NCBI C++ ToolKit
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CVDBGraphSeqIterator Class Reference

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

+ Collaboration diagram for CVDBGraphSeqIterator:

Public Types

enum  EContentFlags {
  fGraphMain = 1<<0 , fGraphQ0 = 1<<1 , fGraphQ10 = 1<<2 , fGraphQ50 = 1<<3 ,
  fGraphQ90 = 1<<4 , fGraphQ100 = 1<<5 , fGraphQAll , fGraphMainAsTable = 1<<8 ,
  fGraphMainAsGraph = 1<<9 , fGraphMainAsBest = (fGraphMainAsTable | fGraphMainAsGraph) , fGraphZoomQ0 = 1<<11 , fGraphZoomQ10 = 1<<12 ,
  fGraphZoomQ50 = 1<<13 , fGraphZoomQ90 = 1<<14 , fGraphZoomQ100 = 1<<15 , fGraphZoomQAll ,
  fDefaultContent = fGraphQAll
}
 
typedef CVDBGraphDb_Impl::SSeqInfo SSeqInfo
 
typedef CVDBGraphDb_Impl::SGraphTableCursor SGraphTableCursor
 
typedef CVDBGraphDb_Impl::TSeqInfoList::const_iterator TSeqInfoIter
 
typedef int TContentFlags
 

Public Member Functions

 CVDBGraphSeqIterator (void)
 
 CVDBGraphSeqIterator (const CVDBGraphDb &db)
 
 CVDBGraphSeqIterator (const CVDBGraphDb &db, const CSeq_id_Handle &seq_id)
 
bool operator! (void) const
 
 operator const void * (void) const
 
const SSeqInfo & GetInfo (void) const
 
const SSeqInfo & operator* (void) const
 
const SSeqInfo * operator-> (void) const
 
CVDBGraphSeqIterator & operator++ (void)
 
const string & GetSeqId (void) const
 
const CSeq_id_Handle & GetSeq_id_Handle (void) const
 
TSeqPos GetSeqLength (void) const
 
CRef< CSeq_annot > GetAnnot (COpenRange< TSeqPos > range, const string &annot_name=kEmptyStr, TContentFlags content=fDefaultContent) const
 
bool SeqTableIsSmaller (COpenRange< TSeqPos > range) const
 

Protected Member Functions

CVDBGraphDb_Impl & GetDb (void) const
 
CRef< CSeq_graph > x_MakeGraph (const string &annot_name, CSeq_loc &loc, const SSeqInfo &info, const COpenRange< TSeqPos > &range, TSeqPos step, SGraphTableCursor &cursor, CVDBColumn &column, int level) const
 
CRef< CSeq_table > x_MakeTable (const string &annot_name, CSeq_loc &loc, const SSeqInfo &info, const COpenRange< TSeqPos > &range, SGraphTableCursor &cursor) const
 
bool x_SeqTableIsSmaller (COpenRange< TSeqPos > range, SGraphTableCursor &cursor) const
 

Private Attributes

CVDBGraphDb m_Db
 
CVDBGraphDb_Impl::SSeqInfo m_Info
 

Detailed Description

Definition at line 189 of file graphread.hpp.

Member Typedef Documentation

◆ SGraphTableCursor

typedef CVDBGraphDb_Impl::SGraphTableCursor CVDBGraphSeqIterator::SGraphTableCursor

Definition at line 193 of file graphread.hpp.

◆ SSeqInfo

typedef CVDBGraphDb_Impl::SSeqInfo CVDBGraphSeqIterator::SSeqInfo

Definition at line 192 of file graphread.hpp.

◆ TContentFlags

typedef int CVDBGraphSeqIterator::TContentFlags

Definition at line 263 of file graphread.hpp.

◆ TSeqInfoIter

typedef CVDBGraphDb_Impl::TSeqInfoList::const_iterator CVDBGraphSeqIterator::TSeqInfoIter

Definition at line 194 of file graphread.hpp.

Member Enumeration Documentation

◆ EContentFlags

enum CVDBGraphSeqIterator::EContentFlags
Enumerator
fGraphMain 
fGraphQ0 
fGraphQ10 
fGraphQ50 
fGraphQ90 
fGraphQ100 
fGraphQAll 
fGraphMainAsTable 
fGraphMainAsGraph 
fGraphMainAsBest 
fGraphZoomQ0 
fGraphZoomQ10 
fGraphZoomQ50 
fGraphZoomQ90 
fGraphZoomQ100 
fGraphZoomQAll 
fDefaultContent 

Definition at line 232 of file graphread.hpp.

