#include <ncbi_pch.hpp>
#include <corelib/ncbiutil.hpp>
#include <corelib/ncbi_param.hpp>
#include <util/line_reader.hpp>
#include <util/static_map.hpp>
#include <util/util_misc.hpp>
#include <util/bitset/ncbi_bitset.hpp>
#include <serial/serialimpl.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/seq_id_handle.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Textseq_id.hpp>
#include <objects/seqloc/Giimport_id.hpp>
#include <objects/seqloc/Patent_seq_id.hpp>
#include <objects/seqloc/PDB_seq_id.hpp>
#include <objects/biblio/Id_pat.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Date.hpp>
#include <objects/general/Date_std.hpp>
#include <objects/misc/error_codes.hpp>
#include <corelib/ncbistre.hpp>
#include "accguide2.inc"

Include dependency graph for Seq_id.cpp:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes
struct	SAccGuide

struct	SAccGuide::SSubMap

struct	SAccGuide::SHints

Macros
#define	NCBI_USE_ERRCODE_X Objects_SeqId

Typedefs
typedef SStaticPair< const char *, CSeq_id::E_Choice >	TChoiceMapEntry

typedef CStaticPairArrayMap< CTempString, CSeq_id::E_Choice, PNocase_Generic< CTempString > >	TChoiceMap

typedef SStaticPair< const char *, CSeq_id::EAccessionInfo >	TAccInfoMapEntry

typedef CStaticPairArrayMap< CTempString, CSeq_id::EAccessionInfo, PNocase_Generic< CTempString > >	TAccInfoMap

Functions
	DEFINE_STATIC_ARRAY_MAP_WITH_COPY (CStaticArraySet< string >, kSupportedRawDbtags, sc_SupportedRawDbtags)

static void	s_SplitVersion (const CTempString &acc_in, CTempString &acc, int &ver)

void	x_Assign (CObject_id &dst, const CObject_id &src)

void	x_Assign (CGiimport_id &dst, const CGiimport_id &src)

void	x_Assign (CTextseq_id &dst, const CTextseq_id &src)

void	x_Assign (CDbtag &dst, const CDbtag &src)

void	x_Assign (CPatent_seq_id &dst, const CPatent_seq_id &src)

void	x_Assign (CDate &dst, const CDate &src)

void	x_Assign (CPDB_seq_id &dst, const CPDB_seq_id &src)

bool	CanCmpAcc (CSeq_id::E_Choice choice)

	DEFINE_STATIC_ARRAY_MAP_WITH_COPY (TChoiceMap, sc_ChoiceMap, sc_ChoiceArray)

static bool	s_HasFastaTag (const CTempString &s)

static CSeq_id::E_Choice	s_CheckForFastaTag (const CTempString &s)

	DEFINE_STATIC_ARRAY_MAP_WITH_COPY (TAccInfoMap, sc_AccInfoMap, sc_AccInfoArray)

static CRef< SAccGuide > *	s_CreateGuide (void)

static void	x_GetLabel_Type (const CSeq_id &id, string *label, CSeq_id::TLabelFlags flags)

static void	x_GetLabel_Content (const CSeq_id &id, string label, CSeq_id::TLabelFlags flags, int version)

CTextseq_id *	s_GetTextseq_id (const CSeq_id::E_Choice &choice, CSeq_id &match)

	NCBI_PARAM_DECL (bool, SeqId, PreferAccessionOverGi)

	NCBI_PARAM_DEF_EX (bool, SeqId, PreferAccessionOverGi, false, eParam_NoThread, SEQ_ID_PREFER_ACCESSION_OVER_GI)

typedef	NCBI_PARAM_TYPE (SeqId, PreferAccessionOverGi) TPreferAccessionOverGi

	NCBI_PARAM_DECL (bool, SeqId, AvoidGi)

	NCBI_PARAM_DEF_EX (bool, SeqId, AvoidGi, false, eParam_NoThread, SEQ_ID_AVOID_GI)

typedef	NCBI_PARAM_TYPE (SeqId, AvoidGi) TAvoidGi

Variables
static const char *	sc_SupportedRawDbtags []

static const TChoiceMapEntry	sc_ChoiceArray []

static const char *const	s_TextId [CSeq_id::e_MaxChoice+1]

static const TAccInfoMapEntry	sc_AccInfoArray []

static const char	kDigits [] = "0123456789"

static const unsigned int	kMaxSmallSpecialDigits = 9

static const bm::bvector ::size_type	kBVSizes [kMaxSmallSpecialDigits+1]

static const SAccGuide::TAccInfo	kUnrecognized = static_cast<SAccGuide::TAccInfo>(-1)

static CSafeStatic< CRef< SAccGuide > >	s_Guide (s_CreateGuide, NULL)

Macro Definition Documentation

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X Objects_SeqId

Definition at line 74 of file Seq_id.cpp.

