SValidatorContext Struct Reference

Search Toolkit Book for SValidatorContext

#include <objtools/validator/validator_context.hpp>

Collaboration diagram for SValidatorContext:

Public Types
using	TSeqIdSet = set< CConstRef< CSeq_id >, PPtrLess< CConstRef< CSeq_id > >>
using	FIdInBlob = function< bool(const CSeq_id &id)>
using	taxupdate_func_t = function< CRef< CTaxon3_reply >(const vector< CRef< COrg_ref > > &list)>

Public Attributes
bool	PreprocessHugeFile {false}
bool	PostprocessHugeFile {false}
bool	IsPatent {false}
bool	IsPDB {false}
bool	IsRefSeq {false}
string	HugeSetId
atomic_bool	CheckECNumFileStatus {true}
bool	NoBioSource {false}
bool	NoPubsFound {false}
bool	NoCitSubsFound {false}
bool	CurrTpaAssembly {false}
int	JustTpaAssembly {0}
int	TpaAssemblyHist {0}
int	TpaNoHistYesGI {0}
std::atomic< size_t >	NumGenes {0}
std::atomic< size_t >	NumGeneXrefs {0}
once_flag	DescriptorsOnceFlag
once_flag	SubmitBlockOnceFlag
once_flag	WgsSetInSeqSubmitOnceFlag
once_flag	ClassNotSetOnceFlag
once_flag	ProteinHaveGeneralIDOnceFlag
FIdInBlob	IsIdInBlob {nullptr}
taxupdate_func_t	m_taxon_update

Detailed Description

Definition at line 48 of file validator_context.hpp.

Member Typedef Documentation

FIdInBlob

using SValidatorContext::FIdInBlob = function<bool(const CSeq_id& id)>

Definition at line 74 of file validator_context.hpp.

taxupdate_func_t

using SValidatorContext::taxupdate_func_t = function<CRef<CTaxon3_reply>(const vector<CRef<COrg_ref> >& list)>

Definition at line 76 of file validator_context.hpp.

TSeqIdSet

using SValidatorContext::TSeqIdSet = set<CConstRef<CSeq_id>, PPtrLess<CConstRef<CSeq_id> >>

Definition at line 50 of file validator_context.hpp.

Member Data Documentation

CheckECNumFileStatus

atomic_bool SValidatorContext::CheckECNumFileStatus {true}

Definition at line 58 of file validator_context.hpp.

Referenced by CSingleFeatValidator::x_ReportECNumFileStatus().

ClassNotSetOnceFlag

once_flag SValidatorContext::ClassNotSetOnceFlag

Definition at line 71 of file validator_context.hpp.

Referenced by CValidError_bioseqset::ValidateBioseqSet().

CurrTpaAssembly

bool SValidatorContext::CurrTpaAssembly {false}

Definition at line 62 of file validator_context.hpp.

Referenced by CHugeFileValidator::UpdateValidatorContext().

DescriptorsOnceFlag

once_flag SValidatorContext::DescriptorsOnceFlag

Definition at line 68 of file validator_context.hpp.

Referenced by CValidError_bioseqset::ValidateBioseqSet().

HugeSetId

string SValidatorContext::HugeSetId

Definition at line 57 of file validator_context.hpp.

Referenced by CValidError_imp::PostErr(), and CHugeFileValidator::UpdateValidatorContext().

IsIdInBlob

FIdInBlob SValidatorContext::IsIdInBlob {nullptr}

Definition at line 75 of file validator_context.hpp.

Referenced by CValidError_imp::IsFarSequence(), and CHugeFileValidator::UpdateValidatorContext().

IsPatent

bool SValidatorContext::IsPatent {false}

Definition at line 54 of file validator_context.hpp.

Referenced by CHugeFileValidator::UpdateValidatorContext().

IsPDB

bool SValidatorContext::IsPDB {false}

Definition at line 55 of file validator_context.hpp.

Referenced by CHugeFileValidator::UpdateValidatorContext().

IsRefSeq

bool SValidatorContext::IsRefSeq {false}

Definition at line 56 of file validator_context.hpp.

Referenced by CHugeFileValidator::UpdateValidatorContext().

JustTpaAssembly

int SValidatorContext::JustTpaAssembly {0}

Definition at line 63 of file validator_context.hpp.

Referenced by CHugeFileValidator::UpdateValidatorContext().

m_taxon_update

taxupdate_func_t SValidatorContext::m_taxon_update

Definition at line 77 of file validator_context.hpp.

NoBioSource

bool SValidatorContext::NoBioSource {false}

Definition at line 59 of file validator_context.hpp.

Referenced by CHugeFileValidator::UpdateValidatorContext().

NoCitSubsFound

bool SValidatorContext::NoCitSubsFound {false}

Definition at line 61 of file validator_context.hpp.

Referenced by CHugeFileValidator::UpdateValidatorContext().

NoPubsFound

bool SValidatorContext::NoPubsFound {false}

Definition at line 60 of file validator_context.hpp.

Referenced by CHugeFileValidator::UpdateValidatorContext().

NumGenes

std::atomic<size_t> SValidatorContext::NumGenes {0}

Definition at line 66 of file validator_context.hpp.

Referenced by CHugeFileValidator::ReportPostErrors().

NumGeneXrefs

std::atomic<size_t> SValidatorContext::NumGeneXrefs {0}

Definition at line 67 of file validator_context.hpp.

Referenced by CHugeFileValidator::ReportPostErrors().

PostprocessHugeFile

bool SValidatorContext::PostprocessHugeFile {false}

Definition at line 53 of file validator_context.hpp.

Referenced by CValidError_bioseq::ValidateBioseqContext().

PreprocessHugeFile

bool SValidatorContext::PreprocessHugeFile {false}

Definition at line 52 of file validator_context.hpp.

Referenced by CHugeFileValidator::UpdateValidatorContext().

ProteinHaveGeneralIDOnceFlag

once_flag SValidatorContext::ProteinHaveGeneralIDOnceFlag

Definition at line 72 of file validator_context.hpp.

SubmitBlockOnceFlag

once_flag SValidatorContext::SubmitBlockOnceFlag

Definition at line 69 of file validator_context.hpp.

TpaAssemblyHist

int SValidatorContext::TpaAssemblyHist {0}

Definition at line 64 of file validator_context.hpp.

Referenced by CHugeFileValidator::UpdateValidatorContext().

TpaNoHistYesGI

int SValidatorContext::TpaNoHistYesGI {0}

Definition at line 65 of file validator_context.hpp.

Referenced by CHugeFileValidator::UpdateValidatorContext().

WgsSetInSeqSubmitOnceFlag

once_flag SValidatorContext::WgsSetInSeqSubmitOnceFlag

Definition at line 70 of file validator_context.hpp.

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The documentation for this struct was generated from the following file:

• include/objtools/validator/validator_context.hpp