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CInDelInfo Class Reference

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#include <algo/gnomon/gnomon_model.hpp>

+ Collaboration diagram for CInDelInfo:

Classes

struct  SSource
 

Public Types

enum  EType { eDel , eIns , eMism }
 
enum  EStatus { eGenomeNotCorrect , eGenomeCorrect , eUnknown }
 

Public Member Functions

 CInDelInfo (TSignedSeqPos l, int len, EType type, const string &v=kEmptyStr, const SSource &s=SSource())
 
TSignedSeqPos Loc () const
 
int Len () const
 
int InDelEnd () const
 
bool IsInsertion () const
 
bool IsDeletion () const
 
bool IsMismatch () const
 
bool IntersectingWith (TSignedSeqPos a, TSignedSeqPos b) const
 
bool operator< (const CInDelInfo &fsi) const
 
bool operator!= (const CInDelInfo &fsi) const
 
bool operator== (const CInDelInfo &fsi) const
 
string GetInDelV () const
 
const SSourceGetSource () const
 
EType GetType () const
 
void SetStatus (EStatus s)
 
EStatus GetStatus () const
 
void SetLoc (TSignedSeqPos l)
 

Private Member Functions

void Init (TSignedSeqPos l, int len, EType type, const string &v, const SSource &s)
 

Private Attributes

TSignedSeqPos m_loc
 
int m_len
 
EType m_type
 
EStatus m_status
 
string m_indelv
 
SSource m_source
 

Detailed Description

Definition at line 100 of file gnomon_model.hpp.

Member Enumeration Documentation

◆ EStatus

Enumerator
eGenomeNotCorrect 
eGenomeCorrect 
eUnknown 

Definition at line 111 of file gnomon_model.hpp.

◆ EType

Enumerator
eDel 
eIns 
eMism 

Definition at line 110 of file gnomon_model.hpp.

Constructor & Destructor Documentation

◆ CInDelInfo()

CInDelInfo::CInDelInfo ( TSignedSeqPos  l,
int  len,
EType  type,
const string v = kEmptyStr,
const SSource s = SSource() 
)
inline

Definition at line 113 of file gnomon_model.hpp.

References Init(), and len.

Member Function Documentation

◆ GetInDelV()

string CInDelInfo::GetInDelV ( ) const
inline

Definition at line 139 of file gnomon_model.hpp.

References m_indelv.

Referenced by BuildGFF3Gap(), and Init().

◆ GetSource()

const SSource& CInDelInfo::GetSource ( ) const
inline

Definition at line 140 of file gnomon_model.hpp.

References m_source.

◆ GetStatus()

EStatus CInDelInfo::GetStatus ( ) const
inline

Definition at line 143 of file gnomon_model.hpp.

References m_status.

Referenced by BuildGFF3Gap().

◆ GetType()

EType CInDelInfo::GetType ( ) const
inline

Definition at line 141 of file gnomon_model.hpp.

References m_type.

◆ InDelEnd()

int CInDelInfo::InDelEnd ( ) const
inline

Definition at line 117 of file gnomon_model.hpp.

References IsInsertion(), IsMismatch(), Len(), and Loc().

Referenced by BuildGFF3Gap(), and OverlappingIndel().

◆ Init()

void CInDelInfo::Init ( TSignedSeqPos  l,
int  len,
EType  type,
const string v,
const SSource s 
)
inlineprivate

◆ IntersectingWith()

bool CInDelInfo::IntersectingWith ( TSignedSeqPos  a,
TSignedSeqPos  b 
) const
inline

Definition at line 121 of file gnomon_model.hpp.

References a, b, IsDeletion(), IsInsertion(), IsMismatch(), Len(), and Loc().

◆ IsDeletion()

bool CInDelInfo::IsDeletion ( ) const
inline

◆ IsInsertion()

bool CInDelInfo::IsInsertion ( ) const
inline

◆ IsMismatch()

bool CInDelInfo::IsMismatch ( ) const
inline

Definition at line 120 of file gnomon_model.hpp.

References eMism, and m_type.

Referenced by AlignModelToSeqalign(), InDelEnd(), Init(), and IntersectingWith().

◆ Len()

int CInDelInfo::Len ( ) const
inline

◆ Loc()

TSignedSeqPos CInDelInfo::Loc ( ) const
inline

◆ operator!=()

bool CInDelInfo::operator!= ( const CInDelInfo fsi) const
inline

Definition at line 137 of file gnomon_model.hpp.

◆ operator<()

bool CInDelInfo::operator< ( const CInDelInfo fsi) const
inline

Definition at line 126 of file gnomon_model.hpp.

References m_indelv, m_len, m_loc, and m_type.

◆ operator==()

bool CInDelInfo::operator== ( const CInDelInfo fsi) const
inline

Definition at line 138 of file gnomon_model.hpp.

◆ SetLoc()

void CInDelInfo::SetLoc ( TSignedSeqPos  l)
inline

Definition at line 144 of file gnomon_model.hpp.

References m_loc.

◆ SetStatus()

void CInDelInfo::SetStatus ( EStatus  s)
inline

Definition at line 142 of file gnomon_model.hpp.

References m_status.

Member Data Documentation

◆ m_indelv

string CInDelInfo::m_indelv
private

Definition at line 165 of file gnomon_model.hpp.

Referenced by GetInDelV(), Init(), and operator<().

◆ m_len

int CInDelInfo::m_len
private

Definition at line 162 of file gnomon_model.hpp.

Referenced by Init(), Len(), and operator<().

◆ m_loc

TSignedSeqPos CInDelInfo::m_loc
private

Definition at line 160 of file gnomon_model.hpp.

Referenced by Init(), Loc(), operator<(), and SetLoc().

◆ m_source

SSource CInDelInfo::m_source
private

Definition at line 166 of file gnomon_model.hpp.

Referenced by GetSource(), and Init().

◆ m_status

EStatus CInDelInfo::m_status
private

Definition at line 164 of file gnomon_model.hpp.

Referenced by GetStatus(), Init(), and SetStatus().

◆ m_type

EType CInDelInfo::m_type
private

Definition at line 163 of file gnomon_model.hpp.

Referenced by GetType(), Init(), IsDeletion(), IsInsertion(), IsMismatch(), and operator<().


The documentation for this class was generated from the following file:
Modified on Wed Feb 21 09:54:47 2024 by modify_doxy.py rev. 669887