NCBI C++ ToolKit
Typedefs | Functions
huge_file_validator.cpp File Reference
#include <ncbi_pch.hpp>
#include <objtools/edit/huge_asn_reader.hpp>
#include <objtools/validator/validatorp.hpp>
#include <objtools/validator/validator_context.hpp>
#include <objtools/validator/validerror_bioseq.hpp>
#include <objtools/validator/validerror_format.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/valerr/ValidErrItem.hpp>
#include <objects/valerr/ValidError.hpp>
#include <objmgr/util/sequence.hpp>
#include <serial/objhook.hpp>
#include <objtools/readers/objhook_lambdas.hpp>
#include <objtools/validator/huge_file_validator.hpp>
+ Include dependency graph for huge_file_validator.cpp:

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Typedefs

using TBioseqInfo = CHugeAsnReader::TBioseqInfo
 

Functions

 USING_SCOPE (edit)
 
static bool s_IsTSAContig (const TBioseqInfo &info, const CHugeAsnReader &reader)
 
static bool s_IsGpipe (const TBioseqInfo &info)
 
static bool s_CuratedRefSeq (const string &accession)
 
static bool s_IsNoncuratedRefSeq (const list< CConstRef< CSeq_id >> &ids)
 
bool g_IsCuratedRefSeq (const TBioseqInfo &info)
 
static bool s_IsMaster (const TBioseqInfo &info)
 
static bool s_IsWGS (const TBioseqInfo &info, const CHugeAsnReader &reader)
 
static bool s_IsWGSMaster (const TBioseqInfo &info, const CHugeAsnReader &reader)
 
static bool s_x_ReportMissingCitSub (const TBioseqInfo &info, const CHugeAsnReader &reader, bool IsRefSeq)
 
static bool s_x_ReportMissingPubs (const TBioseqInfo &info, const CHugeAsnReader &reader)
 
static string s_GetBioseqAcc (const CSeq_id &id, int *version)
 
static string s_GetIdString (const list< CConstRef< CSeq_id >> &ids, int *version)
 
void s_PostErr (EDiagSev severity, EErrType errorType, const string &message, const string &desc, CRef< CValidError > &pErrors)
 
void s_PostErr (EDiagSev severity, EErrType errorType, const string &message, const string &desc, IValidError &errors)
 
static bool s_IsNa (CSeq_inst::EMol mol)
 
static void s_UpdateGlobalInfo (const CPubdesc &pub, CHugeFileValidator::TGlobalInfo &globalInfo)
 
static void s_UpdateGlobalInfo (const CSeq_id &id, CHugeFileValidator::TGlobalInfo &globalInfo)
 
static void s_UpdateGlobalInfo (const CMolInfo &molInfo, CHugeFileValidator::TGlobalInfo &globalInfo)
 
static bool s_DropErrorItem (const CHugeFileValidator::TGlobalInfo &globalInfo, const string &hugeSetId, const CValidErrItem &item)
 
string g_GetHugeSetIdString (const CHugeAsnReader &reader)
 
void g_PostprocessErrors (const CHugeFileValidator::TGlobalInfo &globalInfo, const string &hugeSetId, CRef< CValidError > &pErrors)
 
void g_PostprocessErrors (const CHugeFileValidator::TGlobalInfo &globalInfo, const string &hugeSetId, list< CRef< CValidErrItem >> &errors)
 

Typedef Documentation

◆ TBioseqInfo

Definition at line 54 of file huge_file_validator.cpp.

Function Documentation

◆ g_GetHugeSetIdString()

string g_GetHugeSetIdString ( const CHugeAsnReader reader)

◆ g_IsCuratedRefSeq()

bool g_IsCuratedRefSeq ( const TBioseqInfo info)

Definition at line 101 of file huge_file_validator.cpp.

References info, and s_CuratedRefSeq().

Referenced by CHugeFileValidator::x_ReportMissingPubs().

◆ g_PostprocessErrors() [1/2]

void g_PostprocessErrors ( const CHugeFileValidator::TGlobalInfo globalInfo,
const string hugeSetId,
CRef< CValidError > &  pErrors 
)

◆ g_PostprocessErrors() [2/2]

void g_PostprocessErrors ( const CHugeFileValidator::TGlobalInfo globalInfo,
const string hugeSetId,
list< CRef< CValidErrItem >> &  errors 
)

Definition at line 654 of file huge_file_validator.cpp.

