Search Toolkit Book for CWGSProteinIterator

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

Inheritance diagram for CWGSProteinIterator:

Collaboration diagram for CWGSProteinIterator:

Public Types
typedef NCBI_WGS_hash	THash

typedef CBioseq::TAnnot	TAnnotSet

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
	CWGSProteinIterator (void)

	CWGSProteinIterator (const CWGSDb &wgs_db)

	CWGSProteinIterator (const CWGSDb &wgs_db, TVDBRowId row)

	CWGSProteinIterator (const CWGSDb &wgs_db, CTempString acc)

	~CWGSProteinIterator (void)

void	Reset (void)

	CWGSProteinIterator (const CWGSProteinIterator &iter)

CWGSProteinIterator &	operator= (const CWGSProteinIterator &iter)

	DECLARE_OPERATOR_BOOL (m_CurrId< m_FirstBadId)

CWGSProteinIterator &	operator++ (void)

TVDBRowId	GetCurrentRowId (void) const

TVDBRowId	GetFirstGoodRowId (void) const

TVDBRowId	GetFirstBadRowId (void) const

TVDBRowCount	GetRemainingCount (void) const

TVDBRowCount	GetSize (void) const

CWGSProteinIterator &	SelectRow (TVDBRowId row)

bool	HasGi (void) const

CSeq_id::TGi	GetGi (void) const

CTempString	GetAccession (void) const

int	GetAccVersion (void) const

CRef< CSeq_id >	GetAccSeq_id (void) const

CRef< CSeq_id >	GetGiSeq_id (void) const

CRef< CSeq_id >	GetGeneralSeq_id (void) const

CRef< CSeq_id >	GetGeneralOrPatentSeq_id (void) const

CTempString	GetProteinName (void) const

CTempString	GetProductName (void) const

bool	HasTaxId (void) const

TTaxId	GetTaxId (void) const

bool	HasSeqHash (void) const

THash	GetSeqHash (void) const

TVDBRowIdRange	GetLocFeatRowIdRange (void) const

size_t	GetProductFeatCount (void) const

TVDBRowId	GetProductFeatRowId (size_t index) const

TVDBRowId	GetBestProductFeatRowId (void) const

TVDBRowId	GetProductFeatRowId (void) const

TVDBRowId	GetReplacedByRowId (void) const

TVDBRowId	GetReplacesRowId (void) const

CRef< CSeq_id >	GetId (TFlags flags=fDefaultFlags) const

void	GetIds (CBioseq::TId &ids, TFlags flags=fDefaultFlags) const

bool	HasRefAcc (void) const

CTempString	GetRefAcc (void) const

NCBI_gb_state	GetGBState (void) const

NCBI_gb_state	GetRawGBState (void) const

NCBI_gb_state	GetGBState (EGBStateType type) const

bool	HasPublicComment (void) const

CTempString	GetPublicComment (void) const

TSeqPos	GetSeqLength (void) const

bool	HasSeq_descr (TFlags flags=fDefaultFlags) const

CRef< CSeq_descr >	GetSeq_descr (TFlags flags=fDefaultFlags) const

bool	HasTitle (void) const

CTempString	GetTitle (void) const

bool	HasAnnotSet (void) const

void	GetAnnotSet (TAnnotSet &annot_set, TFlags flags=fDefaultFlags) const

CRef< CSeq_inst >	GetSeq_inst (TFlags flags=fDefaultFlags) const

CRef< CBioseq >	GetBioseq (TFlags flags=fDefaultFlags) const

CRef< CSeq_entry >	GetSeq_entry (TFlags flags=fDefaultFlags) const

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

Protected Member Functions
void	x_Init (const CWGSDb &wgs_db)

void	x_Cur () const

CWGSDb_Impl &	GetDb (void) const

void	x_ReportInvalid (const char *method) const

void	x_CheckValid (const char *method) const

void	x_CreateBioseq (SWGSCreateInfo &info) const

void	x_CreateEntry (SWGSCreateInfo &info) const

Private Attributes
CWGSDb	m_Db

CRef< CWGSDb_Impl::SProt0TableCursor >	m_Cur0

CRef< CWGSDb_Impl::SProtTableCursor >	m_Cur

TVDBRowId	m_CurrId

TVDBRowId	m_FirstGoodId

TVDBRowId	m_FirstBadId

Friends
struct	SWGSCreateInfo

struct	SWGSFeatChunkInfo

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

Detailed Description

Definition at line 1407 of file wgsread.hpp.

