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NCBI C++ ToolKit: CSNPDb_Impl Class Reference
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#include <sra/readers/sra/snpread.hpp>
typedef vector< SSeqInfo > TSeqInfoList typedef map< CSeq_id_Handle, size_t > TSeqInfoMapBySeq_id typedef vector< STrackInfo > TTrackInfoList typedef map< string, size_t > TTrackInfoMapByName 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...
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 CSNPDb_Impl (CVDBMgr &mgr, CTempString path_or_acc) virtual ~CSNPDb_Impl (void) const string & GetDbPath (void) const const TSeqInfoList & GetSeqInfoList (void) const const TSeqInfoMapBySeq_id & GetSeqInfoMapBySeq_id (void) const const TTrackInfoList & GetTrackInfoList (void) const const TTrackInfoMapByName & GetTrackInfoMapByName (void) const TTrackInfoList::const_iterator FindTrack (const string &name) const TSeqInfoList::const_iterator FindSeq (const string &accession, int version) TSeqInfoList::const_iterator FindSeq (const CSeq_id_Handle &seq_id) TSeqPos GetPageSize (void) const TSeqPos GetOverviewZoom (void) const TSeqPos GetCoverageZoom (void) const 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...
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
Definition at line 180 of file snpread.hpp.
◆ TSeq2PageMap ◆ TSeqInfoList ◆ TSeqInfoMapBySeq_id ◆ TTrackInfoList ◆ TTrackInfoMapByName ◆ CSNPDb_Impl()
Definition at line 316 of file snpread.cpp.
References CSraException::eNotFoundDb, CSraException::GetErrCode(), CSeq_id_Handle::GetHandle(), CVDBCursor::GetMaxRowId(), CSraException::GetRC(), CSNPDb_Impl::SSeqInfo::SPageSet::GetRowIdEnd(), CSNPDb_Impl::SSeqInfo::SPageSet::GetSeqPosEnd(), i, info, kPageSize, kPreloadSeqList, CSNPDb_Impl::STrackTableCursor::m_Cursor, m_Db, m_ExtraTable, m_FeatTable, m_GraphTable, m_Mgr, CSNPDb_Impl::SSeqInfo::SPageSet::m_PageCount, m_PageTable, CSNPDb_Impl::SSeqInfo::SPageSet::m_RowId, m_SeqAccIndex, m_SeqList, m_SeqMapBySeq_id, CSNPDb_Impl::SSeqInfo::SPageSet::m_SeqPos, m_SeqTable, m_TrackList, m_TrackMapByName, NCBI_THROW2_FMT, Page(), Put(), row, Seq(), table, and NStr::TrimSuffixInPlace().
◆ ~CSNPDb_Impl() CSNPDb_Impl::~CSNPDb_Impl ( void ) virtual
Definition at line 447 of file snpread.cpp.
◆ Extra() ◆ ExtraTable() ◆ Feat() ◆ FeatTable() ◆ FindSeq() [1/2] CSNPDb_Impl::TSeqInfoList::const_iterator CSNPDb_Impl::FindSeq ( const CSeq_id_Handle & seq_id ) ◆ FindSeq() [2/2] CSNPDb_Impl::TSeqInfoList::const_iterator CSNPDb_Impl::FindSeq ( const string & accession, int version ) ◆ FindTrack() CSNPDb_Impl::TTrackInfoList::const_iterator CSNPDb_Impl::FindTrack ( const string & name ) const ◆ GetCoverageZoom() TSeqPos CSNPDb_Impl::GetCoverageZoom ( void ) const ◆ GetDbPath() ◆ GetOverviewZoom() TSeqPos CSNPDb_Impl::GetOverviewZoom ( void ) const ◆ GetPageSize() TSeqPos CSNPDb_Impl::GetPageSize ( void ) const ◆ GetSeqInfoList() ◆ GetSeqInfoMapBySeq_id() ◆ GetTrackInfoList() ◆ GetTrackInfoMapByName() ◆ Graph() ◆ GraphTable() ◆ Page() ◆ PageTable() ◆ Put() [1/5] ◆ Put() [2/5] ◆ Put() [3/5] ◆ Put() [4/5] ◆ Put() [5/5] ◆ Seq() ◆ SeqTable() ◆ x_GetGraphVDBRowId() TVDBRowId CSNPDb_Impl::x_GetGraphVDBRowId ( TSeqInfoList::const_iterator seq, TTrackInfoList::const_iterator track ) protected ◆ x_GetPageVDBRowRange() CRange< TVDBRowId > CSNPDb_Impl::x_GetPageVDBRowRange ( TSeqInfoList::const_iterator seq ) protected ◆ x_GetSeqVDBIndex() size_t CSNPDb_Impl::x_GetSeqVDBIndex ( TSeqInfoList::const_iterator seq ) const inlineprotected ◆ x_GetSeqVDBRowId() TVDBRowId CSNPDb_Impl::x_GetSeqVDBRowId ( TSeqInfoList::const_iterator seq ) const inlineprotected ◆ x_GetTrackVDBIndex() size_t CSNPDb_Impl::x_GetTrackVDBIndex ( TTrackInfoList::const_iterator track ) const inlineprotected ◆ x_GetTrackVDBRowId() TVDBRowId CSNPDb_Impl::x_GetTrackVDBRowId ( TTrackInfoList::const_iterator track ) const inlineprotected ◆ x_Update() void CSNPDb_Impl::x_Update ( TSeqInfoList::const_iterator seq ) protected
Definition at line 537 of file snpread.cpp.
References _ASSERT, map_checker< Container >::begin(), map_checker< Container >::end(), CSeq_id_Handle::GetHandle(), CSNPDb_Impl::SSeqInfo::SPageSet::GetRowIdEnd(), CSNPDb_Impl::SSeqInfo::SPageSet::GetSeqPosEnd(), info, kPageSize, map_checker< Container >::lower_bound(), m_Mutex, CSNPDb_Impl::SSeqInfo::SPageSet::m_PageCount, CSNPDb_Impl::SSeqInfo::SPageSet::m_RowId, m_Seq2PageMap, m_SeqList, CSNPDb_Impl::SSeqInfo::SPageSet::m_SeqPos, m_TrackList, Page(), Put(), row, and Seq().
Referenced by CSNPDbSeqIterator::CSNPDbSeqIterator(), FindSeq(), and CSNPDbSeqIterator::operator++().
◆ CSNPDbFeatIterator ◆ CSNPDbGraphIterator ◆ CSNPDbPageIterator ◆ CSNPDbSeqIterator ◆ CSNPDbTrackIterator ◆ m_Db ◆ m_DbPath ◆ m_Extra ◆ m_ExtraTable ◆ m_Feat ◆ m_FeatTable ◆ m_Graph ◆ m_GraphTable ◆ m_Mgr ◆ m_Mutex ◆ m_Page ◆ m_PageTable ◆ m_Seq ◆ m_Seq2PageMap ◆ m_SeqAccIndex ◆ m_SeqList ◆ m_SeqMapBySeq_id ◆ m_SeqTable ◆ m_TrackList ◆ m_TrackMapByName
The documentation for this class was generated from the following files:
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