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CAlignCommon Class Reference

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#include <algo/gnomon/aligncollapser.hpp>

Public Types

typedef vector< SIntronTintrons
 

Public Member Functions

 CAlignCommon ()
 
 CAlignCommon (const CGeneModel &align)
 
const TintronsGetIntrons () const
 
CAlignModel GetAlignment (const SAlignIndividual &ali, const deque< char > &target_id_pool) const
 
int GetFlags () const
 
bool isSR () const
 
bool isEST () const
 
bool isPolyA () const
 
bool isCap () const
 
bool isUnknown () const
 
bool isPlus () const
 
bool isMinus () const
 
bool operator< (const CAlignCommon &cas) const
 

Private Types

enum  {
  esr = 1 , eest = 2 , epolya = 4 , ecap = 8 ,
  eunknownorientation = 16 , eplus = 32 , eminus = 64
}
 

Private Attributes

Tintrons m_introns
 
int m_flags
 

Detailed Description

Definition at line 78 of file aligncollapser.hpp.

Member Typedef Documentation

◆ Tintrons

Definition at line 80 of file aligncollapser.hpp.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum
private
Enumerator
esr 
eest 
epolya 
ecap 
eunknownorientation 
eplus 
eminus 

Definition at line 103 of file aligncollapser.hpp.

Constructor & Destructor Documentation

◆ CAlignCommon() [1/2]

CAlignCommon::CAlignCommon ( )
inline

Definition at line 81 of file aligncollapser.hpp.

◆ CAlignCommon() [2/2]

CAlignCommon::CAlignCommon ( const CGeneModel align)

Member Function Documentation

◆ GetAlignment()

CAlignModel CAlignCommon::GetAlignment ( const SAlignIndividual ali,
const deque< char > &  target_id_pool 
) const

◆ GetFlags()

int CAlignCommon::GetFlags ( ) const
inline

Definition at line 85 of file aligncollapser.hpp.

References m_flags.

◆ GetIntrons()

const Tintrons& CAlignCommon::GetIntrons ( ) const
inline

◆ isCap()

bool CAlignCommon::isCap ( ) const
inline

◆ isEST()

bool CAlignCommon::isEST ( ) const
inline

◆ isMinus()

bool CAlignCommon::isMinus ( ) const
inline

Definition at line 92 of file aligncollapser.hpp.

References eminus, and m_flags.

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

◆ isPlus()

bool CAlignCommon::isPlus ( ) const
inline

◆ isPolyA()

bool CAlignCommon::isPolyA ( ) const
inline

◆ isSR()

bool CAlignCommon::isSR ( ) const
inline

Definition at line 86 of file aligncollapser.hpp.

References esr, and m_flags.

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

◆ isUnknown()

bool CAlignCommon::isUnknown ( ) const
inline

Definition at line 90 of file aligncollapser.hpp.

References eunknownorientation, and m_flags.

Referenced by CAlignCollapser::FilterAlignments(), and GetAlignment().

◆ operator<()

bool CAlignCommon::operator< ( const CAlignCommon cas) const
inline

Definition at line 93 of file aligncollapser.hpp.

References m_flags, and m_introns.

Member Data Documentation

◆ m_flags

int CAlignCommon::m_flags
private

◆ m_introns

Tintrons CAlignCommon::m_introns
private

Definition at line 113 of file aligncollapser.hpp.

Referenced by CAlignCommon(), GetAlignment(), GetIntrons(), and operator<().


The documentation for this class was generated from the following files:
Modified on Wed May 22 11:33:58 2024 by modify_doxy.py rev. 669887