Member Typedef Documentation

◆ TAnnotSet

typedef CBioseq::TAnnot CWGSProteinIterator::TAnnotSet

Definition at line 1502 of file wgsread.hpp.

◆ THash

typedef NCBI_WGS_hash CWGSProteinIterator::THash

Definition at line 1464 of file wgsread.hpp.

Constructor & Destructor Documentation

◆ CWGSProteinIterator() [1/5]

CWGSProteinIterator::CWGSProteinIterator ( void )

Definition at line 7042 of file wgsread.cpp.

◆ CWGSProteinIterator() [2/5]

CWGSProteinIterator::CWGSProteinIterator ( const CWGSDb & wgs_db )

explicit

Definition at line 7071 of file wgsread.cpp.

References x_Init().

◆ CWGSProteinIterator() [3/5]

CWGSProteinIterator::CWGSProteinIterator	(	const CWGSDb &	wgs_db,
		TVDBRowId	row
	)

Definition at line 7077 of file wgsread.cpp.

References row, SelectRow(), and x_Init().

◆ CWGSProteinIterator() [4/5]

CWGSProteinIterator::CWGSProteinIterator	(	const CWGSDb &	wgs_db,
		CTempString	acc
	)

Definition at line 7084 of file wgsread.cpp.

References m_CurrId, m_FirstBadId, m_FirstGoodId, CWGSDb::ParseProteinRow(), row, SelectRow(), and x_Init().

◆ ~CWGSProteinIterator()

CWGSProteinIterator::~CWGSProteinIterator ( void )

Definition at line 7097 of file wgsread.cpp.

References Reset().

◆ CWGSProteinIterator() [5/5]

CWGSProteinIterator::CWGSProteinIterator ( const CWGSProteinIterator & iter )

Definition at line 7048 of file wgsread.cpp.

Member Function Documentation

◆ DECLARE_OPERATOR_BOOL()

CWGSProteinIterator::DECLARE_OPERATOR_BOOL ( )

◆ GetAccession()

CTempString CWGSProteinIterator::GetAccession ( void ) const

Definition at line 7168 of file wgsread.cpp.

References m_Cur0, m_CurrId, PROFILE, and x_CheckValid().

Referenced by GetAccSeq_id().

◆ GetAccSeq_id()

CRef< CSeq_id > CWGSProteinIterator::GetAccSeq_id ( void ) const

Definition at line 7189 of file wgsread.cpp.

References CTempString::empty(), GetAccession(), CWGSDb_Impl::GetAccSeq_id(), GetAccVersion(), GetDb(), CWGSDb_Impl::GetProteinSeq_id(), m_CurrId, and PROFILE.

Referenced by GetId(), and GetIds().

◆ GetAccVersion()

int CWGSProteinIterator::GetAccVersion ( void ) const

Definition at line 7181 of file wgsread.cpp.

References m_Cur0, m_CurrId, PROFILE, and x_CheckValid().

Referenced by GetAccSeq_id(), and CWGSClient::IsCorrectVersion().

◆ GetAnnotSet()

void CWGSProteinIterator::GetAnnotSet	(	TAnnotSet &	annot_set,
		TFlags	flags = `fDefaultFlags`
	)		const

Definition at line 7597 of file wgsread.cpp.

References flags, SWGSDb_Defs::fSeqAnnot, m_Cur, m_CurrId, sx_AddAnnotBytes(), x_CheckValid(), and x_Cur().

