#include <sra/readers/sra/wgsread.hpp>

Inheritance diagram for CWGSDb_Impl:

Collaboration diagram for CWGSDb_Impl:

Classes
struct	SAmbiguityInfo

struct	SFeatTableCursor

struct	SGiIdxTableCursor

struct	SProt0TableCursor

struct	SProtAccInfo

struct	SProtIdxTableCursor

struct	SProtTableCursor

struct	SScfTableCursor

struct	SSeq0TableCursor

struct	SSeq4naTableCursor

struct	SSeqTableCursor

Public Types
enum	ERowType { eRowType_contig = 0 , eRowType_scaffold = 'S' , eRowType_protein = 'P' }

enum	EAllowRowType { fAllowRowType_contig = 1<<0 , fAllowRowType_scaffold = 1<<1 , fAllowRowType_protein = 1<<2 }

enum	EGnlIdFlags { fGnlId_NoWGSVersion = 1<<0 , fGnlId_NoWGSId = 1<<1 , fGnlId_Default = 0 }

typedef char	TRowType

typedef list< CRef< CSeqdesc > >	TMasterDescr

typedef CSimpleBufferT< char >	TMasterDescrBytes

typedef COpenRange< TIntId >	TGiRange

typedef vector< TGiRange >	TGiRanges

typedef COpenRange< Uint4 >	TIdRange

typedef map< SProtAccInfo, TIdRange >	TProtAccRanges

Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Types inherited from SWGSDb_Defs
enum	EFlags { fIds_gi = 1<<0 , fIds_acc = 1<<1 , fIds_gnl = 1<<2 , fMaskIds = fIds_gi\|fIds_acc\|fIds_gnl , fDefaultIds = fIds_gi\|fIds_acc\|fIds_gnl , fInst_ncbi4na = 0<<3 , fInst_delta = 1<<3 , fMaskInst = fInst_ncbi4na\|fInst_delta , fDefaultInst = fInst_delta , fSeqDescr = 1<<4 , fNucProtDescr = 1<<12 , fMasterDescr = 1<<5 , fMasterDescrMark = 1<<13 , fSeqDescrObj = 1<<14 , fMaskDescr = fSeqDescr\|fNucProtDescr\|fMasterDescr , fDefaultDescr = fSeqDescr\|fNucProtDescr\|fMasterDescr , fSeqAnnot = 1<<6 , fQualityGraph = 1<<7 , fMaskAnnot = fSeqAnnot\|fQualityGraph , fDefaultAnnot = fSeqAnnot\|fQualityGraph , fSplitQualityGraph = 1<<8 , fSplitSeqData = 1<<9 , fSplitProducts = 1<<10 , fSplitFeatures = 1<<11 , fSplitAll = fSplitQualityGraph \| fSplitSeqData \| fSplitProducts \| fSplitFeatures , fSplitMask = fSplitQualityGraph \| fSplitSeqData \| fSplitProducts \| fSplitFeatures , fDefaultSplit = fSplitAll , fDefaultFlags = fDefaultIds\|fDefaultDescr\|fDefaultAnnot\|fDefaultInst\|fDefaultSplit }

enum	EFeatLocIdType : Int1 { eFeatLocIdUninitialized = -1 , eFeatLocIdGi = 0 , eFeatLocIdAccVer , eFeatLocIdAccNoVer }

enum	EGBStateType { eGBStateZero = 0 , eGBStateRaw = 1 , eGBStateProject = 2 , eGBStateAll = 3 }

typedef int	TSplitVersion

typedef int	TChunkId

Public Member Functions
	CWGSDb_Impl (CVDBMgr &mgr, CTempString path_or_acc, CTempString vol_path=CTempString())

virtual	~CWGSDb_Impl (void)

const string &	GetIdPrefix (void) const

const string &	GetIdPrefixWithVersion (void) const

const string &	GetWGSPath (void) const

	DECLARE_SAFE_FLAGS_TYPE (EAllowRowType, TAllowRowType)

TVDBRowId	ParseRow (CTempString acc, bool *is_scaffold) const

Uint4	GetIdRowDigits (void) const

bool	IsTSA (void) const

	DECLARE_SAFE_FLAGS_TYPE (EGnlIdFlags, TGnlIdFlags)

CRef< CSeq_id >	GetGeneralSeq_id (CTempString prefix, CTempString tag) const

CRef< CSeq_id >	GetGeneralSeq_id (CTempString tag, TGnlIdFlags gnl_id_flags=fGnlId_Default) const

CRef< CSeq_id >	GetPatentSeq_id (int id) const

CRef< CSeq_id >	GetGeneralOrPatentSeq_id (CTempString str, TVDBRowId row, TGnlIdFlags gnl_id_flags=fGnlId_Default) const

CRef< CSeq_id >	GetAccSeq_id (CTempString acc, int version) const

CRef< CSeq_id >	GetAccSeq_id (ERowType type, TVDBRowId row_id, int version) const

CRef< CSeq_id >	GetMasterSeq_id (void) const

TGi	GetMasterGi (void) const

CRef< CSeq_id >	GetContigSeq_id (TVDBRowId row_id) const

CRef< CSeq_id >	GetScaffoldSeq_id (TVDBRowId row_id) const

CRef< CSeq_id >	GetProteinSeq_id (TVDBRowId row_id) const

CSeq_inst::TMol	GetContigMolType (void) const

CSeq_inst::TMol	GetScaffoldMolType (void) const

CSeq_inst::TMol	GetProteinMolType (void) const

CRef< CSeq_entry >	GetMasterSeq_entry (void) const

bool	IsSetMasterDescr (void) const

const TMasterDescr &	GetMasterDescr (void) const

size_t	GetMasterDescrBytes (TMasterDescrBytes &buffer)

CRef< CSeq_entry >	GetMasterDescrEntry (void)

void	AddMasterDescr (CSeq_descr &descr, const CBioseq *main_seq=0, TFlags flags=fDefaultFlags) const

void	ResetMasterDescr (void)

void	SetMasterDescr (const TMasterDescr &descr, int filter)

bool	LoadMasterDescr (int filter)

void	SetPatentId (CRef< CSeq_id > id)

bool	HasPatentId () const

const CRef< CSeq_id > &	GetPatentId (void) const

pair< TGi, TGi >	GetNucGiRange (void)

pair< TGi, TGi >	GetProtGiRange (void)

pair< TVDBRowId, bool >	GetGiRowId (TGi gi)

TVDBRowId	GetNucGiRowId (TGi gi)

TVDBRowId	GetProtGiRowId (TGi gi)

TVDBRowId	GetContigNameRowId (const string &name)

TVDBRowId	GetScaffoldNameRowId (const string &name)

TVDBRowId	GetProteinNameRowId (const string &name)

TVDBRowId	GetProductNameRowId (const string &name)

TVDBRowId	GetProtAccRowId (const string &acc, int version=-1)

TGiRanges	GetNucGiRanges (void)

TGiRanges	GetProtGiRanges (void)

TProtAccRanges	GetProtAccRanges (void)

EFeatLocIdType	GetFeatLocIdType ()

EFeatLocIdType	DetermineFeatLocIdType ()

bool	HasStandardFeatLocIdType ()

NCBI_gb_state	GetProjectGBState () const

const string &	GetReplacedBy () const

bool	IsReplaced () const

bool	HasCommonTaxId (void) const

TTaxId	GetCommonTaxId (void) const

bool	CanHaveGis ()

TVDBRowCount	GetTotalFeatureCount ()

bool	HasFeatures ()

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Public Member Functions inherited from SWGSDb_Defs
	DECLARE_SAFE_FLAGS_TYPE (EFlags, TFlags)

Static Public Member Functions
static string	NormalizePathOrAccession (CTempString path_or_acc, CTempString vol_path=CTempString())

static pair< TVDBRowId, ERowType >	ParseRowType (CTempString acc, TAllowRowType allow)

static TVDBRowId	ParseContigRow (CTempString acc)

static TVDBRowId	ParseScaffoldRow (CTempString acc)

static TVDBRowId	ParseProteinRow (CTempString acc)

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Protected Member Functions
const CVDBTable &	SeqTable (void)

const CVDBTable &	ScfTable (void)

const CVDBTable &	ProtTable (void)

const CVDBTable &	FeatTable (void)

const CVDBTable &	GiIdxTable (void)

const CVDBTable &	ProtIdxTable (void)

const CVDBTableIndex &	ProtAccIndex (void)

const CVDBTableIndex &	ContigNameIndex (void)

const CVDBTableIndex &	ScaffoldNameIndex (void)

const CVDBTableIndex &	ProteinNameIndex (void)

const CVDBTableIndex &	ProductNameIndex (void)

CRef< SSeq0TableCursor >	Seq0 (TVDBRowId row=0)

CRef< SSeqTableCursor >	Seq (TVDBRowId row=0)

CRef< SSeq4naTableCursor >	Seq4na (TVDBRowId row=0)

CRef< SScfTableCursor >	Scf (TVDBRowId row=0)

CRef< SProt0TableCursor >	Prot0 (TVDBRowId row=0)

CRef< SProtTableCursor >	Prot (TVDBRowId row=0)

