NCBI C++ ToolKit
Classes | Public Types | Public Member Functions | Private Attributes | List of all members
CCDSInfo Class Reference

Search Toolkit Book for CCDSInfo

#include <algo/gnomon/gnomon_model.hpp>

+ Collaboration diagram for CCDSInfo:

Classes

struct  SPStop
 

Public Types

enum  EStatus { eSelenocysteine , eGenomeNotCorrect , eGenomeCorrect , eUnknown }
 
typedef vector< SPStop > TPStops
 

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 TPStops & PStops () 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

enum CCDSInfo::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

Definition at line 284 of file gnomon_model.hpp.

References _ASSERT, Invariant(), and m_p_stops.

Referenced by CChain::ClipChain(), CSeqScores::CSeqScores(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CParse::GetGenes(), CGnomonEngine::GetScore(), MapFromEditedToOrig(), MapFromOrigToEdited(), ParseAttributes(), CGnomonAnnotator::Predict(), CChainer::CChainerImpl::ReplicatePStops(), and CChain::RestoreReasonableConfirmedStart().

◆ 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

Definition at line 237 of file gnomon_model.hpp.

References ReadingFrame(), Start(), and Stop().

Referenced by CChain::CChain(), CGeneModel::CdsInvariant(), CChain::ClipLowCoverageUTR(), CollectAttributes(), CAnnotationASN1::CImplementationData::create_cdregion_feature(), CAnnotationASN1::CImplementationData::create_internal_feature(), Cut(), CGeneSelector::FilterGenes(), CChainer::CChainerImpl::FindOptimalChainForProtein(), CGeneModel::GetCdsDnaSequence(), CGeneModel::GetProtein(), CChainer::CChainerImpl::GoodCDNAScore(), Invariant(), CChainer::CChainerImpl::MakeChains(), CGnomonAnnotator::Predict(), CChain::RemoveFshiftsFromUTRs(), CChainer::CChainerImpl::ReplacePseudoGeneSeeds(), CChain::RestoreReasonableConfirmedStart(), CChain::SetConfirmedEnds(), and CChainer::CChainerImpl::SetFlagsForChains().

◆ Clear()

void CCDSInfo::Clear ( void  )

Definition at line 661 of file gnomon_model.cpp.

References BadScore(), COpenRange< TSignedSeqPos >::GetEmpty(), m_confirmed_start, m_confirmed_stop, m_max_cds_limits, m_p_stops, m_reading_frame, m_reading_frame_from_proteins, m_start, m_stop, and SetScore().

Referenced by Clip(), Cut(), CGnomonEngine::GetScore(), CChain::RestoreReasonableConfirmedStart(), and SetReadingFrame().

◆ Clear5PrimeCdsLimit()

void CCDSInfo::Clear5PrimeCdsLimit ( )

Definition at line 448 of file gnomon_model.cpp.

References _ASSERT, COpenRange< TSignedSeqPos >::GetWhole(), COpenRange< TSignedSeqPos >::GetWholeFrom(), COpenRange< TSignedSeqPos >::GetWholeTo(), HasStop(), Invariant(), m_max_cds_limits, Precede(), ReadingFrame(), CRange_Base::SetFrom(), CRange_Base::SetTo(), and Stop().

Referenced by CChain::ClipChain(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), and CGnomonEngine::GetScore().

◆ ClearPStops()

void CCDSInfo::ClearPStops ( )
inline

Definition at line 286 of file gnomon_model.hpp.

References m_p_stops.

Referenced by CChain::ClipChain(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CGnomonEngine::GetScore(), CGnomonAnnotator::Predict(), and CChainer::CChainerImpl::ReplicatePStops().

◆ Clip()

void CCDSInfo::Clip ( TSignedSeqRange  limits)

Definition at line 575 of file gnomon_model.cpp.

References _ASSERT, BadScore(), Clear(), Empty(), COpenRange< Position >::Empty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), COpenRange< TSignedSeqPos >::GetWholeFrom(), COpenRange< TSignedSeqPos >::GetWholeTo(), HasStart(), HasStop(), Invariant(), limits, m_confirmed_start, m_confirmed_stop, m_max_cds_limits, m_p_stops, m_reading_frame, m_reading_frame_from_proteins, m_start, m_stop, ReadingFrame(), CRange_Base::SetFrom(), SetScore(), and CRange_Base::SetTo().