Referenced by x_CreateBioseq().

◆ GetBestProductFeatRowId()

TVDBRowId CWGSProteinIterator::GetBestProductFeatRowId ( void ) const

Definition at line 7480 of file wgsread.cpp.

References m_Cur, m_CurrId, row, x_CheckValid(), and x_Cur().

Referenced by CWGSFileInfo::SAccFileInfo::GetRootFileInfo().

◆ GetBioseq()

CRef< CBioseq > CWGSProteinIterator::GetBioseq ( TFlags flags = fDefaultFlags ) const

Definition at line 7694 of file wgsread.cpp.

References eFromFlags, flags, info, m_Db, x_CheckValid(), and x_CreateBioseq().

◆ GetCurrentRowId()

TVDBRowId CWGSProteinIterator::GetCurrentRowId ( void ) const

inline

Definition at line 1428 of file wgsread.hpp.

References m_CurrId.

Referenced by GetRemainingCount().

◆ GetDb()

CWGSDb_Impl& CWGSProteinIterator::GetDb ( void ) const

inlineprotected

Definition at line 1518 of file wgsread.hpp.

References CRef< C, Locker >::GetNCObject(), and m_Db.

Referenced by SWGSFeatChunkInfo::CreateChunkInfo(), GetAccSeq_id(), GetGeneralOrPatentSeq_id(), GetId(), GetSeq_descr(), GetSeq_inst(), GetTaxId(), HasSeq_descr(), HasTaxId(), Reset(), and x_Cur().

◆ GetFirstBadRowId()

TVDBRowId CWGSProteinIterator::GetFirstBadRowId ( void ) const

inline

Definition at line 1434 of file wgsread.hpp.

References m_FirstBadId.

Referenced by GetRemainingCount(), and GetSize().

◆ GetFirstGoodRowId()

TVDBRowId CWGSProteinIterator::GetFirstGoodRowId ( void ) const

inline

Definition at line 1431 of file wgsread.hpp.

References m_FirstGoodId.

Referenced by GetSize().

◆ GetGBState() [1/2]

NCBI_gb_state CWGSProteinIterator::GetGBState ( EGBStateType type ) const

Definition at line 7367 of file wgsread.cpp.

References SWGSDb_Defs::eGBStateProject, SWGSDb_Defs::eGBStateRaw, GetRawGBState(), m_Db, and x_CheckValid().

◆ GetGBState() [2/2]

NCBI_gb_state CWGSProteinIterator::GetGBState ( void ) const

Definition at line 7361 of file wgsread.cpp.

References SWGSDb_Defs::eGBStateAll.

Referenced by CWGSClient::HasMigrated(), CWGSClient::HasSpecialState(), and CWGSFileInfo::SAccFileInfo::IsMigrated().

◆ GetGeneralOrPatentSeq_id()

CRef< CSeq_id > CWGSProteinIterator::GetGeneralOrPatentSeq_id ( void ) const

Definition at line 7205 of file wgsread.cpp.

References GetDb(), CWGSDb_Impl::GetGeneralOrPatentSeq_id(), GetProteinName(), m_Cur0, and m_CurrId.

Referenced by GetGeneralSeq_id(), GetId(), and GetIds().

◆ GetGeneralSeq_id()

CRef< CSeq_id > CWGSProteinIterator::GetGeneralSeq_id ( void ) const

Definition at line 7211 of file wgsread.cpp.

References GetGeneralOrPatentSeq_id().

◆ GetGi()

CSeq_id::TGi CWGSProteinIterator::GetGi ( void ) const

Definition at line 7155 of file wgsread.cpp.

References CVDBValue::empty(), m_Cur0, m_CurrId, s_ToGi(), x_CheckValid(), and ZERO_GI.

Referenced by SWGSFeatChunkInfo::CreateChunkInfo(), CWGSClient::GetGi(), GetGiSeq_id(), and HasGi().