CRef< SFeatTableCursor >	Feat (TVDBRowId row=0)

CRef< SGiIdxTableCursor >	GiIdx (TVDBRowId row=0)

CRef< SProtIdxTableCursor >	ProtIdx (TVDBRowId row=0)

void	Put (CRef< SSeq0TableCursor > &curs, TVDBRowId row=0)

void	Put (CRef< SSeqTableCursor > &curs, TVDBRowId row=0)

void	Put (CRef< SSeq4naTableCursor > &curs, TVDBRowId row=0)

void	Put (CRef< SScfTableCursor > &curs, TVDBRowId row=0)

void	Put (CRef< SProt0TableCursor > &curs, TVDBRowId row=0)

void	Put (CRef< SProtTableCursor > &curs, TVDBRowId row=0)

void	Put (CRef< SFeatTableCursor > &curs, TVDBRowId row=0)

void	Put (CRef< SGiIdxTableCursor > &curs, TVDBRowId row=0)

void	Put (CRef< SProtIdxTableCursor > &curs, TVDBRowId row=0)

CRef< SAmbiguityInfo >	GetAmbiguityInfo (TVDBRowId row)

void	PutAmbiguityInfo (CRef< SAmbiguityInfo > &ambiguity)

CRef< CSeq_id >	GetGeneralOrPatentSeq_id (CTempString str, const SSeq0TableCursor &cur, TVDBRowId row) const

CRef< CSeq_id >	GetGeneralOrPatentSeq_id (CTempString str, const SScfTableCursor &cur, TVDBRowId row) const

CRef< CSeq_id >	GetGeneralOrPatentSeq_id (CTempString str, const SProt0TableCursor &cur, TVDBRowId row) const

void	OpenTable (CVDBTable &table, atomic< bool > &table_is_opened, const char *table_name)

void	OpenIndex (const CVDBTable &table, CVDBTableIndex &index, atomic< Int1 > &index_is_opened, const char index_name, const char backup_index_name=0)

void	OpenScfTable (void)

void	OpenProtTable (void)

void	OpenFeatTable (void)

void	OpenGiIdxTable (void)

void	OpenProtIdxTable (void)

void	OpenProtAccIndex (void)

void	OpenContigNameIndex (void)

void	OpenScaffoldNameIndex (void)

void	OpenProteinNameIndex (void)

void	OpenProductNameIndex (void)

TVDBRowId	Lookup (const string &name, const CVDBTableIndex &index, bool upcase)

void	x_InitIdParams (void)

void	x_LoadMasterDescr (int filter)

void	x_SortGiRanges (TGiRanges &ranges)

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Private Types
typedef limited_resource_map< TVDBRowId, CRef< SAmbiguityInfo >, size_t >	TAmbiguityCache

Private Attributes
CVDBMgr	m_Mgr

string	m_WGSPath

CVDB	m_Db

CVDBTable	m_SeqTable

string	m_IdPrefixWithVersion

string	m_IdPrefix

string	m_IdPrefixDbWithVersion

string	m_IdPrefixDb

int	m_IdVersion

Uint4	m_IdRowDigits

CFastMutex	m_TableMutex

atomic< bool >	m_ScfTableIsOpened

atomic< bool >	m_ProtTableIsOpened

atomic< bool >	m_FeatTableIsOpened

atomic< bool >	m_GiIdxTableIsOpened

atomic< bool >	m_ProtIdxTableIsOpened

atomic< Int1 >	m_ProtAccIndexIsOpened

atomic< Int1 >	m_ContigNameIndexIsOpened

atomic< Int1 >	m_ScaffoldNameIndexIsOpened

atomic< Int1 >	m_ProteinNameIndexIsOpened

atomic< Int1 >	m_ProductNameIndexIsOpened

CVDBTable	m_ScfTable

CVDBTable	m_ProtTable

CVDBTable	m_FeatTable

CVDBTable	m_GiIdxTable

CVDBTable	m_ProtIdxTable

CVDBObjectCache< SSeq0TableCursor >	m_Seq0

CVDBObjectCache< SSeqTableCursor >	m_Seq

CVDBObjectCache< SScfTableCursor >	m_Scf

CVDBObjectCache< SProt0TableCursor >	m_Prot0

CVDBObjectCache< SProtTableCursor >	m_Prot

CVDBObjectCache< SFeatTableCursor >	m_Feat

CVDBObjectCache< SGiIdxTableCursor >	m_GiIdx

CVDBObjectCache< SProtIdxTableCursor >	m_ProtIdx

CVDBTableIndex	m_ProtAccIndex

CVDBTableIndex	m_ContigNameIndex

CVDBTableIndex	m_ScaffoldNameIndex

CVDBTableIndex	m_ProteinNameIndex

CVDBTableIndex	m_ProductNameIndex

CFastMutex	m_AmbiguityCacheMutex

TAmbiguityCache	m_AmbiguityCache

CSeq_inst::TMol	m_ContigMolType

bool	m_IsSetMasterDescr

bool	m_HasNoDefaultGnlId

bool	m_HasCommonTaxId

atomic< EFeatLocIdType >	m_FeatLocIdType

CRef< CSeq_entry >	m_MasterEntry

TMasterDescr	m_MasterDescr

CRef< CSeq_id >	m_PatentId

NCBI_gb_state	m_ProjectGBState

CSeq_id::E_Choice	m_SeqIdType

string	m_ReplacedBy

TTaxId	m_CommonTaxId

Friends
class	CWGSSeqIterator

class	CWGSScaffoldIterator

class	CWGSGiIterator

class	CWGSProteinIterator

class	CWGSFeatureIterator

Additional Inherited Members
Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Static Public Attributes inherited from SWGSDb_Defs
static const TSplitVersion	kDefaultSplitVersion = 0

Detailed Description

Definition at line 201 of file wgsread.hpp.

Member Typedef Documentation

◆ TAmbiguityCache

typedef limited_resource_map<TVDBRowId, CRef<SAmbiguityInfo>, size_t> CWGSDb_Impl::TAmbiguityCache

private

Definition at line 632 of file wgsread.hpp.

◆ TGiRange

typedef COpenRange<TIntId> CWGSDb_Impl::TGiRange

Definition at line 360 of file wgsread.hpp.

◆ TGiRanges

typedef vector<TGiRange> CWGSDb_Impl::TGiRanges

Definition at line 361 of file wgsread.hpp.

◆ TIdRange

typedef COpenRange<Uint4> CWGSDb_Impl::TIdRange

Definition at line 398 of file wgsread.hpp.

◆ TMasterDescr

typedef list< CRef<CSeqdesc> > CWGSDb_Impl::TMasterDescr

Definition at line 305 of file wgsread.hpp.

◆ TMasterDescrBytes

typedef CSimpleBufferT<char> CWGSDb_Impl::TMasterDescrBytes

Definition at line 314 of file wgsread.hpp.

◆ TProtAccRanges

typedef map<SProtAccInfo, TIdRange> CWGSDb_Impl::TProtAccRanges

Definition at line 399 of file wgsread.hpp.

◆ TRowType

typedef char CWGSDb_Impl::TRowType

Definition at line 231 of file wgsread.hpp.

Member Enumeration Documentation

◆ EAllowRowType

enum CWGSDb_Impl::EAllowRowType

Enumerator
fAllowRowType_contig
fAllowRowType_scaffold
fAllowRowType_protein

Definition at line 232 of file wgsread.hpp.

◆ EGnlIdFlags

enum CWGSDb_Impl::EGnlIdFlags

Enumerator
fGnlId_NoWGSVersion
fGnlId_NoWGSId
fGnlId_Default

Definition at line 273 of file wgsread.hpp.

◆ ERowType

enum CWGSDb_Impl::ERowType

Enumerator
eRowType_contig
eRowType_scaffold
eRowType_protein

Definition at line 226 of file wgsread.hpp.

Constructor & Destructor Documentation

◆ CWGSDb_Impl()

CWGSDb_Impl::CWGSDb_Impl	(	CVDBMgr &	mgr,
		CTempString	path_or_acc,
		CTempString	vol_path = `CTempString()`
	)

Definition at line 843 of file wgsread.cpp.

References m_Db, m_SeqTable, m_WGSPath, PROFILE, and x_InitIdParams().

◆ ~CWGSDb_Impl()

CWGSDb_Impl::~CWGSDb_Impl ( void )

virtual

Definition at line 877 of file wgsread.cpp.

Member Function Documentation

◆ AddMasterDescr()

void CWGSDb_Impl::AddMasterDescr	(	CSeq_descr &	descr,
		const CBioseq *	main_seq = `0`,
		TFlags	flags = `fDefaultFlags`
	)		const

◆ CanHaveGis()

bool CWGSDb_Impl::CanHaveGis ( )

Definition at line 3659 of file wgsread.cpp.

References CVDBValue::eMissing_Allow, Put(), Seq(), and rapidjson::value.

Referenced by DetermineFeatLocIdType().

◆ ContigNameIndex()

const CVDBTableIndex& CWGSDb_Impl::ContigNameIndex ( void )

inlineprotected

Definition at line 497 of file wgsread.hpp.