Constructor & Destructor Documentation

◆ CVDBGraphSeqIterator() [1/3]

CVDBGraphSeqIterator::CVDBGraphSeqIterator ( void  )
inline

Definition at line 196 of file graphread.hpp.

◆ CVDBGraphSeqIterator() [2/3]

CVDBGraphSeqIterator::CVDBGraphSeqIterator ( const CVDBGraphDb &  db)
explicit

Definition at line 330 of file graphread.cpp.

References CRef< C, Locker >::GetNCObject(), CVDBGraphDb_Impl::GetSeqInfoAtRow(), and m_Info.

◆ CVDBGraphSeqIterator() [3/3]

CVDBGraphSeqIterator::CVDBGraphSeqIterator ( const CVDBGraphDb &  db,
const CSeq_id_Handle &  seq_id 
)

Definition at line 337 of file graphread.cpp.

References CRef< C, Locker >::GetNCObject(), CVDBGraphDb_Impl::GetSeqInfo(), and m_Info.

Member Function Documentation

◆ GetAnnot()

CRef< CSeq_annot > CVDBGraphSeqIterator::GetAnnot ( COpenRange< TSeqPos >  range,
const string &  annot_name = kEmptyStr,
TContentFlags  content = fDefaultContent 
) const

Definition at line 669 of file graphread.cpp.

References CUser_object::AddField(), COpenRange< Position >::Empty(), f, fGraphMain, fGraphMainAsGraph, fGraphMainAsTable, fGraphQ0, fGraphQ10, fGraphQ100, fGraphQ50, fGraphQ90, fGraphQAll, fGraphZoomQ0, fGraphZoomQ10, fGraphZoomQ100, fGraphZoomQ50, fGraphZoomQ90, fGraphZoomQAll, GetDb(), GetInfo(), COpenRange< Position >::GetToOpen(), info, CSeq_annot_Base::IsSetData(), min(), NCBI_THROW, CVDBGraphDb_Impl::Put(), compile_time_bits::range(), SerialClone(), CSeq_annot_Base::SetData(), CSeq_annot_Base::SetDesc(), CSeq_loc::SetInt(), CAnnotdesc_Base::SetName(), COpenRange< Position >::SetToOpen(), CUser_object_Base::SetType(), CAnnotdesc_Base::SetUser(), table, x_MakeGraph(), x_MakeTable(), and x_SeqTableIsSmaller().

Referenced by CVDBGraphDataLoader_Impl::GetChunkOnce(), and CVDBGraphDataLoader_Impl::LoadFullEntry().

◆ GetDb()

CVDBGraphDb_Impl& CVDBGraphSeqIterator::GetDb ( void  ) const
inlineprotected

Definition at line 274 of file graphread.hpp.

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

Referenced by GetAnnot(), and SeqTableIsSmaller().

◆ GetInfo()

const CVDBGraphDb_Impl::SSeqInfo & CVDBGraphSeqIterator::GetInfo ( void  ) const

Definition at line 352 of file graphread.cpp.

References m_Info, and NCBI_THROW.

Referenced by GetAnnot(), GetSeq_id_Handle(), GetSeqId(), GetSeqLength(), operator*(), operator++(), operator->(), SeqTableIsSmaller(), and x_SeqTableIsSmaller().

◆ GetSeq_id_Handle()

const CSeq_id_Handle& CVDBGraphSeqIterator::GetSeq_id_Handle ( void  ) const
inline

Definition at line 223 of file graphread.hpp.

References GetInfo(), and CVDBGraphDb_Impl::SSeqInfo::m_Seq_id_Handle.

Referenced by CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ GetSeqId()

const string& CVDBGraphSeqIterator::GetSeqId ( void  ) const
inline

Definition at line 220 of file graphread.hpp.

References GetInfo(), and CVDBGraphDb_Impl::SSeqInfo::m_SeqId.

◆ GetSeqLength()

TSeqPos CVDBGraphSeqIterator::GetSeqLength ( void  ) const
inline

Definition at line 227 of file graphread.hpp.

References GetInfo(), and CVDBGraphDb_Impl::SSeqInfo::m_SeqLength.

Referenced by CVDBGraphDataLoader_Impl::GetChunkOnce(), and CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ operator const void *()

CVDBGraphSeqIterator::operator const void * ( void  ) const
inline

Definition at line 206 of file graphread.hpp.

◆ operator!()

bool CVDBGraphSeqIterator::operator! ( void  ) const
inline

Definition at line 203 of file graphread.hpp.

