CSparseAlnGraphicDataSource Class Reference

Search Toolkit Book for CSparseAlnGraphicDataSource

#include <sparsealn_graphic_ds.hpp>

Inheritance diagram for CSparseAlnGraphicDataSource:

[legend]Collaboration diagram for CSparseAlnGraphicDataSource:

[legend]List of all members.

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Detailed Description

Definition at line 45 of file sparsealn_graphic_ds.hpp.

Public Types
typedef IAlnExplorer::TNumrow	TNumrow
typedef IAlnExplorer::TResidue	TResidue
Public Member Functions
	CSparseAlnGraphicDataSource (CConstRef< CSparseAln > sparseAlign)
	CSparseAlnGraphicDataSource.
virtual	~CSparseAlnGraphicDataSource ()
virtual TSignedSeqPos	GetSeqPosFromSeqPos (TNumrow for_row, TNumrow row, TSeqPos seq_pos) const
IAlnGraphicDataSource implementation
virtual IAlnExplorer::EAlignType	GetAlignType () const
virtual TNumrow	GetNumRows (void) const
	number of rows in alignment
virtual TSeqPos	GetAlnStart (void) const
virtual TSeqPos	GetAlnStop (void) const
virtual TSeqPos	GetSeqStart (TNumrow row) const
virtual TSeqPos	GetSeqStop (TNumrow row) const
virtual TNumrow	GetAnchor (void) const
	Anchoring methods.
virtual const objects::CSeq_id &	GetSeqId (TNumrow row) const
virtual const objects::CBioseq_Handle &	GetBioseqHandle (TNumrow row) const
virtual bool	IsPositiveStrand (TNumrow row) const
virtual bool	IsNegativeStrand (TNumrow row) const
virtual TSignedSeqPos	GetSeqPosFromAlnPos (TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const
virtual IAlnSegmentIterator *	CreateSegmentIterator (TNumrow row, const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flag) const
virtual string &	GetAlnSeqString (string &buffer, TNumrow row, const IAlnExplorer::TSignedRange &aln_rng) const
Protected Attributes
CConstRef< CSparseAln >	m_Alignment

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Member Typedef Documentation

typedef IAlnExplorer::TNumrow CSparseAlnGraphicDataSource::TNumrow

Reimplemented from IAlnGraphicDataSource. Definition at line 50 of file sparsealn_graphic_ds.hpp.

typedef IAlnExplorer::TResidue CSparseAlnGraphicDataSource::TResidue

Reimplemented from IAlnGraphicDataSource. Definition at line 51 of file sparsealn_graphic_ds.hpp.

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Constructor & Destructor Documentation

CSparseAlnGraphicDataSource::CSparseAlnGraphicDataSource (  CConstRef< CSparseAln >  sparseAlign  )

CSparseAlnGraphicDataSource. Definition at line 52 of file sparsealn_graphic_ds.cpp.

CSparseAlnGraphicDataSource::~CSparseAlnGraphicDataSource (   )  [virtual]

Definition at line 58 of file sparsealn_graphic_ds.cpp.

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Member Function Documentation

IAlnSegmentIterator * CSparseAlnGraphicDataSource::CreateSegmentIterator (  TNumrow  row, const IAlnExplorer::TSignedRange &  range, IAlnSegmentIterator::EFlags  flag )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 185 of file sparsealn_graphic_ds.cpp. References m_Alignment.

IAlnExplorer::EAlignType CSparseAlnGraphicDataSource::GetAlignType (   )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 63 of file sparsealn_graphic_ds.cpp. References CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, IAlnExplorer::fDNA, IAlnExplorer::fInvalid, IAlnExplorer::fMixed, IAlnExplorer::fProtein, GetBioseqHandle(), and GetNumRows().

string & CSparseAlnGraphicDataSource::GetAlnSeqString (  string &  buffer, TNumrow  row, const IAlnExplorer::TSignedRange &  aln_rng )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 193 of file sparsealn_graphic_ds.cpp. References m_Alignment.

TSeqPos CSparseAlnGraphicDataSource::GetAlnStart (  void   )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 121 of file sparsealn_graphic_ds.cpp. References m_Alignment.

TSeqPos CSparseAlnGraphicDataSource::GetAlnStop (  void   )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 127 of file sparsealn_graphic_ds.cpp. References m_Alignment.

CSparseAlnGraphicDataSource::TNumrow CSparseAlnGraphicDataSource::GetAnchor (  void   )  const [virtual]

Anchoring methods. Implements IAlnGraphicDataSource. Definition at line 151 of file sparsealn_graphic_ds.cpp. References m_Alignment.

const objects::CBioseq_Handle & CSparseAlnGraphicDataSource::GetBioseqHandle (  TNumrow  row  )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 201 of file sparsealn_graphic_ds.cpp. References m_Alignment. Referenced by GetAlignType().

CSparseAlnGraphicDataSource::TNumrow CSparseAlnGraphicDataSource::GetNumRows (  void   )  const [virtual]

number of rows in alignment Implements IAlnGraphicDataSource. Definition at line 115 of file sparsealn_graphic_ds.cpp. References m_Alignment. Referenced by GetAlignType().

const CSeq_id & CSparseAlnGraphicDataSource::GetSeqId (  TNumrow  row  )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 157 of file sparsealn_graphic_ds.cpp. References m_Alignment.

TSignedSeqPos CSparseAlnGraphicDataSource::GetSeqPosFromAlnPos (  TNumrow  for_row, TSeqPos  aln_pos, IAlnExplorer::ESearchDirection  dir = IAlnExplorer::eNone, bool  try_reverse_dir = true )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 176 of file sparsealn_graphic_ds.cpp. References m_Alignment. Referenced by GetSeqPosFromSeqPos().

TSignedSeqPos CSparseAlnGraphicDataSource::GetSeqPosFromSeqPos (  TNumrow  for_row, TNumrow  row, TSeqPos  seq_pos )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 207 of file sparsealn_graphic_ds.cpp. References GetSeqPosFromAlnPos(), and m_Alignment.

TSeqPos CSparseAlnGraphicDataSource::GetSeqStart (  TNumrow  row  )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 133 of file sparsealn_graphic_ds.cpp. References m_Alignment.

TSeqPos CSparseAlnGraphicDataSource::GetSeqStop (  TNumrow  row  )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 139 of file sparsealn_graphic_ds.cpp. References m_Alignment.

bool CSparseAlnGraphicDataSource::IsNegativeStrand (  TNumrow  row  )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 170 of file sparsealn_graphic_ds.cpp. References m_Alignment.

bool CSparseAlnGraphicDataSource::IsPositiveStrand (  TNumrow  row  )  const [virtual]

Implements IAlnGraphicDataSource. Definition at line 163 of file sparsealn_graphic_ds.cpp.

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Member Data Documentation

CConstRef<CSparseAln> CSparseAlnGraphicDataSource::m_Alignment [protected]

Definition at line 91 of file sparsealn_graphic_ds.hpp. Referenced by CreateSegmentIterator(), GetAlnSeqString(), GetAlnStart(), GetAlnStop(), GetAnchor(), GetBioseqHandle(), GetNumRows(), GetSeqId(), GetSeqPosFromAlnPos(), GetSeqPosFromSeqPos(), GetSeqStart(), GetSeqStop(), and IsNegativeStrand().

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

• include/gui/widgets/seq_graphic/sparsealn_graphic_ds.hpp
• src/gui/widgets/seq_graphic/sparsealn_graphic_ds.cpp

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