CAlignCollapser::CPartialString Class Reference

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#include <algo/gnomon/aligncollapser.hpp>

Public Member Functions
void	Init (const CSeqVector &sv, TSignedSeqPos from, TSignedSeqPos to)
char &	operator[] (TSignedSeqPos p)
const char &	operator[] (TSignedSeqPos p) const
TSignedSeqPos	FullLength () const
string	substr (TSignedSeqPos p, TSignedSeqPos l) const
void	ToUpper ()

Private Attributes
string	m_string
TSignedSeqPos	m_shift = 0

Detailed Description

Definition at line 168 of file aligncollapser.hpp.

Member Function Documentation

FullLength()

TSignedSeqPos CAlignCollapser::CPartialString::FullLength ( ) const

inline

Definition at line 177 of file aligncollapser.hpp.

References m_shift, and m_string.

Referenced by CAlignCollapser::CleanSelfTranscript(), and CAlignCollapser::GetCollapsedAlgnments().

Init()

void CAlignCollapser::CPartialString::Init ( const CSeqVector &  sv, TSignedSeqPos  from, TSignedSeqPos  to  )

inline

Definition at line 170 of file aligncollapser.hpp.

References CSeqVector::GetSeqData(), m_shift, and m_string.

Referenced by CAlignCollapser::InitContig().

operator[]() [1/2]

char& CAlignCollapser::CPartialString::operator[] ( TSignedSeqPos  p )

inline

Definition at line 175 of file aligncollapser.hpp.

References m_shift, and m_string.

operator[]() [2/2]

const char& CAlignCollapser::CPartialString::operator[] ( TSignedSeqPos  p ) const

inline

Definition at line 176 of file aligncollapser.hpp.

References m_shift, and m_string.

substr()

string CAlignCollapser::CPartialString::substr ( TSignedSeqPos  p, TSignedSeqPos  l  ) const

inline

Definition at line 178 of file aligncollapser.hpp.

References l(), m_shift, and m_string.

Referenced by CAlignCollapser::CleanSelfTranscript().

ToUpper()

void CAlignCollapser::CPartialString::ToUpper ( )

inline

Definition at line 179 of file aligncollapser.hpp.

References m_string, and toupper().

Referenced by CAlignCollapser::FilterAlignments().

Member Data Documentation

m_shift

TSignedSeqPos CAlignCollapser::CPartialString::m_shift = 0

private

Definition at line 185 of file aligncollapser.hpp.

Referenced by FullLength(), Init(), operator[](), and substr().

m_string

string CAlignCollapser::CPartialString::m_string

private

Definition at line 184 of file aligncollapser.hpp.

Referenced by FullLength(), Init(), operator[](), substr(), and ToUpper().

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

• include/algo/gnomon/aligncollapser.hpp