NCBI C++ ToolKit
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CSparseRowHandle Class Reference

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CSparseRowHandle. More...

#include <gui/widgets/aln_multiple/sparse_row_handle.hpp>

+ Inheritance diagram for CSparseRowHandle:
+ Collaboration diagram for CSparseRowHandle:

Public Member Functions

 CSparseRowHandle (CSparseAln &aln, TNumrow row)
 CSparseRowHandle. More...
 
virtual ~CSparseRowHandle ()
 
virtual TNumrow GetRowNum () const
 
const stringGetText () const
 
virtual TSignedSeqPos GetSeqAlnStart () const
 
virtual TSignedSeqPos GetSeqAlnStop () const
 
virtual IAlnExplorer::TSignedRange GetSeqAlnRange () const
 
virtual TSignedSeqPos GetSeqStart () const
 
virtual TSignedSeqPos GetSeqStop () const
 
virtual bool IsNegativeStrand () const
 
virtual TSignedSeqPos GetAlnPosFromSeqPos (TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const
 
virtual TSignedSeqPos GetSeqPosFromAlnPos (TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const
 
virtual IAlnSegmentIteratorCreateSegmentIterator (const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flag) const
 
virtual bool CanGetSeqString () const
 
virtual stringGetSeqString (string &buffer, const IAlnExplorer::TRange &seq_rng) const
 
virtual stringGetAlnSeqString (string &buffer, const IAlnExplorer::TSignedRange &aln_rng) const
 
virtual bool CanGetBioseqHandle () const
 
virtual const objects::CBioseq_Handle & GetBioseqHandle () const
 
virtual const objects::CSeq_id & GetSeq_id () const
 
virtual objects::CScope & GetScope () const
 
bool UsesAATranslation () const
 
virtual bool IsNucProtAlignment () const
 
virtual size_t GetBaseWidth () const
 
virtual int GetGenCode () const
 
- Public Member Functions inherited from IAlignRowHandle
virtual bool IsAnchor () const
 
void UseExternalOrganismLookup (bool f)
 
virtual bool IsConsensus () const
 
virtual TSeqPos GetSeqLength () const
 
virtual const stringGetOrgLabel (bool fExtOrgLookup=false) const
 
virtual int GetTaxId (bool fExtOrgLookup=false) const
 
virtual void GetTaxonomy (string &taxonomy, bool fExtOrgLookup=false) const
 
virtual void GetIsolationSource (string &value) const
 
virtual void GetCountry (string &value) const
 
virtual void GetCollectionDate (string &value) const
 
virtual void GetHost (string &value) const
 
virtual void GetGeneSymbol (string &value) const
 
virtual double GetPctIdentity () const
 
virtual double GetPctCoverage () const
 
virtual int GetMismatches () const
 

Protected Attributes

CSparseAlnm_Alignment
 
TNumrow m_Row
 
string m_Text
 
int m_GenCode = -1
 
- Protected Attributes inherited from IAlignRowHandle
bool m_fExtOrgLookup = false
 
string m_OrgLabel
 
int m_TaxId = 0
 

Additional Inherited Members

- Public Types inherited from IAlignRowHandle
typedef IAlnExplorer::TNumrow TNumrow
 
typedef IAlnExplorer::TResidue TResidue
 
- Protected Member Functions inherited from IAlignRowHandle
virtual ~IAlignRowHandle ()
 

Detailed Description

CSparseRowHandle.

Definition at line 47 of file sparse_row_handle.hpp.

Constructor & Destructor Documentation

◆ CSparseRowHandle()

CSparseRowHandle::CSparseRowHandle ( CSparseAln aln,
TNumrow  row 
)

CSparseRowHandle.

Definition at line 46 of file sparse_row_handle.cpp.

◆ ~CSparseRowHandle()

CSparseRowHandle::~CSparseRowHandle ( )
virtual

Definition at line 53 of file sparse_row_handle.cpp.

Member Function Documentation

◆ CanGetBioseqHandle()

bool CSparseRowHandle::CanGetBioseqHandle ( ) const
virtual

Implements IAlignRowHandle.

Definition at line 155 of file sparse_row_handle.cpp.

◆ CanGetSeqString()

bool CSparseRowHandle::CanGetSeqString ( ) const
virtual

Implements IAlignRowHandle.

Definition at line 135 of file sparse_row_handle.cpp.

◆ CreateSegmentIterator()

IAlnSegmentIterator * CSparseRowHandle::CreateSegmentIterator ( const IAlnExplorer::TSignedRange range,
IAlnSegmentIterator::EFlags  flag 
) const
virtual

◆ GetAlnPosFromSeqPos()

TSignedSeqPos CSparseRowHandle::GetAlnPosFromSeqPos ( TSeqPos  seq_pos,
IAlnExplorer::ESearchDirection  dir = IAlnExplorer::eNone,
bool  try_reverse_dir = true 
) const
virtual

Implements IAlignRowHandle.

Definition at line 111 of file sparse_row_handle.cpp.

References CSparseAln::GetAlnPosFromSeqPos(), m_Alignment, and m_Row.

◆ GetAlnSeqString()

string & CSparseRowHandle::GetAlnSeqString ( string buffer,
const IAlnExplorer::TSignedRange aln_rng 
) const
virtual

Implements IAlignRowHandle.

Definition at line 148 of file sparse_row_handle.cpp.

References buffer, CSparseAln::GetAlnSeqString(), m_Alignment, and m_Row.

◆ GetBaseWidth()

size_t CSparseRowHandle::GetBaseWidth ( ) const
virtual

Implements IAlignRowHandle.

