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

shared_ptr<SValidatorContext> pContext,

SetOptions(

options);

Reset(

initialInferenceCount,

notJustLocalOrGeneral,

hasRefSeq);

* scope =

);

Validate(

& pubdesc,

* scope =

);

GetTSANStretchErrors(

& seq);

GetTSAConflictingBiomolTechErrors (

& seq);

()

{

(m_NumTopSetSiblings > 1000)

;

; }

IsHugeFileMode()

;

IsHugeSet(

& bioseqSet)

;

RaiseGenomeSeverity(

et);

ValidateSubSource(

& subsrc,

& obj,

*

=

,

isViral =

,

isInfluenzaOrSars2 =

);

ValidateOrgRef(

& orgref,

& obj,

*

,

checkForUndefinedSpecies =

,

is_single_cell_amplification =

);

IsSyntheticConstruct (

& src);

& prefix,

& obj,

lowerSev =

);

(

)

IsNoPubs()

;

IsNoCitSubPubs()

;

IsNoBioSource()

;

IsPatent()

;

IsRefSeq()

;

IsEmbl()

;

IsDdbj()

;

IsGpipe()

;

IsLocalGeneralOnly()

;

HasGiOrAccnVer()

;

IsGenomic()

;

IsSeqSubmit()

;

IsSmallGenomeSet()

;

IsGenbank()

;

DoesAnyFeatLocHaveGI()

;

DoesAnyProductLocHaveGI()

;

DoesAnyGeneHaveLocusTag()

;

DoesAnyProteinHaveGeneralID()

;

IsINSDInSep()

;

IsGeneious()

;

(

)

{

m_HasRefSeq; }

IsFarSequence(

&

);

AddBioseqWithNoPub(

& seq);

AddBioseqWithNoBiosource(

& seq);

IsWGSIntermediate(

& seq);

IsTSAIntermediate(

& seq);

ReportMissingBiosource(

& se);

IsSerialNumberInComment(

& comment);

RequireLocalProduct(

* sid)

;

x_Init(

options,

initialInferenceCount,

notJustLocalOrGeneral,

hasRefSeq);

m_scopeToRestore(scope), m_scopeOriginalValue(scope) { }

x_AddValidErrItem(

sev,

& accession,

InitializeSourceQualTags();

IsMixedStrands(

& loc);

HasTitle(

& title);

HasIsoJTA(

& title);

FindCollidingSerialNumbers (

& obj);

s_IsSalmonellaGenus(

& taxname);

x_InitLocCheck(SLocCheck&

,

& prefix);

x_CheckForStrandChange(SLocCheck&

);

x_ReportPCRSeqProblem(

& primer_kind,

x_CheckPCRPrimer(

& primer,

& primer_kind,

x_DowngradeForMissingAffil(

& cs);

unique_ptr<CTaxValidationAndCleanup> x_CreateTaxValidator()

;

unique_ptr<CValidatorEntryInfo> m_pEntryInfo = make_unique<CValidatorEntryInfo>();

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

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

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

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

@OrgMod.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::

Base class for all serializable objects.

CScopeRestorer(CRef< CScope > &scope)

CRef< CScope > & m_scopeToRestore

CRef< CScope > m_scopeOriginalValue

CRef< CObjectManager > m_ObjMgr

bool DoRubiscoTest() const

void PostErr(EDiagSev sv, EErrType et, const string &msg, TDesc ds)

const CSeq_entry_Handle & GetTSEH()

bool ReportSpliceAsError() const

void AddToPseudoCount(size_t num)

bool m_NewStrainValidation

bool IsLatLonCheckState() const

size_t GetGeneCount(void) const

bool m_ValidateAlignments

void IncrementGeneCount()

bool IsRemoteFetch() const

void AddToTpaWithHistoryCount(size_t num)

bool IsSuppressContext() const

bool m_FarFetchCDSproducts

CValidator::TProgressCallback m_PrgCallback

bool m_GenerateGoldenFile

IValidError * m_ErrRepository

size_t m_NumMisplacedGraphs

bool m_NotJustLocalOrGeneral

void AddToMisplacedFeatureCount(size_t num)

void IncrementMisplacedFeatureCount()

bool IsValidateAlignments() const

size_t m_NumTopSetSiblings

const CConstRef< CSeq_annot > & GetSeqAnnot()

void ResetSmallGenomeSetMisplacedCount()

void ResetTpaWithoutHistoryCount()

bool GenerateGoldenFile() const

bool IsStandaloneAnnot() const

CConstRef< CSeq_feat > GetCachedGene(const CSeq_feat *f)

