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CSeqsRange Class Reference

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#include <objmgr/split/id_range.hpp>

+ Collaboration diagram for CSeqsRange:

Public Types

typedef COneSeqRange::TRange TRange
 
typedef map< CSeq_id_Handle, COneSeqRange > TRanges
 
typedef TRanges::const_iterator const_iterator
 

Public Member Functions

 CSeqsRange (void)
 
 ~CSeqsRange (void)
 
CNcbiOstream & Print (CNcbiOstream &out) const
 
const_iterator begin (void) const
 
const_iterator end (void) const
 
size_t size (void) const
 
bool empty (void) const
 
void clear (void)
 
CSeq_id_Handle GetSingleId (void) const
 
void Add (const CSeq_id_Handle &id, const COneSeqRange &loc)
 
void Add (const CSeq_id_Handle &id, const TRange &range)
 
void Add (const CSeqsRange &seqs_range)
 
void Add (const CHandleRangeMap &hrmap)
 
void Add (const CSeq_loc &loc, const CBlobSplitterImpl &impl)
 
void Add (const CSeq_feat &obj, const CBlobSplitterImpl &impl)
 
void Add (const CSeq_align &obj, const CBlobSplitterImpl &impl)
 
void Add (const CSeq_graph &obj, const CBlobSplitterImpl &impl)
 
void Add (const CDense_seg &denseg, const CBlobSplitterImpl &impl)
 
void Add (const CDense_diag &diag, const CBlobSplitterImpl &impl)
 
void Add (const CPacked_seg &packed, const CBlobSplitterImpl &impl)
 
void Add (const CSpliced_seg &spliced, const CBlobSplitterImpl &impl)
 
void Add (const CSparse_seg &sparse, const CBlobSplitterImpl &impl)
 
void Add (const CSeq_table &table, const CBlobSplitterImpl &impl)
 
void Add (const CSeqTableLocColumns &loc, const CSeq_table &table, const CBlobSplitterImpl &impl)
 
int Compare (const CSeqsRange &other) const
 

Private Attributes

TRanges m_Ranges
 

Detailed Description

Definition at line 96 of file id_range.hpp.

Member Typedef Documentation

◆ const_iterator

typedef TRanges::const_iterator CSeqsRange::const_iterator

Definition at line 106 of file id_range.hpp.

◆ TRange

typedef COneSeqRange::TRange CSeqsRange::TRange

Definition at line 104 of file id_range.hpp.

◆ TRanges

typedef map<CSeq_id_Handle, COneSeqRange> CSeqsRange::TRanges

Definition at line 105 of file id_range.hpp.

Constructor & Destructor Documentation

◆ CSeqsRange()

CSeqsRange::CSeqsRange ( void  )

Definition at line 95 of file id_range.cpp.

◆ ~CSeqsRange()

CSeqsRange::~CSeqsRange ( void  )

Definition at line 100 of file id_range.cpp.

Member Function Documentation

◆ Add() [1/15]

void CSeqsRange::Add ( const CDense_diag &  diag,
const CBlobSplitterImpl &  impl 
)

Definition at line 248 of file id_range.cpp.

References ERR_POST_X, CDense_diag_Base::GetDim(), CSeq_id_Handle::GetHandle(), CDense_diag_Base::GetIds(), CDense_diag_Base::GetLen(), CDense_diag_Base::GetStarts(), i, len, m_Ranges, min(), and Warning().

◆ Add() [2/15]

void CSeqsRange::Add ( const CDense_seg &  denseg,
const CBlobSplitterImpl &  impl 
)

Definition at line 216 of file id_range.cpp.

References ERR_POST_X, CDense_seg_Base::GetDim(), CSeq_id_Handle::GetHandle(), CDense_seg_Base::GetIds(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CDense_seg_Base::GetStarts(), m_Ranges, min(), and Warning().

◆ Add() [3/15]

void CSeqsRange::Add ( const CHandleRangeMap &  hrmap)

Definition at line 151 of file id_range.cpp.

References ITERATE, and m_Ranges.

