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CCDSInfo Class Reference

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#include <algo/gnomon/gnomon_model.hpp>

+ Collaboration diagram for CCDSInfo:

Classes

struct  SPStop
 

Public Types

enum  EStatus { eSelenocysteine , eGenomeNotCorrect , eGenomeCorrect , eUnknown }
 
typedef vector< SPStopTPStops
 

Public Member Functions

 CCDSInfo (bool gcoords=true)
 
bool operator== (const CCDSInfo &another) const
 
bool IsMappedToGenome () const
 
CCDSInfo MapFromOrigToEdited (const CAlignMap &amap) const
 
CCDSInfo MapFromEditedToOrig (const CAlignMap &amap) const
 
TSignedSeqRange ReadingFrame () const
 
TSignedSeqRange ProtReadingFrame () const
 
TSignedSeqRange Cds () const
 
TSignedSeqRange MaxCdsLimits () const
 
TSignedSeqRange Start () const
 
TSignedSeqRange Stop () const
 
bool HasStart () const
 
bool HasStop () const
 
bool ConfirmedStart () const
 
bool ConfirmedStop () const
 
bool OpenCds () const
 
double Score () const
 
void SetReadingFrame (TSignedSeqRange r, bool protein=false)
 
void SetStart (TSignedSeqRange r, bool confirmed=false)
 
void SetStop (TSignedSeqRange r, bool confirmed=false)
 
void Set5PrimeCdsLimit (TSignedSeqPos p)
 
void Clear5PrimeCdsLimit ()
 
void SetScore (double score, bool open=false)
 
void CombineWith (const CCDSInfo &another_cds_info)
 
void Remap (const CRangeMapper &mapper)
 
void Clip (TSignedSeqRange limits)
 
void Cut (TSignedSeqRange hole)
 
void Clear ()
 
int Strand () const
 
const TPStopsPStops () const
 
bool PStop (bool includeall=true) const
 
void AddPStop (SPStop stp)
 
void AddPStop (TSignedSeqRange r, EStatus status)
 
void ClearPStops ()
 
bool Invariant () const
 

Private Attributes

TSignedSeqRange m_start
 
TSignedSeqRange m_stop
 
TSignedSeqRange m_reading_frame
 
TSignedSeqRange m_reading_frame_from_proteins
 
TSignedSeqRange m_max_cds_limits
 
bool m_confirmed_start
 
bool m_confirmed_stop
 
TPStops m_p_stops
 
bool m_open
 
double m_score
 
bool m_genomic_coordinates
 

Detailed Description

Definition at line 223 of file gnomon_model.hpp.

Member Typedef Documentation

◆ TPStops

typedef vector<SPStop> CCDSInfo::TPStops

Definition at line 281 of file gnomon_model.hpp.

Member Enumeration Documentation

◆ EStatus

Enumerator
eSelenocysteine 
eGenomeNotCorrect 
eGenomeCorrect 
eUnknown 

Definition at line 265 of file gnomon_model.hpp.

Constructor & Destructor Documentation

◆ CCDSInfo()

CCDSInfo::CCDSInfo ( bool  gcoords = true)
inline

Definition at line 225 of file gnomon_model.hpp.

Member Function Documentation

◆ AddPStop() [1/2]

void CCDSInfo::AddPStop ( SPStop  stp)
inline

◆ AddPStop() [2/2]

void CCDSInfo::AddPStop ( TSignedSeqRange  r,
EStatus  status 
)

Definition at line 472 of file gnomon_model.cpp.

References _ASSERT, Invariant(), m_p_stops, and r().

◆ Cds()

TSignedSeqRange CCDSInfo::Cds ( ) const
inline

◆ Clear()

void CCDSInfo::Clear ( void  )

◆ Clear5PrimeCdsLimit()

void CCDSInfo::Clear5PrimeCdsLimit ( )

◆ ClearPStops()

void CCDSInfo::ClearPStops ( )
inline

◆ Clip()

void CCDSInfo::Clip ( TSignedSeqRange  limits)

◆ CombineWith()

void CCDSInfo::CombineWith ( const CCDSInfo another_cds_info)

◆ ConfirmedStart()

bool CCDSInfo::ConfirmedStart ( ) const
inline

◆ ConfirmedStop()

bool CCDSInfo::ConfirmedStop ( ) const
inline

◆ Cut()

void CCDSInfo::Cut ( TSignedSeqRange  hole)