◆ GetGiSeq_id()

CRef< CSeq_id > CWGSProteinIterator::GetGiSeq_id ( void ) const

Definition at line 7217 of file wgsread.cpp.

References GetGi(), PROFILE, CSeq_id_Base::SetGi(), and ZERO_GI.

Referenced by GetId(), and GetIds().

◆ GetId()

CRef< CSeq_id > CWGSProteinIterator::GetId ( TFlags flags = fDefaultFlags ) const

Definition at line 7230 of file wgsread.cpp.

References SWGSDb_Defs::fIds_acc, SWGSDb_Defs::fIds_gi, SWGSDb_Defs::fIds_gnl, flags, GetAccSeq_id(), GetDb(), GetGeneralOrPatentSeq_id(), GetGiSeq_id(), m_CurrId, and NCBI_THROW_FMT.

Referenced by SWGSFeatChunkInfo::CreateChunkInfo(), and GetSeq_inst().

◆ GetIds()

void CWGSProteinIterator::GetIds	(	CBioseq::TId &	ids,
		TFlags	flags = `fDefaultFlags`
	)		const

Definition at line 7260 of file wgsread.cpp.

References SWGSDb_Defs::fIds_acc, SWGSDb_Defs::fIds_gi, SWGSDb_Defs::fIds_gnl, flags, GetAccSeq_id(), GetGeneralOrPatentSeq_id(), GetGiSeq_id(), and PROFILE.

Referenced by x_CreateBioseq(), and SWGSCreateInfo::x_CreateProtSet().

◆ GetLocFeatRowIdRange()

TVDBRowIdRange CWGSProteinIterator::GetLocFeatRowIdRange ( void ) const

Definition at line 7436 of file wgsread.cpp.

References CVDBValue::empty(), m_Cur, m_CurrId, NCBI_THROW_FMT, x_CheckValid(), and x_Cur().

Referenced by x_CreateBioseq().

◆ GetProductFeatCount()

size_t CWGSProteinIterator::GetProductFeatCount ( void ) const

Definition at line 7458 of file wgsread.cpp.

References m_Cur, m_CurrId, x_CheckValid(), and x_Cur().

◆ GetProductFeatRowId() [1/2]

TVDBRowId CWGSProteinIterator::GetProductFeatRowId ( size_t index ) const

Definition at line 7469 of file wgsread.cpp.

References m_Cur, m_CurrId, x_CheckValid(), and x_Cur().

◆ GetProductFeatRowId() [2/2]

TVDBRowId CWGSProteinIterator::GetProductFeatRowId ( void ) const

Definition at line 7492 of file wgsread.cpp.

References m_Cur, m_CurrId, row, x_CheckValid(), and x_Cur().

◆ GetProductName()

CTempString CWGSProteinIterator::GetProductName ( void ) const

Definition at line 7294 of file wgsread.cpp.

References m_Cur, m_CurrId, x_CheckValid(), and x_Cur().

◆ GetProteinName()

CTempString CWGSProteinIterator::GetProteinName ( void ) const

Definition at line 7287 of file wgsread.cpp.

References m_Cur0, m_CurrId, and x_CheckValid().

Referenced by GetGeneralOrPatentSeq_id().

◆ GetPublicComment()

CTempString CWGSProteinIterator::GetPublicComment ( void ) const

Definition at line 7406 of file wgsread.cpp.

References m_Cur, m_CurrId, string, x_CheckValid(), and x_Cur().

◆ GetRawGBState()

NCBI_gb_state CWGSProteinIterator::GetRawGBState ( void ) const

Definition at line 7382 of file wgsread.cpp.

References m_Cur, m_CurrId, x_CheckValid(), and x_Cur().

Referenced by GetGBState().

◆ GetRefAcc()

CTempString CWGSProteinIterator::GetRefAcc ( void ) const

Definition at line 7353 of file wgsread.cpp.

References m_Cur, m_CurrId, x_CheckValid(), and x_Cur().

