#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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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) ◆ CResidueVec ◆ CSupportInfoSet ◆ TAlignModelCluster ◆ TAlignModelClusterSet ◆ TAlignModelList ◆ TDVec ◆ TGeneModelCluster ◆ TGeneModelClusterSet ◆ TGeneModelList ◆ TInDels ◆ TIVec ◆ TResidue ◆ EResidueNames ◆ EStrand ◆ BadScore()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] ◆ Complement() [2/2] ◆ Enclosed() ◆ GetAlignParts()template<class Model >
list<Model> GetAlignParts ( const Model & algn, bool settrimflags ) ◆ Include() [1/2]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] ◆ IsStartCodon() ◆ IsStopCodon() ◆ MapAlignsToOrigContig() ◆ operator<<() [1/3] ◆ operator<<() [2/3] ◆ operator<<() [3/3] ◆ operator>>() [1/2] ◆ operator>>() [2/2] ◆ OtherStrand() ◆ Precede()Definition at line 74 of file gnomon_model.hpp.
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 897 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() ◆ k_aa_table ◆ k_toMinusRetroSearch is an open source project built by @garambo | Open a GitHub Issue
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