◆ HasStart()

bool CCDSInfo::HasStart ( ) const
inline

◆ HasStop()

bool CCDSInfo::HasStop ( ) const
inline

◆ Invariant()

bool CCDSInfo::Invariant ( ) const
inline

◆ IsMappedToGenome()

bool CCDSInfo::IsMappedToGenome ( ) const
inline

◆ MapFromEditedToOrig()

CCDSInfo CCDSInfo::MapFromEditedToOrig ( const CAlignMap amap) const

◆ MapFromOrigToEdited()

CCDSInfo CCDSInfo::MapFromOrigToEdited ( const CAlignMap amap) const

◆ MaxCdsLimits()

TSignedSeqRange CCDSInfo::MaxCdsLimits ( ) const
inline

◆ OpenCds()

bool CCDSInfo::OpenCds ( ) const
inline

◆ operator==()

bool CCDSInfo::operator== ( const CCDSInfo another) const

◆ ProtReadingFrame()

TSignedSeqRange CCDSInfo::ProtReadingFrame ( ) const
inline

◆ PStop()

bool CCDSInfo::PStop ( bool  includeall = true) const

◆ PStops()

const TPStops& CCDSInfo::PStops ( ) const
inline

◆ ReadingFrame()

TSignedSeqRange CCDSInfo::ReadingFrame ( ) const
inline

◆ Remap()

void CCDSInfo::Remap ( const CRangeMapper mapper)

◆ Score()

double CCDSInfo::Score ( ) const
inline

◆ Set5PrimeCdsLimit()

void CCDSInfo::Set5PrimeCdsLimit ( TSignedSeqPos  p)

◆ SetReadingFrame()

void CCDSInfo::SetReadingFrame ( TSignedSeqRange  r,
bool  protein = false 
)

◆ SetScore()

void CCDSInfo::SetScore ( double  score,
bool  open = false 
)

◆ SetStart()

void CCDSInfo::SetStart ( TSignedSeqRange  r,
bool  confirmed = false 
)

◆ SetStop()

void CCDSInfo::SetStop ( TSignedSeqRange  r,
bool  confirmed = false 
)

◆ Start()

TSignedSeqRange CCDSInfo::Start ( ) const
inline

◆ Stop()

TSignedSeqRange CCDSInfo::Stop ( ) const
inline

◆ Strand()

int CCDSInfo::Strand ( ) const

Member Data Documentation

◆ m_confirmed_start

bool CCDSInfo::m_confirmed_start
private

Definition at line 347 of file gnomon_model.hpp.

Referenced by Clear(), Clip(), CombineWith(), ConfirmedStart(), Cut(), operator==(), and SetStart().

◆ m_confirmed_stop

bool CCDSInfo::m_confirmed_stop
private

Definition at line 347 of file gnomon_model.hpp.

Referenced by Clear(), Clip(), CombineWith(), ConfirmedStop(), Cut(), operator==(), and SetStop().

◆ m_genomic_coordinates

bool CCDSInfo::m_genomic_coordinates
private

Definition at line 353 of file gnomon_model.hpp.

Referenced by IsMappedToGenome(), and operator==().

◆ m_max_cds_limits

TSignedSeqRange CCDSInfo::m_max_cds_limits
private

◆ m_open

bool CCDSInfo::m_open
private

Definition at line 350 of file gnomon_model.hpp.

Referenced by OpenCds(), operator==(), SetScore(), and SetStart().

◆ m_p_stops

TPStops CCDSInfo::m_p_stops
private

◆ m_reading_frame

TSignedSeqRange CCDSInfo::m_reading_frame
private

◆ m_reading_frame_from_proteins

TSignedSeqRange CCDSInfo::m_reading_frame_from_proteins
private

◆ m_score

double CCDSInfo::m_score
private

Definition at line 351 of file gnomon_model.hpp.

Referenced by operator==(), Score(), and SetScore().

◆ m_start

TSignedSeqRange CCDSInfo::m_start
private

Definition at line 342 of file gnomon_model.hpp.

Referenced by Clear(), Clip(), CombineWith(), Cut(), operator==(), Remap(), SetStart(), and Start().

◆ m_stop

TSignedSeqRange CCDSInfo::m_stop
private

Definition at line 342 of file gnomon_model.hpp.

Referenced by Clear(), Clip(), CombineWith(), Cut(), operator==(), Remap(), SetStop(), and Stop().


The documentation for this class was generated from the following files:
Modified on Sat Feb 24 07:48:04 2024 by modify_doxy.py rev. 669887