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CValidError_feat Class Reference

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#include <objtools/validator/validerror_feat.hpp>

+ Inheritance diagram for CValidError_feat:
+ Collaboration diagram for CValidError_feat:

Public Types

enum  EInferenceValidCode {
  eInferenceValidCode_valid = 0 , eInferenceValidCode_empty , eInferenceValidCode_bad_prefix , eInferenceValidCode_bad_body ,
  eInferenceValidCode_single_field , eInferenceValidCode_spaces , eInferenceValidCode_comment , eInferenceValidCode_same_species_misused ,
  eInferenceValidCode_bad_accession , eInferenceValidCode_bad_accession_version , eInferenceValidCode_accession_version_not_public , eInferenceValidCode_bad_accession_type ,
  eInferenceValidCode_unrecognized_database
}
 

Public Member Functions

 CValidError_feat (CValidError_imp &imp)
 
 ~CValidError_feat () override
 
void SetScope (CScope &scope)
 
void SetTSE (CSeq_entry_Handle seh)
 
void ValidateSeqFeat (const CSeq_feat &feat)
 
void ValidateSeqFeatContext (const CSeq_feat &feat, const CBioseq &seq)
 
bool DoesCDSHaveShortIntrons (const CSeq_feat &feat)
 
bool IsIntronShort (const CSeq_feat &feat)
 
bool GetTSACDSOnMinusStrandErrors (const CSeq_feat &feat, const CBioseq &seq)
 

Static Public Member Functions

static vector< string > GetAccessionsFromInferenceString (string inference, string &prefix, string &remainder, bool &same_species)
 
static bool GetPrefixAndAccessionFromInferenceAccession (string inf_accession, string &prefix, string &accession)
 
static EInferenceValidCode ValidateInferenceAccession (string accession, bool fetch_accession, bool is_similar_to, CScope *scope=nullptr)
 
static EInferenceValidCode ValidateInference (string inference, bool fetch_accession, CScope *scope=nullptr)
 

Private Member Functions

CBioseq_Handle x_GetCachedBsh (const CSeq_loc &loc)
 
void ValidateSeqFeatXref (const CSeq_feat &feat)
 
void ValidateSeqFeatXref (const CSeqFeatXref &xref, const CSeq_feat &feat)
 
void x_ValidateSeqFeatExceptXref (const CSeq_feat &feat)
 
void ValidateOneFeatXrefPair (const CSeq_feat &feat, const CSeq_feat &far_feat)
 
bool IsOverlappingGenePseudo (const CSeq_feat &feat)
 
bool x_HasNonReciprocalXref (const CSeq_feat &feat, const CFeat_id &id, CSeqFeatData::ESubtype subtype)
 

Static Private Member Functions

static bool HasNonReciprocalXref (const CSeq_feat &feat, const CFeat_id &id, CSeqFeatData::ESubtype subtype, const CTSE_Handle &tse)
 

Private Attributes

CSeq_entry_Handle m_TSE
 
CGeneCache m_GeneCache
 
CCacheImpl m_SeqCache
 

Detailed Description

Definition at line 108 of file validerror_feat.hpp.

Member Enumeration Documentation

◆ EInferenceValidCode

enum CValidError_feat::EInferenceValidCode
Enumerator
eInferenceValidCode_valid 
eInferenceValidCode_empty 
eInferenceValidCode_bad_prefix 
eInferenceValidCode_bad_body 
eInferenceValidCode_single_field 
eInferenceValidCode_spaces 
eInferenceValidCode_comment 
eInferenceValidCode_same_species_misused 
eInferenceValidCode_bad_accession 
eInferenceValidCode_bad_accession_version 
eInferenceValidCode_accession_version_not_public 
eInferenceValidCode_bad_accession_type 
eInferenceValidCode_unrecognized_database 

Definition at line 121 of file validerror_feat.hpp.

Constructor & Destructor Documentation

◆ CValidError_feat()

CValidError_feat::CValidError_feat ( CValidError_imp &  imp)

Definition at line 107 of file validerror_feat.cpp.

◆ ~CValidError_feat()

CValidError_feat::~CValidError_feat ( )
override

Definition at line 113 of file validerror_feat.cpp.

Member Function Documentation

◆ DoesCDSHaveShortIntrons()

bool CValidError_feat::DoesCDSHaveShortIntrons ( const CSeq_feat &  feat)

Definition at line 506 of file validerror_feat.cpp.

