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IAlignRowHandle Class Referenceabstract

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IAlignRowHandle provides an abstract way to access alignment row data. More...

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

+ Inheritance diagram for IAlignRowHandle:

Public Types

typedef IAlnExplorer::TNumrow TNumrow
 
typedef IAlnExplorer::TResidue TResidue
 

Public Member Functions

virtual TNumrow GetRowNum () const =0
 
virtual const stringGetText () const =0
 
virtual TSignedSeqPos GetSeqAlnStart () const =0
 
virtual TSignedSeqPos GetSeqAlnStop () const =0
 
virtual IAlnExplorer::TSignedRange GetSeqAlnRange () const =0
 
virtual TSignedSeqPos GetSeqStart () const =0
 
virtual TSignedSeqPos GetSeqStop () const =0
 
virtual bool IsNegativeStrand () const =0
 
virtual TSignedSeqPos GetAlnPosFromSeqPos (TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0
 
virtual TSignedSeqPos GetSeqPosFromAlnPos (TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0
 
virtual IAlnSegmentIteratorCreateSegmentIterator (const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) const =0
 
virtual bool CanGetSeqString () const =0
 
virtual stringGetSeqString (string &buffer, const IAlnExplorer::TRange &seq_rng) const =0
 
virtual stringGetAlnSeqString (string &buffer, const IAlnExplorer::TSignedRange &aln_rng) const =0
 
virtual bool CanGetBioseqHandle () const =0
 
virtual const objects::CBioseq_Handle & GetBioseqHandle () const =0
 
virtual const objects::CSeq_id & GetSeq_id () const =0
 
virtual bool UsesAATranslation () const =0
 
virtual bool IsNucProtAlignment () const =0
 
virtual size_t GetBaseWidth () const =0
 
virtual int GetGenCode () const =0
 
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 Member Functions

virtual ~IAlignRowHandle ()
 

Protected Attributes

bool m_fExtOrgLookup = false
 
string m_OrgLabel
 
int m_TaxId = 0
 

Detailed Description

IAlignRowHandle provides an abstract way to access alignment row data.

IAlignRowHandle-inherited classes are supposed to provide proprietary interface depending on the nature of data being represented.

Definition at line 58 of file alnmulti_ds.hpp.

Member Typedef Documentation

◆ TNumrow

Definition at line 61 of file alnmulti_ds.hpp.

◆ TResidue

Definition at line 62 of file alnmulti_ds.hpp.

Constructor & Destructor Documentation

◆ ~IAlignRowHandle()

virtual IAlignRowHandle::~IAlignRowHandle ( )
inlineprotectedvirtual

Definition at line 131 of file alnmulti_ds.hpp.

Member Function Documentation

◆ CanGetBioseqHandle()

virtual bool IAlignRowHandle::CanGetBioseqHandle ( ) const
pure virtual

◆ CanGetSeqString()

virtual bool IAlignRowHandle::CanGetSeqString ( ) const
pure virtual

◆ CreateSegmentIterator()

virtual IAlnSegmentIterator* IAlignRowHandle::CreateSegmentIterator ( const IAlnExplorer::TSignedRange range,
IAlnSegmentIterator::EFlags  flags 
) const
pure virtual

◆ GetAlnPosFromSeqPos()

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

◆ GetAlnSeqString()

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

◆ GetBaseWidth()

virtual size_t IAlignRowHandle::GetBaseWidth ( ) const
pure virtual

◆ GetBioseqHandle()

virtual const objects::CBioseq_Handle& IAlignRowHandle::GetBioseqHandle ( ) const
pure virtual

◆ GetCollectionDate()

virtual void IAlignRowHandle::GetCollectionDate ( string value) const
inlinevirtual

Definition at line 122 of file alnmulti_ds.hpp.

Referenced by CAlnVecRow::GetColumnText().

◆ GetCountry()

virtual void IAlignRowHandle::GetCountry ( string value) const
inlinevirtual

Definition at line 121 of file alnmulti_ds.hpp.

Referenced by CAlnVecRow::GetColumnText().

◆ GetGenCode()

virtual int IAlignRowHandle::GetGenCode ( ) const
pure virtual

◆ GetGeneSymbol()

virtual void IAlignRowHandle::GetGeneSymbol ( string value) const
inlinevirtual

Definition at line 124 of file alnmulti_ds.hpp.

Referenced by CAlnVecRow::GetColumnText().

◆ GetHost()

virtual void IAlignRowHandle::GetHost ( string value) const
inlinevirtual

Definition at line 123 of file alnmulti_ds.hpp.

Referenced by CAlnVecRow::GetColumnText().

◆ GetIsolationSource()

virtual void IAlignRowHandle::GetIsolationSource ( string value) const
inlinevirtual

Definition at line 120 of file alnmulti_ds.hpp.