Referenced by CGeneModel::Clip(), and CGnomonAnnotator_Base::MapOneModelToEditedContig().

◆ CombineWith()

void CCDSInfo::CombineWith ( const CCDSInfo &  another_cds_info)

Definition at line 505 of file gnomon_model.cpp.

References _ASSERT, BadScore(), COpenRange< Position >::Empty(), COpenRange< TSignedSeqPos >::GetEmpty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), HasStart(), HasStop(), Include(), Invariant(), m_confirmed_start, m_confirmed_stop, m_max_cds_limits, m_p_stops, m_reading_frame, m_reading_frame_from_proteins, m_start, m_stop, Precede(), CRange_Base::SetFrom(), SetScore(), CRange_Base::SetTo(), ct::sort(), and Stop().

Referenced by CChain::CChain(), and CGeneModel::CombineCdsInfo().

◆ ConfirmedStart()

bool CCDSInfo::ConfirmedStart ( ) const
inline

Definition at line 244 of file gnomon_model.hpp.

References m_confirmed_start.

Referenced by CollectAttributes(), CGeneModel::ConfirmedStart(), CGnomonEngine::GetScore(), Invariant(), MapFromEditedToOrig(), MapFromOrigToEdited(), CGnomonEngine::SelectBestReadingFrame(), and CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments().

◆ ConfirmedStop()

bool CCDSInfo::ConfirmedStop ( ) const
inline

Definition at line 245 of file gnomon_model.hpp.

References m_confirmed_stop.

Referenced by CollectAttributes(), CGeneModel::ConfirmedStop(), CGnomonEngine::GetScore(), Invariant(), MapFromEditedToOrig(), MapFromOrigToEdited(), CChain::RestoreReasonableConfirmedStart(), CGnomonEngine::SelectBestReadingFrame(), and CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments().

◆ Cut()

void CCDSInfo::Cut ( TSignedSeqRange  hole)

Definition at line 611 of file gnomon_model.cpp.

References _ASSERT, BadScore(), Cds(), Clear(), Empty(), ERASE_ITERATE, COpenRange< TSignedSeqPos >::GetEmpty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), COpenRange< TSignedSeqPos >::GetWholeFrom(), COpenRange< TSignedSeqPos >::GetWholeTo(), Include(), COpenRange< Position >::IntersectingWith(), Invariant(), m_confirmed_start, m_confirmed_stop, m_max_cds_limits, m_p_stops, m_reading_frame, m_reading_frame_from_proteins, m_start, m_stop, CRange_Base::SetFrom(), SetScore(), CRange_Base::SetTo(), and VECTOR_ERASE.

Referenced by CGeneModel::CutExons().

◆ HasStart()

bool CCDSInfo::HasStart ( ) const
inline

Definition at line 242 of file gnomon_model.hpp.

References COpenRange< Position >::NotEmpty(), and Start().

Referenced by CGeneModel::CdsInvariant(), Clip(), CollectAttributes(), CombineWith(), CAnnotationASN1::CImplementationData::create_internal_feature(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CGeneModel::HasStart(), Invariant(), CChainer::CChainerImpl::LRCanChainItoJ(), CChainer::CChainerImpl::LRIinit(), MapFromEditedToOrig(), MapFromOrigToEdited(), SChainMember::MarkUnwantedCopiesForChain(), printGFF3(), CChainer::CChainerImpl::RightLeft(), CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments(), SetScore(), Strand(), and CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes().

◆ HasStop()

bool CCDSInfo::HasStop ( ) const
inline

Definition at line 243 of file gnomon_model.hpp.

References COpenRange< Position >::NotEmpty(), and Stop().

Referenced by CChainer::CChainerImpl::CanIncludeJinI(), CGeneModel::CdsInvariant(), Clear5PrimeCdsLimit(), Clip(), CollectAttributes(), CombineWith(), CChainer::CChainerImpl::FindOptimalChainForProtein(), CGeneModel::HasStop(), Invariant(), CChainer::CChainerImpl::LRCanChainItoJ(), MapFromEditedToOrig(), MapFromOrigToEdited(), printGFF3(), CChainer::CChainerImpl::RightLeft(), CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments(), and Strand().

