#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 SSource &	GetSource () 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

enum CInDelInfo::EStatus

Enumerator
eGenomeNotCorrect
eGenomeCorrect
eUnknown

Definition at line 111 of file gnomon_model.hpp.

◆ EType

enum CInDelInfo::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(), l(), 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

Definition at line 147 of file gnomon_model.hpp.

References _ASSERT, eIns, ctll::empty(), eUnknown, GetInDelV(), IsDeletion(), IsMismatch(), l(), Len(), len, m_indelv, m_len, m_loc, m_source, m_status, m_type, and type.

Referenced by CInDelInfo().

◆ 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

Definition at line 119 of file gnomon_model.hpp.

References eDel, and m_type.

Referenced by BuildGFF3Gap(), CChainer::CChainerImpl::FsTouch(), Init(), IntersectingWith(), and OverlappingIndel().

◆ IsInsertion()

bool CInDelInfo::IsInsertion ( ) const

inline

Definition at line 118 of file gnomon_model.hpp.

References eIns, and m_type.

Referenced by AlignModelToSeqalign(), BuildGFF3Gap(), CChainer::CChainerImpl::FsTouch(), InDelEnd(), and IntersectingWith().

◆ 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

Definition at line 116 of file gnomon_model.hpp.

References m_len.

Referenced by AlignModelToSeqalign(), BuildGFF3Gap(), CChainer::CChainerImpl::FsTouch(), InDelEnd(), Init(), and IntersectingWith().

◆ Loc()

TSignedSeqPos CInDelInfo::Loc ( ) const

inline

Definition at line 115 of file gnomon_model.hpp.

References m_loc.

Referenced by AlignModelToSeqalign(), BuildGFF3Gap(), CChainer::CChainerImpl::FsTouch(), InDelEnd(), and IntersectingWith().

◆ 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 l(), and 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:

include/algo/gnomon/gnomon_model.hpp

Classes

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Enumeration Documentation

◆ EStatus

◆ EType

Constructor & Destructor Documentation

◆ CInDelInfo()

Member Function Documentation

◆ GetInDelV()

◆ GetSource()

◆ GetStatus()

◆ GetType()

◆ InDelEnd()

◆ Init()

◆ IntersectingWith()

◆ IsDeletion()

◆ IsInsertion()

◆ IsMismatch()

◆ Len()

◆ Loc()

◆ operator!=()

◆ operator<()

◆ operator==()

◆ SetLoc()

◆ SetStatus()

Member Data Documentation

◆ m_indelv

◆ m_len

◆ m_loc

◆ m_source

◆ m_status

◆ m_type