References m_ContigNameIndex, m_ContigNameIndexIsOpened, and OpenContigNameIndex().

Referenced by GetContigNameRowId().

◆ DECLARE_SAFE_FLAGS_TYPE() [1/2]

CWGSDb_Impl::DECLARE_SAFE_FLAGS_TYPE	(	EAllowRowType	,
		TAllowRowType
	)

◆ DECLARE_SAFE_FLAGS_TYPE() [2/2]

CWGSDb_Impl::DECLARE_SAFE_FLAGS_TYPE	(	EGnlIdFlags	,
		TGnlIdFlags
	)

◆ DetermineFeatLocIdType()

CWGSDb_Impl::EFeatLocIdType CWGSDb_Impl::DetermineFeatLocIdType ( )

Definition at line 3712 of file wgsread.cpp.

References Begin(), CanHaveGis(), CTempString::data(), SWGSDb_Defs::eFeatLocIdAccNoVer, SWGSDb_Defs::eFeatLocIdAccVer, SWGSDb_Defs::eFeatLocIdGi, Feat(), CSeq_feat_Base::GetLocation(), HasStandardFeatLocIdType(), i, PROFILE, Put(), Seq(), and CTempString::size().

Referenced by GetFeatLocIdType().

◆ Feat()

CRef< CWGSDb_Impl::SFeatTableCursor > CWGSDb_Impl::Feat ( TVDBRowId row = 0 )

inlineprotected

Definition at line 961 of file wgsread.cpp.

References FeatTable(), m_Feat, row, and table.

Referenced by DetermineFeatLocIdType(), GetTotalFeatureCount(), and CWGSFeatureIterator::x_Init().

◆ FeatTable()

const CVDBTable& CWGSDb_Impl::FeatTable ( void )

inlineprotected

Definition at line 473 of file wgsread.hpp.

References m_FeatTable, m_FeatTableIsOpened, and OpenFeatTable().

Referenced by Feat().

◆ GetAccSeq_id() [1/2]

CRef< CSeq_id > CWGSDb_Impl::GetAccSeq_id	(	CTempString	acc,
		int	version
	)		const

Definition at line 2913 of file wgsread.cpp.

References CSeq_id_Base::e_not_set, CTempString::empty(), m_SeqIdType, PROFILE, sx_SetAccession(), sx_SetVersion(), and dtl::version.

Referenced by CWGSSeqIterator::GetAccSeq_id(), CWGSScaffoldIterator::GetAccSeq_id(), CWGSProteinIterator::GetAccSeq_id(), GetContigSeq_id(), GetProteinSeq_id(), and GetScaffoldSeq_id().

◆ GetAccSeq_id() [2/2]

CRef< CSeq_id > CWGSDb_Impl::GetAccSeq_id	(	ERowType	type,
		TVDBRowId	row_id,
		int	version
	)		const

Definition at line 2932 of file wgsread.cpp.

References eRowType_contig, m_IdPrefixWithVersion, m_IdRowDigits, str(), sx_SetVersion(), and dtl::version.

◆ GetAmbiguityInfo()

CRef< CWGSDb_Impl::SAmbiguityInfo > CWGSDb_Impl::GetAmbiguityInfo ( TVDBRowId row )

protected

Definition at line 2211 of file wgsread.cpp.

References limited_resource_map< Key, Value, Resource, Less >::get(), GetWGSPath(), m_AmbiguityCache, m_AmbiguityCacheMutex, row, and s_GlobalAmbiguityCache.

Referenced by CWGSSeqIterator::SAmbiguityAccess::SAmbiguityAccess().

◆ GetCommonTaxId()

TTaxId CWGSDb_Impl::GetCommonTaxId ( void ) const

inline

Definition at line 422 of file wgsread.hpp.

References m_CommonTaxId.

Referenced by CWGSSeqIterator::GetTaxId(), and CWGSProteinIterator::GetTaxId().

◆ GetContigMolType()

CSeq_inst::TMol CWGSDb_Impl::GetContigMolType ( void ) const

Definition at line 2987 of file wgsread.cpp.

References m_ContigMolType.

Referenced by IsTSA().

◆ GetContigNameRowId()

TVDBRowId CWGSDb_Impl::GetContigNameRowId ( const string & name )

Definition at line 3564 of file wgsread.cpp.

References ContigNameIndex(), CVDBValue::eMissing_Allow, Lookup(), m_ContigNameIndexIsOpened, Put(), compile_time_bits::range(), Seq(), and rapidjson::value.

Referenced by CWGSDb::GetContigNameRowId().

◆ GetContigSeq_id()

CRef< CSeq_id > CWGSDb_Impl::GetContigSeq_id ( TVDBRowId row_id ) const

Definition at line 2969 of file wgsread.cpp.

References eRowType_contig, and GetAccSeq_id().

◆ GetFeatLocIdType()

CWGSDb_Impl::EFeatLocIdType CWGSDb_Impl::GetFeatLocIdType ( )

Definition at line 3771 of file wgsread.cpp.

References DetermineFeatLocIdType(), SWGSDb_Defs::eFeatLocIdUninitialized, and m_FeatLocIdType.

Referenced by SWGSFeatChunkInfo::CreateChunkInfo().

◆ GetGeneralOrPatentSeq_id() [1/4]

CRef< CSeq_id > CWGSDb_Impl::GetGeneralOrPatentSeq_id	(	CTempString	str,
		const SProt0TableCursor &	cur,
		TVDBRowId	row
	)		const

protected

Definition at line 2893 of file wgsread.cpp.

References fGnlId_NoWGSVersion, GetGeneralSeq_id(), GetPatentSeq_id(), HasPatentId(), str(), and sx_GetStringId().

◆ GetGeneralOrPatentSeq_id() [2/4]

CRef< CSeq_id > CWGSDb_Impl::GetGeneralOrPatentSeq_id	(	CTempString	str,
		const SScfTableCursor &	cur,
		TVDBRowId	row
	)		const

protected

Definition at line 2872 of file wgsread.cpp.

References GetGeneralSeq_id(), GetPatentSeq_id(), HasPatentId(), str(), and sx_GetStringId().

◆ GetGeneralOrPatentSeq_id() [3/4]

CRef< CSeq_id > CWGSDb_Impl::GetGeneralOrPatentSeq_id	(	CTempString	str,
		const SSeq0TableCursor &	cur,
		TVDBRowId	row
	)		const

protected

Definition at line 2851 of file wgsread.cpp.

References GetGeneralSeq_id(), GetPatentSeq_id(), HasPatentId(), str(), and sx_GetStringId().

◆ GetGeneralOrPatentSeq_id() [4/4]

CRef< CSeq_id > CWGSDb_Impl::GetGeneralOrPatentSeq_id	(	CTempString	str,
		TVDBRowId	row,
		TGnlIdFlags	gnl_id_flags = `fGnlId_Default`
	)		const

Definition at line 2832 of file wgsread.cpp.

References fGnlId_NoWGSId, GetGeneralSeq_id(), GetPatentSeq_id(), HasPatentId(), str(), and sx_GetStringId().

Referenced by CWGSSeqIterator::GetGeneralOrPatentSeq_id(), and CWGSProteinIterator::GetGeneralOrPatentSeq_id().

◆ GetGeneralSeq_id() [1/2]

CRef< CSeq_id > CWGSDb_Impl::GetGeneralSeq_id	(	CTempString	prefix,
		CTempString	tag
	)		const

Definition at line 2777 of file wgsread.cpp.

References CTempString::empty(), CDbtag_Base::SetDb(), sx_SetTag(), and tag.

Referenced by GetGeneralOrPatentSeq_id(), and CWGSScaffoldIterator::GetGeneralOrPatentSeq_id().

◆ GetGeneralSeq_id() [2/2]

CRef< CSeq_id > CWGSDb_Impl::GetGeneralSeq_id	(	CTempString	tag,
		TGnlIdFlags	gnl_id_flags = `fGnlId_Default`
	)		const

Definition at line 2793 of file wgsread.cpp.

References fGnlId_NoWGSVersion, m_HasNoDefaultGnlId, m_IdPrefixDb, m_IdPrefixDbWithVersion, NPOS, CDbtag_Base::SetDb(), NStr::StartsWith(), sx_SetTag(), and tag.

◆ GetGiRowId()

pair< TVDBRowId, bool > CWGSDb_Impl::GetGiRowId ( TGi gi )

Definition at line 3482 of file wgsread.cpp.

References CVDBValue::eMissing_Allow, GI_TO, GiIdx(), Put(), and rapidjson::value.

Referenced by CWGSDb::GetGiRowId().

◆ GetIdPrefix()

const string& CWGSDb_Impl::GetIdPrefix ( void ) const

inline

Definition at line 209 of file wgsread.hpp.

References m_IdPrefix.

◆ GetIdPrefixWithVersion()

const string& CWGSDb_Impl::GetIdPrefixWithVersion ( void ) const

inline

Definition at line 212 of file wgsread.hpp.

References m_IdPrefixWithVersion.

◆ GetIdRowDigits()

Uint4 CWGSDb_Impl::GetIdRowDigits ( void ) const

inline

Definition at line 267 of file wgsread.hpp.