◆ Invariant()

bool CCDSInfo::Invariant ( ) const
inline

Definition at line 288 of file gnomon_model.hpp.

References _ASSERT, BadScore(), Cds(), ConfirmedStart(), ConfirmedStop(), Empty(), COpenRange< TSignedSeqPos >::GetWholeFrom(), COpenRange< TSignedSeqPos >::GetWholeTo(), HasStart(), HasStop(), Include(), MaxCdsLimits(), OpenCds(), Precede(), ProtReadingFrame(), ReadingFrame(), Score(), Start(), and Stop().

Referenced by AddPStop(), Clear5PrimeCdsLimit(), Clip(), CombineWith(), Cut(), Remap(), Set5PrimeCdsLimit(), SetReadingFrame(), SetScore(), SetStart(), and SetStop().

◆ IsMappedToGenome()

bool CCDSInfo::IsMappedToGenome ( ) const
inline

Definition at line 231 of file gnomon_model.hpp.

References m_genomic_coordinates.

Referenced by CGeneModel::CdsInvariant(), CollectAttributes(), CGeneSelector::FilterGenes(), CGeneModel::GetCdsDnaSequence(), CGeneModel::GetProtein(), CGnomonEngine::GetScore(), MapFromEditedToOrig(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), printGFF3(), and SModelData::SModelData().

◆ MapFromEditedToOrig()

CCDSInfo CCDSInfo::MapFromEditedToOrig ( const CAlignMap &  amap) const

Definition at line 285 of file gnomon_model.cpp.

References _ASSERT, AddPStop(), ConfirmedStart(), ConfirmedStop(), CAlignMap::FShiftedLen(), COpenRange< TSignedSeqPos >::GetWhole(), HasStart(), HasStop(), i, IsMappedToGenome(), ITERATE, CAlignMap::MapEditedToOrig(), CAlignMap::MapRangeEditedToOrig(), MaxCdsLimits(), COpenRange< Position >::NotEmpty(), OpenCds(), Precede(), ProtReadingFrame(), PStops(), ReadingFrame(), Score(), Set5PrimeCdsLimit(), SetReadingFrame(), SetScore(), SetStart(), SetStop(), Start(), and Stop().

Referenced by CChainer::FindSelenoproteinsClipProteinsToStartStop(), CGnomonEngine::GetScore(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), readGFF3(), RestoreModelAttributes(), and CChain::SetConfirmedEnds().

◆ MapFromOrigToEdited()

CCDSInfo CCDSInfo::MapFromOrigToEdited ( const CAlignMap &  amap) const

Definition at line 346 of file gnomon_model.cpp.

References _ASSERT, AddPStop(), ConfirmedStart(), ConfirmedStop(), COpenRange< TSignedSeqPos >::GetWhole(), HasStart(), HasStop(), i, ITERATE, CAlignMap::MapOrigToEdited(), CAlignMap::MapRangeOrigToEdited(), MaxCdsLimits(), COpenRange< Position >::NotEmpty(), OpenCds(), Precede(), ProtReadingFrame(), PStops(), ReadingFrame(), Score(), Set5PrimeCdsLimit(), SetReadingFrame(), SetScore(), SetStart(), SetStop(), Start(), and Stop().

Referenced by CGeneModel::CdsInvariant(), CollectAttributes(), CGeneSelector::FilterGenes(), CGeneModel::GetCdsDnaSequence(), CGeneModel::GetProtein(), CGnomonEngine::GetScore(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGnomonAnnotator_Base::MapOneModelToOrigContig(), printGFF3(), CChain::SetConfirmedEnds(), and SModelData::SModelData().

◆ MaxCdsLimits()

TSignedSeqRange CCDSInfo::MaxCdsLimits ( ) const
inline

Definition at line 238 of file gnomon_model.hpp.

References m_max_cds_limits.

