Search Toolkit Book for CAlignMap
#include <algo/gnomon/gnomon_model.hpp>
Definition at line 630 of file gnomon_model.hpp.
◆ EEdgeType ◆ ERangeEnd ◆ CAlignMap() [1/5] ◆ CAlignMap() [2/5] ◆ CAlignMap() [3/5] ◆ CAlignMap() [4/5]Definition at line 515 of file gnomon_seq.cpp.
References _ASSERT, eBoundary, eGgap, eMinus, Empty(), ePlus, eSplice, f, i, InsertIndelRangesForInterval(), ITERATE, m_edited_ranges, m_orientation, m_orig_ranges, and ReverseComplement().
◆ CAlignMap() [5/5]Definition at line 572 of file gnomon_seq.cpp.
References _ASSERT, eBoundary, eGgap, eMinus, Empty(), eSplice, CRange_Base::GetFrom(), CRange_Base::GetTo(), i, InsertIndelRangesForInterval(), m_edited_ranges, m_orientation, m_orig_ranges, m_target_len, and ReverseComplement().
◆ EditedSequence()template<class In , class Out >
template void CAlignMap::EditedSequence< string, string > ( const In & original_sequence, Out & edited_sequence, bool includeholes =false ) const
Definition at line 631 of file gnomon_seq.cpp.
References a, b, eBoundary, eMinus, ePlus, eSplice, i, int, ITERATE, l(), m_edited_ranges, m_orientation, m_orig_ranges, ReverseComplement(), and TargetLen().
Referenced by CAlignCollapser::AddAlignment(), CSeqScores::ConstructSequenceAndMaps(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CGeneModel::GetCdsDnaSequence(), CGnomonEngine::GetScore(), CSeqScores::Init(), CChain::SetConfirmedEnds(), SModelData::SModelData(), ProjectCDS::transform_align(), and RemoveTrailingNs::transform_model().
◆ FindLowerRange() ◆ FShiftedLen() [1/3] ◆ FShiftedLen() [2/3] ◆ FShiftedLen() [3/3]Definition at line 992 of file gnomon_seq.cpp.
References eBoundary, COpenRange< Position >::GetLength(), i, Include(), int, len, m_edited_ranges, m_orig_ranges, and MapRangeOrigToEdited().
Referenced by CChain::AddAllMembersAndCoverage(), CChain::CalculateDropLimits(), CAlignMap(), CChain::CChain(), CChain::ClipLowCoverageUTR(), CAlignCollapser::ClipNotSupportedFlanks(), EffectiveExonLength(), CAlignCollapser::FilterAlignments(), CChainer::CChainerImpl::FilterOutChimeras(), CChainer::CChainerImpl::FindOptimalChainForProtein(), CChainer::CChainerImpl::FindOverlappingWithTrusted(), CGeneModel::FShiftedLen(), CParse::GetGenes(), InframeFraction(), CGene::IsAlternative(), CChainer::CChainerImpl::LRCanChainItoJ(), CChainer::CChainerImpl::LRIinit(), CCDSInfo::MapFromEditedToOrig(), CAlignCollapser::RemoveNotSupportedIntronsFromProt(), CChain::RestoreReasonableConfirmedStart(), CChainer::CChainerImpl::RightLeft(), CGnomonEngine::SelectBestReadingFrame(), CChain::SetConsistentCoverage(), CChainer::CChainerImpl::SetFlagsForChains(), and CutShortPartialExons::transform_align().
◆ FShiftedMove() ◆ InsertIndelRangesForInterval() ◆ InsertOneToOneRange() void CAlignMap::InsertOneToOneRange ( TSignedSeqPos orig_start, TSignedSeqPos edited_start, TSignedSeqPos len, const string & mism, TSignedSeqPos left_orige, TSignedSeqPos left_edite, TSignedSeqPos right_orige, TSignedSeqPos right_edite, EEdgeType left_type, EEdgeType right_type, const string & left_edit_extra_seq, const string & right_edit_extra_seq ) private ◆ MapAtoB() ◆ MapEditedToOrig()Definition at line 902 of file gnomon_seq.cpp.
References eMinus, eSinglePoint, m_edited_ranges, m_orientation, m_orig_ranges, and MapAtoB().
Referenced by CChain::CalculateDropLimits(), CSeqScores::ConstructSequenceAndMaps(), FindStartsStops(), FShiftedMove(), CGnomonEngine::GetScore(), CSeqScores::Init(), CCDSInfo::MapFromEditedToOrig(), CGnomonEngine::PartialModelStepBack(), CParse::PrintInfo(), SPhyloCSFSlice::Score(), CGnomonEngine::SelectBestReadingFrame(), CChain::SetConfirmedEnds(), ProjectCDS::transform_align(), and CGeneModel::TrimEdgesToFrameInOtherAlignGaps().
◆ MapOrigToEdited()Definition at line 893 of file gnomon_seq.cpp.
References eMinus, eSinglePoint, m_edited_ranges, m_orientation, m_orig_ranges, and MapAtoB().