References abs, CSeq_id::Assign(), CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CBioseq_Handle::GetId(), CSeq_feat_Base::GetLocation(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetLocation(), and m_Scope.

◆ GetAccessionsFromInferenceString()

vector< string > CValidError_feat::GetAccessionsFromInferenceString ( string  inference,
string &  prefix,
string &  remainder,
bool &  same_species 
)
static

Definition at line 406 of file validerror_feat.cpp.

References NStr::eNocase, NStr::Equal(), CInferencePrefixList::GetPrefixAndRemainder(), NStr::IsBlank(), NStr::Split(), NStr::StartsWith(), and NStr::TruncateSpacesInPlace().

Referenced by CValidError_imp::Validate(), and ValidateInference().

◆ GetPrefixAndAccessionFromInferenceAccession()

bool CValidError_feat::GetPrefixAndAccessionFromInferenceAccession ( string  inf_accession,
string &  prefix,
string &  accession 
)
static

Definition at line 264 of file validerror_feat.cpp.

References NStr::Find(), and NStr::TruncateSpacesInPlace().

Referenced by CValidError_imp::Validate(), and ValidateInferenceAccession().

◆ GetTSACDSOnMinusStrandErrors()

bool CValidError_feat::GetTSACDSOnMinusStrandErrors ( const CSeq_feat &  feat,
const CBioseq &  seq 
)

Definition at line 167 of file validerror_feat.cpp.

References CSeqdesc_Base::e_Molinfo, CMolInfo_Base::eBiomol_transcribed_RNA, eDiag_Warning, eErr_SEQ_FEAT_CDSonMinusStrandTranscribedRNA, eNa_strand_minus, CMolInfo_Base::eTech_tsa, CMolInfo_Base::GetBiomol(), CScope::GetBioseqHandle(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), CSeqdesc_Base::GetMolinfo(), CSeq_loc::GetStrand(), CMolInfo_Base::GetTech(), CSeqFeatData_Base::IsCdregion(), CMolInfo_Base::IsSetBiomol(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetLocation(), CMolInfo_Base::IsSetTech(), and m_Scope.

Referenced by CValidError_imp::GetTSACDSOnMinusStrandErrors(), and ValidateSeqFeatContext().

◆ HasNonReciprocalXref()

static bool CValidError_feat::HasNonReciprocalXref ( const CSeq_feat &  feat,
const CFeat_id &  id,
CSeqFeatData::ESubtype  subtype,
const CTSE_Handle &  tse 
)
staticprivate

◆ IsIntronShort()

bool CValidError_feat::IsIntronShort ( const CSeq_feat &  feat)

Definition at line 571 of file validerror_feat.cpp.

References eExtreme_Positional, CSeqFeatData::eSubtype_intron, CBioseq_Handle::GetBioseqLength(), CSeq_feat_Base::GetData(), GetLength(), CSeq_feat_Base::GetLocation(), CSeqFeatData::GetSubtype(), IsOrganelle(), IsOverlappingGenePseudo(), CSeq_feat_Base::IsSetData(), CSeq_feat_Base::IsSetLocation(), CSeq_feat_Base::IsSetPseudo(), m_Scope, and x_GetCachedBsh().

◆ IsOverlappingGenePseudo()

bool CValidError_feat::IsOverlappingGenePseudo ( const CSeq_feat &  feat)
private

Definition at line 554 of file validerror_feat.cpp.

References CGeneCache::GetGeneFromCache(), CSeq_feat::GetGeneXref(), m_GeneCache, m_Scope, and CSingleFeatValidator::s_IsPseudo().

Referenced by IsIntronShort().

◆ SetScope()

void CValidError_feat::SetScope ( CScope &  scope)
inline

Definition at line 114 of file validerror_feat.hpp.

References m_Scope.

Referenced by CValidError_imp::Validate(), CValidError_bioseq::ValidateBioseq(), and CValidError_annot::ValidateSeqAnnot().

◆ SetTSE()

void CValidError_feat::SetTSE ( CSeq_entry_Handle  seh)

Definition at line 118 of file validerror_feat.cpp.

References CValidator::CCacheImpl::Clear(), CGeneCache::Clear(), m_GeneCache, m_SeqCache, and m_TSE.