Referenced by CChainer::CChainerImpl::CanIncludeJinI(), CGeneModel::CdsInvariant(), CChain::ClipChain(), CollectAttributes(), CAnnotationASN1::CImplementationData::create_cdregion_feature(), CAnnotationASN1::CImplementationData::create_internal_feature(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), ExtendedMaxCdsLimits(), CChainer::CChainerImpl::FindContainedAlignments(), CChainer::CChainerImpl::FindOptimalChainForProtein(), CGnomonEngine::GetScore(), CSeqScores::Init(), Invariant(), CChainer::CChainerImpl::LRCanChainItoJ(), CChainer::CChainerImpl::LRIinit(), MapFromEditedToOrig(), MapFromOrigToEdited(), CGeneModel::MaxCdsLimits(), CGeneModel::OpenLeftEnd(), CGeneModel::OpenRightEnd(), printGFF3(), and CChainer::CChainerImpl::RightLeft().

◆ OpenCds()

bool CCDSInfo::OpenCds ( ) const
inline

Definition at line 247 of file gnomon_model.hpp.

References m_open.

Referenced by CollectAttributes(), Invariant(), MapFromEditedToOrig(), MapFromOrigToEdited(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGeneModel::OpenCds(), readGFF3(), and RestoreModelAttributes().

◆ operator==()

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

Definition at line 269 of file gnomon_model.cpp.

References a, m_confirmed_start, m_confirmed_stop, m_genomic_coordinates, m_max_cds_limits, m_open, m_p_stops, m_reading_frame, m_reading_frame_from_proteins, m_score, m_start, and m_stop.

◆ ProtReadingFrame()

TSignedSeqRange CCDSInfo::ProtReadingFrame ( ) const
inline

Definition at line 236 of file gnomon_model.hpp.

References m_reading_frame_from_proteins.

Referenced by CChain::CalculateSupportAndWeightFromMembers(), CollectAttributes(), CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CChainer::CChainerImpl::FindGeneSeeds(), FindStartsStops(), CParse::GetGenes(), CGnomonEngine::GetScore(), CChainer::CChainerImpl::GoodCDNAScore(), Invariant(), CChainer::CChainerImpl::MakeChains(), MapFromEditedToOrig(), MapFromOrigToEdited(), ParseAttributes(), CChain::RestoreReasonableConfirmedStart(), CChain::SetBestPlacement(), and CChainer::CChainerImpl::SetFlagsForChains().

◆ PStop()

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

Definition at line 670 of file gnomon_model.cpp.

References eGenomeNotCorrect, eSelenocysteine, ITERATE, and m_p_stops.

Referenced by CChain::ClipChain(), CGeneModel::PStop(), and CChainer::CChainerImpl::ReplicatePStops().

◆ PStops()

const TPStops& CCDSInfo::PStops ( ) const
inline

Definition at line 282 of file gnomon_model.hpp.

References m_p_stops.

Referenced by CChain::CalculateSupportAndWeightFromMembers(), CChain::ClipChain(), CollectAttributes(), CAnnotationASN1::CImplementationData::create_cdregion_feature(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CParse::GetGenes(), CGeneModel::GetProtein(), CGnomonEngine::GetScore(), CGeneModel::IdenticalAlign(), MapFromEditedToOrig(), MapFromOrigToEdited(), CGnomonAnnotator::Predict(), CChainer::CChainerImpl::ReplicatePStops(), and CChain::RestoreReasonableConfirmedStart().

◆ ReadingFrame()

TSignedSeqRange CCDSInfo::ReadingFrame ( ) const
inline

Definition at line 235 of file gnomon_model.hpp.

References m_reading_frame.

Referenced by CChain::CalculateSupportAndWeightFromMembers(), CChainer::CChainerImpl::CanIncludeJinI(), Cds(), CGeneModel::CdsInvariant(), Clear5PrimeCdsLimit(), Clip(), CGeneModel::CombineCdsInfo(), CAnnotationASN1::CImplementationData::create_internal_feature(), CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CGeneSelector::FilterGenes(), CChainer::CChainerImpl::FindOptimalChainForProtein(), CGnomonEngine::GetScore(), Invariant(), CGeneModel::isNMD(), CChainer::CChainerImpl::LRCanChainItoJ(), CChainer::CChainerImpl::LRIinit(), MapFromEditedToOrig(), MapFromOrigToEdited(), SChainMember::MarkIncluded(), SChainMember::MarkPostponed(), SChainMember::MarkUnwantedCopiesForChain(), ParseAttributes(), printGFF3(), readGFF3(), CGeneModel::ReadingFrame(), RestoreModelAttributes(), CChain::RestoreReasonableConfirmedStart(), CChainer::CChainerImpl::RightLeft(), CChain::SetConfirmedEnds(), CChainer::CChainerImpl::SetFlagsForChains(), and Strand().