References m_IdRowDigits.

◆ GetMasterDescr()

const TMasterDescr& CWGSDb_Impl::GetMasterDescr ( void ) const

inline

Definition at line 310 of file wgsread.hpp.

References m_MasterDescr.

Referenced by AddMasterDescr(), and CWGSScaffoldIterator::HasSeq_descr().

◆ GetMasterDescrBytes()

size_t CWGSDb_Impl::GetMasterDescrBytes ( TMasterDescrBytes & buffer )

Definition at line 3022 of file wgsread.cpp.

References buffer, CKMDataNode::eMissing_Allow, CKMDataNode::GetData(), CKMDataNode::GetSize(), SeqTable(), and ncbi::grid::netcache::search::fields::size.

Referenced by GetMasterDescrEntry().

◆ GetMasterDescrEntry()

CRef< CSeq_entry > CWGSDb_Impl::GetMasterDescrEntry ( void )

Definition at line 3043 of file wgsread.cpp.

References buffer, CBioseq_Base::GetId(), GetMasterDescrBytes(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::IsSeq(), m_MasterEntry, m_TableMutex, SetPatentId(), and str().

Referenced by x_LoadMasterDescr().

◆ GetMasterGi()

TGi CWGSDb_Impl::GetMasterGi ( void ) const

Definition at line 3284 of file wgsread.cpp.

References CSeq_id_Base::GetGi(), CBioseq_Base::GetId(), CSeq_entry_Base::GetSeq(), ITERATE, m_MasterEntry, and ZERO_GI.

◆ GetMasterSeq_entry()

CRef< CSeq_entry > CWGSDb_Impl::GetMasterSeq_entry ( void ) const

Definition at line 3238 of file wgsread.cpp.

References CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eRepr_virtual, GetMasterSeq_id(), m_MasterDescr, m_MasterEntry, CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_inst_Base::SetMol(), CSeq_inst_Base::SetRepr(), and CSeq_entry_Base::SetSeq().

◆ GetMasterSeq_id()

CRef< CSeq_id > CWGSDb_Impl::GetMasterSeq_id ( void ) const

Definition at line 2953 of file wgsread.cpp.

References m_IdPrefix, m_IdRowDigits, m_IdVersion, and sx_SetVersion().

Referenced by GetMasterSeq_entry().

◆ GetNucGiRange()

pair< TGi, TGi > CWGSDb_Impl::GetNucGiRange ( void )

Definition at line 3310 of file wgsread.cpp.

References GiIdx(), Put(), and s_ToGi().

Referenced by CWGSDb::GetNucGiRange().

◆ GetNucGiRanges()

CWGSDb_Impl::TGiRanges CWGSDb_Impl::GetNucGiRanges ( void )

Definition at line 3369 of file wgsread.cpp.

References GI_TO, i, Put(), s_ToGi(), Seq(), and x_SortGiRanges().

Referenced by CWGSDb::GetNucGiRanges().

◆ GetNucGiRowId()

TVDBRowId CWGSDb_Impl::GetNucGiRowId ( TGi gi )

Definition at line 3507 of file wgsread.cpp.

References CVDBValue::eMissing_Allow, GI_TO, GiIdx(), Put(), and rapidjson::value.

Referenced by CWGSDb::GetNucGiRowId().

◆ GetPatentId()

const CRef<CSeq_id>& CWGSDb_Impl::GetPatentId ( void ) const

inline

Definition at line 331 of file wgsread.hpp.

References m_PatentId.

◆ GetPatentSeq_id()

CRef< CSeq_id > CWGSDb_Impl::GetPatentSeq_id ( int id ) const

Definition at line 2821 of file wgsread.cpp.

References CRef< C, Locker >::GetNCObject(), m_PatentId, CPatent_seq_id_Base::SetCit(), CSeq_id_Base::SetPatent(), and CPatent_seq_id_Base::SetSeqid().

Referenced by GetGeneralOrPatentSeq_id().

◆ GetProductNameRowId()

TVDBRowId CWGSDb_Impl::GetProductNameRowId ( const string & name )

Definition at line 3600 of file wgsread.cpp.

References Lookup(), m_ProductNameIndexIsOpened, and ProductNameIndex().

Referenced by CWGSDb::GetProductNameRowId().

◆ GetProjectGBState()

NCBI_gb_state CWGSDb_Impl::GetProjectGBState ( ) const

inline

Definition at line 408 of file wgsread.hpp.

References m_ProjectGBState.

Referenced by HasStandardFeatLocIdType().

◆ GetProtAccRanges()

CWGSDb_Impl::TProtAccRanges CWGSDb_Impl::GetProtAccRanges ( void )

Definition at line 3445 of file wgsread.cpp.

References CTempString::empty(), map_checker< Container >::end(), i, info, map_checker< Container >::insert(), map_checker< Container >::lower_bound(), Prot0(), Put(), and compile_time_bits::range().

Referenced by CWGSDb::GetProtAccRanges().

◆ GetProtAccRowId()

TVDBRowId CWGSDb_Impl::GetProtAccRowId	(	const string &	acc,
		int	version = `-1`
	)

Definition at line 3607 of file wgsread.cpp.

References CVDBValue::eMissing_Allow, CVDBValue::empty(), NStr::Equal(), prot, Prot0(), ProtIdx(), Put(), compile_time_bits::range(), CVDBValue::size(), tmp, NStr::ToUpper(), and rapidjson::value.

Referenced by CWGSDb::GetProtAccRowId().

◆ GetProteinMolType()

CSeq_inst::TMol CWGSDb_Impl::GetProteinMolType ( void ) const

Definition at line 2999 of file wgsread.cpp.

References CSeq_inst_Base::eMol_aa.

◆ GetProteinNameRowId()

TVDBRowId CWGSDb_Impl::GetProteinNameRowId ( const string & name )

Definition at line 3593 of file wgsread.cpp.

References Lookup(), m_ProteinNameIndexIsOpened, and ProteinNameIndex().

Referenced by CWGSDb::GetProteinNameRowId().

◆ GetProteinSeq_id()

CRef< CSeq_id > CWGSDb_Impl::GetProteinSeq_id ( TVDBRowId row_id ) const

Definition at line 2981 of file wgsread.cpp.

References eRowType_protein, and GetAccSeq_id().

Referenced by CWGSProteinIterator::GetAccSeq_id().

◆ GetProtGiRange()

pair< TGi, TGi > CWGSDb_Impl::GetProtGiRange ( void )

Definition at line 3330 of file wgsread.cpp.

References GiIdx(), Put(), and s_ToGi().

Referenced by CWGSDb::GetProtGiRange().

◆ GetProtGiRanges()

CWGSDb_Impl::TGiRanges CWGSDb_Impl::GetProtGiRanges ( void )

Definition at line 3401 of file wgsread.cpp.

Referenced by CWGSDb::GetProtGiRanges().

◆ GetProtGiRowId()

TVDBRowId CWGSDb_Impl::GetProtGiRowId ( TGi gi )

Definition at line 3525 of file wgsread.cpp.

References CVDBValue::eMissing_Allow, GI_TO, GiIdx(), Put(), and rapidjson::value.

Referenced by CWGSDb::GetProtGiRowId().

◆ GetReplacedBy()

const string& CWGSDb_Impl::GetReplacedBy ( ) const

inline

Definition at line 411 of file wgsread.hpp.

References m_ReplacedBy.

◆ GetScaffoldMolType()

CSeq_inst::TMol CWGSDb_Impl::GetScaffoldMolType ( void ) const

Definition at line 2993 of file wgsread.cpp.

References CSeq_inst_Base::eMol_dna.

◆ GetScaffoldNameRowId()

TVDBRowId CWGSDb_Impl::GetScaffoldNameRowId ( const string & name )

Definition at line 3586 of file wgsread.cpp.

References Lookup(), m_ScaffoldNameIndexIsOpened, and ScaffoldNameIndex().

Referenced by CWGSDb::GetScaffoldNameRowId().

◆ GetScaffoldSeq_id()

CRef< CSeq_id > CWGSDb_Impl::GetScaffoldSeq_id ( TVDBRowId row_id ) const

Definition at line 2975 of file wgsread.cpp.

References eRowType_scaffold, and GetAccSeq_id().

Referenced by CWGSScaffoldIterator::GetAccSeq_id().

◆ GetTotalFeatureCount()

TVDBRowCount CWGSDb_Impl::GetTotalFeatureCount ( )

Definition at line 3677 of file wgsread.cpp.

References Feat(), and Put().

Referenced by HasFeatures().

◆ GetWGSPath()

const string& CWGSDb_Impl::GetWGSPath ( void ) const

inline

Definition at line 215 of file wgsread.hpp.

References m_WGSPath.

Referenced by GetAmbiguityInfo(), CWGSDb::GetWGSPath(), HasStandardFeatLocIdType(), and PutAmbiguityInfo().

◆ GiIdx()

CRef< CWGSDb_Impl::SGiIdxTableCursor > CWGSDb_Impl::GiIdx ( TVDBRowId row = 0 )

inlineprotected

Definition at line 975 of file wgsread.cpp.