CConstRef< CSeq_annot > m_SeqAnnot

bool IsValidateIdSet() const

TSuppressed m_SuppressedErrors

bool IsLocusTagGeneralMatch() const

bool IgnoreInferences() const

CValidator::CProgressInfo m_PrgInfo

void AddToGeneXrefCount(size_t num)

bool ForceInferences() const

const CTSE_Handle & GetTSE_Handle()

bool ValidateInferenceAccessions() const

size_t m_NumMisplacedFeatures

void IncrementMisplacedGraphCount()

void IncrementPseudogeneCount()

bool m_ValidateInferenceAccessions

bool m_LocusTagGeneralMatch

vector< CConstRef< CBioseq > > m_BioseqWithNoSource

const CSeq_annot & TAnnot

bool IsRequireTaxonID() const

void ResetGeneXrefCount()

bool IsSeqSubmitParent() const

size_t m_NumTpaWithHistory

const CSeq_graph & TGraph

void AddToMisplacedGraphCount(size_t num)

size_t m_NumTpaWithoutHistory

bool NewStrainValidation() const

bool IsGenomeSubmission() const

void ResetPseudogeneCount()

void AddToGeneCount(size_t num)

void IncrementGeneXrefCount()

void AddToSmallGenomeSetMisplacedCount(size_t num)

bool IsLatLonIgnoreWater() const

bool m_ReportSpliceAsError

bool IsFarFetchCDSproducts() const

void ResetTpaWithHistoryCount()

void AddToTpaWithoutHistoryCount(size_t num)

void IncrementTpaWithHistoryCount()

bool IsValidateExons() const

size_t GetCumulativeInferenceCount(void) const

size_t m_NumSmallGenomeSetMisplaced

map< CSubSource::TSubtype, int > TCount

bool IgnoreExceptions() const

vector< CConstRef< CSeq_id > > m_InitialSeqIds

bool m_FarFetchMRNAproducts

void ResetCumulativeInferenceCount()

void SetFarFetchFailure()

CBioSourceKind m_biosource_kind

CConstRef< CSeq_entry > m_TSE

void IncrementTpaWithoutHistoryCount()

bool IsRefSeqConventions() const

bool IsIndexerVersion() const

bool IsRequireISOJTA() const

CGeneCache & GetGeneCache()

map< const CSeq_feat *, const CSeq_annot * > & TFeatAnnotMap

void AddToCumulativeInferenceCount(size_t num)

void IncrementSmallGenomeSetMisplacedCount()

size_t m_CumulativeInferenceCount

const CSeq_align & TAlign

void IncrementPseudoCount()

vector< int > m_PubSerialNumbers

void AddToPseudogeneCount(size_t num)

bool HasRefSeq(void) const

void ResetMisplacedGraphCount()

const CSeq_entry & TEntry

shared_ptr< SValidatorContext > m_pContext

const CSeq_entry & GetTSE() const

bool IsFarFetchMRNAproducts() const

bool DoCompareVDJCtoCDS() const

bool ShouldSubdivide() const

void IncrementCumulativeInferenceCount()

void ResetMisplacedFeatureCount()

size_t GetGeneXrefCount(void) const

CValidError_imp(const CValidError_imp &)

Cache various information for one validation run.

static const CTSE_Handle kEmptyTSEHandle

bool(* TProgressCallback)(CProgressInfo *)

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

API (CDeflineGenerator) for computing sequences' titles ("definitions").

static const struct name_t names[]

static const char * str(char *buf, int n)

SStrictId_Entrez::TId TEntrezId

TEntrezId type for entrez ids which require the same strictness as TGi.

SStrictId_Tax::TId TTaxId

Taxon id type.

EDiagSev

Severity level for the posted diagnostics.

#define NCBI_STD_DEPRECATED(message)

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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

ENa_strand

strand of nucleic acid

const string version

version string

std::istream & in(std::istream &in_, double &x_)

static wxString GetContext(const wxString &str, int pos)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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