◆ Remap()

void CCDSInfo::Remap ( const CRangeMapper &  mapper)

Definition at line 487 of file gnomon_model.cpp.

References _ASSERT, Invariant(), m_max_cds_limits, m_p_stops, m_reading_frame, m_reading_frame_from_proteins, m_start, m_stop, NON_CONST_ITERATE, and COpenRange< Position >::NotEmpty().

Referenced by CGeneModel::Remap().

◆ Score()

double CCDSInfo::Score ( ) const
inline

Definition at line 248 of file gnomon_model.hpp.

References m_score.

Referenced by CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CChainer::CChainerImpl::DuplicateUTRs(), Invariant(), MapFromEditedToOrig(), MapFromOrigToEdited(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), MemberIsCoding(), ScoreOrder::operator()(), ParseAttributes(), CGnomonAnnotator::Predict(), CGeneModel::Score(), CChain::SetConfirmedStartStopForCompleteProteins(), and CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes().

◆ Set5PrimeCdsLimit()

void CCDSInfo::Set5PrimeCdsLimit ( TSignedSeqPos  p)

Definition at line 461 of file gnomon_model.cpp.

References _ASSERT, CRange_Base::GetFrom(), Invariant(), m_max_cds_limits, m_reading_frame, CRange_Base::SetFrom(), and CRange_Base::SetTo().

Referenced by CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CGnomonEngine::GetScore(), MapFromEditedToOrig(), MapFromOrigToEdited(), ParseAttributes(), and CGnomonAnnotator::Predict().

◆ SetReadingFrame()

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

Definition at line 389 of file gnomon_model.cpp.

References _ASSERT, Clear(), COpenRange< Position >::Empty(), COpenRange< TSignedSeqPos >::GetWhole(), Invariant(), m_max_cds_limits, m_reading_frame, m_reading_frame_from_proteins, and r().

Referenced by CChain::CalculateSupportAndWeightFromMembers(), CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CParse::GetGenes(), CGnomonEngine::GetScore(), MapFromEditedToOrig(), MapFromOrigToEdited(), ParseAttributes(), readGFF3(), RestoreModelReadingFrame(), CChain::RestoreReasonableConfirmedStart(), CChainer::CChainerImpl::SetFlagsForChains(), and ProjectCDS::transform_align().

◆ SetScore()

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

Definition at line 479 of file gnomon_model.cpp.

References _ASSERT, HasStart(), Invariant(), m_open, and m_score.

Referenced by Clear(), Clip(), CombineWith(), Cut(), CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CParse::GetGenes(), CGnomonEngine::GetScore(), MapFromEditedToOrig(), MapFromOrigToEdited(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), ParseAttributes(), CGnomonAnnotator::Predict(), readGFF3(), RestoreModelAttributes(), CChain::SetConfirmedStartStopForCompleteProteins(), CChain::SetOpenForPartialyAlignedProteins(), RemoveTrailingNs::transform_model(), and CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes().

◆ SetStart()

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

Definition at line 407 of file gnomon_model.cpp.

References _ASSERT, Invariant(), m_confirmed_start, m_open, m_start, and r().

Referenced by CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CParse::GetGenes(), CGnomonEngine::GetScore(), MapFromEditedToOrig(), MapFromOrigToEdited(), ParseAttributes(), CChain::RestoreReasonableConfirmedStart(), CChain::SetConfirmedStartStopForCompleteProteins(), CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments(), and ProjectCDS::transform_align().

◆ SetStop()

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

Definition at line 419 of file gnomon_model.cpp.

References _ASSERT, CRange_Base::GetFrom(), CRange_Base::GetTo(), COpenRange< TSignedSeqPos >::GetWholeFrom(), COpenRange< TSignedSeqPos >::GetWholeTo(), Invariant(), m_confirmed_stop, m_max_cds_limits, m_p_stops, m_reading_frame, m_stop, COpenRange< Position >::NotEmpty(), Precede(), r(), CRange_Base::SetFrom(), and CRange_Base::SetTo().