Definition at line 195 of file sparse_row_handle.cpp.

References CSparseAln::GetBaseWidth(), m_Alignment, and m_Row.

◆ GetBioseqHandle()

const objects::CBioseq_Handle & CSparseRowHandle::GetBioseqHandle ( void  ) const
virtual

Implements IAlignRowHandle.

Definition at line 161 of file sparse_row_handle.cpp.

References CSparseAln::GetBioseqHandle(), m_Alignment, and m_Row.

Referenced by GetGenCode().

◆ GetGenCode()

int CSparseRowHandle::GetGenCode ( ) const
virtual

Implements IAlignRowHandle.

Definition at line 200 of file sparse_row_handle.cpp.

References GetBioseqHandle(), CSeqUtils::GetGenCode(), and m_GenCode.

◆ GetRowNum()

CSparseRowHandle::TNumrow CSparseRowHandle::GetRowNum ( ) const
virtual

Implements IAlignRowHandle.

Definition at line 58 of file sparse_row_handle.cpp.

References m_Row.

◆ GetScope()

objects::CScope & CSparseRowHandle::GetScope ( void  ) const
virtual

Definition at line 172 of file sparse_row_handle.cpp.

References CSparseAln::GetScope(), and m_Alignment.

Referenced by GetText().

◆ GetSeq_id()

const objects::CSeq_id & CSparseRowHandle::GetSeq_id ( void  ) const
virtual

Implements IAlignRowHandle.

Definition at line 166 of file sparse_row_handle.cpp.

References CSparseAln::GetSeqId(), m_Alignment, and m_Row.

Referenced by GetText().

◆ GetSeqAlnRange()

IAlnExplorer::TSignedRange CSparseRowHandle::GetSeqAlnRange ( ) const
virtual

Implements IAlignRowHandle.

Definition at line 105 of file sparse_row_handle.cpp.

References CSparseAln::GetSeqAlnRange(), m_Alignment, and m_Row.

◆ GetSeqAlnStart()

TSignedSeqPos CSparseRowHandle::GetSeqAlnStart ( ) const
virtual

Implements IAlignRowHandle.

Definition at line 75 of file sparse_row_handle.cpp.

References CSparseAln::GetSeqAlnStart(), m_Alignment, and m_Row.

◆ GetSeqAlnStop()

TSignedSeqPos CSparseRowHandle::GetSeqAlnStop ( ) const
virtual

Implements IAlignRowHandle.

Definition at line 81 of file sparse_row_handle.cpp.

References CSparseAln::GetSeqAlnStop(), m_Alignment, and m_Row.

◆ GetSeqPosFromAlnPos()

TSignedSeqPos CSparseRowHandle::GetSeqPosFromAlnPos ( TSeqPos  aln_pos,
IAlnExplorer::ESearchDirection  dir = IAlnExplorer::eNone,
bool  try_reverse_dir = true 
) const
virtual

Implements IAlignRowHandle.

Definition at line 119 of file sparse_row_handle.cpp.

References CSparseAln::GetSeqPosFromAlnPos(), m_Alignment, and m_Row.

◆ GetSeqStart()

TSignedSeqPos CSparseRowHandle::GetSeqStart ( ) const
virtual

Implements IAlignRowHandle.

Definition at line 87 of file sparse_row_handle.cpp.

References CSparseAln::GetSeqStart(), m_Alignment, and m_Row.

◆ GetSeqStop()

TSignedSeqPos CSparseRowHandle::GetSeqStop ( ) const
virtual

Implements IAlignRowHandle.

Definition at line 93 of file sparse_row_handle.cpp.

References CSparseAln::GetSeqStop(), m_Alignment, and m_Row.

◆ GetSeqString()

string & CSparseRowHandle::GetSeqString ( string buffer,
const IAlnExplorer::TRange seq_rng 
) const
virtual

Implements IAlignRowHandle.

Definition at line 141 of file sparse_row_handle.cpp.

References buffer, CSparseAln::GetSeqString(), m_Alignment, and m_Row.

◆ GetText()

const string & CSparseRowHandle::GetText ( void  ) const
virtual

◆ IsNegativeStrand()

bool CSparseRowHandle::IsNegativeStrand ( ) const
virtual

Implements IAlignRowHandle.

Definition at line 99 of file sparse_row_handle.cpp.

References CSparseAln::IsNegativeStrand(), m_Alignment, and m_Row.

◆ IsNucProtAlignment()

bool CSparseRowHandle::IsNucProtAlignment ( ) const
virtual

◆ UsesAATranslation()

bool CSparseRowHandle::UsesAATranslation ( ) const
virtual

Implements IAlignRowHandle.

Definition at line 177 of file sparse_row_handle.cpp.

References CSparseAln::GetBioseqHandle(), m_Alignment, and m_Row.

Member Data Documentation

◆ m_Alignment

CSparseAln& CSparseRowHandle::m_Alignment
protected

◆ m_GenCode

int CSparseRowHandle::m_GenCode = -1
mutableprotected

Definition at line 90 of file sparse_row_handle.hpp.

Referenced by GetGenCode().

◆ m_Row

TNumrow CSparseRowHandle::m_Row
protected

◆ m_Text

string CSparseRowHandle::m_Text
mutableprotected

Definition at line 89 of file sparse_row_handle.hpp.

Referenced by GetText().


The documentation for this class was generated from the following files:
Modified on Fri Apr 12 17:15:24 2024 by modify_doxy.py rev. 669887