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:

Go to the source code of this file.

Go to the SVN repository for this file.

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

)

Definition at line 287 of file valid_pub.cpp.

References CTitle_Base::C_E::e_Name, ePubStatus_aheadofprint, ePubStatus_epublish, ITERATE, journal(), and NStr::StartsWith().

Referenced by CValidError_imp::ValidatePubArticle(), and CValidError_imp::ValidatePubArticleNoPMID().

IsInpress()

static bool IsInpress ( const CCit_jour &  jour )

static

Definition at line 309 of file valid_pub.cpp.

References CImprint_Base::ePrepub_in_press, CCit_jour_Base::GetImp(), CImprint_Base::GetPrepub(), CCit_jour_Base::IsSetImp(), and CImprint_Base::IsSetPrepub().

Referenced by CValidError_imp::ValidatePubArticle().

s_CitGenIsJustBackBoneIDNumber()

static bool s_CitGenIsJustBackBoneIDNumber ( const CCit_gen &  gen )

static

Definition at line 213 of file valid_pub.cpp.

References gen, and NStr::StartsWith().

Referenced by CValidError_imp::ValidatePubGen(), and CValidError_imp::ValidatePubHasAuthor().

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

Definition at line 939 of file valid_pub.cpp.

References CSeqdesc_Base::e_Molinfo, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, FOR_EACH_DESCRIPTOR_ON_SEQENTRY, FOR_EACH_SEQENTRY_ON_SEQSET, CSeq_entry_Base::GetSet(), and CSeq_entry_Base::IsSet().

Referenced by CValidError_imp::IsHtg().

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

Definition at line 923 of file valid_pub.cpp.

References FOR_EACH_SEQID_ON_BIOSEQ, and CTextseq_id_Base::IsSetAccession().

Referenced by CValidError_imp::x_DowngradeForMissingAffil().

s_IsTSA_Contig()

static bool s_IsTSA_Contig ( const CBioseq &  seq )

static

Definition at line 1262 of file valid_pub.cpp.

References CMolInfo_Base::GetTech(), IF_EXISTS_CLOSEST_MOLINFO, and NCBI_TECH.

Referenced by CValidError_imp::ReportMissingPubs().

s_IsWgs_Contig()

static bool s_IsWgs_Contig ( const CBioseq &  seq )

static

Definition at line 1250 of file valid_pub.cpp.

References CSeq_inst_Base::eRepr_virtual, CBioseq_Base::GetInst(), CSeq_inst_Base::GetRepr(), CMolInfo_Base::GetTech(), IF_EXISTS_CLOSEST_MOLINFO, and NCBI_TECH.

Referenced by CValidError_imp::ReportMissingPubs().