Typedef Documentation

◆ TAccInfoMap

typedef CStaticPairArrayMap<CTempString, CSeq_id::EAccessionInfo, PNocase_Generic<CTempString> > TAccInfoMap

Definition at line 863 of file Seq_id.cpp.

◆ TAccInfoMapEntry

typedef SStaticPair<const char*, CSeq_id::EAccessionInfo> TAccInfoMapEntry

Definition at line 645 of file Seq_id.cpp.

◆ TChoiceMap

typedef CStaticPairArrayMap<CTempString, CSeq_id::E_Choice, PNocase_Generic<CTempString> > TChoiceMap

Definition at line 568 of file Seq_id.cpp.

◆ TChoiceMapEntry

typedef SStaticPair<const char*, CSeq_id::E_Choice> TChoiceMapEntry

Definition at line 524 of file Seq_id.cpp.

Function Documentation

◆ CanCmpAcc()

bool CanCmpAcc ( CSeq_id::E_Choice choice )

inline

Definition at line 392 of file Seq_id.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, and CSeq_id_Base::e_Tpg.

Referenced by CSeq_id::Compare().

◆ DEFINE_STATIC_ARRAY_MAP_WITH_COPY() [1/3]

DEFINE_STATIC_ARRAY_MAP_WITH_COPY	(	CStaticArraySet< string >	,
		kSupportedRawDbtags	,
		sc_SupportedRawDbtags
	)

◆ DEFINE_STATIC_ARRAY_MAP_WITH_COPY() [2/3]

DEFINE_STATIC_ARRAY_MAP_WITH_COPY	(	TAccInfoMap	,
		sc_AccInfoMap	,
		sc_AccInfoArray
	)

◆ DEFINE_STATIC_ARRAY_MAP_WITH_COPY() [3/3]

DEFINE_STATIC_ARRAY_MAP_WITH_COPY	(	TChoiceMap	,
		sc_ChoiceMap	,
		sc_ChoiceArray
	)

◆ NCBI_PARAM_DECL() [1/2]

NCBI_PARAM_DECL	(	bool	,
		SeqId	,
		AvoidGi
	)

◆ NCBI_PARAM_DECL() [2/2]

NCBI_PARAM_DECL	(	bool	,
		SeqId	,
		PreferAccessionOverGi
	)

◆ NCBI_PARAM_DEF_EX() [1/2]

NCBI_PARAM_DEF_EX	(	bool	,
		SeqId	,
		AvoidGi	,
		false	,
		eParam_NoThread	,
		SEQ_ID_AVOID_GI
	)

◆ NCBI_PARAM_DEF_EX() [2/2]

NCBI_PARAM_DEF_EX	(	bool	,
		SeqId	,
		PreferAccessionOverGi	,
		false	,
		eParam_NoThread	,
		SEQ_ID_PREFER_ACCESSION_OVER_GI
	)

◆ NCBI_PARAM_TYPE() [1/2]

typedef NCBI_PARAM_TYPE	(	SeqId	,
		AvoidGi
	)

◆ NCBI_PARAM_TYPE() [2/2]

typedef NCBI_PARAM_TYPE	(	SeqId	,
		PreferAccessionOverGi
	)

◆ s_CheckForFastaTag()

static CSeq_id::E_Choice s_CheckForFastaTag ( const CTempString & s )

static

Definition at line 632 of file Seq_id.cpp.

References CSeq_id_Base::e_not_set, CTempString::size(), CTempString::substr(), and CSeq_id::WhichInverseSeqId().

Referenced by CSeq_id::Set().

◆ s_CreateGuide()

static CRef<SAccGuide>* s_CreateGuide ( void )

static

Definition at line 1627 of file Seq_id.cpp.

