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NCBI C++ ToolKit: CSNPDbSeqIterator Class Reference

Search Toolkit Book for CSNPDbSeqIterator

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

enum   EFlags {
  fZoomPage = 1<<0 , fNoGaps = 1<<1 , fNoSNPFeat = 1<<2 , fNoCoverageGraph = 1<<3 ,
  fNoOverviewGraph = 1<<4 , fOnlySNPFeat = fNoCoverageGraph | fNoOverviewGraph , fOverviewWithZoomAlways = 1<<5 , fOverviewWithZoomNever = 1<<6 ,
  fDefaultFlags = 0
}   typedef CSNPDb_Impl::TSeqInfoList  TList   typedef TList::value_type  TInfo   typedef vector< CRef< CSeq_annot > >  TAnnotSet   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     CSNPDbSeqIterator (void)     CSNPDbSeqIterator (const CSNPDb &db)     CSNPDbSeqIterator (const CSNPDb &db, size_t seq_index)     CSNPDbSeqIterator (const CSNPDb &db, const string &accession, int version)     CSNPDbSeqIterator (const CSNPDb &db, const CSeq_id_Handle &seq_id)   void  Reset (void)     DECLARE_OPERATOR_BOOL (m_Db &&m_Iter !=GetList().end())   const TInfo &  operator* (void) const   const TInfo *  operator-> (void) const   CSNPDbSeqIterator &  operator++ (void)   CRef< CSeq_id >  GetSeqId (void) const   const CSeq_id_Handle &  GetSeqIdHandle (void) const   TSeqPos  GetSeqLength (void) const   bool  IsCircular (void) const   TSeqPos  GetPageSize (void) const   TSeqPos  GetOverviewZoom (void) const   TSeqPos  GetCoverageZoom (void) const   TSeqPos  GetMaxSNPLength (void) const   Uint8  GetSNPCount (CRange< TSeqPos > range) const   Uint8  GetSNPCount (void) const   CRange< TSeqPos >  GetSNPRange (void) const   TVDBRowId  GetVDBRowId (void) const   size_t  GetVDBSeqIndex (void) const   CRange< TVDBRowId >  GetPageVDBRowRange (void) const   TVDBRowId  GetGraphVDBRowId () const     DECLARE_SAFE_FLAGS_TYPE (EFlags, TFlags)   CRef< CSeq_graph >  GetOverviewGraph (CRange< TSeqPos > range, TFlags flags=fDefaultFlags) const   CRef< CSeq_annot >  GetOverviewAnnot (CRange< TSeqPos > range, const string &annot_name, TFlags flags=fDefaultFlags) const   CRef< CSeq_annot >  GetOverviewAnnot (CRange< TSeqPos > range, TFlags flags=fDefaultFlags) const   CRef< CSeq_graph >  GetCoverageGraph (CRange< TSeqPos > range) const   CRef< CSeq_annot >  GetCoverageAnnot (CRange< TSeqPos > range, const string &annot_name, TFlags flags=fDefaultFlags) const   CRef< CSeq_annot >  GetCoverageAnnot (CRange< TSeqPos > range, TFlags flags=fDefaultFlags) const   CRef< CSeq_annot >  GetFeatAnnot (CRange< TSeqPos > range, const SFilter &filter, TFlags flags=fDefaultFlags) const   CRef< CSeq_annot >  GetFeatAnnot (CRange< TSeqPos > range, TFlags flags=fDefaultFlags) const   TAnnotSet  GetTableFeatAnnots (CRange< TSeqPos > range, const string &annot_name, const SFilter &filter, TFlags flags=fDefaultFlags) const   TAnnotSet  GetTableFeatAnnots (CRange< TSeqPos > range, const SFilter &filter, TFlags flags=fDefaultFlags) const   TAnnotSet  GetTableFeatAnnots (CRange< TSeqPos > range, TFlags flags=fDefaultFlags) const   TAnnotSet  GetTableFeatAnnots (CRange< TSeqPos > range, const string &annot_name, TFlags flags=fDefaultFlags) const   CRef< CSeq_entry >  GetEntry (const string &base_name, TFlags flags=fDefaultFlags) const   pair< CRef< CID2S_Split_Info >, TSplitVersion >  GetSplitInfoAndVersion (const string &base_name, TFlags flags=fDefaultFlags) const   CRef< CID2S_Chunk >  GetChunkForVersion (const string &base_name, TChunkId chunk_id, TSplitVersion split_version) const   CSNPDb_Impl &  GetDb (void) const   const SFilter &  GetFilter () const   void  SetTrack (const CSNPDbTrackIterator &track)  

Definition at line 473 of file snpread.hpp.

