagSet, NStr::Equal(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_ProductBioseq, CSingleFeatValidator::m_Scope, CSingleFeatValidator::PostErr(), CSeqVector::SetCoding(), CSeqVector::size(), and CSeqTranslator::Translate().

Referenced by Validate().

◆ x_ValidateExceptText()

void CCdregionValidator::x_ValidateExceptText ( const string &  text)
overrideprotectedvirtual

Reimplemented from CSingleFeatValidator.

Definition at line 136 of file cdregion_validator.cpp.

References eDiag_Warning, eErr_SEQ_FEAT_TranslExceptAndRnaEditing, NStr::FindNoCase(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::IsSetCode_break(), CSingleFeatValidator::m_Feat, NPOS, CSingleFeatValidator::PostErr(), text(), and CSingleFeatValidator::x_ValidateExceptText().

◆ x_ValidateFarProducts()

void CCdregionValidator::x_ValidateFarProducts ( )
protected

Definition at line 1177 of file cdregion_validator.cpp.

References CBioseq_set_Base::eClass_nuc_prot, eDiag_Error, eErr_SEQ_FEAT_CDSmRNAmismatch, CSeqFeatData::eSubtype_mRNA, CScope::GetBioseqHandle(), CScope::GetBioseqHandleFromTSE(), CSeq_feat_Base::GetData(), CGeneCache::GetFeatTreeFromCache(), CValidError_imp::GetGeneCache(), CSeq_loc::GetId(), CSeq_feat_Base::GetProduct(), CMappedFeat::GetProduct(), CMappedFeat::GetSeq_feat(), CScope::GetSeq_featHandle(), CSeqFeatData_Base::IsCdregion(), CValidError_imp::IsFarSequence(), CValidError_imp::IsRefSeq(), CValidError_imp::IsRemoteFetch(), CSeq_feat_Base::IsSetProduct(), CSeq_feat_Handle::IsSetProduct(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_Imp, CSingleFeatValidator::m_ProductIsFar, CSingleFeatValidator::m_Scope, CSingleFeatValidator::PostErr(), and CValidError_imp::PostErr().

Referenced by Validate().

◆ x_ValidateFeatComment()

void CCdregionValidator::x_ValidateFeatComment ( )
overrideprotectedvirtual

Reimplemented from CSingleFeatValidator.

Definition at line 86 of file cdregion_validator.cpp.

References DoesCodingRegionHaveTerminalCodeBreak(), CBioseq_Handle::eCoding_Iupac, eDiag_Error, eDiag_Info, eErr_SEQ_FEAT_BadCDScomment, eErr_SEQ_FEAT_EcNumberInCDSComment, CSeqFeatData::eSubtype_prot, NStr::Find(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CSeq_feat_Handle::GetData(), GetLastCodonLoc(), GetLength(), CSeqFeatData_Base::GetProt(), CSeqVector::GetSeqData(), HasECnumberPattern(), CSeq_feat_Base::IsSetComment(), CProt_ref_Base::IsSetEc(), len, CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_Imp, CSingleFeatValidator::m_ProductBioseq, CSingleFeatValidator::m_Scope, NPOS, CSingleFeatValidator::PostErr(), CValidError_imp::PostErr(), and CSingleFeatValidator::x_ValidateFeatComment().

◆ x_ValidateGeneticCode()

void CCdregionValidator::x_ValidateGeneticCode ( )
protected

Definition at line 959 of file cdregion_validator.cpp.

References CCdregion_Base::CanGetCode(), CBioSource_Base::CanGetGenome(), CSeqdesc_Base::e_Source, eDiag_Error, eDiag_Warning, eErr_SEQ_FEAT_GenCodeInvalid, eErr_SEQ_FEAT_GenCodeMismatch, NStr::Find(), CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetExcept_text(), CBioSource_Base::GetGenome(), CGenetic_code::GetId(), CSeqdesc_Base::GetSource(), NStr::IntToString(), IsGeneticCodeValid(), IsPlastid(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_LocationBioseq, CSingleFeatValidator::PostErr(), s_GetStrictGenCode(), and s_PlastidTxt.

Referenced by Validate().

◆ x_ValidateParentPartialness() [1/2]

void CCdregionValidator::x_ValidateParentPartialness ( )
protected

Definition at line 1871 of file cdregion_validator.cpp.

References CSeqFeatData_Base::e_Rna, eOverlap_Contains, CSeqFeatData::eSubtype_mRNA, CSeq_feat_Base::GetLocation(), GetmRNAforCDS(), GetOverlappingFeatures(), CSingleFeatValidator::m_Feat, m_Gene, and CSingleFeatValidator::m_Scope.

Referenced by Validate().

◆ x_ValidateParentPartialness() [2/2]

void CCdregionValidator::x_ValidateParentPartialness ( const CSeq_loc &  parent_loc,
const string &  parent_name 
)
protected

Definition at line 1804 of file cdregion_validator.cpp.

References CBioseq_Handle::eCoding_Iupac, eDiag_Info, eDiag_Warning, eErr_SEQ_FEAT_PartialProblemMismatch3Prime, eErr_SEQ_FEAT_PartialProblemMismatch5Prime, eExtreme_Biological, eNa_strand_minus, NStr::EqualNocase(), CSeq_inst_Base::eRepr_delta, CBioseq_Handle::GetBioseqLength(), CSeq_feat_Base::GetData(), CSeqFeatData_Base::GetGene(), CBioseq_Handle::GetInst(), CSeq_feat_Base::GetLocation(), CGene_ref_Base::GetLocus(), CSeq_inst_Base::GetRepr(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::GetStrand(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CBioseq_Handle::IsSetInst(), CGene_ref_Base::IsSetLocus(), CSeq_inst_Base::IsSetRepr(), CSeq_loc::IsSetStrand(), CSingleFeatValidator::m_Feat, m_Gene, CSingleFeatValidator::m_LocationBioseq, CSingleFeatValidator::PostErr(), and x_CheckPosNOrGap().