◆ GetRemainingCount()

TVDBRowCount CWGSProteinIterator::GetRemainingCount ( void ) const

inline

Definition at line 1437 of file wgsread.hpp.

References GetCurrentRowId(), and GetFirstBadRowId().

◆ GetReplacedByRowId()

TVDBRowId CWGSProteinIterator::GetReplacedByRowId ( void ) const

Definition at line 7504 of file wgsread.cpp.

References m_Cur, m_CurrId, rapidjson::value, x_CheckValid(), and x_Cur().

Referenced by GetSeq_inst().

◆ GetReplacesRowId()

TVDBRowId CWGSProteinIterator::GetReplacesRowId ( void ) const

Definition at line 7523 of file wgsread.cpp.

References m_Cur, m_CurrId, rapidjson::value, x_CheckValid(), and x_Cur().

Referenced by GetSeq_inst().

◆ GetSeq_descr()

CRef< CSeq_descr > CWGSProteinIterator::GetSeq_descr ( TFlags flags = fDefaultFlags ) const

Definition at line 7561 of file wgsread.cpp.

References CWGSDb_Impl::AddMasterDescr(), CTempString::empty(), flags, SWGSDb_Defs::fMasterDescr, SWGSDb_Defs::fSeqDescr, CSeq_descr_Base::Get(), GetDb(), GetTitle(), m_Cur, m_CurrId, CRef< C, Locker >::Reset(), CSeq_descr_Base::Set(), CSeqdesc_Base::SetTitle(), sx_AddDescrBytes(), x_CheckValid(), and x_Cur().

Referenced by x_CreateBioseq().

◆ GetSeq_entry()

CRef< CSeq_entry > CWGSProteinIterator::GetSeq_entry ( TFlags flags = fDefaultFlags ) const

Definition at line 7703 of file wgsread.cpp.

References eFromFlags, flags, info, m_Db, x_CheckValid(), and x_CreateEntry().

Referenced by CWGSClient::GetWGSData().

◆ GetSeq_inst()

CRef< CSeq_inst > CWGSProteinIterator::GetSeq_inst ( TFlags flags = fDefaultFlags ) const

Definition at line 7607 of file wgsread.cpp.

References CSeq_inst_Base::eRepr_raw, GetDb(), GetId(), GetReplacedByRowId(), GetReplacesRowId(), GetSeqLength(), m_Cur, m_CurrId, m_Db, PROFILE, CSeq_inst_Base::SetHist(), CSeq_inst_Base::SetLength(), CSeq_inst_Base::SetMol(), CSeq_hist_Base::SetReplaced_by(), CSeq_hist_Base::SetReplaces(), CSeq_inst_Base::SetRepr(), CSeq_inst_Base::SetSeq_data(), x_CheckValid(), and x_Cur().

Referenced by x_CreateBioseq().

◆ GetSeqHash()

CWGSProteinIterator::THash CWGSProteinIterator::GetSeqHash ( void ) const

Definition at line 7331 of file wgsread.cpp.

References HasSeqHash(), m_Cur, and m_CurrId.

Referenced by CWGSClient::GetBioseqInfo().

◆ GetSeqLength()

TSeqPos CWGSProteinIterator::GetSeqLength ( void ) const

Definition at line 7337 of file wgsread.cpp.

References m_Cur, m_CurrId, x_CheckValid(), and x_Cur().

Referenced by CWGSClient::GetBioseqInfo(), and GetSeq_inst().

◆ GetSize()

TVDBRowCount CWGSProteinIterator::GetSize ( void ) const

inline

Definition at line 1440 of file wgsread.hpp.

References GetFirstBadRowId(), and GetFirstGoodRowId().

◆ GetTaxId()

TTaxId CWGSProteinIterator::GetTaxId ( void ) const

Definition at line 7312 of file wgsread.cpp.

References CWGSDb_Impl::GetCommonTaxId(), GetDb(), m_Cur, m_CurrId, s_GetTaxId(), x_CheckValid(), and x_Cur().

