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CSNPDbPageIterator Class Reference

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

+ Inheritance diagram for CSNPDbPageIterator:
+ Collaboration diagram for CSNPDbPageIterator:

Public Member Functions

 CSNPDbPageIterator (void)
 
 CSNPDbPageIterator (const CSNPDb &db, const CSeq_id_Handle &ref_id, TSeqPos ref_pos=0, TSeqPos window=0, ESearchMode search_mode=eSearchByOverlap)
 
 CSNPDbPageIterator (const CSNPDb &db, const CSeq_id_Handle &ref_id, COpenRange< TSeqPos > ref_range, ESearchMode search_mode=eSearchByOverlap)
 
 CSNPDbPageIterator (const CSNPDbSeqIterator &seq, COpenRange< TSeqPos > ref_range, ESearchMode search_mode=eSearchByOverlap)
 
 CSNPDbPageIterator (const CSNPDbPageIterator &iter)
 
 ~CSNPDbPageIterator (void)
 
CSNPDbPageIteratoroperator= (const CSNPDbPageIterator &iter)
 
CSNPDbPageIteratorSelect (COpenRange< TSeqPos > ref_range, ESearchMode search_mode=eSearchByOverlap)
 
void Reset (void)
 
 DECLARE_OPERATOR_BOOL (m_CurrPagePos< m_SearchRange.GetToOpen())
 
CSNPDbPageIteratoroperator++ (void)
 
const CRange< TSeqPos > & GetSearchRange (void) const
 
ESearchMode GetSearchMode (void) const
 
CRef< CSeq_idGetSeqId (void) const
 
CSeq_id_Handle GetSeqIdHandle (void) const
 
TSeqPos GetPageSize (void) const
 
TSeqPos GetPagePos (void) const
 
CRange< TSeqPosGetPageRange (void) const
 
TVDBRowId GetPageRowId (void) const
 
const CSNPDbSeqIteratorGetRefIter (void) const
 
TVDBRowId GetFirstFeatRowId (void) const
 
TVDBRowCount GetFeatCount (void) const
 
void SetTrack (const CSNPDbTrackIterator &track)
 

Protected Member Functions

CSNPDb_ImplGetDb (void) const
 
const CSNPDb_Impl::SPageTableCursorCur (void) const
 
CSNPDb_Impl::TSeqInfoList::const_iterator x_GetSeqIter () const
 
CSNPDb_Impl::TTrackInfoList::const_iterator x_GetTrackIter () const
 
TVDBRowId x_GetSeqVDBRowId () const
 
TVDBRowId x_GetTrackVDBRowId () const
 
CRange< TVDBRowIdx_GetPageVDBRowRange () const
 
TVDBRowId x_GetGraphVDBRowId () const
 
void x_ReportInvalid (const char *method) const
 
void x_CheckValid (const char *method) const
 
void x_Next (void)
 

Private Attributes

CSNPDbSeqIterator m_SeqIter
 
CRef< CSNPDb_Impl::SPageTableCursorm_Cur
 
CRef< CSNPDb_Impl::SGraphTableCursorm_GraphCur
 
TVDBRowId m_LastGraphRowId
 
CRange< TSeqPosm_SearchRange
 
size_t m_CurrPageSet
 
TVDBRowId m_CurrPageRowId
 
TSeqPos m_CurrPagePos
 
ESearchMode m_SearchMode
 

Friends

class CSNPDbFeatIterator
 

Additional Inherited Members

- Public Types inherited from SSNPDb_Defs
enum  ESearchMode { eSearchByOverlap , eSearchByStart }
 
enum  EFeatSubtype {
  eFeatSubtype_unknown = 0 , eFeatSubtype_identity = 1 , eFeatSubtype_inversion = 2 , eFeatSubtype_single_nucleotide_variation = 3 ,
  eFeatSubtype_multi_nucleotide_variation = 4 , eFeatSubtype_deletion_insertion = 5 , eFeatSubtype_deletion = 6 , eFeatSubtype_insertion = 7 ,
  eFeatSubtype_str = 8
}
 