◆ x_ValidateProductId()

void CCdregionValidator::x_ValidateProductId ( )
protected

Definition at line 1669 of file cdregion_validator.cpp.

References eDiag_Error, eErr_SEQ_FEAT_MissingCDSproduct, eExtreme_Biological, NStr::Find(), CSeq_feat_Base::GetExcept_text(), GetLength(), CSeq_feat_Base::GetLocation(), NStr::IsBlank(), CSeq_feat_Base::IsSetExcept(), CSeq_feat_Base::IsSetExcept_text(), CSeq_feat_Base::IsSetLocation(), CSeq_feat_Base::IsSetProduct(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_Scope, NPOS, and CSingleFeatValidator::PostErr().

Referenced by Validate().

◆ x_ValidateProductPartials()

void CCdregionValidator::x_ValidateProductPartials ( )
protected

Definition at line 1774 of file cdregion_validator.cpp.

References eDiag_Warning, eErr_SEQ_FEAT_PartialsInconsistentCDSProtein, CSeqFeatData::eSubtype_prot, CSeq_feat_Base::GetLocation(), CBioseq_Handle::GetTopLevelEntry(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_LocationBioseq, CSingleFeatValidator::m_ProductBioseq, PartialsSame(), CSingleFeatValidator::PostErr(), and prot.

Referenced by Validate().

◆ x_ValidateQuals()

void CCdregionValidator::x_ValidateQuals ( )
protected

Definition at line 804 of file cdregion_validator.cpp.

References CGb_qual_Base::CanGetQual(), eDiag_Error, eDiag_Warning, eErr_SEQ_FEAT_CodonQualifierUsed, eErr_SEQ_FEAT_InvalidCodonStart, eErr_SEQ_FEAT_MissingExceptionFlag, eErr_SEQ_FEAT_WrongQualOnCDS, eErr_SEQ_FEAT_WrongQualOnFeature, CCdregion_Base::eFrame_not_set, NStr::EqualNocase(), FOR_EACH_GBQUAL_ON_FEATURE, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CGb_qual_Base::GetQual(), CSeq_feat_Base::IsSetExcept(), CCdregion_Base::IsSetFrame(), ncbi::grid::netcache::search::fields::key, CSingleFeatValidator::m_Feat, and CSingleFeatValidator::PostErr().

Referenced by Validate().

◆ x_ValidateSeqFeatLoc()

void CCdregionValidator::x_ValidateSeqFeatLoc ( )
overrideprotectedvirtual

Reimplemented from CSingleFeatValidator.

Definition at line 1010 of file cdregion_validator.cpp.

References eDiag_Warning, eErr_SEQ_FEAT_ShortExon, CSeq_feat_Base::GetLocation(), CSingleFeatValidator::m_Feat, NStr::NumericToString(), CSingleFeatValidator::PostErr(), and CSingleFeatValidator::x_ValidateSeqFeatLoc().

◆ x_ValidateTrans()

void CCdregionValidator::x_ValidateTrans ( )
protected

Definition at line 196 of file cdregion_validator.cpp.

References CCDSTranslationProblems::CalculateTranslationProblems(), CCDSTranslationProblems::eCDSTranslationProblem_UnableToFetch, CSeq_feat_Base::GetProduct(), CCDSTranslationProblems::GetTranslationProblemFlags(), CValidError_imp::GetTSE(), CCDSTranslationProblems::HasException(), CValidError_imp::IgnoreExceptions(), CValidError_imp::IsFarFetchCDSproducts(), CValidError_imp::IsGED(), CValidError_imp::IsGenomic(), CValidError_imp::IsGpipe(), CValidError_imp::IsRefSeq(), CSeq_entry_Base::IsSeq(), CValidError_imp::IsStandaloneAnnot(), CValidError_imp::IsTPE(), CSingleFeatValidator::m_Feat, CSingleFeatValidator::m_Imp, CSingleFeatValidator::m_LocationBioseq, CSingleFeatValidator::m_ProductBioseq, CSingleFeatValidator::m_Scope, s_LocIdType(), CValidError_imp::SetFarFetchFailure(), CCDSTranslationProblems::UnableToTranslate(), CValidError_imp::x_IsFarFetchFailure(), x_ReportTranslationProblems(), and x_ValidateCodebreak().

Referenced by Validate().

Member Data Documentation

◆ m_Gene

CConstRef<CSeq_feat> CCdregionValidator::m_Gene
protected

Definition at line 246 of file single_feat_validator.hpp.

Referenced by CCdregionValidator(), Validate(), and x_ValidateParentPartialness().

◆ m_GeneIsPseudo

bool CCdregionValidator::m_GeneIsPseudo
protected

Definition at line 247 of file single_feat_validator.hpp.

Referenced by CCdregionValidator(), Validate(), x_IsProductMisplaced(), x_ReportOrigProteinId(), and x_ValidateBadMRNAOverlap().

The documentation for this class was generated from the following files:
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Modified on Fri Sep 20 14:58:31 2024 by modify_doxy.py rev. 669887