Referenced by CChainer::CChainerImpl::CanIncludeJinI(), CSeqScores::ConstructSequenceAndMaps(), CChainer::CChainerImpl::FilterOutChimeras(), CChainer::CChainerImpl::FindOverlappingWithTrusted(), FShiftedMove(), CSeqScores::Init(), CGene::IsAlternative(), CChain::MainPeaks(), CCDSInfo::MapFromOrigToEdited(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CChain::RestoreReasonableConfirmedStart(), CChain::SetConfirmedStartStopForCompleteProteins(), CChainer::CChainerImpl::SetFlagsForChains(), CGeneModel::TranscriptExon(), CGeneModel::TranscriptLimits(), and ProjectCDS::transform_align().
◆ MapRangeAtoB() [1/2] ◆ MapRangeAtoB() [2/2] ◆ MapRangeEditedToOrig()Definition at line 965 of file gnomon_seq.cpp.
References eMinus, COpenRange< Position >::Empty(), COpenRange< TSignedSeqPos >::GetEmpty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), COpenRange< TSignedSeqPos >::GetWholeFrom(), COpenRange< TSignedSeqPos >::GetWholeTo(), m_edited_ranges, m_orientation, m_orig_ranges, MapRangeAtoB(), and offset.
Referenced by CAlignCollapser::CleanSelfTranscript(), CChain::ClipLowCoverageUTR(), SPhyloCSFSlice::CompactRange(), CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CParse::GetGenes(), CGnomonEngine::GetScore(), CCDSInfo::MapFromEditedToOrig(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CGnomonAnnotator_Base::MapOneModelToOrigContig(), CGnomonEngine::SelectBestReadingFrame(), and ProjectCDS::transform_align().
◆ MapRangeOrigToEdited() [1/2] ◆ MapRangeOrigToEdited() [2/2]Definition at line 937 of file gnomon_seq.cpp.
References COpenRange< Position >::Empty(), ePlus, COpenRange< TSignedSeqPos >::GetEmpty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), COpenRange< TSignedSeqPos >::GetWholeFrom(), COpenRange< TSignedSeqPos >::GetWholeTo(), m_edited_ranges, m_orientation, m_orig_ranges, MapRangeAtoB(), and offset.
Referenced by CChain::AddAllMembersAndCoverage(), CChain::CalculateDropLimits(), CChain::CChain(), CChain::ClipChain(), CChain::ClipLowCoverageUTR(), CAnnotationASN1::CImplementationData::create_internal_feature(), CAnnotationASN1::CImplementationData::create_packed_int_seqloc(), CAlignCollapser::FillGapsInAlignmentAndAddToGenomicGaps(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), FindStartsStops(), FShiftedLen(), CParse::GetGenes(), CGeneModel::isNMD(), CChain::MainPeaks(), CCDSInfo::MapFromOrigToEdited(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CIndelMapper::operator()(), CAlignModel::PolyALen(), readGFF3(), CAlignModel::RecalculateAlignMap(), CAlignCollapser::RemoveNotSupportedIntronsFromTranscript(), RestoreModelReadingFrame(), CChain::SetConfirmedEnds(), CChain::SetConfirmedStartStopForCompleteProteins(), CChainer::CChainerImpl::SetConfirmedStartStopForProteinAlignments(), CChain::SetConsistentCoverage(), CGeneModel::TranscriptExon(), CGeneModel::TranscriptLimits(), and CGeneModel::TrimEdgesToFrameInOtherAlignGaps().
◆ MoveOrigin() ◆ Orientation() EStrand CAlignMap::Orientation ( ) const inline ◆ ShrinkToRealPoints()Definition at line 763 of file gnomon_seq.cpp.
References _ASSERT, a, b, eMinus, ePlus, FindLowerRange(), COpenRange< TSignedSeqPos >::GetEmpty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), Include(), m_edited_ranges, m_orientation, m_orig_ranges, and COpenRange< Position >::NotEmpty().
Referenced by CAlignCollapser::AddAlignment(), CGeneModel::Clip(), CAlignCollapser::ClipNotSupportedFlanks(), CChainer::CChainerImpl::CreateChainsForPartialProteins(), EffectiveExonLength(), CAlignCollapser::FilterAlignments(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), InframeFraction(), CChain::MainPeaks(), CGnomonAnnotator_Base::MapOneModelToEditedContig(), CAlignCollapser::RemoveNotSupportedIntronsFromProt(), CAlignCollapser::RemoveNotSupportedIntronsFromTranscript(), CChain::SetConfirmedEnds(), CutShortPartialExons::transform_align(), CChainer::CChainerImpl::TrimAlignmentsIncludedInDifferentGenes(), TrimAlignment::TrimProtein(), and TrimAlignment::TrimTranscript().
◆ ShrinkToRealPointsOnEdited()Definition at line 697 of file gnomon_seq.cpp.
References _ASSERT, a, b, eMinus, FindLowerRange(), COpenRange< TSignedSeqPos >::GetEmpty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), COpenRange< TSignedSeqPos >::GetWholeFrom(), COpenRange< TSignedSeqPos >::GetWholeTo(), Include(), m_edited_ranges, m_orientation, COpenRange< Position >::NotEmpty(), and offset.
Referenced by SPhyloCSFSlice::CompactRange(), and CGnomonAnnotator_Base::MapOneModelToOrigContig().
◆ TargetLen() int CAlignMap::TargetLen ( ) const inline ◆ m_edited_ranges ◆ m_orientation ◆ m_orig_ranges ◆ m_target_len int CAlignMap::m_target_len privateThe documentation for this class was generated from the following files:
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