enum  EFeatSubtypeChar {
  eFeatSubtypeChar_unknown = 'U' , eFeatSubtypeChar_identity = '-' , eFeatSubtypeChar_inversion = 'V' , eFeatSubtypeChar_single_nucleotide_variation = 'S' ,
  eFeatSubtypeChar_multi_nucleotide_variation = 'M' , eFeatSubtypeChar_deletion_insertion = 'L' , eFeatSubtypeChar_deletion = 'D' , eFeatSubtypeChar_insertion = 'I' ,
  eFeatSubtypeChar_str = 'R'
}
 
typedef Uint8 TFilter
 
typedef int TSplitVersion
 
typedef int TChunkId
 

Detailed Description

Definition at line 641 of file snpread.hpp.

Constructor & Destructor Documentation

◆ CSNPDbPageIterator() [1/5]

CSNPDbPageIterator::CSNPDbPageIterator ( void  )

Definition at line 1875 of file snpread.cpp.

◆ CSNPDbPageIterator() [2/5]

CSNPDbPageIterator::CSNPDbPageIterator ( const CSNPDb db,
const CSeq_id_Handle ref_id,
TSeqPos  ref_pos = 0,
TSeqPos  window = 0,
ESearchMode  search_mode = eSearchByOverlap 
)

Definition at line 1884 of file snpread.cpp.

References kInvalidSeqPos, and Select().

◆ CSNPDbPageIterator() [3/5]

CSNPDbPageIterator::CSNPDbPageIterator ( const CSNPDb db,
const CSeq_id_Handle ref_id,
COpenRange< TSeqPos ref_range,
ESearchMode  search_mode = eSearchByOverlap 
)

Definition at line 1896 of file snpread.cpp.

References compile_time_bits::range(), and Select().

◆ CSNPDbPageIterator() [4/5]

CSNPDbPageIterator::CSNPDbPageIterator ( const CSNPDbSeqIterator seq,
COpenRange< TSeqPos ref_range,
ESearchMode  search_mode = eSearchByOverlap 
)

Definition at line 1906 of file snpread.cpp.

References compile_time_bits::range(), and Select().

◆ CSNPDbPageIterator() [5/5]

CSNPDbPageIterator::CSNPDbPageIterator ( const CSNPDbPageIterator iter)

Definition at line 1915 of file snpread.cpp.

◆ ~CSNPDbPageIterator()

CSNPDbPageIterator::~CSNPDbPageIterator ( void  )

Definition at line 1940 of file snpread.cpp.

References Reset().

Member Function Documentation

◆ Cur()

const CSNPDb_Impl::SPageTableCursor& CSNPDbPageIterator::Cur ( void  ) const
inlineprotected

Definition at line 721 of file snpread.hpp.

References m_Cur.

Referenced by GetFeatCount(), and GetFirstFeatRowId().

◆ DECLARE_OPERATOR_BOOL()

CSNPDbPageIterator::DECLARE_OPERATOR_BOOL ( )

◆ GetDb()

CSNPDb_Impl& CSNPDbPageIterator::GetDb ( void  ) const
inlineprotected

◆ GetFeatCount()

TVDBRowCount CSNPDbPageIterator::GetFeatCount ( void  ) const

Definition at line 2022 of file snpread.cpp.

References Cur(), GetPageRowId(), and x_CheckValid().

◆ GetFirstFeatRowId()

TVDBRowId CSNPDbPageIterator::GetFirstFeatRowId ( void  ) const

Definition at line 2015 of file snpread.cpp.

References Cur(), GetPageRowId(), and x_CheckValid().

Referenced by CSNPDbFeatIterator::x_InitPage().

◆ GetPagePos()

TSeqPos CSNPDbPageIterator::GetPagePos ( void  ) const
inline

Definition at line 692 of file snpread.hpp.