Referenced by CAlnVecRow::GetColumnText().

◆ GetMismatches()

virtual int IAlignRowHandle::GetMismatches ( void  ) const
inlinevirtual

Definition at line 128 of file alnmulti_ds.hpp.

Referenced by CAlnVecRow::GetColumnAsSeqPos(), and CAlnVecRow::GetColumnText().

◆ GetOrgLabel()

const string & IAlignRowHandle::GetOrgLabel ( bool  fExtOrgLookup = false) const
virtual

◆ GetPctCoverage()

virtual double IAlignRowHandle::GetPctCoverage ( ) const
inlinevirtual

Definition at line 127 of file alnmulti_ds.hpp.

Referenced by CAlnVecRow::GetColumnAsFloat(), and CAlnVecRow::GetColumnText().

◆ GetPctIdentity()

virtual double IAlignRowHandle::GetPctIdentity ( ) const
inlinevirtual

Definition at line 126 of file alnmulti_ds.hpp.

Referenced by CAlnVecRow::GetColumnAsFloat(), and CAlnVecRow::GetColumnText().

◆ GetRowNum()

virtual TNumrow IAlignRowHandle::GetRowNum ( ) const
pure virtual

◆ GetSeq_id()

virtual const objects::CSeq_id& IAlignRowHandle::GetSeq_id ( ) const
pure virtual

Implemented in CSparseRowHandle, and CAlnVecRowHandle.

Referenced by IsConsensus().

◆ GetSeqAlnRange()

virtual IAlnExplorer::TSignedRange IAlignRowHandle::GetSeqAlnRange ( ) const
pure virtual

◆ GetSeqAlnStart()

virtual TSignedSeqPos IAlignRowHandle::GetSeqAlnStart ( ) const
pure virtual

◆ GetSeqAlnStop()

virtual TSignedSeqPos IAlignRowHandle::GetSeqAlnStop ( ) const
pure virtual

◆ GetSeqLength()

TSeqPos IAlignRowHandle::GetSeqLength ( void  ) const
inlinevirtual

◆ GetSeqPosFromAlnPos()

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

◆ GetSeqStart()

virtual TSignedSeqPos IAlignRowHandle::GetSeqStart ( ) const
pure virtual

◆ GetSeqStop()

virtual TSignedSeqPos IAlignRowHandle::GetSeqStop ( ) const
pure virtual

◆ GetSeqString()

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

◆ GetTaxId()

int IAlignRowHandle::GetTaxId ( bool  fExtOrgLookup = false) const
virtual

◆ GetTaxonomy()

void IAlignRowHandle::GetTaxonomy ( string taxonomy,
bool  fExtOrgLookup = false 
) const
virtual

◆ GetText()

virtual const string& IAlignRowHandle::GetText ( ) const
pure virtual

◆ IsAnchor()

virtual bool IAlignRowHandle::IsAnchor ( ) const
inlinevirtual

Reimplemented in CAlnVecRowHandle.

Definition at line 105 of file alnmulti_ds.hpp.

Referenced by CAlnVecRow::x_HitTest(), and CAlnVecRow::x_RenderTracks().

◆ IsConsensus()

bool IAlignRowHandle::IsConsensus ( ) const
inlinevirtual

Definition at line 275 of file alnmulti_ds.hpp.

References GetSeq_id(), and GetSeqIdString().

◆ IsNegativeStrand()

virtual bool IAlignRowHandle::IsNegativeStrand ( ) const
pure virtual

◆ IsNucProtAlignment()

virtual bool IAlignRowHandle::IsNucProtAlignment ( ) const
pure virtual

◆ UseExternalOrganismLookup()

void IAlignRowHandle::UseExternalOrganismLookup ( bool  f)
inline

Definition at line 109 of file alnmulti_ds.hpp.

References f(), and m_fExtOrgLookup.

◆ UsesAATranslation()

virtual bool IAlignRowHandle::UsesAATranslation ( ) const
pure virtual

Member Data Documentation

◆ m_fExtOrgLookup

bool IAlignRowHandle::m_fExtOrgLookup = false
protected

Definition at line 133 of file alnmulti_ds.hpp.

Referenced by UseExternalOrganismLookup().

◆ m_OrgLabel

string IAlignRowHandle::m_OrgLabel
mutableprotected

Definition at line 134 of file alnmulti_ds.hpp.

Referenced by GetOrgLabel().

◆ m_TaxId

int IAlignRowHandle::m_TaxId = 0
mutableprotected

Definition at line 135 of file alnmulti_ds.hpp.

Referenced by GetTaxId().


The documentation for this class was generated from the following files:
Modified on Sun Jun 16 04:32:02 2024 by modify_doxy.py rev. 669887