References GiIdxTable(), m_GiIdx, row, and table.

Referenced by GetGiRowId(), GetNucGiRange(), GetNucGiRowId(), GetProtGiRange(), GetProtGiRowId(), and CWGSGiIterator::x_Init().

◆ GiIdxTable()

const CVDBTable& CWGSDb_Impl::GiIdxTable ( void )

inlineprotected

Definition at line 479 of file wgsread.hpp.

References m_GiIdxTable, m_GiIdxTableIsOpened, and OpenGiIdxTable().

Referenced by GiIdx().

◆ HasCommonTaxId()

bool CWGSDb_Impl::HasCommonTaxId ( void ) const

inline

Definition at line 418 of file wgsread.hpp.

References m_HasCommonTaxId.

Referenced by CWGSSeqIterator::HasTaxId().

◆ HasFeatures()

bool CWGSDb_Impl::HasFeatures ( )

Definition at line 3688 of file wgsread.cpp.

References GetTotalFeatureCount().

◆ HasPatentId()

bool CWGSDb_Impl::HasPatentId ( ) const

inline

Definition at line 327 of file wgsread.hpp.

References m_PatentId.

Referenced by GetGeneralOrPatentSeq_id().

◆ HasStandardFeatLocIdType()

bool CWGSDb_Impl::HasStandardFeatLocIdType ( )

Definition at line 3694 of file wgsread.cpp.

References GetProjectGBState(), GetWGSPath(), IsReplaced(), NCBI_gb_state_eWGSGenBankMissing, and NPOS.

Referenced by DetermineFeatLocIdType().

◆ IsReplaced()

bool CWGSDb_Impl::IsReplaced ( void ) const

inline

Definition at line 414 of file wgsread.hpp.

References m_ReplacedBy.

Referenced by HasStandardFeatLocIdType().

◆ IsSetMasterDescr()

bool CWGSDb_Impl::IsSetMasterDescr ( void ) const

inline

Definition at line 307 of file wgsread.hpp.

References m_IsSetMasterDescr.

Referenced by LoadMasterDescr().

◆ IsTSA()

bool CWGSDb_Impl::IsTSA ( void ) const

Definition at line 2771 of file wgsread.cpp.

References CSeq_inst_Base::eMol_rna, and GetContigMolType().

Referenced by x_InitIdParams().

◆ LoadMasterDescr()

bool CWGSDb_Impl::LoadMasterDescr ( int filter )

Definition at line 3012 of file wgsread.cpp.

References IsSetMasterDescr(), NCBI_PARAM_TYPE, and x_LoadMasterDescr().

Referenced by CWGSDb::LoadMasterDescr().

◆ Lookup()

TVDBRowId CWGSDb_Impl::Lookup	(	const string &	name,
		const CVDBTableIndex &	index,
		bool	upcase
	)

inlineprotected

Definition at line 3544 of file wgsread.cpp.

References CVDBTableIndex::Find(), NStr::IsUpper(), compile_time_bits::range(), tmp, and NStr::ToUpper().

Referenced by GetContigNameRowId(), GetProductNameRowId(), GetProteinNameRowId(), and GetScaffoldNameRowId().

◆ NormalizePathOrAccession()

string CWGSDb_Impl::NormalizePathOrAccession	(	CTempString	path_or_acc,
		CTempString	vol_path = `CTempString()`
	)

static

Definition at line 2322 of file wgsread.cpp.

References CTempString::empty(), CTempString::find(), CVPath::IsPlainAccession(), ITERATE, LOG_POST, CDirEntry::MakePath(), NCBI_PARAM_TYPE, CTempString::size(), NStr::Split(), string, CTempString::substr(), and Warning().

Referenced by CWGSDataLoader_Impl::OpenWGSFileOnce().

◆ OpenContigNameIndex()

void CWGSDb_Impl::OpenContigNameIndex ( void )

protected

Definition at line 2449 of file wgsread.cpp.

References m_ContigNameIndex, m_ContigNameIndexIsOpened, OpenIndex(), and SeqTable().

Referenced by ContigNameIndex().

◆ OpenFeatTable()

void CWGSDb_Impl::OpenFeatTable ( void )

protected

Definition at line 2431 of file wgsread.cpp.

References m_FeatTable, m_FeatTableIsOpened, and OpenTable().

Referenced by FeatTable().

◆ OpenGiIdxTable()

void CWGSDb_Impl::OpenGiIdxTable ( void )

protected

Definition at line 2437 of file wgsread.cpp.

References m_GiIdxTable, m_GiIdxTableIsOpened, and OpenTable().

Referenced by GiIdxTable().

◆ OpenIndex()

void CWGSDb_Impl::OpenIndex	(	const CVDBTable &	table,
		CVDBTableIndex &	index,
		atomic< Int1 > &	index_is_opened,
		const char *	index_name,
		const char *	backup_index_name = `0`
	)

inlineprotected

Definition at line 2388 of file wgsread.cpp.

References CVDBTableIndex::eMissing_Allow, m_TableMutex, and table.

Referenced by OpenContigNameIndex(), OpenProductNameIndex(), OpenProtAccIndex(), OpenProteinNameIndex(), and OpenScaffoldNameIndex().

◆ OpenProductNameIndex()

void CWGSDb_Impl::OpenProductNameIndex ( void )

protected

Definition at line 2470 of file wgsread.cpp.

References m_ProductNameIndex, m_ProductNameIndexIsOpened, OpenIndex(), and ProtTable().

Referenced by ProductNameIndex().

◆ OpenProtAccIndex()

void CWGSDb_Impl::OpenProtAccIndex ( void )

protected

Definition at line 2477 of file wgsread.cpp.

References m_ProtAccIndex, m_ProtAccIndexIsOpened, OpenIndex(), and ProtTable().

Referenced by ProtAccIndex().

◆ OpenProteinNameIndex()

void CWGSDb_Impl::OpenProteinNameIndex ( void )

protected

Definition at line 2463 of file wgsread.cpp.

References m_ProteinNameIndex, m_ProteinNameIndexIsOpened, OpenIndex(), and ProtTable().

Referenced by ProteinNameIndex().

◆ OpenProtIdxTable()

void CWGSDb_Impl::OpenProtIdxTable ( void )

protected

Definition at line 2443 of file wgsread.cpp.

References m_ProtIdxTable, m_ProtIdxTableIsOpened, and OpenTable().

Referenced by ProtIdxTable().

◆ OpenProtTable()

void CWGSDb_Impl::OpenProtTable ( void )

protected

Definition at line 2425 of file wgsread.cpp.

References m_ProtTable, m_ProtTableIsOpened, and OpenTable().

Referenced by ProtTable().

◆ OpenScaffoldNameIndex()

void CWGSDb_Impl::OpenScaffoldNameIndex ( void )

protected

Definition at line 2456 of file wgsread.cpp.

References m_ScaffoldNameIndex, m_ScaffoldNameIndexIsOpened, OpenIndex(), and ScfTable().

Referenced by ScaffoldNameIndex().

◆ OpenScfTable()

void CWGSDb_Impl::OpenScfTable ( void )

protected

Definition at line 2419 of file wgsread.cpp.

References m_ScfTable, m_ScfTableIsOpened, and OpenTable().

Referenced by ScfTable().

◆ OpenTable()

void CWGSDb_Impl::OpenTable	(	CVDBTable &	table,
		atomic< bool > &	table_is_opened,
		const char *	table_name
	)

inlineprotected

Definition at line 2375 of file wgsread.cpp.

References CVDBTable::eMissing_Allow, m_Db, m_TableMutex, table, and table_name.

Referenced by OpenFeatTable(), OpenGiIdxTable(), OpenProtIdxTable(), OpenProtTable(), and OpenScfTable().

◆ ParseContigRow()

static TVDBRowId CWGSDb_Impl::ParseContigRow ( CTempString acc )

inlinestatic

Definition at line 252 of file wgsread.hpp.

References fAllowRowType_contig, and ParseRowType().

Referenced by CWGSDb::ParseContigRow().

◆ ParseProteinRow()

static TVDBRowId CWGSDb_Impl::ParseProteinRow ( CTempString acc )

inlinestatic

Definition at line 264 of file wgsread.hpp.

References fAllowRowType_protein, and ParseRowType().

Referenced by CWGSDb::ParseProteinRow().

◆ ParseRow()

TVDBRowId CWGSDb_Impl::ParseRow	(	CTempString	acc,
		bool *	is_scaffold
	)		const

Definition at line 2523 of file wgsread.cpp.

References eRowType_scaffold, fAllowRowType_contig, fAllowRowType_scaffold, and ParseRowType().

Referenced by CWGSDb::ParseRow().

◆ ParseRowType()

pair< TVDBRowId, CWGSDb_Impl::ERowType > CWGSDb_Impl::ParseRowType	(	CTempString	acc,
		TAllowRowType	allow
	)

static

Definition at line 2485 of file wgsread.cpp.

References eRowType_contig, eRowType_protein, eRowType_scaffold, fAllowRowType_contig, fAllowRowType_protein, fAllowRowType_scaffold, NStr::fConvErr_NoThrow, CTempString::find_first_of(), NPOS, row, CTempString::size(), and CTempString::substr().

