NCBI C++ ToolKit
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CWGSProteinIterator Class Reference

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 }
 
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)
 
CWGSProteinIteratoroperator= (const CWGSProteinIterator &iter)
 
 DECLARE_OPERATOR_BOOL (m_CurrId< m_FirstBadId)
 
CWGSProteinIteratoroperator++ (void)
 
TVDBRowId GetCurrentRowId (void) const
 
TVDBRowId GetFirstGoodRowId (void) const
 
TVDBRowId GetFirstBadRowId (void) const
 
TVDBRowCount GetRemainingCount (void) const
 
TVDBRowCount GetSize (void) const
 
CWGSProteinIteratorSelectRow (TVDBRowId row)
 
bool HasGi (void) const
 
CSeq_id::TGi GetGi (void) const
 
CTempString GetAccession (void) const
 
int GetAccVersion (void) const
 
CRef< CSeq_idGetAccSeq_id (void) const
 
CRef< CSeq_idGetGiSeq_id (void) const
 
CRef< CSeq_idGetGeneralSeq_id (void) const
 
CRef< CSeq_idGetGeneralOrPatentSeq_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_idGetId (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
 
bool HasPublicComment (void) const
 
CTempString GetPublicComment (void) const
 
TSeqPos GetSeqLength (void) const
 
bool HasSeq_descr (TFlags flags=fDefaultFlags) const
 
CRef< CSeq_descrGetSeq_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_instGetSeq_inst (TFlags flags=fDefaultFlags) const
 
CRef< CBioseqGetBioseq (TFlags flags=fDefaultFlags) const
 
CRef< CSeq_entryGetSeq_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_ImplGetDb (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::SProt0TableCursorm_Cur0
 
CRef< CWGSDb_Impl::SProtTableCursorm_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 1395 of file wgsread.hpp.

Member Typedef Documentation

◆ TAnnotSet

Definition at line 1488 of file wgsread.hpp.

◆ THash

Definition at line 1452 of file wgsread.hpp.

Constructor & Destructor Documentation

◆ CWGSProteinIterator() [1/5]

CWGSProteinIterator::CWGSProteinIterator ( void  )

Definition at line 6992 of file wgsread.cpp.

◆ CWGSProteinIterator() [2/5]

CWGSProteinIterator::CWGSProteinIterator ( const CWGSDb wgs_db)
explicit

Definition at line 7021 of file wgsread.cpp.

References x_Init().

◆ CWGSProteinIterator() [3/5]

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

Definition at line 7027 of file wgsread.cpp.

References SelectRow(), and x_Init().

◆ CWGSProteinIterator() [4/5]

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

◆ ~CWGSProteinIterator()

CWGSProteinIterator::~CWGSProteinIterator ( void  )

Definition at line 7047 of file wgsread.cpp.

References Reset().

◆ CWGSProteinIterator() [5/5]

CWGSProteinIterator::CWGSProteinIterator ( const CWGSProteinIterator iter)

Definition at line 6998 of file wgsread.cpp.

Member Function Documentation

◆ DECLARE_OPERATOR_BOOL()

CWGSProteinIterator::DECLARE_OPERATOR_BOOL ( )

◆ GetAccession()

CTempString CWGSProteinIterator::GetAccession ( void  ) const

Definition at line 7118 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

◆ GetAccVersion()

int CWGSProteinIterator::GetAccVersion ( void  ) const

Definition at line 7131 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 7522 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

◆ GetBioseq()

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

Definition at line 7619 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 1416 of file wgsread.hpp.

References m_CurrId.

Referenced by GetRemainingCount().

◆ GetDb()

CWGSDb_Impl& CWGSProteinIterator::GetDb ( void  ) const
inlineprotected

◆ GetFirstBadRowId()

TVDBRowId CWGSProteinIterator::GetFirstBadRowId ( void  ) const
inline

Definition at line 1422 of file wgsread.hpp.

References m_FirstBadId.

Referenced by GetRemainingCount(), and GetSize().

◆ GetFirstGoodRowId()

TVDBRowId CWGSProteinIterator::GetFirstGoodRowId ( void  ) const
inline

Definition at line 1419 of file wgsread.hpp.

References m_FirstGoodId.

Referenced by GetSize().

◆ GetGBState()

NCBI_gb_state CWGSProteinIterator::GetGBState ( void  ) const

◆ GetGeneralOrPatentSeq_id()

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

◆ GetGeneralSeq_id()

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

Definition at line 7161 of file wgsread.cpp.

References GetGeneralOrPatentSeq_id().

◆ GetGi()

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

◆ GetGiSeq_id()

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

Definition at line 7167 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

◆ GetIds()

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

◆ GetLocFeatRowIdRange()

TVDBRowIdRange CWGSProteinIterator::GetLocFeatRowIdRange ( void  ) const

Definition at line 7361 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 7383 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 7394 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 7417 of file wgsread.cpp.