◆ s_GetTextseq_id()

CTextseq_id* s_GetTextseq_id	(	const CSeq_id::E_Choice &	choice,
		CSeq_id &	match
	)

Definition at line 3230 of file Seq_id.cpp.

References CSeq_id_Base::e_Ddbj, CSeq_id_Base::e_Embl, CSeq_id_Base::e_Genbank, CSeq_id_Base::e_Gpipe, CSeq_id_Base::e_Named_annot_track, CSeq_id_Base::e_Other, CSeq_id_Base::e_Pir, CSeq_id_Base::e_Prf, CSeq_id_Base::e_Swissprot, CSeq_id_Base::e_Tpd, CSeq_id_Base::e_Tpe, CSeq_id_Base::e_Tpg, and match().

Referenced by CSeq_id::GetMatchingTextseqIds().

◆ s_HasFastaTag()

static bool s_HasFastaTag ( const CTempString & s )

inlinestatic

Definition at line 618 of file Seq_id.cpp.

References CTempString::size().

Referenced by CSeq_id::ParseIDs().

◆ s_SplitVersion()

static void s_SplitVersion	(	const CTempString &	acc_in,
		CTempString &	acc,
		int &	ver
	)

static

Definition at line 151 of file Seq_id.cpp.

References CTempString::empty(), NCBI_THROW, NStr::SplitInTwo(), and NStr::StringToNonNegativeInt().

Referenced by CSeq_id::Set().

◆ x_Assign() [1/7]

void x_Assign	(	CDate &	dst,
		const CDate &	src
	)

inline

Definition at line 287 of file Seq_id.cpp.

References CSerialObject::Assign().

◆ x_Assign() [2/7]

void x_Assign	(	CDbtag &	dst,
		const CDbtag &	src
	)

inline

Definition at line 271 of file Seq_id.cpp.

References CDbtag_Base::GetDb(), CDbtag_Base::GetTag(), CDbtag_Base::SetDb(), CDbtag_Base::SetTag(), and x_Assign().

◆ x_Assign() [3/7]

void x_Assign	(	CGiimport_id &	dst,
		const CGiimport_id &	src
	)

inline

Definition at line 222 of file Seq_id.cpp.

References CGiimport_id_Base::GetDb(), CGiimport_id_Base::GetId(), CGiimport_id_Base::GetRelease(), CGiimport_id_Base::IsSetDb(), CGiimport_id_Base::IsSetRelease(), CGiimport_id_Base::ResetDb(), CGiimport_id_Base::ResetRelease(), CGiimport_id_Base::SetDb(), CGiimport_id_Base::SetId(), and CGiimport_id_Base::SetRelease().

◆ x_Assign() [4/7]

void x_Assign	(	CObject_id &	dst,
		const CObject_id &	src
	)

inline

Examples: /home/coremake/doxygen/cxx/include/corelib/ncbistr.hpp.

Definition at line 203 of file Seq_id.cpp.

References CObject_id_Base::e_Id, CObject_id_Base::e_not_set, CObject_id_Base::e_Str, CObject_id_Base::GetId(), CObject_id_Base::GetStr(), NCBI_THROW, CObject_id_Base::Reset(), CObject_id_Base::SetId(), CObject_id_Base::SetStr(), and CObject_id_Base::Which().

Referenced by CSeq_id::Assign(), CBamException::CBamException(), CErrnoTemplExceptionEx< CBDB_Exception, CBDB_StrErrAdapt::GetErrCode, CBDB_StrErrAdapt::GetErrCodeString >::CErrnoTemplExceptionEx(), CParseTemplException< CSeqsetException >::CParseTemplException(), CSraException::CSraException(), and x_Assign().

◆ x_Assign() [5/7]

void x_Assign	(	CPatent_seq_id &	dst,
		const CPatent_seq_id &	src
	)

inline

Definition at line 279 of file Seq_id.cpp.

References CPatent_seq_id_Base::GetCit(), CPatent_seq_id_Base::GetSeqid(), CPatent_seq_id_Base::SetCit(), and CPatent_seq_id_Base::SetSeqid().