Referenced by ParseContigRow(), ParseProteinRow(), ParseRow(), and ParseScaffoldRow().

◆ ParseScaffoldRow()

static TVDBRowId CWGSDb_Impl::ParseScaffoldRow ( CTempString acc )

inlinestatic

Definition at line 258 of file wgsread.hpp.

References fAllowRowType_scaffold, and ParseRowType().

Referenced by CWGSDb::ParseScaffoldRow().

◆ ProductNameIndex()

const CVDBTableIndex& CWGSDb_Impl::ProductNameIndex ( void )

inlineprotected

Definition at line 515 of file wgsread.hpp.

References m_ProductNameIndex, m_ProductNameIndexIsOpened, and OpenProductNameIndex().

Referenced by GetProductNameRowId().

◆ Prot()

CRef< CWGSDb_Impl::SProtTableCursor > CWGSDb_Impl::Prot ( TVDBRowId row = 0 )

inlineprotected

Definition at line 947 of file wgsread.cpp.

References m_Prot, ProtTable(), row, and table.

Referenced by CWGSProteinIterator::x_Cur().

◆ Prot0()

CRef< CWGSDb_Impl::SProt0TableCursor > CWGSDb_Impl::Prot0 ( TVDBRowId row = 0 )

inlineprotected

Definition at line 933 of file wgsread.cpp.

References m_Prot0, ProtTable(), row, and table.

Referenced by GetProtAccRanges(), GetProtAccRowId(), and CWGSProteinIterator::x_Init().

◆ ProtAccIndex()

const CVDBTableIndex& CWGSDb_Impl::ProtAccIndex ( void )

inlineprotected

Definition at line 491 of file wgsread.hpp.

References m_ProtAccIndex, m_ProtAccIndexIsOpened, and OpenProtAccIndex().

◆ ProteinNameIndex()

const CVDBTableIndex& CWGSDb_Impl::ProteinNameIndex ( void )

inlineprotected

Definition at line 509 of file wgsread.hpp.

References m_ProteinNameIndex, m_ProteinNameIndexIsOpened, and OpenProteinNameIndex().

Referenced by GetProteinNameRowId().

◆ ProtIdx()

CRef< CWGSDb_Impl::SProtIdxTableCursor > CWGSDb_Impl::ProtIdx ( TVDBRowId row = 0 )

inlineprotected

Definition at line 989 of file wgsread.cpp.

References m_ProtIdx, ProtIdxTable(), row, and table.

Referenced by GetProtAccRowId().

◆ ProtIdxTable()

const CVDBTable& CWGSDb_Impl::ProtIdxTable ( void )

inlineprotected

Definition at line 485 of file wgsread.hpp.

References m_ProtIdxTable, m_ProtIdxTableIsOpened, and OpenProtIdxTable().

Referenced by ProtIdx().

◆ ProtTable()

const CVDBTable& CWGSDb_Impl::ProtTable ( void )

inlineprotected

Definition at line 467 of file wgsread.hpp.

References m_ProtTable, m_ProtTableIsOpened, and OpenProtTable().

Referenced by OpenProductNameIndex(), OpenProtAccIndex(), OpenProteinNameIndex(), Prot(), and Prot0().

◆ Put() [1/9]

void CWGSDb_Impl::Put	(	CRef< SFeatTableCursor > &	curs,
		TVDBRowId	row = `0`
	)

inlineprotected

Definition at line 1045 of file wgsread.cpp.

References m_Feat, and row.

◆ Put() [2/9]

void CWGSDb_Impl::Put	(	CRef< SGiIdxTableCursor > &	curs,
		TVDBRowId	row = `0`
	)

inlineprotected

Definition at line 1052 of file wgsread.cpp.

References m_GiIdx, and row.

◆ Put() [3/9]

void CWGSDb_Impl::Put	(	CRef< SProt0TableCursor > &	curs,
		TVDBRowId	row = `0`
	)

inlineprotected

Definition at line 1031 of file wgsread.cpp.

References m_Prot0, and row.

◆ Put() [4/9]

void CWGSDb_Impl::Put	(	CRef< SProtIdxTableCursor > &	curs,
		TVDBRowId	row = `0`
	)

inlineprotected

Definition at line 1059 of file wgsread.cpp.

References m_ProtIdx, and row.

◆ Put() [5/9]

void CWGSDb_Impl::Put	(	CRef< SProtTableCursor > &	curs,
		TVDBRowId	row = `0`
	)

inlineprotected

Definition at line 1038 of file wgsread.cpp.

References m_Prot, and row.

◆ Put() [6/9]

void CWGSDb_Impl::Put	(	CRef< SScfTableCursor > &	curs,
		TVDBRowId	row = `0`
	)

inlineprotected

Definition at line 1024 of file wgsread.cpp.

References m_Scf, and row.

◆ Put() [7/9]

void CWGSDb_Impl::Put	(	CRef< SSeq0TableCursor > &	curs,
		TVDBRowId	row = `0`
	)

inlineprotected

Definition at line 1003 of file wgsread.cpp.

References m_Seq0, and row.

Referenced by CanHaveGis(), DetermineFeatLocIdType(), GetContigNameRowId(), GetGiRowId(), GetNucGiRange(), GetNucGiRanges(), GetNucGiRowId(), GetProtAccRanges(), GetProtAccRowId(), GetProtGiRange(), GetProtGiRowId(), GetTotalFeatureCount(), CWGSGiIterator::Reset(), CWGSProteinIterator::Reset(), CWGSFeatureIterator::Reset(), and x_InitIdParams().

◆ Put() [8/9]

void CWGSDb_Impl::Put	(	CRef< SSeq4naTableCursor > &	curs,
		TVDBRowId	row = `0`
	)

inlineprotected

Definition at line 1017 of file wgsread.cpp.

◆ Put() [9/9]

void CWGSDb_Impl::Put	(	CRef< SSeqTableCursor > &	curs,
		TVDBRowId	row = `0`
	)

inlineprotected

Definition at line 1010 of file wgsread.cpp.

References m_Seq, and row.

◆ PutAmbiguityInfo()

void CWGSDb_Impl::PutAmbiguityInfo ( CRef< SAmbiguityInfo > & ambiguity )

protected

Definition at line 2223 of file wgsread.cpp.

References GetWGSPath(), info, m_AmbiguityCache, m_AmbiguityCacheMutex, limited_resource_map< Key, Value, Resource, Less >::put(), and s_GlobalAmbiguityCache.

Referenced by CWGSSeqIterator::SAmbiguityAccess::~SAmbiguityAccess().

◆ ResetMasterDescr()

void CWGSDb_Impl::ResetMasterDescr ( void )

Definition at line 3005 of file wgsread.cpp.

References m_IsSetMasterDescr, and m_MasterDescr.

◆ ScaffoldNameIndex()

const CVDBTableIndex& CWGSDb_Impl::ScaffoldNameIndex ( void )

inlineprotected

Definition at line 503 of file wgsread.hpp.

References m_ScaffoldNameIndex, m_ScaffoldNameIndexIsOpened, and OpenScaffoldNameIndex().

Referenced by GetScaffoldNameRowId().

◆ Scf()

CRef< CWGSDb_Impl::SScfTableCursor > CWGSDb_Impl::Scf ( TVDBRowId row = 0 )

inlineprotected

Definition at line 919 of file wgsread.cpp.

References m_Scf, row, ScfTable(), and table.

Referenced by CWGSScaffoldIterator::x_Init().

◆ ScfTable()

const CVDBTable& CWGSDb_Impl::ScfTable ( void )

inlineprotected

Definition at line 461 of file wgsread.hpp.

References m_ScfTable, m_ScfTableIsOpened, and OpenScfTable().

Referenced by OpenScaffoldNameIndex(), and Scf().

◆ Seq()

CRef< CWGSDb_Impl::SSeqTableCursor > CWGSDb_Impl::Seq ( TVDBRowId row = 0 )

inlineprotected

Definition at line 895 of file wgsread.cpp.

References m_Seq, row, and SeqTable().

Referenced by CanHaveGis(), DetermineFeatLocIdType(), GetContigNameRowId(), GetNucGiRanges(), and CWGSSeqIterator::x_Init().

◆ Seq0()

CRef< CWGSDb_Impl::SSeq0TableCursor > CWGSDb_Impl::Seq0 ( TVDBRowId row = 0 )

inlineprotected

Definition at line 883 of file wgsread.cpp.

References m_Seq0, row, and SeqTable().

Referenced by CWGSSeqIterator::x_Init(), and x_InitIdParams().

◆ Seq4na()

CRef< CWGSDb_Impl::SSeq4naTableCursor > CWGSDb_Impl::Seq4na ( TVDBRowId row = 0 )

inlineprotected

Definition at line 907 of file wgsread.cpp.

References SeqTable().

Referenced by CWGSDb_Impl::SAmbiguityInfo::x_Calculate4na(), and CWGSDb_Impl::SAmbiguityInfo::x_CalculateAmbiguityMask().

