Org_ref.cpp File Reference

#include <ncbi_pch.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Dbtag.hpp>
#include "common_tax.inc"

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Macros
#define	MAKE_COMMON(o1, o2, o3, Field)   if (o1.IsSet##Field() && o2.IsSet##Field() && NStr::Equal(o1.Get##Field(), o2.Get##Field())) o3.Set##Field(o1.Get##Field());
#define	NO_FLAG(a, f)   (( a & f ) == 0)

Typedefs
typedef map< string, CRef< COrg_ref >, PNocase >	TOrgrefMap

Functions
bool	s_FindWholeWord (string taxname, string value)
void	s_MakeCommonStringList (const list< string > &list1, const list< string > &list2, list< string > &list3)
	DEFINE_STATIC_FAST_MUTEX (s_OrgRefMapMutex)
static void	s_ProcessOrgRefMapLine (const CTempString &line)
static void	s_InitializeOrgRefMap (void)

Variables
static const char *const	s_taxonName = "taxon"
static const string	s_nomenclature = "nomenclature="
static TOrgrefMap	s_OrgRefMap
static vector< string >	s_CommonTaxnameList
static bool	s_OrgRefMapInitialized = false

Macro Definition Documentation

MAKE_COMMON

#define MAKE_COMMON	(		o1,
			o2,
			o3,
			Field
	)		if (o1.IsSet##Field() && o2.IsSet##Field() && NStr::Equal(o1.Get##Field(), o2.Get##Field())) o3.Set##Field(o1.Get##Field());

Definition at line 261 of file Org_ref.cpp.

NO_FLAG

#define NO_FLAG	(		a,
			f
	)		(( a & f ) == 0)

Definition at line 515 of file Org_ref.cpp.

Typedef Documentation

TOrgrefMap

typedef map<string, CRef<COrg_ref>, PNocase> TOrgrefMap

Definition at line 342 of file Org_ref.cpp.

Function Documentation

DEFINE_STATIC_FAST_MUTEX()

DEFINE_STATIC_FAST_MUTEX

(

s_OrgRefMapMutex

)

s_FindWholeWord()

bool s_FindWholeWord	(	string	taxname,
		string	value
	)

Definition at line 200 of file Org_ref.cpp.

References NStr::Find(), isalpha(), NStr::IsBlank(), and rapidjson::value.

Referenced by COrg_ref::IsSubspeciesValid(), and COrg_ref::IsVarietyValid().

s_InitializeOrgRefMap()

static void s_InitializeOrgRefMap ( void  )

static

Definition at line 415 of file Org_ref.cpp.

References ILineReader::AtEOF(), CRef< C, Locker >::Empty(), file, g_FindDataFile(), i, LOG_POST, NCBI_CATCH, ILineReader::New(), s_OrgRefMapInitialized, and s_ProcessOrgRefMapLine().

Referenced by COrg_ref::GetTaxnameList(), and COrg_ref::TableLookup().

s_MakeCommonStringList()

void s_MakeCommonStringList	(	const list< string > &	list1,
		const list< string > &	list2,
		list< string > &	list3
	)

Definition at line 263 of file Org_ref.cpp.

References NStr::Equal(), and ITERATE.

Referenced by COrg_ref::MakeCommon().

s_ProcessOrgRefMapLine()

static void s_ProcessOrgRefMapLine ( const CTempString &  line )

static

Definition at line 351 of file Org_ref.cpp.

References NStr::Equal(), NStr::IsBlank(), kEmptyStr, NON_CONST_ITERATE, s_CommonTaxnameList, s_OrgRefMap, COrg_ref_Base::SetCommon(), CDbtag_Base::SetDb(), COrg_ref_Base::SetDb(), COrg_ref_Base::SetOrgname(), CDbtag_Base::SetTag(), COrg_ref_Base::SetTaxname(), NStr::Split(), NStr::StringToNonNegativeInt(), t, and NStr::TruncateSpacesInPlace().

Referenced by s_InitializeOrgRefMap().

Variable Documentation

s_CommonTaxnameList

vector<string> s_CommonTaxnameList

static

Definition at line 344 of file Org_ref.cpp.

Referenced by COrg_ref::GetTaxnameList(), and s_ProcessOrgRefMapLine().

s_nomenclature

const string s_nomenclature = "nomenclature="

static

Definition at line 69 of file Org_ref.cpp.

s_OrgRefMap

TOrgrefMap s_OrgRefMap

static

Definition at line 343 of file Org_ref.cpp.

Referenced by s_ProcessOrgRefMapLine(), and COrg_ref::TableLookup().

s_OrgRefMapInitialized

bool s_OrgRefMapInitialized = false

static

Definition at line 345 of file Org_ref.cpp.

Referenced by s_InitializeOrgRefMap().

s_taxonName

const char* const s_taxonName = "taxon"

static

Definition at line 68 of file Org_ref.cpp.

Referenced by COrg_ref::FilterOutParts(), COrg_ref::GetTaxId(), and COrg_ref::SetTaxId().