◆ x_Assign() [6/7]

void x_Assign	(	CPDB_seq_id &	dst,
		const CPDB_seq_id &	src
	)

inline

Definition at line 294 of file Seq_id.cpp.

References CPDB_seq_id_Base::GetChain(), CPDB_seq_id_Base::GetChain_id(), CPDB_seq_id_Base::GetMol(), CPDB_seq_id_Base::GetRel(), CPDB_seq_id_Base::IsSetChain(), CPDB_seq_id_Base::IsSetChain_id(), CPDB_seq_id_Base::IsSetRel(), CPDB_seq_id_Base::ResetChain(), CPDB_seq_id_Base::ResetChain_id(), CPDB_seq_id_Base::ResetRel(), CPDB_seq_id_Base::SetChain(), CPDB_seq_id_Base::SetChain_id(), CPDB_seq_id_Base::SetMol(), and CPDB_seq_id_Base::SetRel().

◆ x_Assign() [7/7]

void x_Assign	(	CTextseq_id &	dst,
		const CTextseq_id &	src
	)

inline

Definition at line 241 of file Seq_id.cpp.

◆ x_GetLabel_Content()

static void x_GetLabel_Content	(	const CSeq_id &	id,
		string *	label,
		CSeq_id::TLabelFlags	flags,
		int *	version
	)

inlinestatic

Definition at line 1926 of file Seq_id.cpp.

References CSeq_id_Base::e_General, CSeq_id_Base::e_Gi, CSeq_id_Base::e_Gibbmt, CSeq_id_Base::e_Gibbsq, CSeq_id_Base::e_Giim, CSeq_id_Base::e_Local, CSeq_id_Base::e_not_set, CSeq_id_Base::e_Patent, CSeq_id_Base::e_Pdb, CSeq_id::fLabel_GeneralDbIsContent, CSeq_id::fLabel_Version, flags, CAliasBase< TPrim >::Get(), CTextseq_id_Base::GetAccession(), CId_pat_Base::C_Id::GetApp_number(), CPDB_seq_id_Base::GetChain(), CPDB_seq_id_Base::GetChain_id(), CId_pat_Base::GetCountry(), CDbtag_Base::GetDb(), GetId(), CId_pat_Base::GetId(), CObject_id_Base::GetId(), CPDB_seq_id_Base::GetMol(), CTextseq_id_Base::GetName(), CId_pat_Base::C_Id::GetNumber(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), CTextseq_id_Base::GetVersion(), NStr::IntToString(), CObject_id_Base::IsId(), CId_pat_Base::C_Id::IsNumber(), CTextseq_id_Base::IsSetAccession(), CPDB_seq_id_Base::IsSetChain(), CPDB_seq_id_Base::IsSetChain_id(), CTextseq_id_Base::IsSetName(), CTextseq_id_Base::IsSetVersion(), CObject_id_Base::IsStr(), label, NULL, NStr::NumericToString(), str(), NStr::ToUpper(), and version.

Referenced by CSeq_id::GetLabel().

◆ x_GetLabel_Type()

static void x_GetLabel_Type	(	const CSeq_id &	id,
		string *	label,
		CSeq_id::TLabelFlags	flags
	)

inlinestatic

Definition at line 1893 of file Seq_id.cpp.

References _ASSERT, CSeq_id_Base::e_General, CSeq_id_Base::e_MaxChoice, CSeq_id_Base::e_Patent, CSeq_id::fLabel_GeneralDbIsContent, flags, label, and s_TextId.

Referenced by CSeq_id::GetLabel().

Variable Documentation

◆ kBVSizes

const bm::bvector ::size_type kBVSizes[kMaxSmallSpecialDigits+1]

static

Initial value:

Definition at line 873 of file Seq_id.cpp.

Referenced by SAccGuide::x_AddSpecial(), and SAccGuide::x_SplitSpecial().

◆ kDigits

const char kDigits[] = "0123456789"

static

Definition at line 866 of file Seq_id.cpp.

Referenced by SAccGuide::AddRule(), CSeq_id::IdentifyAccession(), and CSeq_id::x_IdentifyAccession().

◆ kMaxSmallSpecialDigits

const unsigned int kMaxSmallSpecialDigits = 9

static

Definition at line 872 of file Seq_id.cpp.

Referenced by SAccGuide::x_AddSpecial(), and SAccGuide::x_SplitSpecial().