◆ Add() [4/15]

void CSeqsRange::Add ( const CPacked_seg &  packed,
const CBlobSplitterImpl &  impl 
)

Definition at line 269 of file id_range.cpp.

References CPacked_seg_Base::GetDim(), CSeq_id_Handle::GetHandle(), CPacked_seg_Base::GetIds(), CPacked_seg_Base::GetLens(), CPacked_seg_Base::GetNumseg(), CPacked_seg_Base::GetPresent(), CPacked_seg_Base::GetStarts(), and m_Ranges.

◆ Add() [5/15]

void CSeqsRange::Add ( const CSeq_align &  obj,
const CBlobSplitterImpl &  impl 
)

Definition at line 177 of file id_range.cpp.

References Add(), CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Packed, CSeq_align_Base::C_Segs::e_Sparse, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::C_Segs::GetDisc(), CSeq_align_Base::C_Segs::GetPacked(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSparse(), CSeq_align_Base::C_Segs::GetSpliced(), CSeq_align_Base::C_Segs::GetStd(), ITERATE, and CSeq_align_Base::C_Segs::Which().

◆ Add() [6/15]

void CSeqsRange::Add ( const CSeq_feat &  obj,
const CBlobSplitterImpl &  impl 
)

Definition at line 168 of file id_range.cpp.

References Add(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), and CSeq_feat_Base::IsSetProduct().

◆ Add() [7/15]

void CSeqsRange::Add ( const CSeq_graph &  obj,
const CBlobSplitterImpl &  impl 
)

Definition at line 373 of file id_range.cpp.

References Add(), and CSeq_graph_Base::GetLoc().

◆ Add() [8/15]

void CSeqsRange::Add ( const CSeq_id_Handle &  id,
const COneSeqRange &  loc 
)

Definition at line 131 of file id_range.cpp.

References m_Ranges.

Referenced by CLocObjects_SplitInfo::Add(), CSeq_annot_SplitInfo::Add(), Add(), CAnnotObject_SplitInfo::CAnnotObject_SplitInfo(), CBioseq_SplitInfo::CBioseq_SplitInfo(), CSeq_descr_SplitInfo::CSeq_descr_SplitInfo(), CSeq_hist_SplitInfo::CSeq_hist_SplitInfo(), and CSeq_data_SplitInfo::SetSeq_data().

◆ Add() [9/15]

void CSeqsRange::Add ( const CSeq_id_Handle &  id,
const TRange &  range 
)

Definition at line 137 of file id_range.cpp.

References m_Ranges, and compile_time_bits::range().

◆ Add() [10/15]

void CSeqsRange::Add ( const CSeq_loc &  loc,
const CBlobSplitterImpl &  impl 
)

Definition at line 159 of file id_range.cpp.

References Add(), CHandleRangeMap::AddLocation(), and CHandleRangeMap::SetMasterSeq().

◆ Add() [11/15]

void CSeqsRange::Add ( const CSeq_table &  table,
const CBlobSplitterImpl &  impl 
)

Definition at line 379 of file id_range.cpp.

References Add(), info, and table.

◆ Add() [12/15]

void CSeqsRange::Add ( const CSeqsRange &  seqs_range)

Definition at line 143 of file id_range.cpp.

References ITERATE, m_Ranges, and compile_time_bits::range().

◆ Add() [13/15]

void CSeqsRange::Add ( const CSeqTableLocColumns &  loc,
const CSeq_table &  table,
const CBlobSplitterImpl &  impl 
)

Definition at line 395 of file id_range.cpp.

References Add(), CSeqTableLocColumns::GetLoc(), CSeqTableLocColumns::IsRealLoc(), CSeqTableLocColumns::IsSet(), ncbi::grid::netcache::search::fields::key, row, CSeqTableLocColumns::SetTableKeyAndIndex(), and table.

◆ Add() [14/15]

void CSeqsRange::Add ( const CSparse_seg &  sparse,
const CBlobSplitterImpl &  impl 
)

Definition at line 331 of file id_range.cpp.