References m_Info, and CVDBGraphDb_Impl::SSeqInfo::m_RowSize.

◆ operator*()

const SSeqInfo& CVDBGraphSeqIterator::operator* ( void  ) const
inline

Definition at line 211 of file graphread.hpp.

References GetInfo().

◆ operator++()

CVDBGraphSeqIterator & CVDBGraphSeqIterator::operator++ ( void  )

Definition at line 345 of file graphread.cpp.

References GetInfo(), m_Db, and m_Info.

◆ operator->()

const SSeqInfo* CVDBGraphSeqIterator::operator-> ( void  ) const
inline

Definition at line 214 of file graphread.hpp.

References GetInfo().

◆ SeqTableIsSmaller()

bool CVDBGraphSeqIterator::SeqTableIsSmaller ( COpenRange< TSeqPos >  range) const

Definition at line 651 of file graphread.cpp.

References GetDb(), GetInfo(), info, CVDBGraphDb_Impl::Put(), compile_time_bits::range(), and x_SeqTableIsSmaller().

Referenced by CVDBGraphDataLoader_Impl::LoadFullEntry(), and CVDBGraphDataLoader_Impl::LoadSplitEntry().

◆ x_MakeGraph()

CRef< CSeq_graph > CVDBGraphSeqIterator::x_MakeGraph ( const string &  annot_name,
CSeq_loc &  loc,
const SSeqInfo &  info,
const COpenRange< TSeqPos > &  range,
TSeqPos  step,
SGraphTableCursor &  cursor,
CVDBColumn &  column,
int  level 
) const
protected

Definition at line 374 of file graphread.cpp.

References column, info, NStr::IntToString(), kMax_I4, kMax_Int, kMax_UI1, kMin_I4, CVDBGraphDb_Impl::SGraphTableCursor::m_Cursor, max(), min(), NCBI_THROW, compile_time_bits::range(), row, CSeq_graph_Base::SetA(), CInt_graph_Base::SetAxis(), CReal_graph_Base::SetAxis(), CSeq_graph_Base::SetComment(), CSeq_graph_Base::SetComp(), CSeq_graph_Base::SetGraph(), CSeq_graph_Base::SetLoc(), CInt_graph_Base::SetMax(), CReal_graph_Base::SetMax(), CInt_graph_Base::SetMin(), CReal_graph_Base::SetMin(), CSeq_graph_Base::SetNumval(), CSeq_graph_Base::SetTitle(), CInt_graph_Base::SetValues(), CReal_graph_Base::SetValues(), CVDBValue::size(), and sx_Assign().

Referenced by GetAnnot().

◆ x_MakeTable()

CRef< CSeq_table > CVDBGraphSeqIterator::x_MakeTable ( const string &  annot_name,
CSeq_loc &  loc,
const SSeqInfo &  info,
const COpenRange< TSeqPos > &  range,
SGraphTableCursor &  cursor 
) const
protected

Definition at line 493 of file graphread.cpp.

References cnt, CSeqTable_column_info_Base::eField_id_location_from, CSeqTable_column_info_Base::eField_id_location_id, i, info, kMax_I4, kMax_Int, kMin_I4, min(), NCBI_THROW, compile_time_bits::range(), row, CSeqTable_column_Base::SetData(), CSeqTable_column_Base::SetDefault(), CSeqTable_column_Base::SetHeader(), CSeq_loc::SetInt(), ncbi::grid::netcache::search::fields::size, and table.

Referenced by GetAnnot().

◆ x_SeqTableIsSmaller()

bool CVDBGraphSeqIterator::x_SeqTableIsSmaller ( COpenRange< TSeqPos >  range,
SGraphTableCursor &  cursor 
) const
protected

Definition at line 609 of file graphread.cpp.

References GetInfo(), info, int, kMax_I4, kMax_UI1, kMin_I4, compile_time_bits::range(), and row.

Referenced by GetAnnot(), and SeqTableIsSmaller().

Member Data Documentation

◆ m_Db

CVDBGraphDb CVDBGraphSeqIterator::m_Db
private

Definition at line 296 of file graphread.hpp.

Referenced by GetDb(), and operator++().

◆ m_Info

CVDBGraphDb_Impl::SSeqInfo CVDBGraphSeqIterator::m_Info
private

Definition at line 297 of file graphread.hpp.

Referenced by CVDBGraphSeqIterator(), GetInfo(), operator!(), and operator++().

The documentation for this class was generated from the following files:
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Modified on Fri Sep 20 14:57:49 2024 by modify_doxy.py rev. 669887