NCBI C++ ToolKit
Classes | Typedefs | Enumerations | Functions | Variables
gnomon_model.hpp File Reference
#include <corelib/ncbiobj.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbi_limits.hpp>
#include <set>
#include <vector>
#include <algorithm>
#include <math.h>
#include <objmgr/seq_vector_ci.hpp>
#include <util/range.hpp>
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Classes

class  CSupportInfo
 
class  CInDelInfo
 
struct  CInDelInfo::SSource
 
class  CRangeMapper
 
class  CModelExon
 
class  CCDSInfo
 
struct  CCDSInfo::SPStop
 
class  CGeneModel
 
class  CAlignMap
 
struct  CAlignMap::SMapRangeEdge
 
class  CAlignMap::SMapRange
 
class  CAlignModel
 
struct  setcontig
 
struct  getcontig
 
class  CModelCluster< Model >
 
class  CModelClusterSet< Cluster >
 
class  EResidue
 

Typedefs

typedef objects::CSeqVectorTypes::TResidue TResidue
 
typedef vector< TResidueCResidueVec
 
typedef vector< intTIVec
 
typedef vector< double > TDVec
 
typedef set< CSupportInfoCSupportInfoSet
 
typedef vector< CInDelInfoTInDels
 
typedef CModelCluster< CGeneModelTGeneModelCluster
 
typedef CModelCluster< CAlignModelTAlignModelCluster
 
typedef list< CGeneModelTGeneModelList
 
typedef list< CAlignModelTAlignModelList
 
typedef CModelClusterSet< TGeneModelClusterTGeneModelClusterSet
 
typedef CModelClusterSet< TAlignModelClusterTAlignModelClusterSet
 

Enumerations

enum  EStrand { ePlus , eMinus }
 
enum  EResidueNames {
  enA , enC , enG , enT ,
  enN
}
 

Functions

 USING_SCOPE (objects)
 
double BadScore ()
 
EStrand OtherStrand (EStrand s)
 
bool Precede (TSignedSeqRange l, TSignedSeqRange r)
 
bool Include (TSignedSeqRange big, TSignedSeqRange small)
 
bool Include (TSignedSeqRange r, TSignedSeqPos p)
 
bool Enclosed (TSignedSeqRange big, TSignedSeqRange small)
 
template<class Res >
bool IsStartCodon (const Res *seq, int strand=ePlus)
 
template<class Res >
bool IsStopCodon (const Res *seq, int strand=ePlus)
 
CNcbiOstreamoperator<< (CNcbiOstream &s, const setcontig &c)
 
CNcbiIstreamoperator>> (CNcbiIstream &s, const getcontig &c)
 
CNcbiIstreamoperator>> (CNcbiIstream &s, CAlignModel &a)
 
CNcbiOstreamoperator<< (CNcbiOstream &s, const CAlignModel &a)
 
CNcbiOstreamoperator<< (CNcbiOstream &s, const CGeneModel &a)
 
TResidue Complement (TResidue c)
 
EResidue Complement (EResidue c)
 
template<class BidirectionalIterator >
void ReverseComplement (const BidirectionalIterator &first, const BidirectionalIterator &last)
 
template<class Model >
list< Model > GetAlignParts (const Model &algn, bool settrimflags)
 
void MapAlignsToOrigContig (TAlignModelList &aligns, const TInDels &corrections, int contig_size)
 

Variables

const EResidue k_toMinus [5]
 
const char *const k_aa_table
 

Typedef Documentation

◆ CResidueVec

typedef vector<TResidue> CResidueVec

Definition at line 69 of file gnomon_model.hpp.

◆ CSupportInfoSet

Definition at line 96 of file gnomon_model.hpp.

◆ TAlignModelCluster

Definition at line 814 of file gnomon_model.hpp.

◆ TAlignModelClusterSet

Definition at line 839 of file gnomon_model.hpp.

◆ TAlignModelList

Definition at line 817 of file gnomon_model.hpp.

◆ TDVec

typedef vector<double> TDVec

Definition at line 71 of file gnomon_model.hpp.

◆ TGeneModelCluster

Definition at line 813 of file gnomon_model.hpp.

◆ TGeneModelClusterSet

Definition at line 838 of file gnomon_model.hpp.

◆ TGeneModelList

typedef list<CGeneModel> TGeneModelList

Definition at line 816 of file gnomon_model.hpp.

◆ TInDels

typedef vector<CInDelInfo> TInDels

Definition at line 169 of file gnomon_model.hpp.

