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NCBI C++ ToolKit: include/objtools/validator/validerror_feat.hpp Source File

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34 #ifndef VALIDATOR___VALIDERROR_FEAT__HPP 35 #define VALIDATOR___VALIDERROR_FEAT__HPP 117 void

ValidateSeqFeat(

122

eInferenceValidCode_valid = 0,

134

eInferenceValidCode_unrecognized_database

137 static

vector<string> GetAccessionsFromInferenceString (

string

inference,

string

&prefix,

string

&remainder,

bool

&same_species);

138 static bool

GetPrefixAndAccessionFromInferenceAccession (

string

inf_accession,

string

&prefix,

string

&accession);

139 static

EInferenceValidCode ValidateInferenceAccession (

string

accession,

bool

fetch_accession,

bool

is_similar_to,

CScope

* scope =

nullptr

);

140 static

EInferenceValidCode ValidateInference(

string

inference,

bool

fetch_accession,

CScope

* scope =

nullptr

);

143 bool

DoesCDSHaveShortIntrons(

const CSeq_feat

& feat);

144 bool

IsIntronShort(

const CSeq_feat

& feat);

145 bool

GetTSACDSOnMinusStrandErrors(

const CSeq_feat

& feat,

const CBioseq

& seq);

155 void

ValidateSeqFeatXref(

const CSeq_feat

& feat);

157 void

x_ValidateSeqFeatExceptXref(

const CSeq_feat

& feat);

164 bool

IsOverlappingGenePseudo(

const CSeq_feat

& feat);

static CRef< CScope > m_Scope

@Auth_list.hpp User-defined methods of the data storage class.

@Imp_feat.hpp User-defined methods of the data storage class.

@Pubdesc.hpp User-defined methods of the data storage class.

@RNA_ref.hpp User-defined methods of the data storage class.

namespace ncbi::objects::

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

void SetScope(CScope &scope)

@ eInferenceValidCode_bad_prefix

@ eInferenceValidCode_spaces

@ eInferenceValidCode_bad_accession_version

@ eInferenceValidCode_comment

@ eInferenceValidCode_same_species_misused

@ eInferenceValidCode_empty

@ eInferenceValidCode_bad_body

@ eInferenceValidCode_single_field

@ eInferenceValidCode_bad_accession

@ eInferenceValidCode_bad_accession_type

@ eInferenceValidCode_accession_version_not_public

Cache various information for one validation run.

Include a standard set of the NCBI C++ Toolkit most basic headers.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_VALIDATOR_EXPORT

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