◆ SeqTable()

const CVDBTable& CWGSDb_Impl::SeqTable ( void )

inlineprotected

Definition at line 458 of file wgsread.hpp.

References m_SeqTable.

Referenced by GetMasterDescrBytes(), OpenContigNameIndex(), Seq(), Seq0(), Seq4na(), and x_InitIdParams().

◆ SetMasterDescr()

void CWGSDb_Impl::SetMasterDescr	(	const TMasterDescr &	descr,
		int	filter
	)

Definition at line 3140 of file wgsread.cpp.

References CWGSDb::eDescr_skip, CWGSDb::eDescrDefaultFilter, CWGSDb::eDescrNoFilter, CWGSDb::GetMasterDescrType(), ITERATE, m_IsSetMasterDescr, m_MasterDescr, Ref(), and SerialClone().

Referenced by CWGSDb::SetMasterDescr(), and x_LoadMasterDescr().

◆ SetPatentId()

void CWGSDb_Impl::SetPatentId ( CRef< CSeq_id > id )

Definition at line 3258 of file wgsread.cpp.

References m_PatentId.

Referenced by GetMasterDescrEntry().

◆ x_InitIdParams()

void CWGSDb_Impl::x_InitIdParams ( void )

protected

Definition at line 2239 of file wgsread.cpp.

References CKMDataNode::eMissing_Allow, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_rna, CTempString::find_first_of(), IsTSA(), m_CommonTaxId, m_ContigMolType, m_HasCommonTaxId, m_HasNoDefaultGnlId, m_IdPrefix, m_IdPrefixDb, m_IdPrefixDbWithVersion, m_IdPrefixWithVersion, m_IdRowDigits, m_IdVersion, m_ProjectGBState, m_ReplacedBy, m_SeqIdType, NCBI_THROW_FMT, Put(), Seq0(), SeqTable(), ncbi::grid::netcache::search::fields::size, CTempString::substr(), rapidjson::value, and ZERO_TAX_ID.

Referenced by CWGSDb_Impl().

◆ x_LoadMasterDescr()

void CWGSDb_Impl::x_LoadMasterDescr ( int filter )

protected

Definition at line 3097 of file wgsread.cpp.

References GetMasterDescrEntry(), and SetMasterDescr().

Referenced by LoadMasterDescr().

◆ x_SortGiRanges()

void CWGSDb_Impl::x_SortGiRanges ( TGiRanges & ranges )

protected

Definition at line 3350 of file wgsread.cpp.

References i, and ct::sort().

Referenced by GetNucGiRanges().

Friends And Related Function Documentation

◆ CWGSFeatureIterator

friend class CWGSFeatureIterator

friend

Definition at line 437 of file wgsread.hpp.

◆ CWGSGiIterator

friend class CWGSGiIterator

friend

Definition at line 435 of file wgsread.hpp.

◆ CWGSProteinIterator

friend class CWGSProteinIterator

friend

Definition at line 436 of file wgsread.hpp.

◆ CWGSScaffoldIterator

friend class CWGSScaffoldIterator

friend

Definition at line 434 of file wgsread.hpp.

◆ CWGSSeqIterator

friend class CWGSSeqIterator

friend

Definition at line 433 of file wgsread.hpp.

Member Data Documentation

◆ m_AmbiguityCache

TAmbiguityCache CWGSDb_Impl::m_AmbiguityCache

private

Definition at line 633 of file wgsread.hpp.

Referenced by GetAmbiguityInfo(), and PutAmbiguityInfo().

◆ m_AmbiguityCacheMutex

CFastMutex CWGSDb_Impl::m_AmbiguityCacheMutex

private

Definition at line 631 of file wgsread.hpp.

Referenced by GetAmbiguityInfo(), and PutAmbiguityInfo().

◆ m_CommonTaxId

TTaxId CWGSDb_Impl::m_CommonTaxId

private

Definition at line 646 of file wgsread.hpp.

Referenced by GetCommonTaxId(), and x_InitIdParams().

◆ m_ContigMolType

CSeq_inst::TMol CWGSDb_Impl::m_ContigMolType

private

Definition at line 635 of file wgsread.hpp.

Referenced by GetContigMolType(), and x_InitIdParams().

◆ m_ContigNameIndex

CVDBTableIndex CWGSDb_Impl::m_ContigNameIndex

private

Definition at line 626 of file wgsread.hpp.

Referenced by ContigNameIndex(), and OpenContigNameIndex().

◆ m_ContigNameIndexIsOpened

atomic<Int1> CWGSDb_Impl::m_ContigNameIndexIsOpened

private

Definition at line 607 of file wgsread.hpp.

Referenced by ContigNameIndex(), GetContigNameRowId(), and OpenContigNameIndex().

◆ m_Db

CVDB CWGSDb_Impl::m_Db

private

Definition at line 591 of file wgsread.hpp.

Referenced by CWGSDb_Impl(), OpenTable(), and CWGSSeqIterator::Reset().

◆ m_Feat

CVDBObjectCache<SFeatTableCursor> CWGSDb_Impl::m_Feat

private

Definition at line 622 of file wgsread.hpp.

Referenced by Feat(), and Put().

◆ m_FeatLocIdType

atomic<EFeatLocIdType> CWGSDb_Impl::m_FeatLocIdType

private

Definition at line 639 of file wgsread.hpp.

Referenced by GetFeatLocIdType().

◆ m_FeatTable

CVDBTable CWGSDb_Impl::m_FeatTable

private

Definition at line 613 of file wgsread.hpp.

Referenced by FeatTable(), and OpenFeatTable().

◆ m_FeatTableIsOpened

atomic<bool> CWGSDb_Impl::m_FeatTableIsOpened

private

Definition at line 603 of file wgsread.hpp.

Referenced by FeatTable(), and OpenFeatTable().

◆ m_GiIdx

CVDBObjectCache<SGiIdxTableCursor> CWGSDb_Impl::m_GiIdx

private

Definition at line 623 of file wgsread.hpp.

Referenced by GiIdx(), and Put().

◆ m_GiIdxTable

CVDBTable CWGSDb_Impl::m_GiIdxTable

private

Definition at line 614 of file wgsread.hpp.

Referenced by GiIdxTable(), and OpenGiIdxTable().

◆ m_GiIdxTableIsOpened

atomic<bool> CWGSDb_Impl::m_GiIdxTableIsOpened

private

Definition at line 604 of file wgsread.hpp.

Referenced by GiIdxTable(), and OpenGiIdxTable().

◆ m_HasCommonTaxId

bool CWGSDb_Impl::m_HasCommonTaxId

private

Definition at line 638 of file wgsread.hpp.

Referenced by HasCommonTaxId(), and x_InitIdParams().

◆ m_HasNoDefaultGnlId

bool CWGSDb_Impl::m_HasNoDefaultGnlId

private

Definition at line 637 of file wgsread.hpp.

Referenced by GetGeneralSeq_id(), and x_InitIdParams().

◆ m_IdPrefix

string CWGSDb_Impl::m_IdPrefix

private

Definition at line 594 of file wgsread.hpp.

Referenced by GetIdPrefix(), GetMasterSeq_id(), and x_InitIdParams().

◆ m_IdPrefixDb

string CWGSDb_Impl::m_IdPrefixDb

private

Definition at line 596 of file wgsread.hpp.

Referenced by GetGeneralSeq_id(), and x_InitIdParams().

◆ m_IdPrefixDbWithVersion

string CWGSDb_Impl::m_IdPrefixDbWithVersion

private

Definition at line 595 of file wgsread.hpp.

Referenced by GetGeneralSeq_id(), and x_InitIdParams().

◆ m_IdPrefixWithVersion

string CWGSDb_Impl::m_IdPrefixWithVersion

private

Definition at line 593 of file wgsread.hpp.

Referenced by GetAccSeq_id(), GetIdPrefixWithVersion(), and x_InitIdParams().

◆ m_IdRowDigits

Uint4 CWGSDb_Impl::m_IdRowDigits

private

Definition at line 598 of file wgsread.hpp.

Referenced by GetAccSeq_id(), GetIdRowDigits(), GetMasterSeq_id(), and x_InitIdParams().

◆ m_IdVersion

int CWGSDb_Impl::m_IdVersion

private

Definition at line 597 of file wgsread.hpp.

Referenced by GetMasterSeq_id(), and x_InitIdParams().

◆ m_IsSetMasterDescr

bool CWGSDb_Impl::m_IsSetMasterDescr

private

Definition at line 636 of file wgsread.hpp.

Referenced by IsSetMasterDescr(), ResetMasterDescr(), and SetMasterDescr().

◆ m_MasterDescr

TMasterDescr CWGSDb_Impl::m_MasterDescr

private

Definition at line 641 of file wgsread.hpp.

Referenced by GetMasterDescr(), GetMasterSeq_entry(), ResetMasterDescr(), and SetMasterDescr().

◆ m_MasterEntry

CRef<CSeq_entry> CWGSDb_Impl::m_MasterEntry

private

Definition at line 640 of file wgsread.hpp.

Referenced by GetMasterDescrEntry(), GetMasterGi(), and GetMasterSeq_entry().

