CSNPDbPageIterator Class Reference

Search Toolkit Book for CSNPDbPageIterator

#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)
CSNPDbPageIterator &	operator= (const CSNPDbPageIterator &iter)
CSNPDbPageIterator &	Select (COpenRange< TSeqPos > ref_range, ESearchMode search_mode=eSearchByOverlap)
void	Reset (void)
	DECLARE_OPERATOR_BOOL (m_CurrPagePos< m_SearchRange.GetToOpen())
CSNPDbPageIterator &	operator++ (void)
const CRange< TSeqPos > &	GetSearchRange (void) const
ESearchMode	GetSearchMode (void) const
CRef< CSeq_id >	GetSeqId (void) const
CSeq_id_Handle	GetSeqIdHandle (void) const
TSeqPos	GetPageSize (void) const
TSeqPos	GetPagePos (void) const
CRange< TSeqPos >	GetPageRange (void) const
TVDBRowId	GetPageRowId (void) const
const CSNPDbSeqIterator &	GetRefIter (void) const
TVDBRowId	GetFirstFeatRowId (void) const
TVDBRowCount	GetFeatCount (void) const
void	SetTrack (const CSNPDbTrackIterator &track)

Protected Member Functions
CSNPDb_Impl &	GetDb (void) const
const CSNPDb_Impl::SPageTableCursor &	Cur (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< TVDBRowId >	x_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::SPageTableCursor >	m_Cur
CRef< CSNPDb_Impl::SGraphTableCursor >	m_GraphCur
TVDBRowId	m_LastGraphRowId
CRange< TSeqPos >	m_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

Definition at line 718 of file snpread.hpp.

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

Referenced by CSNPDbFeatIterator::GetDb(), GetPageSize(), Reset(), Select(), x_GetSeqVDBRowId(), and x_GetTrackVDBRowId().

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

Definition at line 704 of file snpread.hpp.

References m_SeqIter.

Referenced by GetDb(), CSNPDbFeatIterator::GetRefIter(), GetSeqId(), GetSeqIdHandle(), x_GetGraphVDBRowId(), x_GetPageVDBRowRange(), x_GetSeqIter(), and x_GetTrackIter().

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

)

Definition at line 1922 of file snpread.cpp.

References m_Cur, m_CurrPagePos, m_CurrPageRowId, m_CurrPageSet, m_GraphCur, m_LastGraphRowId, m_SearchMode, m_SearchRange, m_SeqIter, and Reset().

Reset()

void CSNPDbPageIterator::Reset

(

void

)

Definition at line 1860 of file snpread.cpp.

References _ASSERT, GetDb(), kInvalidSeqPos, m_Cur, m_CurrPagePos, m_CurrPageRowId, m_GraphCur, m_LastGraphRowId, m_SeqIter, CSNPDb_Impl::Put(), and CSNPDbSeqIterator::Reset().

Referenced by operator=(), CSNPDbFeatIterator::Reset(), and ~CSNPDbPageIterator().

Select()

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

Definition at line 1947 of file snpread.cpp.

References COpenRange< Position >::Empty(), SSNPDb_Defs::eSearchByOverlap, GetDb(), COpenRange< Position >::GetFrom(), kInvalidSeqPos, kMaxSNPLength, kPageSize, m_Cur, m_CurrPagePos, m_CurrPageRowId, m_CurrPageSet, CSNPDb_Impl::SSeqInfo::SPageSet::m_PageCount, CSNPDb_Impl::SSeqInfo::SPageSet::m_RowId, m_SearchMode, m_SearchRange, m_SeqIter, CSNPDb_Impl::SSeqInfo::SPageSet::m_SeqPos, and CSNPDb_Impl::Page().

Referenced by CSNPDbPageIterator(), and CSNPDbFeatIterator::Select().

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

Definition at line 725 of file snpread.hpp.

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

Referenced by CSNPDbFeatIterator::x_GetSeqIter(), and x_GetSeqVDBRowId().

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().

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

• include/sra/readers/sra/snpread.hpp
• src/sra/readers/sra/snpread.cpp