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

◆ GetProductName()

CTempString CWGSProteinIterator::GetProductName ( void  ) const

Definition at line 7244 of file wgsread.cpp.

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

◆ GetProteinName()

CTempString CWGSProteinIterator::GetProteinName ( void  ) const

Definition at line 7237 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 7331 of file wgsread.cpp.

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

◆ GetRefAcc()

CTempString CWGSProteinIterator::GetRefAcc ( void  ) const

Definition at line 7303 of file wgsread.cpp.

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

◆ GetRemainingCount()

TVDBRowCount CWGSProteinIterator::GetRemainingCount ( void  ) const
inline

Definition at line 1425 of file wgsread.hpp.

References GetCurrentRowId(), and GetFirstBadRowId().

◆ GetReplacedByRowId()

TVDBRowId CWGSProteinIterator::GetReplacedByRowId ( void  ) const

Definition at line 7429 of file wgsread.cpp.

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

Referenced by GetSeq_inst().

◆ GetReplacesRowId()

TVDBRowId CWGSProteinIterator::GetReplacesRowId ( void  ) const

Definition at line 7448 of file wgsread.cpp.

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

Referenced by GetSeq_inst().

◆ GetSeq_descr()

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

◆ GetSeq_entry()

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

Definition at line 7628 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

◆ GetSeqHash()

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

Definition at line 7281 of file wgsread.cpp.

References HasSeqHash(), m_Cur, and m_CurrId.

Referenced by CWGSClient::GetBioseqInfo().

◆ GetSeqLength()

TSeqPos CWGSProteinIterator::GetSeqLength ( void  ) const

Definition at line 7287 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 1428 of file wgsread.hpp.

References GetFirstBadRowId(), and GetFirstGoodRowId().

◆ GetTaxId()

TTaxId CWGSProteinIterator::GetTaxId ( void  ) const

◆ GetTitle()

CTempString CWGSProteinIterator::GetTitle ( void  ) const

Definition at line 7350 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 7514 of file wgsread.cpp.

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

◆ HasGi()

bool CWGSProteinIterator::HasGi ( void  ) const

◆ HasPublicComment()

bool CWGSProteinIterator::HasPublicComment ( void  ) const

Definition at line 7320 of file wgsread.cpp.

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

◆ HasRefAcc()

bool CWGSProteinIterator::HasRefAcc ( void  ) const

Definition at line 7295 of file wgsread.cpp.

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

◆ HasSeq_descr()

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

◆ HasSeqHash()

bool CWGSProteinIterator::HasSeqHash ( void  ) const

Definition at line 7273 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 7252 of file wgsread.cpp.

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

Referenced by CWGSClient::GetBioseqInfo().

◆ HasTitle()

bool CWGSProteinIterator::HasTitle ( void  ) const

Definition at line 7342 of file wgsread.cpp.

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

◆ operator++()

CWGSProteinIterator& CWGSProteinIterator::operator++ ( void  )
inline

Definition at line 1411 of file wgsread.hpp.

References m_CurrId.

◆ operator=()

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

Definition at line 7006 of file wgsread.cpp.

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

◆ Reset()

void CWGSProteinIterator::Reset ( void  )

◆ SelectRow()

CWGSProteinIterator & CWGSProteinIterator::SelectRow ( TVDBRowId  row)

◆ x_CheckValid()

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

◆ x_CreateBioseq()

void CWGSProteinIterator::x_CreateBioseq ( SWGSCreateInfo info) const
protected

◆ x_CreateEntry()

void CWGSProteinIterator::x_CreateEntry ( SWGSCreateInfo info) const
protected

Definition at line 7612 of file wgsread.cpp.

References info, PROFILE, and x_CreateBioseq().

Referenced by GetSeq_entry().

◆ x_Cur()

void CWGSProteinIterator::x_Cur ( ) const
protected

◆ x_Init()

void CWGSProteinIterator::x_Init ( const CWGSDb wgs_db)
protected

◆ x_ReportInvalid()

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

Definition at line 7091 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 1498 of file wgsread.hpp.

◆ SWGSFeatChunkInfo

friend struct SWGSFeatChunkInfo
friend

Definition at line 1499 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

◆ m_CurrId

TVDBRowId CWGSProteinIterator::m_CurrId
private

◆ m_Db

CWGSDb CWGSProteinIterator::m_Db
private

◆ m_FirstBadId

TVDBRowId CWGSProteinIterator::m_FirstBadId
private

Definition at line 1522 of file wgsread.hpp.

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

◆ m_FirstGoodId

TVDBRowId CWGSProteinIterator::m_FirstGoodId
private

The documentation for this class was generated from the following files:
Modified on Sun Feb 25 03:05:45 2024 by modify_doxy.py rev. 669887