NCBI C++ ToolKit
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CAlnScanner Class Reference

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#include "aln_scanner.hpp"
(Private to src/objtools/readers.)

+ Inheritance diagram for CAlnScanner:

Public Types

using TDeflines = vector< TLineInfo >
 

Public Member Functions

 CAlnScanner ()
 
virtual ~CAlnScanner ()
 
virtual void ProcessAlignmentFile (CSequenceInfo &, CLineInput &, SAlignmentFile &)
 

Protected Types

enum class  ESeqIdComparison { eIdentical , eDifferByCase , eDifferentChars , eDifferent }
 
using TLineInfo = SLineInfo
 

Protected Member Functions

virtual void xImportAlignmentData (CSequenceInfo &, CLineInput &)
 
virtual void xAdjustSequenceInfo (CSequenceInfo &)
 
virtual void xVerifyAlignmentData (const CSequenceInfo &)
 
virtual void xExportAlignmentData (SAlignmentFile &alignmentInfo)
 
virtual void xVerifySingleSequenceData (const CSequenceInfo &, const TLineInfo &seqId, const vector< TLineInfo > seqData)
 
ESeqIdComparison xGetExistingSeqIdInfo (const string &seqId, TLineInfo &existingInfo)
 
bool xSeqIdIsEqualToInfoAt (const string &seqId, int index)
 

Protected Attributes

vector< TLineInfomSeqIds
 
vector< vector< TLineInfo > > mSequences
 
vector< TLineInfomDeflines
 

Detailed Description

Definition at line 44 of file aln_scanner.hpp.

Member Typedef Documentation

◆ TDeflines

Definition at line 51 of file aln_scanner.hpp.

◆ TLineInfo

using CAlnScanner::TLineInfo = SLineInfo
protected

Definition at line 48 of file aln_scanner.hpp.

Member Enumeration Documentation

◆ ESeqIdComparison

enum CAlnScanner::ESeqIdComparison
strongprotected
Enumerator
eIdentical 
eDifferByCase 
eDifferentChars 
eDifferent 

Definition at line 65 of file aln_scanner.hpp.

Constructor & Destructor Documentation

◆ CAlnScanner()

CAlnScanner::CAlnScanner ( )
inline

Definition at line 53 of file aln_scanner.hpp.

◆ ~CAlnScanner()

virtual CAlnScanner::~CAlnScanner ( )
inlinevirtual

Definition at line 55 of file aln_scanner.hpp.

Member Function Documentation

◆ ProcessAlignmentFile()

void CAlnScanner::ProcessAlignmentFile ( CSequenceInfo sequenceInfo,
CLineInput iStr,
SAlignmentFile alignInfo 
)
virtual

◆ xAdjustSequenceInfo()

void CAlnScanner::xAdjustSequenceInfo ( CSequenceInfo sequenceInfo)
protectedvirtual

Reimplemented in CAlnScannerSequin, CAlnScannerNexus, and CAlnScannerMultAlign.

Definition at line 75 of file aln_scanner.cpp.

Referenced by ProcessAlignmentFile().

◆ xExportAlignmentData()

void CAlnScanner::xExportAlignmentData ( SAlignmentFile alignmentInfo)
protectedvirtual

◆ xGetExistingSeqIdInfo()

CAlnScanner::ESeqIdComparison CAlnScanner::xGetExistingSeqIdInfo ( const string seqId,
TLineInfo existingInfo 
)
protected

◆ xImportAlignmentData()

void CAlnScanner::xImportAlignmentData ( CSequenceInfo sequenceInfo,
CLineInput iStr 
)
protectedvirtual

◆ xSeqIdIsEqualToInfoAt()

bool CAlnScanner::xSeqIdIsEqualToInfoAt ( const string seqId,
int  index 
)
protected

◆ xVerifyAlignmentData()

void CAlnScanner::xVerifyAlignmentData ( const CSequenceInfo sequenceInfo)
protectedvirtual

Reimplemented in CAlnScannerPhylip.

Definition at line 83 of file aln_scanner.cpp.

References i, mSeqIds, mSequences, and xVerifySingleSequenceData().

Referenced by ProcessAlignmentFile(), and CAlnScannerPhylip::xVerifyAlignmentData().

◆ xVerifySingleSequenceData()

void CAlnScanner::xVerifySingleSequenceData ( const CSequenceInfo sequenceInfo,
const TLineInfo seqId,
const vector< TLineInfo seqData 
)
protectedvirtual

Member Data Documentation

◆ mDeflines

vector<TLineInfo> CAlnScanner::mDeflines
protected

◆ mSeqIds

vector<TLineInfo> CAlnScanner::mSeqIds
protected

◆ mSequences

vector<vector<TLineInfo> > CAlnScanner::mSequences
protected

The documentation for this class was generated from the following files:
Modified on Fri Sep 20 14:57:06 2024 by modify_doxy.py rev. 669887