Referenced by CWGSClient::GetBioseqInfo().

◆ GetTitle()

CTempString CWGSProteinIterator::GetTitle ( void ) const

Definition at line 7425 of file wgsread.cpp.

References m_Cur, m_CurrId, x_CheckValid(), and x_Cur().

Referenced by GetSeq_descr(), and HasSeq_descr().

◆ HasAnnotSet()

bool CWGSProteinIterator::HasAnnotSet ( void ) const

Definition at line 7589 of file wgsread.cpp.

References m_Cur, m_CurrId, x_CheckValid(), and x_Cur().

◆ HasGi()

bool CWGSProteinIterator::HasGi ( void ) const

Definition at line 7149 of file wgsread.cpp.

References GetGi(), m_Cur0, and ZERO_GI.

Referenced by CWGSClient::GetGi(), CWGSClient::HasMigrated(), CWGSClient::HasSpecialState(), and CWGSFileInfo::SAccFileInfo::IsMigrated().

◆ HasPublicComment()

bool CWGSProteinIterator::HasPublicComment ( void ) const

Definition at line 7395 of file wgsread.cpp.

References m_Cur, m_CurrId, x_CheckValid(), and x_Cur().

◆ HasRefAcc()

bool CWGSProteinIterator::HasRefAcc ( void ) const

Definition at line 7345 of file wgsread.cpp.

References m_Cur, x_CheckValid(), and x_Cur().

◆ HasSeq_descr()

bool CWGSProteinIterator::HasSeq_descr ( TFlags flags = fDefaultFlags ) const

Definition at line 7542 of file wgsread.cpp.

References ctll::empty(), flags, SWGSDb_Defs::fMasterDescr, SWGSDb_Defs::fSeqDescr, GetDb(), GetTitle(), m_Cur, m_CurrId, x_CheckValid(), and x_Cur().

◆ HasSeqHash()

bool CWGSProteinIterator::HasSeqHash ( void ) const

Definition at line 7323 of file wgsread.cpp.

References m_Cur, x_CheckValid(), and x_Cur().

Referenced by CWGSClient::GetBioseqInfo(), and GetSeqHash().

◆ HasTaxId()

bool CWGSProteinIterator::HasTaxId ( void ) const

Definition at line 7302 of file wgsread.cpp.

References GetDb(), m_Cur, and x_Cur().

Referenced by CWGSClient::GetBioseqInfo().

◆ HasTitle()

bool CWGSProteinIterator::HasTitle ( void ) const

Definition at line 7417 of file wgsread.cpp.

References m_Cur, m_CurrId, x_CheckValid(), and x_Cur().

◆ operator++()

CWGSProteinIterator& CWGSProteinIterator::operator++ ( void )

inline

Definition at line 1423 of file wgsread.hpp.

References m_CurrId.

◆ operator=()

CWGSProteinIterator & CWGSProteinIterator::operator= ( const CWGSProteinIterator & iter )

Definition at line 7056 of file wgsread.cpp.

References m_Cur, m_Cur0, m_CurrId, m_Db, m_FirstBadId, m_FirstGoodId, and Reset().

◆ Reset()

void CWGSProteinIterator::Reset ( void )

Definition at line 7024 of file wgsread.cpp.

References GetDb(), m_Cur, m_Cur0, m_CurrId, m_Db, m_FirstBadId, m_FirstGoodId, CWGSDb_Impl::Put(), and CRef< C, Locker >::Reset().

Referenced by operator=(), and ~CWGSProteinIterator().

◆ SelectRow()

CWGSProteinIterator & CWGSProteinIterator::SelectRow ( TVDBRowId row )

Definition at line 7129 of file wgsread.cpp.

References m_CurrId, m_FirstBadId, m_FirstGoodId, and row.

Referenced by SWGSFeatChunkInfo::CreateChunkInfo(), CWGSProteinIterator(), SWGSCreateInfo::x_AddProducts(), and SWGSCreateInfo::x_CreateProtSet().

