CAlnVecGraphicDataSource Class Reference

Search Toolkit Book for CAlnVecGraphicDataSource

#include <alnvec_graphic_ds.hpp>

Inheritance diagram for CAlnVecGraphicDataSource:

[legend]Collaboration diagram for CAlnVecGraphicDataSource:

[legend]List of all members.

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Detailed Description

CAlnVecGraphicDataSource - implementation of CAlnGraphicDataSource for CAlnVec-based alignments.

Definition at line 48 of file alnvec_graphic_ds.hpp.

Public Member Functions
	CAlnVecGraphicDataSource (const objects::CAlnVec &aln_mgr)
	~CAlnVecGraphicDataSource ()
virtual TSignedSeqPos	GetSeqPosFromSeqPos (TNumrow for_row, TNumrow row, TSeqPos seq_pos) const
CAlnGraphicDataSource 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, TSearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const
virtual string &	GetAlnSeqString (string &buffer, TNumrow row, const IAlnExplorer::TSignedRange &aln_range) const
virtual IAlnSegmentIterator *	CreateSegmentIterator (TNumrow row, const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) const
Protected Attributes
CConstRef< objects::CAlnVec >	m_AlnVec
Private Member Functions
	CAlnVecGraphicDataSource (const CAlnVecGraphicDataSource &ds)
CAlnVecGraphicDataSource &	operator= (const CAlnVecGraphicDataSource &ds)

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Constructor & Destructor Documentation

CAlnVecGraphicDataSource::CAlnVecGraphicDataSource (  const objects::CAlnVec &  aln_mgr  )

Definition at line 49 of file alnvec_graphic_ds.cpp.

CAlnVecGraphicDataSource::~CAlnVecGraphicDataSource (   )

Definition at line 55 of file alnvec_graphic_ds.cpp.

CAlnVecGraphicDataSource::CAlnVecGraphicDataSource (  const CAlnVecGraphicDataSource &  ds  )  [private]

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Member Function Documentation

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

Definition at line 161 of file alnvec_graphic_ds.cpp. References _ASSERT, IAlnSegmentIterator::eAllSegments, IAlnSegmentIterator::eInsertsOnly, IAlnSegmentIterator::eSkipGaps, IAlnSegmentIterator::eSkipInserts, CAlnMap::fAllChunks, CAlnMap::fInsertsOnly, CAlnMap::fSkipAllGaps, CAlnMap::fSkipInserts, and m_AlnVec.

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

Implements IAlnGraphicDataSource. Definition at line 60 of file alnvec_graphic_ds.cpp. References IAlnExplorer::fInvalid, IAlnExplorer::fMixed, and m_AlnVec.

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

Definition at line 153 of file alnvec_graphic_ds.cpp. References m_AlnVec.

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

Implements IAlnGraphicDataSource. Definition at line 84 of file alnvec_graphic_ds.cpp. References m_AlnVec.

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

Implements IAlnGraphicDataSource. Definition at line 90 of file alnvec_graphic_ds.cpp. References m_AlnVec.

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

Anchoring methods. Implements IAlnGraphicDataSource. Definition at line 114 of file alnvec_graphic_ds.cpp. References m_AlnVec.

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

Definition at line 127 of file alnvec_graphic_ds.cpp. References m_AlnVec.

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

number of rows in alignment Implements IAlnGraphicDataSource. Definition at line 78 of file alnvec_graphic_ds.cpp. References m_AlnVec.

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

Definition at line 121 of file alnvec_graphic_ds.cpp. References m_AlnVec.

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

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

Definition at line 188 of file alnvec_graphic_ds.cpp. References m_AlnVec.

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

Definition at line 96 of file alnvec_graphic_ds.cpp. References m_AlnVec.

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

Definition at line 102 of file alnvec_graphic_ds.cpp. References m_AlnVec.

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

Definition at line 138 of file alnvec_graphic_ds.cpp. References m_AlnVec.

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

Definition at line 132 of file alnvec_graphic_ds.cpp. References m_AlnVec.

CAlnVecGraphicDataSource& CAlnVecGraphicDataSource::operator= (  const CAlnVecGraphicDataSource &  ds  )  [private]

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Member Data Documentation

CConstRef<objects::CAlnVec> CAlnVecGraphicDataSource::m_AlnVec [protected]

Definition at line 93 of file alnvec_graphic_ds.hpp. Referenced by CreateSegmentIterator(), GetAlignType(), GetAlnSeqString(), GetAlnStart(), GetAlnStop(), GetAnchor(), GetBioseqHandle(), GetNumRows(), GetSeqId(), GetSeqPosFromSeqPos(), GetSeqStart(), GetSeqStop(), IsNegativeStrand(), and IsPositiveStrand().

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

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

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