◆ TIVec

typedef vector<int> TIVec

Definition at line 70 of file gnomon_model.hpp.

◆ TResidue

typedef objects::CSeqVectorTypes::TResidue TResidue

Definition at line 67 of file gnomon_model.hpp.

Enumeration Type Documentation

◆ EResidueNames

Enumerator
enA 
enC 
enG 
enT 
enN 

Definition at line 842 of file gnomon_model.hpp.

◆ EStrand

enum EStrand
Enumerator
ePlus 
eMinus 

Definition at line 64 of file gnomon_model.hpp.

Function Documentation

◆ BadScore()

double BadScore ( )
inline

Definition at line 62 of file gnomon_model.hpp.

References max().

Referenced by CGnomonEngine::AcceptorScore(), AddProbabilities(), CIntergenic::BranchScore(), CInternalExon::BranchScore(), CSingleExon::BranchScore(), CLastExon::BranchScore(), CFirstExon::BranchScore(), CIntron::BranchScore(), CalcStateScores(), CGeneModel::CdsInvariant(), CCDSInfo::Clear(), CCDSInfo::Clip(), CExon::ClosingLengthScore(), CLorentz::ClosingScore(), CCDSInfo::CombineWith(), CParse::CParse(), CAnnotationASN1::CImplementationData::create_internal_feature(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), CCDSInfo::Cut(), CGnomonEngine::DonorScore(), CChainer::CChainerImpl::Duplicate5pendsAndShortCDSes(), CChainer::CChainerImpl::DuplicateUTRs(), CChainer::CChainerImpl::FilterOutBadScoreChainsHavingBetterCompatibles(), CChainer::CChainerImpl::FindGeneSeeds(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CCodingPropensity::GetScore(), CGnomonEngine::GetScore(), CChainer::CChainerImpl::GoodCDNAScore(), CSeqScores::Init(), CExon::InitialLengthScore(), CChainMembers::InsertMember(), CCDSInfo::Invariant(), CSeqScores::isConsensusIntron(), CIntron::LengthScore(), CChainer::CChainerImpl::MakeChains(), MemberIsCoding(), SingleExon_Noncoding::model_predicate(), LowSupport_Noncoding::model_predicate(), operator>>(), CGnomonEngine::PointCodingScore(), CGnomonAnnotator::Predict(), SGFFrec::print(), CGnomonAnnotatorArgUtil::ReadArgs(), readGFF3(), CGnomonEngine::Run(), s_EvaluateNewScore(), s_ForwardStep(), s_MakeStep(), s_TooFar(), CWAM_Donor< order >::Score(), CWAM_Acceptor< order >::Score(), CWMM_Start::Score(), CWAM_Stop::Score(), CMC_NonCodingRegion< order >::Score(), CMC3_CodingRegion< order >::Score(), CChainer::CChainerImpl::ScoreCdnas(), CChainer::ScoreCDSes_FilterOutPoorAlignments(), CGnomonEngine::SelectBestReadingFrame(), CIntronParameters::SetSeqLen(), CIntergenicParameters::SetSeqLen(), CLorentz::Through(), CExon::ThroughLengthScore(), CMarkovChain< 0 >::toScore(), CGnomonAnnotator::TryToEliminateAlignmentsFromTail(), CGnomonAnnotator::TryToEliminateOneAlignment(), and CGnomonAnnotator::TryWithoutObviouslyBadAlignments().

◆ Complement() [1/2]

EResidue Complement ( EResidue  c)
inline

Definition at line 883 of file gnomon_model.hpp.

References k_toMinus.

◆ Complement() [2/2]

TResidue Complement ( TResidue  c)
inline

◆ Enclosed()

bool Enclosed ( TSignedSeqRange  big,
TSignedSeqRange  small 
)
inline

Definition at line 77 of file gnomon_model.hpp.

References Include().

◆ GetAlignParts()

template<class Model >
list<Model> GetAlignParts ( const Model &  algn,
bool  settrimflags 
)

◆ Include() [1/2]

bool Include ( TSignedSeqRange  big,
TSignedSeqRange  small 
)
inline

Definition at line 75 of file gnomon_model.hpp.

References CRange_Base::GetFrom(), and CRange_Base::GetTo().