◆ TAnnotSet ◆ TInfo ◆ TList ◆ EFlags Enumerator fZoomPage  fNoGaps  fNoSNPFeat  fNoCoverageGraph  fNoOverviewGraph  fOnlySNPFeat  fOverviewWithZoomAlways  fOverviewWithZoomNever  fDefaultFlags 

Definition at line 543 of file snpread.hpp.

◆ CSNPDbSeqIterator() [1/5] CSNPDbSeqIterator::CSNPDbSeqIterator ( void  ) inline

Definition at line 479 of file snpread.hpp.

◆ CSNPDbSeqIterator() [2/5] CSNPDbSeqIterator::CSNPDbSeqIterator ( const CSNPDb &  db ) explicit ◆ CSNPDbSeqIterator() [3/5] CSNPDbSeqIterator::CSNPDbSeqIterator ( const CSNPDb &  db, size_t  seq_index  ) ◆ CSNPDbSeqIterator() [4/5] ◆ CSNPDbSeqIterator() [5/5] ◆ DECLARE_OPERATOR_BOOL() ◆ DECLARE_SAFE_FLAGS_TYPE() CSNPDbSeqIterator::DECLARE_SAFE_FLAGS_TYPE ( EFlags  , TFlags    ) ◆ GetChunkForVersion()

Definition at line 2994 of file snpread.cpp.

References data, GetCoverageAnnot(), GetCoverageZoom(), GetPageSize(), GetTableFeatAnnots(), i, kChunkIdFeat, kChunkIdGraph, kChunkIdMul, kDefaultFeatChunkPages, kFeatChunkSize, kFeatChunksPerGraphChunk, kGraphChunkSize, kTSEId, NCBI_THROW_FMT, CID2S_Chunk_Base::SetData(), CRange_Base::SetFrom(), COpenRange< Position >::SetToOpen(), sx_AddNew(), and sx_SetZoomLevel().

Referenced by CSNPSeqInfo::LoadAnnotChunk(), and CSNPSeqInfo::LoadChunk().

◆ GetCoverageAnnot() [1/2] ◆ GetCoverageAnnot() [2/2] ◆ GetCoverageGraph() ◆ GetCoverageZoom() TSeqPos CSNPDbSeqIterator::GetCoverageZoom ( void  ) const inline ◆ GetDb()

Definition at line 606 of file snpread.hpp.

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

Referenced by CSNPBlobId::CSNPBlobId(), CSNPDbSeqIterator(), GetCoverageZoom(), CSNPDbPageIterator::GetDb(), GetGraphVDBRowId(), GetList(), GetOverviewZoom(), GetPageSize(), GetPageVDBRowRange(), GetSNPCount(), GetVDBRowId(), GetVDBSeqIndex(), and operator++().

◆ GetEntry()

Definition at line 2866 of file snpread.cpp.

References _ASSERT, flags, fNoCoverageGraph, fNoOverviewGraph, fNoSNPFeat, g(), GetCoverageAnnot(), GetCoverageZoom(), GetOverviewAnnot(), GetOverviewZoom(), GetPageSize(), GetSNPRange(), GetTableFeatAnnots(), CRange_Base::GetTo(), COpenRange< Position >::GetToOpen(), i, kDefaultFeatChunkPages, kFeatChunkSize, kFeatChunksPerGraphChunk, kGraphChunkSize, min(), CBioseq_set_Base::SetAnnot(), CRange_Base::SetFrom(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), COpenRange< Position >::SetToOpen(), sx_AddBits(), sx_CalcFeatChunkPages(), sx_HasNonZero(), sx_SetOverviewName(), and sx_SetZoomLevel().

Referenced by CSNPSeqInfo::LoadAnnotBlob(), and CSNPSeqInfo::LoadBlob().

◆ GetFeatAnnot() [1/2] ◆ GetFeatAnnot() [2/2] ◆ GetFilter() ◆ GetGraphVDBRowId() TVDBRowId CSNPDbSeqIterator::GetGraphVDBRowId ( ) const inline ◆ GetInfo() ◆ GetList() const TList& CSNPDbSeqIterator::GetList ( void  ) const inlineprotected ◆ GetMaxSNPLength() TSeqPos CSNPDbSeqIterator::GetMaxSNPLength ( void  ) const ◆ GetOverviewAnnot() [1/2] ◆ GetOverviewAnnot() [2/2] ◆ GetOverviewGraph() ◆ GetOverviewZoom() TSeqPos CSNPDbSeqIterator::GetOverviewZoom ( void  ) const inline ◆ GetPageSize() TSeqPos CSNPDbSeqIterator::GetPageSize ( void  ) const inline ◆ GetPageVDBRowRange() ◆ GetSeqId() CRef<CSeq_id> CSNPDbSeqIterator::GetSeqId ( void  ) const inline ◆ GetSeqIdHandle() ◆ GetSeqLength() TSeqPos CSNPDbSeqIterator::GetSeqLength ( void  ) const inline ◆ GetSNPCount() [1/2] ◆ GetSNPCount() [2/2] Uint8 CSNPDbSeqIterator::GetSNPCount ( void  ) const ◆ GetSNPRange() ◆ GetSplitInfoAndVersion()