◆ kUnrecognized

const SAccGuide::TAccInfo kUnrecognized = static_cast<SAccGuide::TAccInfo>(-1)

static

Definition at line 971 of file Seq_id.cpp.

Referenced by SAccGuide::AddRule(), and SAccGuide::SHints::FindAccInfo().

◆ s_Guide

CSafeStatic<CRef<SAccGuide> > s_Guide(s_CreateGuide, NULL)	(	s_CreateGuide	,
		NULL
	)

static

Referenced by CSeq_id::LoadAccessionGuide(), and CSeq_id::x_IdentifyAccession().

◆ s_TextId

const char* const s_TextId[CSeq_id::e_MaxChoice+1]

static

Initial value:

=
{   
    "???" , 
    "lcl",  
    "bbs",  
    "bbm",  
    "gim",  
    "gb",   
    "emb",  
    "pir",  
    "sp",   
    "pat",  
            
    "ref",  
    "gnl",  
    "gi",   
    "dbj",  
    "prf",  
    "pdb",  
    "tpg",  
    "tpe",  
    "tpd",  
    "gpp",  
    "nat",  
    ""  
}

Definition at line 572 of file Seq_id.cpp.

Referenced by CSeq_id::WhichFastaTag(), CSeq_id::WriteAsFasta(), x_GetLabel_Type(), and CSeq_id::x_Init().

◆ sc_AccInfoArray

const TAccInfoMapEntry sc_AccInfoArray[]

static

Definition at line 647 of file Seq_id.cpp.

◆ sc_ChoiceArray

const TChoiceMapEntry sc_ChoiceArray[]

static

Definition at line 526 of file Seq_id.cpp.

◆ sc_SupportedRawDbtags

const char* sc_SupportedRawDbtags[]

static

Initial value:

= {
    "ATGC",
    "BCMHGSC",
    "BERKELEY",
    "CELERA",
    "GSDB",
    "HOOD",
    "LANLCHGS",
    "LRG",
    "MIPS",
    "NCBI_EXT_ACC",
    "NCBI_GENOMES",
    "NCBI_MITO",
    "PGEC",
    "PID",
    "SGD",
    "SHGC",
    "SRA",
    "TIGR",
    "UOKNOR",
    "UWGC",
    "WASHU",
    "WIBR",
    "WUGSC",
    "dbGSS",
    "dbSTS"
}

Definition at line 96 of file Seq_id.cpp.

Classes

Macros

Typedefs

Functions

Variables

Macro Definition Documentation

◆ NCBI_USE_ERRCODE_X

Typedef Documentation

◆ TAccInfoMap

◆ TAccInfoMapEntry

◆ TChoiceMap

◆ TChoiceMapEntry

Function Documentation

◆ CanCmpAcc()

◆ DEFINE_STATIC_ARRAY_MAP_WITH_COPY() [1/3]

◆ DEFINE_STATIC_ARRAY_MAP_WITH_COPY() [2/3]

◆ DEFINE_STATIC_ARRAY_MAP_WITH_COPY() [3/3]

◆ NCBI_PARAM_DECL() [1/2]

◆ NCBI_PARAM_DECL() [2/2]

◆ NCBI_PARAM_DEF_EX() [1/2]

◆ NCBI_PARAM_DEF_EX() [2/2]

◆ NCBI_PARAM_TYPE() [1/2]

◆ NCBI_PARAM_TYPE() [2/2]

◆ s_CheckForFastaTag()

◆ s_CreateGuide()

◆ s_GetTextseq_id()

◆ s_HasFastaTag()

◆ s_SplitVersion()

◆ x_Assign() [1/7]

◆ x_Assign() [2/7]

◆ x_Assign() [3/7]

◆ x_Assign() [4/7]

◆ x_Assign() [5/7]

◆ x_Assign() [6/7]

◆ x_Assign() [7/7]

◆ x_GetLabel_Content()

◆ x_GetLabel_Type()

Variable Documentation

◆ kBVSizes

◆ kDigits

◆ kMaxSmallSpecialDigits

◆ kUnrecognized

◆ s_Guide

◆ s_TextId

◆ sc_AccInfoArray

◆ sc_ChoiceArray

◆ sc_SupportedRawDbtags