NCBI C++ ToolKit
Classes | Typedefs | Functions | Variables
reference_item.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <serial/iterator.hpp>
#include <util/static_set.hpp>
#include <objects/biblio/biblio__.hpp>
#include <objects/general/Name_std.hpp>
#include <objects/general/Person_id.hpp>
#include <objects/general/Date.hpp>
#include <objects/general/Date_std.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/medline/Medline_entry.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/pub/Pub_set.hpp>
#include <objects/seqloc/Patent_seq_id.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/biblio/Imprint.hpp>
#include <objects/submit/Submit_block.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <algorithm>
#include <objtools/format/flat_expt.hpp>
#include <objtools/format/text_ostream.hpp>
#include <objtools/format/formatter.hpp>
#include <objtools/format/items/reference_item.hpp>
#include <objtools/format/context.hpp>
#include <objmgr/util/objutil.hpp>
+ Include dependency graph for reference_item.cpp:

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Classes

class  LessThan
 
class  CIsLowercase
 

Typedefs

typedef CStaticArraySet< const char *, PCase_CStrTStaticRemarkSet
 

Functions

 USING_SCOPE (sequence)
 
static bool s_ShouldRemoveRef (const CReferenceItem &prev_ref, const CReferenceItem &curr_ref)
 
static void s_CombineRefs (CReferenceItem &prev_ref, CReferenceItem &curr_ref, CBioseqContext &ctx)
 
static void s_MergeDuplicates (CReferenceItem::TReferences &refs, CBioseqContext &ctx)
 
static bool s_IsOnlySerial (const CPub &pub)
 
static bool PiiOk (const string &str)
 
static void s_RemovePeriod (string &title)
 
static bool s_ContainsNoLowercase (const string &str)
 
 DEFINE_STATIC_ARRAY_MAP (TStaticRemarkSet, sc_Remarks, sc_RemarkText)
 
static CDate::ECompare s_CompareDates (const CDate &d1, const CDate &d2)
 

Variables

static const char *const sc_RemarkText []
 

Typedef Documentation

◆ TStaticRemarkSet

Definition at line 1367 of file reference_item.cpp.

Function Documentation

◆ DEFINE_STATIC_ARRAY_MAP()

DEFINE_STATIC_ARRAY_MAP ( TStaticRemarkSet  ,
sc_Remarks  ,
sc_RemarkText   
)

◆ PiiOk()

static bool PiiOk ( const string str)
static

Definition at line 877 of file reference_item.cpp.

References i, int, NStr::IsBlank(), islower(), isupper(), max(), and str().

Referenced by CReferenceItem::x_Init().

◆ s_CombineRefs()

static void s_CombineRefs ( CReferenceItem prev_ref,
CReferenceItem curr_ref,
CBioseqContext ctx 
)
static

◆ s_CompareDates()

static CDate::ECompare s_CompareDates ( const CDate d1,
const CDate d2 
)
static

◆ s_ContainsNoLowercase()

static bool s_ContainsNoLowercase ( const string str)
static

Definition at line 1297 of file reference_item.cpp.

References str().

Referenced by CReferenceItem::x_CapitalizeTitleIfNecessary().

◆ s_IsOnlySerial()

static bool s_IsOnlySerial ( const CPub pub)
static

Definition at line 560 of file reference_item.cpp.

References gen, CPub_Base::GetGen(), and CPub_Base::IsGen().

Referenced by CReferenceItem::x_CreateUniqueStr().

◆ s_MergeDuplicates()

static void s_MergeDuplicates ( CReferenceItem::TReferences refs,
CBioseqContext ctx 
)
static

◆ s_RemovePeriod()

static void s_RemovePeriod ( string title)
static

Definition at line 1258 of file reference_item.cpp.

References NStr::EndsWith(), and last().

Referenced by CReferenceItem::x_CleanData().

◆ s_ShouldRemoveRef()

static bool s_ShouldRemoveRef ( const CReferenceItem prev_ref,
const CReferenceItem curr_ref 
)
static

◆ USING_SCOPE()

USING_SCOPE ( sequence  )

Variable Documentation

◆ sc_RemarkText

const char* const sc_RemarkText[]
static
Initial value:
= {
"full automatic",
"full staff_entry",
"full staff_review",
"simple automatic",
"simple staff_entry",
"simple staff_review",
"unannotated automatic",
"unannotated staff_entry",
"unannotated staff_review"
}

Definition at line 1356 of file reference_item.cpp.

Modified on Tue Apr 23 07:39:37 2024 by modify_doxy.py rev. 669887