CSequenceInfo Class Reference

Search Toolkit Book for CSequenceInfo

#include <objtools/readers/alnread.hpp>

Public Member Functions
	CSequenceInfo ()
	CSequenceInfo (const string &alphabet, const string &match, const string &missing, const string &beginningGap, const string &middleGap, const string &endGap)
const string &	Alphabet () const
CSequenceInfo &	SetAlphabet (const string &alphabet)
const string &	Match () const
CSequenceInfo &	SetMatch (const string &c)
const string &	Missing () const
CSequenceInfo &	SetMissing (const string &c)
const string &	BeginningGap () const
CSequenceInfo &	SetBeginningGap (const string &c)
const string &	MiddleGap () const
CSequenceInfo &	SetMiddleGap (const string &c)
const string &	EndGap () const
CSequenceInfo &	SetEndGap (const string &c)

Protected Attributes
string	mAlphabet
string	mMatch
string	mMissing
string	mBeginningGap
string	mMiddleGap
string	mEndGap

Detailed Description

Definition at line 58 of file alnread.hpp.

Constructor & Destructor Documentation

CSequenceInfo() [1/2]

CSequenceInfo::CSequenceInfo ( )

inline

Definition at line 61 of file alnread.hpp.

CSequenceInfo() [2/2]

CSequenceInfo::CSequenceInfo ( const string &  alphabet, const string &  match, const string &  missing, const string &  beginningGap, const string &  middleGap, const string &  endGap  )

inline

Definition at line 64 of file alnread.hpp.

Member Function Documentation

Alphabet()

const string& CSequenceInfo::Alphabet ( ) const

inline

Definition at line 80 of file alnread.hpp.

References mAlphabet.

Referenced by ReadAlignmentFile(), CAlnScanner::xVerifySingleSequenceData(), and CAlnScannerMultAlign::xVerifySingleSequenceData().

BeginningGap()

const string& CSequenceInfo::BeginningGap ( ) const

inline

Definition at line 101 of file alnread.hpp.

References mBeginningGap.

Referenced by CAlnScanner::xVerifySingleSequenceData().

EndGap()

const string& CSequenceInfo::EndGap ( ) const

inline

Definition at line 115 of file alnread.hpp.

References mEndGap.

Referenced by CAlnScanner::xVerifySingleSequenceData().

Match()

const string& CSequenceInfo::Match ( void  ) const

inline

Definition at line 87 of file alnread.hpp.

References mMatch.

Referenced by CAlnScanner::xVerifySingleSequenceData().

MiddleGap()

const string& CSequenceInfo::MiddleGap ( ) const

inline

Definition at line 108 of file alnread.hpp.

References mMiddleGap.

Referenced by CAlnScanner::xVerifySingleSequenceData().

Missing()

const string& CSequenceInfo::Missing ( ) const

inline

Definition at line 94 of file alnread.hpp.

References mMissing.

Referenced by CAlnScanner::xVerifySingleSequenceData().

SetAlphabet()

CSequenceInfo& CSequenceInfo::SetAlphabet ( const string &  alphabet )

inline

Definition at line 83 of file alnread.hpp.

References mAlphabet.

SetBeginningGap()

CSequenceInfo& CSequenceInfo::SetBeginningGap ( const string &  c )

inline

Definition at line 104 of file alnread.hpp.

References mBeginningGap.

Referenced by CAlnScannerMultAlign::xAdjustSequenceInfo(), CAlnScannerNexus::xAdjustSequenceInfo(), and CAlnScannerSequin::xAdjustSequenceInfo().

SetEndGap()

CSequenceInfo& CSequenceInfo::SetEndGap ( const string &  c )

inline

Definition at line 118 of file alnread.hpp.

References mEndGap.

Referenced by CAlnScannerMultAlign::xAdjustSequenceInfo(), CAlnScannerNexus::xAdjustSequenceInfo(), and CAlnScannerSequin::xAdjustSequenceInfo().

SetMatch()

CSequenceInfo& CSequenceInfo::SetMatch ( const string &  c )

inline

Definition at line 90 of file alnread.hpp.

References mMatch.

Referenced by CAlnScannerMultAlign::xAdjustSequenceInfo(), CAlnScannerNexus::xAdjustSequenceInfo(), and CAlnScannerSequin::xAdjustSequenceInfo().

SetMiddleGap()

CSequenceInfo& CSequenceInfo::SetMiddleGap ( const string &  c )

inline

Definition at line 111 of file alnread.hpp.

References mMiddleGap.

Referenced by CAlnScannerMultAlign::xAdjustSequenceInfo(), CAlnScannerNexus::xAdjustSequenceInfo(), and CAlnScannerSequin::xAdjustSequenceInfo().

SetMissing()

CSequenceInfo& CSequenceInfo::SetMissing ( const string &  c )

inline

Definition at line 97 of file alnread.hpp.

References mMissing.

Referenced by CAlnScannerMultAlign::xAdjustSequenceInfo(), and CAlnScannerNexus::xAdjustSequenceInfo().

Member Data Documentation

mAlphabet

string CSequenceInfo::mAlphabet

protected

Definition at line 122 of file alnread.hpp.

Referenced by Alphabet(), and SetAlphabet().

mBeginningGap

string CSequenceInfo::mBeginningGap

protected

Definition at line 125 of file alnread.hpp.

Referenced by BeginningGap(), and SetBeginningGap().

mEndGap

string CSequenceInfo::mEndGap

protected

Definition at line 127 of file alnread.hpp.

Referenced by EndGap(), and SetEndGap().

mMatch

string CSequenceInfo::mMatch

protected

Definition at line 123 of file alnread.hpp.

Referenced by Match(), and SetMatch().

mMiddleGap

string CSequenceInfo::mMiddleGap

protected

Definition at line 126 of file alnread.hpp.

Referenced by MiddleGap(), and SetMiddleGap().

mMissing

string CSequenceInfo::mMissing

protected

Definition at line 124 of file alnread.hpp.

Referenced by Missing(), and SetMissing().

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

• include/objtools/readers/alnread.hpp