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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, TSeqPosTShortIntron
 
- 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< TShortIntronx_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_featm_Gene
 
bool m_GeneIsPseudo
 
- Protected Attributes inherited from CSingleFeatValidator
const CSeq_featm_Feat
 
CScopem_Scope
 
CValidError_impm_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

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 
)

Member Function Documentation

◆ IsPlastid()

bool CCdregionValidator::IsPlastid ( int  genome)
staticprotected

◆ MapToNTCoords()

string CCdregionValidator::MapToNTCoords ( TSeqPos  pos)
protected

◆ ReportShortIntrons()

void CCdregionValidator::ReportShortIntrons ( )
protected

◆ Validate()

void CCdregionValidator::Validate ( void  )
overridevirtual

◆ 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

◆ x_CDS3primePartialTest()

bool CCdregionValidator::x_CDS3primePartialTest ( ) const
protected

◆ x_CDS5primePartialTest()

bool CCdregionValidator::x_CDS5primePartialTest ( ) const
protected

◆ 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

◆ x_HasGoodParent()

bool CCdregionValidator::x_HasGoodParent ( )
protected

◆ x_IsProductMisplaced()

bool CCdregionValidator::x_IsProductMisplaced ( ) const
protected

◆ x_ReportOrigProteinId()

bool CCdregionValidator::x_ReportOrigProteinId ( )
overrideprotectedvirtual

◆ x_ReportTranslationMismatches()

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

◆ 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, 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

◆ x_ValidateBadMRNAOverlap()

void CCdregionValidator::x_ValidateBadMRNAOverlap ( )
protected

◆ x_ValidateCDSPartial()

void CCdregionValidator::x_ValidateCDSPartial ( )
protected

◆ x_ValidateCDSPeptides()

void CCdregionValidator::x_ValidateCDSPeptides ( )
protected

◆ x_ValidateCodebreak()

void CCdregionValidator::x_ValidateCodebreak ( )
protected

◆ x_ValidateCommonProduct()

void CCdregionValidator::x_ValidateCommonProduct ( )
protected

◆ x_ValidateConflict()

void CCdregionValidator::x_ValidateConflict ( )
protected

◆ x_ValidateExceptText()

void CCdregionValidator::x_ValidateExceptText ( const string text)
overrideprotectedvirtual

◆ x_ValidateFarProducts()

void CCdregionValidator::x_ValidateFarProducts ( )
protected

◆ x_ValidateFeatComment()

void CCdregionValidator::x_ValidateFeatComment ( )
overrideprotectedvirtual

◆ x_ValidateGeneticCode()

void CCdregionValidator::x_ValidateGeneticCode ( )
protected

◆ x_ValidateParentPartialness() [1/2]

void CCdregionValidator::x_ValidateParentPartialness ( )
protected

◆ x_ValidateParentPartialness() [2/2]

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

◆ x_ValidateProductId()

void CCdregionValidator::x_ValidateProductId ( )
protected

◆ x_ValidateProductPartials()

void CCdregionValidator::x_ValidateProductPartials ( )
protected

◆ x_ValidateQuals()

void CCdregionValidator::x_ValidateQuals ( )
protected

◆ x_ValidateSeqFeatLoc()

void CCdregionValidator::x_ValidateSeqFeatLoc ( )
overrideprotectedvirtual

◆ x_ValidateTrans()

void CCdregionValidator::x_ValidateTrans ( )
protected

Member Data Documentation

◆ m_Gene

CConstRef<CSeq_feat> CCdregionValidator::m_Gene
protected

◆ m_GeneIsPseudo

bool CCdregionValidator::m_GeneIsPseudo
protected

The documentation for this class was generated from the following files:
Modified on Thu Feb 29 12:21:22 2024 by modify_doxy.py rev. 669887