◆ x_CheckValid()

void CWGSProteinIterator::x_CheckValid ( const char * method ) const

inlineprotected

Definition at line 1523 of file wgsread.hpp.

References x_ReportInvalid().

Referenced by GetAccession(), GetAccVersion(), GetAnnotSet(), GetBestProductFeatRowId(), GetBioseq(), GetGBState(), GetGi(), GetLocFeatRowIdRange(), GetProductFeatCount(), GetProductFeatRowId(), GetProductName(), GetProteinName(), GetPublicComment(), GetRawGBState(), GetRefAcc(), GetReplacedByRowId(), GetReplacesRowId(), GetSeq_descr(), GetSeq_entry(), GetSeq_inst(), GetSeqLength(), GetTaxId(), GetTitle(), HasAnnotSet(), HasPublicComment(), HasRefAcc(), HasSeq_descr(), HasSeqHash(), and HasTitle().

◆ x_CreateBioseq()

void CWGSProteinIterator::x_CreateBioseq ( SWGSCreateInfo & info ) const

protected

Definition at line 7638 of file wgsread.cpp.

References _ASSERT, CSeq_entry_Base::e_not_set, CVDBValue::empty(), SWGSDb_Defs::fMaskAnnot, SWGSDb_Defs::fMaskDescr, SWGSDb_Defs::fSeqDescr, GetAnnotSet(), GetIds(), GetLocFeatRowIdRange(), GetSeq_descr(), GetSeq_inst(), info, m_Cur, m_CurrId, PROFILE, and x_Cur().

Referenced by GetBioseq(), SWGSCreateInfo::x_AddProducts(), and x_CreateEntry().

◆ x_CreateEntry()

void CWGSProteinIterator::x_CreateEntry ( SWGSCreateInfo & info ) const

protected

Definition at line 7687 of file wgsread.cpp.

References info, PROFILE, and x_CreateBioseq().

Referenced by GetSeq_entry().

◆ x_Cur()

void CWGSProteinIterator::x_Cur ( ) const

protected

Definition at line 7121 of file wgsread.cpp.

References GetDb(), m_Cur, and CWGSDb_Impl::Prot().

Referenced by GetAnnotSet(), GetBestProductFeatRowId(), GetLocFeatRowIdRange(), GetProductFeatCount(), GetProductFeatRowId(), GetProductName(), GetPublicComment(), GetRawGBState(), GetRefAcc(), GetReplacedByRowId(), GetReplacesRowId(), GetSeq_descr(), GetSeq_inst(), GetSeqLength(), GetTaxId(), GetTitle(), HasAnnotSet(), HasPublicComment(), HasRefAcc(), HasSeq_descr(), HasSeqHash(), HasTaxId(), HasTitle(), and x_CreateBioseq().

◆ x_Init()

void CWGSProteinIterator::x_Init ( const CWGSDb & wgs_db )

protected

Definition at line 7103 of file wgsread.cpp.

References CRef< C, Locker >::GetNCObject(), CVDBCursor::GetRowIdRange(), m_Cur0, m_CurrId, CWGSDb_Impl::SProt0TableCursor::m_Cursor, m_Db, m_FirstBadId, m_FirstGoodId, PROFILE, CWGSDb_Impl::Prot0(), and compile_time_bits::range().

Referenced by CWGSProteinIterator().

◆ x_ReportInvalid()

void CWGSProteinIterator::x_ReportInvalid ( const char * method ) const

protected

Definition at line 7141 of file wgsread.cpp.

References NCBI_THROW_FMT.

Referenced by x_CheckValid().

Friends And Related Function Documentation

◆ SWGSCreateInfo

friend struct SWGSCreateInfo

friend

Definition at line 1512 of file wgsread.hpp.

◆ SWGSFeatChunkInfo

friend struct SWGSFeatChunkInfo

friend

Definition at line 1513 of file wgsread.hpp.