References m_CurrPagePos.

Referenced by GetPageRange(), and CSNPDbFeatIterator::x_GetGraphVDBRowId().

◆ GetPageRange()

CRange<TSeqPos> CSNPDbPageIterator::GetPageRange ( void  ) const
inline

Definition at line 695 of file snpread.hpp.

References GetPagePos(), and GetPageSize().

◆ GetPageRowId()

TVDBRowId CSNPDbPageIterator::GetPageRowId ( void  ) const
inline

Definition at line 700 of file snpread.hpp.

References m_CurrPageRowId.

Referenced by GetFeatCount(), GetFirstFeatRowId(), and CSNPDbFeatIterator::GetPageRowId().

◆ GetPageSize()

TSeqPos CSNPDbPageIterator::GetPageSize ( void  ) const
inline

Definition at line 689 of file snpread.hpp.

References GetDb(), and CSNPDb_Impl::GetPageSize().

Referenced by GetPageRange().

◆ GetRefIter()

const CSNPDbSeqIterator& CSNPDbPageIterator::GetRefIter ( void  ) const
inline

◆ GetSearchMode()

ESearchMode CSNPDbPageIterator::GetSearchMode ( void  ) const
inline

Definition at line 678 of file snpread.hpp.

References m_SearchMode.

Referenced by CSNPDbFeatIterator::GetSearchMode().

◆ GetSearchRange()

const CRange<TSeqPos>& CSNPDbPageIterator::GetSearchRange ( void  ) const
inline

Definition at line 675 of file snpread.hpp.

References m_SearchRange.

Referenced by CSNPDbFeatIterator::GetSearchRange().

◆ GetSeqId()

CRef<CSeq_id> CSNPDbPageIterator::GetSeqId ( void  ) const
inline

Definition at line 682 of file snpread.hpp.

References GetRefIter(), and CSNPDbSeqIterator::GetSeqId().

Referenced by CSNPDbFeatIterator::GetSeqId().

◆ GetSeqIdHandle()

CSeq_id_Handle CSNPDbPageIterator::GetSeqIdHandle ( void  ) const
inline

Definition at line 685 of file snpread.hpp.

References GetRefIter(), and CSNPDbSeqIterator::GetSeqIdHandle().

Referenced by CSNPDbFeatIterator::GetSeqIdHandle().

◆ operator++()

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

Definition at line 670 of file snpread.hpp.

References x_Next().

◆ operator=()

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

◆ Reset()

void CSNPDbPageIterator::Reset ( void  )

◆ Select()

CSNPDbPageIterator & CSNPDbPageIterator::Select ( COpenRange< TSeqPos ref_range,
ESearchMode  search_mode = eSearchByOverlap 
)

◆ SetTrack()

void CSNPDbPageIterator::SetTrack ( const CSNPDbTrackIterator track)
inline

Definition at line 711 of file snpread.hpp.

References m_SeqIter, and CSNPDbSeqIterator::SetTrack().

◆ x_CheckValid()

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

Definition at line 747 of file snpread.hpp.

References x_ReportInvalid().

Referenced by GetFeatCount(), GetFirstFeatRowId(), and x_Next().

◆ x_GetGraphVDBRowId()

TVDBRowId CSNPDbPageIterator::x_GetGraphVDBRowId ( ) const
inlineprotected

Definition at line 742 of file snpread.hpp.

References CSNPDbSeqIterator::GetGraphVDBRowId(), and GetRefIter().

◆ x_GetPageVDBRowRange()

CRange<TVDBRowId> CSNPDbPageIterator::x_GetPageVDBRowRange ( ) const
inlineprotected

Definition at line 739 of file snpread.hpp.

References CSNPDbSeqIterator::GetPageVDBRowRange(), and GetRefIter().