Referenced by CChainer::FindSelenoproteinsClipProteinsToStartStop(), CParse::GetGenes(), CGnomonEngine::GetScore(), MapFromEditedToOrig(), MapFromOrigToEdited(), ParseAttributes(), CChain::RestoreReasonableConfirmedStart(), CChain::SetConfirmedStartStopForCompleteProteins(), CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments(), and ProjectCDS::transform_align().

◆ Start()

TSignedSeqRange CCDSInfo::Start ( ) const
inline

Definition at line 240 of file gnomon_model.hpp.

References m_start.

Referenced by CChainer::CChainerImpl::CanIncludeJinI(), Cds(), CGeneModel::CdsInvariant(), CollectAttributes(), CGeneModel::CombineCdsInfo(), CAnnotationASN1::CImplementationData::create_internal_feature(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), FindStartsStops(), CParse::GetGenes(), CGnomonEngine::GetScore(), HasStart(), Invariant(), CGeneModel::isNMD(), CChainer::CChainerImpl::LRCanChainItoJ(), CChainer::CChainerImpl::LRIinit(), MapFromEditedToOrig(), MapFromOrigToEdited(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGnomonAnnotator::Predict(), printGFF3(), CChain::RestoreReasonableConfirmedStart(), CChainer::CChainerImpl::RightLeft(), CChain::SetConfirmedStartStopForCompleteProteins(), CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments(), and Strand().

◆ Stop()

TSignedSeqRange CCDSInfo::Stop ( ) const
inline

Definition at line 241 of file gnomon_model.hpp.

References m_stop.

Referenced by CChainer::CChainerImpl::CanIncludeJinI(), Cds(), CGeneModel::CdsInvariant(), Clear5PrimeCdsLimit(), CGeneModel::CombineCdsInfo(), CombineWith(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), CChainer::CChainerImpl::FindOptimalChainForProtein(), CGnomonEngine::GetScore(), HasStop(), Invariant(), CGeneModel::isNMD(), CChainer::CChainerImpl::LRCanChainItoJ(), CChainer::CChainerImpl::LRIinit(), MapFromEditedToOrig(), MapFromOrigToEdited(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CChain::RestoreReasonableConfirmedStart(), CChainer::CChainerImpl::RightLeft(), CChain::SetConfirmedStartStopForCompleteProteins(), CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments(), and Strand().

◆ Strand()

int CCDSInfo::Strand ( ) const

Definition at line 561 of file gnomon_model.cpp.

References CRange_Base::GetFrom(), CRange_Base::GetTo(), COpenRange< TSignedSeqPos >::GetWholeFrom(), COpenRange< TSignedSeqPos >::GetWholeTo(), HasStart(), HasStop(), m_max_cds_limits, Precede(), ReadingFrame(), Start(), and Stop().

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

Definition at line 345 of file gnomon_model.hpp.

Referenced by Clear(), Clear5PrimeCdsLimit(), Clip(), CombineWith(), Cut(), MaxCdsLimits(), operator==(), Remap(), Set5PrimeCdsLimit(), SetReadingFrame(), SetStop(), and Strand().

◆ 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

Definition at line 348 of file gnomon_model.hpp.

Referenced by AddPStop(), Clear(), ClearPStops(), Clip(), CombineWith(), Cut(), operator==(), PStop(), PStops(), Remap(), and SetStop().

◆ m_reading_frame

TSignedSeqRange CCDSInfo::m_reading_frame
private

Definition at line 343 of file gnomon_model.hpp.

Referenced by Clear(), Clip(), CombineWith(), Cut(), operator==(), ReadingFrame(), Remap(), Set5PrimeCdsLimit(), SetReadingFrame(), and SetStop().

◆ m_reading_frame_from_proteins

TSignedSeqRange CCDSInfo::m_reading_frame_from_proteins
private

Definition at line 344 of file gnomon_model.hpp.

Referenced by Clear(), Clip(), CombineWith(), Cut(), operator==(), ProtReadingFrame(), Remap(), and SetReadingFrame().

◆ 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:
Generated by doxygen 1.9.0
Modified on Fri Sep 20 14:57:58 2024 by modify_doxy.py rev. 669887