Referenced by CValidError_imp::Validate(), CValidError_bioseq::ValidateBioseq(), and CValidError_annot::ValidateSeqAnnot().

◆ ValidateInference()

CValidError_feat::EInferenceValidCode CValidError_feat::ValidateInference ( string  inference,
bool  fetch_accession,
CScope *  scope = nullptr 
)
static

Definition at line 452 of file validerror_feat.cpp.

References eInferenceValidCode_bad_body, eInferenceValidCode_bad_prefix, eInferenceValidCode_comment, eInferenceValidCode_empty, eInferenceValidCode_same_species_misused, eInferenceValidCode_spaces, eInferenceValidCode_valid, FOR_EACH_CHAR_IN_STRING, GetAccessionsFromInferenceString(), i, NStr::IsBlank(), NStr::StartsWith(), NStr::TruncateSpacesInPlace(), and ValidateInferenceAccession().

Referenced by CSingleFeatValidator::x_ValidateGbQual().

◆ ValidateInferenceAccession()

CValidError_feat::EInferenceValidCode CValidError_feat::ValidateInferenceAccession ( string  accession,
bool  fetch_accession,
bool  is_similar_to,
CScope *  scope = nullptr 
)
static

Definition at line 320 of file validerror_feat.cpp.

References eInferenceValidCode_accession_version_not_public, eInferenceValidCode_bad_accession, eInferenceValidCode_bad_accession_type, eInferenceValidCode_bad_accession_version, eInferenceValidCode_empty, eInferenceValidCode_single_field, eInferenceValidCode_spaces, eInferenceValidCode_unrecognized_database, eInferenceValidCode_valid, NStr::eNocase, NStr::EqualNocase(), NStr::Find(), GetPrefixAndAccessionFromInferenceAccession(), NStr::IsBlank(), isdigit(), CGb_qual::IsLegalInferenceDatabase(), IsSequenceFetchable(), s_IsAllDigitsOrPeriods(), s_IsSraPrefix(), NStr::StartsWith(), and ValidateAccessionFormat().

Referenced by ValidateInference().

◆ ValidateOneFeatXrefPair()

void CValidError_feat::ValidateOneFeatXrefPair ( const CSeq_feat &  feat,
const CSeq_feat &  far_feat 
)
private

Definition at line 668 of file validerror_feat.cpp.

References CSeqFeatData::AllowXref(), Compare(), eContained, eDiag_Error, eDiag_Warning, eErr_SEQ_FEAT_CDSmRNAXrefLocationProblem, eErr_SEQ_FEAT_SeqFeatXrefNotReciprocal, eErr_SEQ_FEAT_SeqFeatXrefProblem, eSame, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eVocabulary_genbank, fCompareOverlapping, FeaturePairIsTwoTypes(), GeneXrefConflicts(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetId(), CSeqFeatData::GetKey(), CSeq_feat_Base::GetLocation(), CSeqFeatData::GetSubtype(), CSeq_feat::HasSeqFeatXref(), CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsGene(), CSeq_feat_Base::IsSetId(), CSeq_feat_Base::IsSetXref(), m_Scope, CSeqFeatData::ProhibitXref(), and x_HasNonReciprocalXref().

Referenced by ValidateSeqFeatXref().

◆ ValidateSeqFeat()

void CValidError_feat::ValidateSeqFeat ( const CSeq_feat &  feat)

Definition at line 157 of file validerror_feat.cpp.

References ValidateSeqFeatXref(), and x_ValidateSeqFeatExceptXref().

Referenced by CValidError_imp::Validate(), and CValidError_annot::ValidateSeqAnnot().

◆ ValidateSeqFeatContext()

void CValidError_feat::ValidateSeqFeatContext ( const CSeq_feat &  feat,
const CBioseq &  seq 
)

Definition at line 193 of file validerror_feat.cpp.

References CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Prot, CSeqFeatData_Base::e_Psec_str, CSeqFeatData_Base::e_Rna, CSeqFeatData_Base::e_Rsite, CSeqFeatData_Base::e_Txinit, eDiag_Error, eDiag_Warning, eErr_SEQ_FEAT_InvalidFeatureForNucleotide, eErr_SEQ_FEAT_InvalidFeatureForProtein, eErr_SEQ_FEAT_InvalidForType, CProt_ref_Base::eProcessed_mature, CProt_ref_Base::eProcessed_preprotein, CProt_ref_Base::eProcessed_signal_peptide, CProt_ref_Base::eProcessed_transit_peptide, CSeq_feat_Base::GetData(), CProt_ref_Base::GetProcessed(), CSeqFeatData_Base::GetProt(), GetTSACDSOnMinusStrandErrors(), CBioseq::IsAa(), CSeqFeatData_Base::IsProt(), CSeq_feat_Base::IsSetData(), CProt_ref_Base::IsSetProcessed(), and CSeqFeatData_Base::Which().