◆ m_Mgr

CVDBMgr CWGSDb_Impl::m_Mgr

private

Definition at line 589 of file wgsread.hpp.

◆ m_PatentId

CRef<CSeq_id> CWGSDb_Impl::m_PatentId

private

Definition at line 642 of file wgsread.hpp.

Referenced by GetPatentId(), GetPatentSeq_id(), HasPatentId(), and SetPatentId().

◆ m_ProductNameIndex

CVDBTableIndex CWGSDb_Impl::m_ProductNameIndex

private

Definition at line 629 of file wgsread.hpp.

Referenced by OpenProductNameIndex(), and ProductNameIndex().

◆ m_ProductNameIndexIsOpened

atomic<Int1> CWGSDb_Impl::m_ProductNameIndexIsOpened

private

Definition at line 610 of file wgsread.hpp.

Referenced by GetProductNameRowId(), OpenProductNameIndex(), and ProductNameIndex().

◆ m_ProjectGBState

NCBI_gb_state CWGSDb_Impl::m_ProjectGBState

private

Definition at line 643 of file wgsread.hpp.

Referenced by GetProjectGBState(), and x_InitIdParams().

◆ m_Prot

CVDBObjectCache<SProtTableCursor> CWGSDb_Impl::m_Prot

private

Definition at line 621 of file wgsread.hpp.

Referenced by Prot(), and Put().

◆ m_Prot0

CVDBObjectCache<SProt0TableCursor> CWGSDb_Impl::m_Prot0

private

Definition at line 620 of file wgsread.hpp.

Referenced by Prot0(), and Put().

◆ m_ProtAccIndex

CVDBTableIndex CWGSDb_Impl::m_ProtAccIndex

private

Definition at line 625 of file wgsread.hpp.

Referenced by OpenProtAccIndex(), and ProtAccIndex().

◆ m_ProtAccIndexIsOpened

atomic<Int1> CWGSDb_Impl::m_ProtAccIndexIsOpened

private

Definition at line 606 of file wgsread.hpp.

Referenced by OpenProtAccIndex(), and ProtAccIndex().

◆ m_ProteinNameIndex

CVDBTableIndex CWGSDb_Impl::m_ProteinNameIndex

private

Definition at line 628 of file wgsread.hpp.

Referenced by OpenProteinNameIndex(), and ProteinNameIndex().

◆ m_ProteinNameIndexIsOpened

atomic<Int1> CWGSDb_Impl::m_ProteinNameIndexIsOpened

private

Definition at line 609 of file wgsread.hpp.

Referenced by GetProteinNameRowId(), OpenProteinNameIndex(), and ProteinNameIndex().

◆ m_ProtIdx

CVDBObjectCache<SProtIdxTableCursor> CWGSDb_Impl::m_ProtIdx

private

Definition at line 624 of file wgsread.hpp.

Referenced by ProtIdx(), and Put().

◆ m_ProtIdxTable

CVDBTable CWGSDb_Impl::m_ProtIdxTable

private

Definition at line 615 of file wgsread.hpp.

Referenced by OpenProtIdxTable(), and ProtIdxTable().

◆ m_ProtIdxTableIsOpened

atomic<bool> CWGSDb_Impl::m_ProtIdxTableIsOpened

private

Definition at line 605 of file wgsread.hpp.

Referenced by OpenProtIdxTable(), and ProtIdxTable().

◆ m_ProtTable

CVDBTable CWGSDb_Impl::m_ProtTable

private

Definition at line 612 of file wgsread.hpp.

Referenced by OpenProtTable(), and ProtTable().

◆ m_ProtTableIsOpened

atomic<bool> CWGSDb_Impl::m_ProtTableIsOpened

private

Definition at line 602 of file wgsread.hpp.

Referenced by OpenProtTable(), and ProtTable().

◆ m_ReplacedBy

string CWGSDb_Impl::m_ReplacedBy

private

Definition at line 645 of file wgsread.hpp.

Referenced by GetReplacedBy(), IsReplaced(), and x_InitIdParams().

◆ m_ScaffoldNameIndex

CVDBTableIndex CWGSDb_Impl::m_ScaffoldNameIndex

private

Definition at line 627 of file wgsread.hpp.

Referenced by OpenScaffoldNameIndex(), and ScaffoldNameIndex().

◆ m_ScaffoldNameIndexIsOpened

atomic<Int1> CWGSDb_Impl::m_ScaffoldNameIndexIsOpened

private

Definition at line 608 of file wgsread.hpp.

Referenced by GetScaffoldNameRowId(), OpenScaffoldNameIndex(), and ScaffoldNameIndex().

◆ m_Scf

CVDBObjectCache<SScfTableCursor> CWGSDb_Impl::m_Scf

private

Definition at line 619 of file wgsread.hpp.

Referenced by Put(), and Scf().

◆ m_ScfTable

CVDBTable CWGSDb_Impl::m_ScfTable

private

Definition at line 611 of file wgsread.hpp.

Referenced by OpenScfTable(), and ScfTable().

◆ m_ScfTableIsOpened

atomic<bool> CWGSDb_Impl::m_ScfTableIsOpened

private

Definition at line 601 of file wgsread.hpp.

Referenced by OpenScfTable(), and ScfTable().

◆ m_Seq

CVDBObjectCache<SSeqTableCursor> CWGSDb_Impl::m_Seq

private

Definition at line 618 of file wgsread.hpp.

Referenced by Put(), and Seq().

◆ m_Seq0

CVDBObjectCache<SSeq0TableCursor> CWGSDb_Impl::m_Seq0

private

Definition at line 617 of file wgsread.hpp.

Referenced by Put(), and Seq0().

◆ m_SeqIdType

CSeq_id::E_Choice CWGSDb_Impl::m_SeqIdType

private

Definition at line 644 of file wgsread.hpp.

Referenced by GetAccSeq_id(), and x_InitIdParams().

◆ m_SeqTable

CVDBTable CWGSDb_Impl::m_SeqTable

private

Definition at line 592 of file wgsread.hpp.

Referenced by CWGSDb_Impl(), and SeqTable().

◆ m_TableMutex

CFastMutex CWGSDb_Impl::m_TableMutex

private

Definition at line 600 of file wgsread.hpp.

Referenced by GetMasterDescrEntry(), OpenIndex(), and OpenTable().

◆ m_WGSPath

string CWGSDb_Impl::m_WGSPath

private

Definition at line 590 of file wgsread.hpp.

Referenced by CWGSDb_Impl(), and GetWGSPath().

The documentation for this class was generated from the following files:

include/sra/readers/sra/wgsread.hpp
src/sra/readers/sra/wgsread.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TAmbiguityCache

◆ TGiRange

◆ TGiRanges

◆ TIdRange

◆ TMasterDescr

◆ TMasterDescrBytes

◆ TProtAccRanges

◆ TRowType

Member Enumeration Documentation

◆ EAllowRowType

◆ EGnlIdFlags

◆ ERowType

Constructor & Destructor Documentation

◆ CWGSDb_Impl()

◆ ~CWGSDb_Impl()

Member Function Documentation

◆ AddMasterDescr()

◆ CanHaveGis()

◆ ContigNameIndex()

◆ DECLARE_SAFE_FLAGS_TYPE() [1/2]

◆ DECLARE_SAFE_FLAGS_TYPE() [2/2]

◆ DetermineFeatLocIdType()

◆ Feat()

◆ FeatTable()

◆ GetAccSeq_id() [1/2]

◆ GetAccSeq_id() [2/2]

◆ GetAmbiguityInfo()

◆ GetCommonTaxId()

◆ GetContigMolType()

◆ GetContigNameRowId()

◆ GetContigSeq_id()

◆ GetFeatLocIdType()

◆ GetGeneralOrPatentSeq_id() [1/4]

◆ GetGeneralOrPatentSeq_id() [2/4]

◆ GetGeneralOrPatentSeq_id() [3/4]

◆ GetGeneralOrPatentSeq_id() [4/4]

◆ GetGeneralSeq_id() [1/2]

◆ GetGeneralSeq_id() [2/2]

◆ GetGiRowId()

◆ GetIdPrefix()

◆ GetIdPrefixWithVersion()

◆ GetIdRowDigits()

◆ GetMasterDescr()

◆ GetMasterDescrBytes()

◆ GetMasterDescrEntry()

◆ GetMasterGi()

◆ GetMasterSeq_entry()

◆ GetMasterSeq_id()

◆ GetNucGiRange()

◆ GetNucGiRanges()

◆ GetNucGiRowId()

◆ GetPatentId()

◆ GetPatentSeq_id()

◆ GetProductNameRowId()

◆ GetProjectGBState()

◆ GetProtAccRanges()

◆ GetProtAccRowId()

◆ GetProteinMolType()

◆ GetProteinNameRowId()

◆ GetProteinSeq_id()

◆ GetProtGiRange()

◆ GetProtGiRanges()

◆ GetProtGiRowId()

◆ GetReplacedBy()

◆ GetScaffoldMolType()

◆ GetScaffoldNameRowId()

◆ GetScaffoldSeq_id()

◆ GetTotalFeatureCount()

◆ GetWGSPath()