References remove_if().

◆ s_CuratedRefSeq()

static bool s_CuratedRefSeq ( const string accession)
static

Definition at line 81 of file huge_file_validator.cpp.

References NStr::StartsWith().

Referenced by g_IsCuratedRefSeq(), and s_IsNoncuratedRefSeq().

◆ s_DropErrorItem()

static bool s_DropErrorItem ( const CHugeFileValidator::TGlobalInfo globalInfo,
const string hugeSetId,
const CValidErrItem item 
)
static

◆ s_GetBioseqAcc()

static string s_GetBioseqAcc ( const CSeq_id id,
int version 
)
static

Definition at line 184 of file huge_file_validator.cpp.

References CSeq_id::eFasta, kEmptyStr, label, and version.

Referenced by s_GetIdString().

◆ s_GetIdString()

static string s_GetIdString ( const list< CConstRef< CSeq_id >> &  ids,
int version 
)
static

Definition at line 196 of file huge_file_validator.cpp.

References eGetId_Best, GetId(), kEmptyStr, Ref(), s_GetBioseqAcc(), and version.

Referenced by g_GetHugeSetIdString().

◆ s_IsGpipe()

static bool s_IsGpipe ( const TBioseqInfo info)
static

Definition at line 70 of file huge_file_validator.cpp.

References info.

Referenced by s_x_ReportMissingPubs().

◆ s_IsMaster()

static bool s_IsMaster ( const TBioseqInfo info)
static

Definition at line 114 of file huge_file_validator.cpp.

References CSeq_inst_Base::eRepr_virtual, g_IsMasterAccession(), and info.

Referenced by s_IsWGSMaster().

◆ s_IsNa()

static bool s_IsNa ( CSeq_inst::EMol  mol)
static

◆ s_IsNoncuratedRefSeq()

static bool s_IsNoncuratedRefSeq ( const list< CConstRef< CSeq_id >> &  ids)
static

Definition at line 90 of file huge_file_validator.cpp.

References s_CuratedRefSeq().

Referenced by s_x_ReportMissingPubs().

◆ s_IsTSAContig()

static bool s_IsTSAContig ( const TBioseqInfo info,
const CHugeAsnReader reader 
)
static

◆ s_IsWGS()

static bool s_IsWGS ( const TBioseqInfo info,
const CHugeAsnReader reader 
)
static

◆ s_IsWGSMaster()

static bool s_IsWGSMaster ( const TBioseqInfo info,
const CHugeAsnReader reader 
)
static

Definition at line 139 of file huge_file_validator.cpp.

References info, s_IsMaster(), and s_IsWGS().

Referenced by s_x_ReportMissingCitSub().

◆ s_PostErr() [1/2]

void s_PostErr ( EDiagSev  severity,
EErrType  errorType,
const string message,
const string desc,
CRef< CValidError > &  pErrors 
)

◆ s_PostErr() [2/2]

void s_PostErr ( EDiagSev  severity,
EErrType  errorType,
const string message,
const string desc,
IValidError errors 
)

Definition at line 230 of file huge_file_validator.cpp.

References IValidError::AddValidErrItem(), and version.

◆ s_UpdateGlobalInfo() [1/3]

static void s_UpdateGlobalInfo ( const CMolInfo molInfo,
CHugeFileValidator::TGlobalInfo globalInfo 
)
static

◆ s_UpdateGlobalInfo() [2/3]

static void s_UpdateGlobalInfo ( const CPubdesc pub,
CHugeFileValidator::TGlobalInfo globalInfo 
)
static

◆ s_UpdateGlobalInfo() [3/3]

static void s_UpdateGlobalInfo ( const CSeq_id id,
CHugeFileValidator::TGlobalInfo globalInfo 
)
static

◆ s_x_ReportMissingCitSub()

static bool s_x_ReportMissingCitSub ( const TBioseqInfo info,
const CHugeAsnReader reader,
bool  IsRefSeq 
)
static

◆ s_x_ReportMissingPubs()

static bool s_x_ReportMissingPubs ( const TBioseqInfo info,
const CHugeAsnReader reader 
)
static

◆ USING_SCOPE()

USING_SCOPE ( edit  )
Modified on Sat May 25 14:15:56 2024 by modify_doxy.py rev. 669887