Referenced by CValidError_bioseq::ValidateSeqFeatContext().

◆ ValidateSeqFeatXref() [1/2]

void CValidError_feat::ValidateSeqFeatXref ( const CSeq_feat &  feat)
private

Definition at line 749 of file validerror_feat.cpp.

References CSeq_feat_Base::GetXref(), and CSeq_feat_Base::IsSetXref().

Referenced by ValidateSeqFeat().

◆ ValidateSeqFeatXref() [2/2]

void CValidError_feat::ValidateSeqFeatXref ( const CSeqFeatXref &  xref,
const CSeq_feat &  feat 
)
private

Definition at line 760 of file validerror_feat.cpp.

References eDiag_Error, eDiag_Warning, eErr_SEQ_FEAT_SeqFeatXrefFeatureMissing, eErr_SEQ_FEAT_SeqFeatXrefProblem, eErr_SEQ_FEAT_UnnecessaryGeneXref, CSeqFeatData::eSubtype_any, CSeq_feat_Base::GetData(), CSeqFeatXref_Base::GetData(), CTSE_Handle::GetFeaturesWithId(), CSeqFeatXref_Base::GetId(), CFeat_id_Base::GetLocal(), CSeq_entry_Handle::GetTSE_Handle(), CSeqFeatData_Base::IsGene(), CFeat_id_Base::IsLocal(), CSeqFeatXref_Base::IsSetData(), CSeqFeatXref_Base::IsSetId(), m_TSE, s_HasId(), ValidateOneFeatXrefPair(), and CSeqFeatData_Base::Which().

◆ x_GetCachedBsh()

CBioseq_Handle CValidError_feat::x_GetCachedBsh ( const CSeq_loc &  loc)
private

Definition at line 128 of file validerror_feat.cpp.

References ctll::empty(), CValidator::CCacheImpl::GetBioseqHandleFromLocation(), CSeq_entry_Handle::GetTSE_Handle(), m_Scope, m_SeqCache, and m_TSE.

Referenced by IsIntronShort().

◆ x_HasNonReciprocalXref()

bool CValidError_feat::x_HasNonReciprocalXref ( const CSeq_feat &  feat,
const CFeat_id &  id,
CSeqFeatData::ESubtype  subtype 
)
private

Definition at line 643 of file validerror_feat.cpp.

References CTSE_Handle::GetFeaturesWithId(), CObject_id_Base::GetId(), CSeq_entry_Handle::GetTSE_Handle(), CSeq_feat_Base::GetXref(), CSeq_feat_Base::IsSetXref(), ITERATE, and m_TSE.

Referenced by ValidateOneFeatXrefPair().

◆ x_ValidateSeqFeatExceptXref()

void CValidError_feat::x_ValidateSeqFeatExceptXref ( const CSeq_feat &  feat)
private

Definition at line 138 of file validerror_feat.cpp.

References eDiag_Fatal, eErr_INTERNAL_Exception, FeatValidatorFactory(), and m_Scope.

Referenced by ValidateSeqFeat().

Member Data Documentation

◆ m_GeneCache

CGeneCache CValidError_feat::m_GeneCache
private

Definition at line 150 of file validerror_feat.hpp.

Referenced by IsOverlappingGenePseudo(), and SetTSE().

◆ m_SeqCache

CCacheImpl CValidError_feat::m_SeqCache
private

Definition at line 151 of file validerror_feat.hpp.

Referenced by SetTSE(), and x_GetCachedBsh().

◆ m_TSE

CSeq_entry_Handle CValidError_feat::m_TSE
private

Definition at line 149 of file validerror_feat.hpp.

Referenced by SetTSE(), ValidateSeqFeatXref(), x_GetCachedBsh(), and x_HasNonReciprocalXref().

The documentation for this class was generated from the following files:
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Modified on Fri Sep 20 14:57:10 2024 by modify_doxy.py rev. 669887