Referenced by AddSupport(), BelongToExon(), CChain::CalculateDropLimits(), CChain::CalculateSupportAndWeightFromMembers(), CChainer::CChainerImpl::CanIncludeJinI(), CGeneModel::CdsInvariant(), CChain::CheckSecondaryCapPolyAEnds(), CMultAlign::CheckWord(), CAlignCollapser::CleanSelfTranscript(), CChain::ClipChain(), CChain::ClipLowCoverageUTR(), CChain::ClipToCap(), CChain::ClipToPolyA(), CGeneModel::CombineCdsInfo(), CChainer::CChainerImpl::CombineCompatibleChains(), CCDSInfo::CombineWith(), CSeqScores::ConstructSequenceAndMaps(), CAnnotationASN1::CImplementationData::create_cdregion_feature(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), CCDSInfo::Cut(), Enclosed(), CAlignCollapser::FilterAlignments(), CChainer::CChainerImpl::FindContainedAlignments(), CChainer::CChainerImpl::FindOptimalChainForProtein(), FindStartsStops(), CGeneModel::FShiftedLen(), CAlignMap::FShiftedLen(), CGnomonEngine::GetScore(), CGene::HarborsRange(), CSeqScores::Init(), CCDSInfo::Invariant(), CGeneModel::IsSubAlignOf(), CChainer::CChainerImpl::LRCanChainItoJ(), CChainer::CChainerImpl::LRIinit(), CChain::MainPeaks(), CChainer::CChainerImpl::MakeChains(), SChainMember::MarkUnwantedCopiesForChain(), CGnomonAnnotator::Predict(), CModelCompare::RangeNestedInIntron(), CChain::RemoveFshiftsFromUTRs(), CChainer::CChainerImpl::ReplicatePStops(), CChain::RestoreReasonableConfirmedStart(), CChainer::CChainerImpl::RightLeft(), CMultAlign::SeqCountsBetweenTwoStrongWords(), CChain::SetConfirmedEnds(), CChain::SetConfirmedStartStopForCompleteProteins(), CChain::SetConsistentCoverage(), CAlignMap::ShrinkToRealPoints(), CAlignMap::ShrinkToRealPointsOnEdited(), CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes(), and CGnomonAnnotator::TryWithoutObviouslyBadAlignments().

◆ Include() [2/2]

bool Include ( TSignedSeqRange  r,
TSignedSeqPos  p 
)
inline

Definition at line 76 of file gnomon_model.hpp.

References r().

◆ IsStartCodon()

template<class Res >
bool IsStartCodon ( const Res *  seq,
int  strand = ePlus 
)

◆ IsStopCodon()

template<class Res >
bool IsStopCodon ( const Res *  seq,
int  strand = ePlus 
)

◆ MapAlignsToOrigContig()

void MapAlignsToOrigContig ( TAlignModelList aligns,
const TInDels corrections,
int  contig_size 
)

◆ operator<<() [1/3]

CNcbiOstream& operator<< ( CNcbiOstream s,
const CAlignModel a 
)

Definition at line 2566 of file gnomon_model.cpp.

References a, eGFF3FileFormat, model_file_format_state, and printGFF3().

◆ operator<<() [2/3]

CNcbiOstream& operator<< ( CNcbiOstream s,
const CGeneModel a 
)

Definition at line 2561 of file gnomon_model.cpp.

References a, and operator<<().

◆ operator<<() [3/3]

CNcbiOstream& operator<< ( CNcbiOstream s,
const setcontig c 
)

Definition at line 1605 of file gnomon_model.cpp.

References contig_stream_state, and setcontig::m_contig.

Referenced by operator<<().

◆ operator>>() [1/2]

CNcbiIstream& operator>> ( CNcbiIstream s,
CAlignModel a 
)

Definition at line 2577 of file gnomon_model.cpp.

References eGFF3FileFormat, model_file_format_state, and readGFF3().

◆ operator>>() [2/2]

CNcbiIstream& operator>> ( CNcbiIstream s,
const getcontig c 
)

◆ OtherStrand()

EStrand OtherStrand ( EStrand  s)
inline

Definition at line 65 of file gnomon_model.hpp.

References eMinus, and ePlus.

Referenced by isGoodIntron().

◆ Precede()

bool Precede ( TSignedSeqRange  l,
TSignedSeqRange  r 
)
inline

◆ ReverseComplement()

template<class BidirectionalIterator >
void ReverseComplement ( const BidirectionalIterator &  first,
const BidirectionalIterator &  last 
)

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ k_aa_table

const char* const k_aa_table
extern

Definition at line 41 of file gnomon_seq.cpp.

◆ k_toMinus

const EResidue k_toMinus[5]
extern

Definition at line 40 of file gnomon_seq.cpp.

Referenced by Complement(), CSeqScores::Init(), and ReverseComplement().

Modified on Sun Apr 21 03:45:08 2024 by modify_doxy.py rev. 669887