Definition at line 2921 of file snpread.cpp.

References _ASSERT, CSeqFeatData_Base::e_Imp, CSeqFeatData::eSubtype_variation, flags, fNoCoverageGraph, fNoOverviewGraph, fNoSNPFeat, g(), GetCoverageZoom(), GetMaxSNPLength(), GetOverviewAnnot(), GetOverviewZoom(), GetPageSize(), GetSeqId(), GetSNPRange(), CRange_Base::GetTo(), COpenRange< Position >::GetToOpen(), i, kChunkIdFeat, kChunkIdGraph, kChunkIdMul, kDefaultFeatChunkPages, kFeatChunkSize, kFeatChunksPerGraphChunk, kGraphChunkSize, kTSEId, CBioseq_set_Base::SetAnnot(), CID2S_Split_Info_Base::SetChunks(), CID2S_Chunk_Info_Base::SetContent(), CID2S_Seq_annot_Info_Base::SetFeat(), CID2S_Seq_annot_Info_Base::SetGraph(), CID2S_Chunk_Info_Base::SetId(), CBioseq_set_Base::SetId(), CID2S_Seq_id_Interval_Base::SetLength(), CID2S_Seq_annot_Info_Base::SetName(), CID2S_Seq_id_Interval_Base::SetSeq_id(), CID2S_Seq_annot_Info_Base::SetSeq_loc(), CBioseq_set_Base::SetSeq_set(), CID2S_Split_Info_Base::SetSkeleton(), CID2S_Seq_id_Interval_Base::SetStart(), CID2S_Feat_type_Info_Base::SetSubtypes(), CID2S_Feat_type_Info_Base::SetType(), sx_AddBits(), sx_AddNew(), sx_CalcFeatChunkPages(), sx_CombineWithZoomLevel(), sx_HasNonZero(), and sx_SetOverviewName().

Referenced by CSNPSeqInfo::LoadAnnotBlob(), and CSNPSeqInfo::LoadBlob().

◆ GetTableFeatAnnots() [1/4] ◆ GetTableFeatAnnots() [2/4] ◆ GetTableFeatAnnots() [3/4] ◆ GetTableFeatAnnots() [4/4] ◆ GetVDBRowId() TVDBRowId CSNPDbSeqIterator::GetVDBRowId ( void  ) const inline ◆ GetVDBSeqIndex() size_t CSNPDbSeqIterator::GetVDBSeqIndex ( void  ) const inline ◆ IsCircular() bool CSNPDbSeqIterator::IsCircular ( void  ) const ◆ operator*() const TInfo& CSNPDbSeqIterator::operator* ( void  ) const inline ◆ operator++() ◆ operator->() const TInfo* CSNPDbSeqIterator::operator-> ( void  ) const inline ◆ Reset() void CSNPDbSeqIterator::Reset ( void  ) ◆ SetTrack() ◆ x_GetSeqIter() TList::const_iterator CSNPDbSeqIterator::x_GetSeqIter ( ) const inlineprotected ◆ x_GetTrackIter() CSNPDb_Impl::TTrackInfoList::const_iterator CSNPDbSeqIterator::x_GetTrackIter ( ) const inlineprotected ◆ CSNPDbGraphIterator ◆ CSNPDbPageIterator ◆ m_Db CSNPDb CSNPDbSeqIterator::m_Db private ◆ m_Iter TList::const_iterator CSNPDbSeqIterator::m_Iter private

Definition at line 634 of file snpread.hpp.

Referenced by CSNPDbSeqIterator(), GetGraphVDBRowId(), GetInfo(), GetPageVDBRowRange(), GetSeqId(), GetSeqIdHandle(), GetSeqLength(), GetVDBRowId(), GetVDBSeqIndex(), operator++(), Reset(), and x_GetSeqIter().

◆ m_TrackIter CSNPDb_Impl::TTrackInfoList::const_iterator CSNPDbSeqIterator::m_TrackIter private

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

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