References ERR_POST_X, CSparse_align_Base::GetFirst_id(), CSparse_align_Base::GetFirst_starts(), CSeq_id_Handle::GetHandle(), CSparse_align_Base::GetLens(), CSparse_align_Base::GetNumseg(), CSparse_seg_Base::GetRows(), CSparse_align_Base::GetSecond_id(), CSparse_align_Base::GetSecond_starts(), CSparse_align_Base::GetSecond_strands(), CSparse_align_Base::IsSetSecond_strands(), ITERATE, len, m_Ranges, min(), and Warning().

◆ Add() [15/15]

void CSeqsRange::Add ( const CSpliced_seg &  spliced,
const CBlobSplitterImpl &  impl 
)

Definition at line 301 of file id_range.cpp.

References CProt_pos_Base::GetAmin(), CSpliced_seg_Base::GetExons(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_id(), CSpliced_seg_Base::GetGenomic_id(), CSpliced_exon_Base::GetGenomic_start(), CSeq_id_Handle::GetHandle(), CProduct_pos_Base::GetNucpos(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::GetProduct_id(), CSpliced_seg_Base::GetProduct_id(), CSpliced_exon_Base::GetProduct_start(), CProduct_pos_Base::GetProtpos(), CProduct_pos_Base::IsNucpos(), CSpliced_exon_Base::IsSetGenomic_id(), CSpliced_seg_Base::IsSetGenomic_id(), CSpliced_exon_Base::IsSetProduct_id(), CSpliced_seg_Base::IsSetProduct_id(), ITERATE, and m_Ranges.

◆ begin()

const_iterator CSeqsRange::begin ( void  ) const
inline

Definition at line 108 of file id_range.hpp.

References map_checker< Container >::begin(), and m_Ranges.

Referenced by CSeq_data_SplitInfo::GetRange().

◆ clear()

void CSeqsRange::clear ( void  )
inline

Definition at line 125 of file id_range.hpp.

References map_checker< Container >::clear(), and m_Ranges.

Referenced by CBioseq_SplitInfo::CBioseq_SplitInfo(), CLocObjects_SplitInfo::clear(), and CSeq_data_SplitInfo::SetSeq_data().

◆ Compare()

int CSeqsRange::Compare ( const CSeqsRange &  other) const

Definition at line 418 of file id_range.cpp.

References map_checker< Container >::begin(), NStr::CompareNocase(), map_checker< Container >::end(), m_Ranges, r1, and r2.

Referenced by CSeq_annot_SplitInfo::Compare().

◆ empty()

bool CSeqsRange::empty ( void  ) const
inline

Definition at line 121 of file id_range.hpp.

References map_checker< Container >::empty(), and m_Ranges.

◆ end()

const_iterator CSeqsRange::end ( void  ) const
inline

Definition at line 112 of file id_range.hpp.

References map_checker< Container >::end(), and m_Ranges.

◆ GetSingleId()

CSeq_id_Handle CSeqsRange::GetSingleId ( void  ) const

Definition at line 121 of file id_range.cpp.

References map_checker< Container >::begin(), m_Ranges, and map_checker< Container >::size().

◆ Print()

CNcbiOstream & CSeqsRange::Print ( CNcbiOstream &  out) const

Definition at line 105 of file id_range.cpp.

References map_checker< Container >::begin(), COpenRange< TSeqPos >::GetWhole(), ITERATE, m_Ranges, out(), and compile_time_bits::range().

◆ size()

size_t CSeqsRange::size ( void  ) const
inline

Definition at line 117 of file id_range.hpp.

References m_Ranges, and map_checker< Container >::size().

Referenced by CAnnotPieces::CountAnnotObjects(), and CSeq_data_SplitInfo::GetRange().

Member Data Documentation

◆ m_Ranges

TRanges CSeqsRange::m_Ranges
private

Definition at line 153 of file id_range.hpp.

Referenced by Add(), begin(), clear(), Compare(), empty(), end(), GetSingleId(), Print(), and size().

The documentation for this class was generated from the following files:
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Modified on Wed Sep 04 15:03:36 2024 by modify_doxy.py rev. 669887