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< TResidue >	CResidueVec
typedef vector< int >	TIVec
typedef vector< double >	TDVec
typedef set< CSupportInfo >	CSupportInfoSet
typedef vector< CInDelInfo >	TInDels
typedef CModelCluster< CGeneModel >	TGeneModelCluster
typedef CModelCluster< CAlignModel >	TAlignModelCluster
typedef list< CGeneModel >	TGeneModelList
typedef list< CAlignModel >	TAlignModelList
typedef CModelClusterSet< TGeneModelCluster >	TGeneModelClusterSet
typedef CModelClusterSet< TAlignModelCluster >	TAlignModelClusterSet

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)
CNcbiOstream &	operator<< (CNcbiOstream &s, const setcontig &c)
CNcbiIstream &	operator>> (CNcbiIstream &s, const getcontig &c)
CNcbiIstream &	operator>> (CNcbiIstream &s, CAlignModel &a)
CNcbiOstream &	operator<< (CNcbiOstream &s, const CAlignModel &a)
CNcbiOstream &	operator<< (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

typedef set<CSupportInfo> CSupportInfoSet

Definition at line 96 of file gnomon_model.hpp.

TAlignModelCluster

typedef CModelCluster<CAlignModel> TAlignModelCluster

Definition at line 814 of file gnomon_model.hpp.

TAlignModelClusterSet

typedef CModelClusterSet<TAlignModelCluster> TAlignModelClusterSet

Definition at line 839 of file gnomon_model.hpp.

TAlignModelList

typedef list<CAlignModel> 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

typedef CModelCluster<CGeneModel> TGeneModelCluster

Definition at line 813 of file gnomon_model.hpp.

TGeneModelClusterSet

typedef CModelClusterSet<TGeneModelCluster> 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

enum 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

Definition at line 855 of file gnomon_model.hpp.

Referenced by ReverseComplement(), and DeBruijn::CDBGraphDigger::SContig::SContig().

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
	)

Definition at line 897 of file gnomon_model.hpp.

References CGeneModel::eRemoveExons, CGeneModel::Exons(), i, ncbi::grid::netcache::search::fields::size, and CGeneModel::Status().

Referenced by CAlignCollapser::AddAlignment(), CChainer::CChainerImpl::CutParts(), and CAlignCollapser::FilterAlignments().

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
	)

Definition at line 108 of file gnomon_seq.cpp.

References res_traits< Res >::_codons(), res_traits< Res >::_rev_codons(), and ePlus.

Referenced by FindStartsStops(), CChain::SetConfirmedEnds(), and ProjectCDS::transform_align().

IsStopCodon()

template<class Res >

bool IsStopCodon	(	const Res *	seq,
		int	strand = ePlus
	)

Definition at line 124 of file gnomon_seq.cpp.

References ePlus, and i.

Referenced by CGnomonEngine::GetScore(), Partial5pCodonIsStop(), CChain::SetConfirmedEnds(), and ProjectCDS::transform_align().

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
	)

Examples

/home/coremake/doxygen/cxx/include/corelib/ncbimisc.hpp.

Definition at line 1609 of file gnomon_model.cpp.

References contig_stream_state, and getcontig::m_contig.

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

Definition at line 74 of file gnomon_model.hpp.

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

Referenced by CModelCompare::CanBeConnectedIntoOne(), CCDSInfo::Clear5PrimeCdsLimit(), CCDSInfo::CombineWith(), CCDSInfo::Invariant(), CCDSInfo::MapFromEditedToOrig(), CCDSInfo::MapFromOrigToEdited(), Precedence::operator()(), RangeOrder::operator()(), CGeneModel::operator<(), CModelCluster< Model >::operator<(), CModelExon::operator<(), CGnomonAnnotator::Predict(), CChain::RestoreReasonableConfirmedStart(), CCDSInfo::SetStop(), CCDSInfo::Strand(), and CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes().

ReverseComplement()

template<class BidirectionalIterator >

void ReverseComplement	(	const BidirectionalIterator &	first,
		const BidirectionalIterator &	last
	)

Definition at line 889 of file gnomon_model.hpp.

References Complement(), first(), i, and last().

Referenced by CDiscrepancyVisitorImpl< _Name >::Autofix(), BOOST_AUTO_TEST_CASE(), CAlignCollapser::CleanSelfTranscript(), CAlignCollapser::FillGapsInAlignmentAndAddToGenomicGaps(), CGeneModel::GetCdsDnaSequence(), CCorrectRNAStrandDlg::GetCommand(), CMixedStrands::GetCommand(), CParse::GetGenes(), GetReverseComplimentSequenceCommand(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGnomonAnnotator_Base::MapOneModelToOrigContig(), CRevCompSequencesDlg::RevCompBioSeq(), DeBruijn::CDBGraphDigger::SContig::ReverseComplement(), CGeneModel::ReverseComplementModel(), and CChain::ValidPolyA().

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().