◆ x_GetSeqIter()

CSNPDb_Impl::TSeqInfoList::const_iterator CSNPDbPageIterator::x_GetSeqIter ( ) const
inlineprotected

◆ x_GetSeqVDBRowId()

TVDBRowId CSNPDbPageIterator::x_GetSeqVDBRowId ( ) const
inlineprotected

Definition at line 732 of file snpread.hpp.

References GetDb(), x_GetSeqIter(), and CSNPDb_Impl::x_GetSeqVDBRowId().

◆ x_GetTrackIter()

CSNPDb_Impl::TTrackInfoList::const_iterator CSNPDbPageIterator::x_GetTrackIter ( ) const
inlineprotected

Definition at line 728 of file snpread.hpp.

References GetRefIter(), and CSNPDbSeqIterator::x_GetTrackIter().

Referenced by x_GetTrackVDBRowId().

◆ x_GetTrackVDBRowId()

TVDBRowId CSNPDbPageIterator::x_GetTrackVDBRowId ( ) const
inlineprotected

Definition at line 735 of file snpread.hpp.

References GetDb(), x_GetTrackIter(), and CSNPDb_Impl::x_GetTrackVDBRowId().

◆ x_Next()

void CSNPDbPageIterator::x_Next ( void  )
protected

Definition at line 1983 of file snpread.cpp.

References kInvalidSeqPos, kPageSize, m_CurrPagePos, m_CurrPageRowId, m_CurrPageSet, m_SeqIter, and x_CheckValid().

Referenced by operator++().

◆ x_ReportInvalid()

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

Definition at line 2007 of file snpread.cpp.

References NCBI_THROW_FMT.

Referenced by x_CheckValid().

Friends And Related Function Documentation

◆ CSNPDbFeatIterator

friend class CSNPDbFeatIterator
friend

Definition at line 716 of file snpread.hpp.

Member Data Documentation

◆ m_Cur

CRef<CSNPDb_Impl::SPageTableCursor> CSNPDbPageIterator::m_Cur
private

Definition at line 758 of file snpread.hpp.

Referenced by Cur(), operator=(), Reset(), and Select().

◆ m_CurrPagePos

TSeqPos CSNPDbPageIterator::m_CurrPagePos
private

Definition at line 766 of file snpread.hpp.

Referenced by GetPagePos(), operator=(), Reset(), Select(), and x_Next().

◆ m_CurrPageRowId

TVDBRowId CSNPDbPageIterator::m_CurrPageRowId
private

Definition at line 765 of file snpread.hpp.

Referenced by GetPageRowId(), operator=(), Reset(), Select(), and x_Next().

◆ m_CurrPageSet

size_t CSNPDbPageIterator::m_CurrPageSet
private

Definition at line 764 of file snpread.hpp.

Referenced by operator=(), Select(), and x_Next().

◆ m_GraphCur

CRef<CSNPDb_Impl::SGraphTableCursor> CSNPDbPageIterator::m_GraphCur
mutableprivate

Definition at line 759 of file snpread.hpp.

Referenced by operator=(), and Reset().

◆ m_LastGraphRowId

TVDBRowId CSNPDbPageIterator::m_LastGraphRowId
mutableprivate

Definition at line 760 of file snpread.hpp.

Referenced by operator=(), and Reset().

◆ m_SearchMode

ESearchMode CSNPDbPageIterator::m_SearchMode
private

Definition at line 768 of file snpread.hpp.

Referenced by GetSearchMode(), operator=(), and Select().

◆ m_SearchRange

CRange<TSeqPos> CSNPDbPageIterator::m_SearchRange
private

Definition at line 762 of file snpread.hpp.

Referenced by GetSearchRange(), operator=(), and Select().

◆ m_SeqIter

CSNPDbSeqIterator CSNPDbPageIterator::m_SeqIter
private

Definition at line 756 of file snpread.hpp.

Referenced by GetRefIter(), operator=(), Reset(), Select(), SetTrack(), and x_Next().


The documentation for this class was generated from the following files:
Modified on Mon Jun 17 05:09:25 2024 by modify_doxy.py rev. 669887