Member Data Documentation

◆ m_Cur

CRef<CWGSDb_Impl::SProtTableCursor> CWGSProteinIterator::m_Cur

private

◆ m_Cur0

CRef<CWGSDb_Impl::SProt0TableCursor> CWGSProteinIterator::m_Cur0

private

Definition at line 1534 of file wgsread.hpp.

Referenced by GetAccession(), GetAccVersion(), GetGeneralOrPatentSeq_id(), GetGi(), GetProteinName(), HasGi(), operator=(), Reset(), and x_Init().

◆ m_CurrId

TVDBRowId CWGSProteinIterator::m_CurrId

private

◆ m_Db

CWGSDb CWGSProteinIterator::m_Db

private

Definition at line 1533 of file wgsread.hpp.

Referenced by GetBioseq(), GetDb(), GetGBState(), GetSeq_entry(), GetSeq_inst(), operator=(), Reset(), and x_Init().

◆ m_FirstBadId

TVDBRowId CWGSProteinIterator::m_FirstBadId

private

Definition at line 1536 of file wgsread.hpp.

Referenced by CWGSProteinIterator(), GetFirstBadRowId(), operator=(), Reset(), SelectRow(), and x_Init().

◆ m_FirstGoodId

TVDBRowId CWGSProteinIterator::m_FirstGoodId

private

Definition at line 1536 of file wgsread.hpp.

Referenced by CWGSProteinIterator(), GetFirstGoodRowId(), operator=(), Reset(), SelectRow(), and x_Init().

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

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

Public Types

Public Member Functions

Protected Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TAnnotSet

◆ THash

Constructor & Destructor Documentation

◆ CWGSProteinIterator() [1/5]

◆ CWGSProteinIterator() [2/5]

◆ CWGSProteinIterator() [3/5]

◆ CWGSProteinIterator() [4/5]

◆ ~CWGSProteinIterator()

◆ CWGSProteinIterator() [5/5]

Member Function Documentation

◆ DECLARE_OPERATOR_BOOL()

◆ GetAccession()

◆ GetAccSeq_id()

◆ GetAccVersion()

◆ GetAnnotSet()

◆ GetBestProductFeatRowId()

◆ GetBioseq()

◆ GetCurrentRowId()

◆ GetDb()

◆ GetFirstBadRowId()

◆ GetFirstGoodRowId()

◆ GetGBState() [1/2]

◆ GetGBState() [2/2]

◆ GetGeneralOrPatentSeq_id()

◆ GetGeneralSeq_id()

◆ GetGi()

◆ GetGiSeq_id()

◆ GetId()

◆ GetIds()

◆ GetLocFeatRowIdRange()

◆ GetProductFeatCount()

◆ GetProductFeatRowId() [1/2]

◆ GetProductFeatRowId() [2/2]

◆ GetProductName()

◆ GetProteinName()

◆ GetPublicComment()

◆ GetRawGBState()

◆ GetRefAcc()

◆ GetRemainingCount()

◆ GetReplacedByRowId()

◆ GetReplacesRowId()

◆ GetSeq_descr()

◆ GetSeq_entry()

◆ GetSeq_inst()

◆ GetSeqHash()

◆ GetSeqLength()

◆ GetSize()

◆ GetTaxId()

◆ GetTitle()

◆ HasAnnotSet()

◆ HasGi()

◆ HasPublicComment()

◆ HasRefAcc()

◆ HasSeq_descr()

◆ HasSeqHash()

◆ HasTaxId()

◆ HasTitle()

◆ operator++()

◆ operator=()

◆ Reset()

◆ SelectRow()

◆ x_CheckValid()

◆ x_CreateBioseq()

◆ x_CreateEntry()

◆ x_Cur()

◆ x_Init()

◆ x_ReportInvalid()

Friends And Related Function Documentation

◆ SWGSCreateInfo

◆ SWGSFeatChunkInfo

Member Data Documentation

◆ m_Cur