NCBI C++ ToolKit
Macros | Functions
valid_pub.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbistr.hpp>
#include <objtools/validator/validerror_desc.hpp>
#include <objtools/validator/validerror_bioseq.hpp>
#include <objects/general/Person_id.hpp>
#include <objects/general/Name_std.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/scope.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/biblio/Author.hpp>
#include <objects/biblio/Auth_list.hpp>
#include <objects/biblio/Cit_art.hpp>
#include <objects/biblio/Cit_book.hpp>
#include <objects/biblio/Cit_gen.hpp>
#include <objects/biblio/Cit_jour.hpp>
#include <objects/biblio/Cit_let.hpp>
#include <objects/biblio/Cit_proc.hpp>
#include <objects/biblio/Cit_sub.hpp>
#include <objects/biblio/PubMedId.hpp>
#include <objects/biblio/PubStatus.hpp>
#include <objects/biblio/Title.hpp>
#include <objects/biblio/Imprint.hpp>
#include <objects/biblio/Affil.hpp>
#include <objects/misc/sequence_macros.hpp>
#include <objtools/validator/validator_context.hpp>
+ Include dependency graph for valid_pub.cpp:

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Macros

#define NCBI_USE_ERRCODE_X   Objtools_Validator
 
#define HAS_VALUE(x)   (std.CanGet##x() && ! NStr::IsBlank(std.Get##x()))
 

Functions

static bool s_CitGenIsJustBackBoneIDNumber (const CCit_gen &gen)
 
bool IsElectronicJournal (const CCit_jour &journal)
 
static bool IsInpress (const CCit_jour &jour)
 
bool s_GetDigits (const string &pages, string &digits)
 
static bool s_IsRefSeqInSep (const CSeq_entry &se, CScope &scope)
 
static bool s_IsHtgInSep (const CSeq_entry &se)
 
static bool s_CuratedRefSeq (const string &accession)
 
static bool s_IsNoncuratedRefSeq (const CBioseq &seq)
 
static bool s_IsGpipe (const CBioseq &seq)
 
static bool s_CuratedRefSeqLowerToWarning (const CBioseq &seq)
 
static bool s_IsWgs_Contig (const CBioseq &seq)
 
static bool s_IsTSA_Contig (const CBioseq &seq)
 

Macro Definition Documentation

◆ HAS_VALUE

#define HAS_VALUE (   x)    (std.CanGet##x() && ! NStr::IsBlank(std.Get##x()))

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   Objtools_Validator

Definition at line 69 of file valid_pub.cpp.

Function Documentation

◆ IsElectronicJournal()

bool IsElectronicJournal ( const CCit_jour journal)

◆ IsInpress()

static bool IsInpress ( const CCit_jour jour)
static

◆ s_CitGenIsJustBackBoneIDNumber()

static bool s_CitGenIsJustBackBoneIDNumber ( const CCit_gen gen)
static

◆ s_CuratedRefSeq()

static bool s_CuratedRefSeq ( const string accession)
static

Definition at line 1150 of file valid_pub.cpp.

References NStr::StartsWith().

Referenced by CValidError_imp::IsNoncuratedRefSeq(), and s_IsNoncuratedRefSeq().

◆ s_CuratedRefSeqLowerToWarning()

static bool s_CuratedRefSeqLowerToWarning ( const CBioseq seq)
static

Definition at line 1234 of file valid_pub.cpp.

References FOR_EACH_SEQID_ON_BIOSEQ, NStr::StartsWith(), and str().

Referenced by CValidError_imp::ReportMissingPubs().

◆ s_GetDigits()

bool s_GetDigits ( const string pages,
string digits 
)

Definition at line 462 of file valid_pub.cpp.

References _ASSERT, isdigit(), and len.

◆ s_IsGpipe()

static bool s_IsGpipe ( const CBioseq seq)
static

Definition at line 1220 of file valid_pub.cpp.

References FOR_EACH_SEQID_ON_BIOSEQ.

Referenced by CValidError_imp::ReportMissingPubs().

◆ s_IsHtgInSep()

static bool s_IsHtgInSep ( const CSeq_entry se)
static

◆ s_IsNoncuratedRefSeq()

static bool s_IsNoncuratedRefSeq ( const CBioseq seq)
static

Definition at line 1158 of file valid_pub.cpp.

References FOR_EACH_SEQID_ON_BIOSEQ, and s_CuratedRefSeq().

Referenced by CValidError_imp::ReportMissingPubs().

◆ s_IsRefSeqInSep()

static bool s_IsRefSeqInSep ( const CSeq_entry se,
CScope scope 
)
static

◆ s_IsTSA_Contig()

static bool s_IsTSA_Contig ( const CBioseq seq)
static

◆ s_IsWgs_Contig()

static bool s_IsWgs_Contig ( const CBioseq seq)
static
Modified on Sat Jun 22 10:41:01 2024 by modify_doxy.py rev. 669887