NCBI C++ ToolKit
Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Static Private Member Functions | Private Attributes | List of all members
CValidError_feat Class Reference

Search Toolkit Book for CValidError_feat

#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< stringGetAccessionsFromInferenceString (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

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)

◆ GetAccessionsFromInferenceString()

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

◆ GetPrefixAndAccessionFromInferenceAccession()

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

◆ GetTSACDSOnMinusStrandErrors()

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

◆ 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)

◆ IsOverlappingGenePseudo()

bool CValidError_feat::IsOverlappingGenePseudo ( const CSeq_feat feat)
private

◆ SetScope()

void CValidError_feat::SetScope ( CScope scope)
inline

◆ SetTSE()

void CValidError_feat::SetTSE ( CSeq_entry_Handle  seh)

◆ ValidateInference()

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

◆ ValidateInferenceAccession()

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

◆ ValidateOneFeatXrefPair()

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

◆ ValidateSeqFeat()

void CValidError_feat::ValidateSeqFeat ( const CSeq_feat feat)

◆ ValidateSeqFeatContext()

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

◆ 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

◆ x_GetCachedBsh()

CBioseq_Handle CValidError_feat::x_GetCachedBsh ( const CSeq_loc loc)
private

◆ x_HasNonReciprocalXref()

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

◆ 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

The documentation for this class was generated from the following files:
Modified on Thu May 30 12:28:22 2024 by modify_doxy.py rev. 669887