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NCBI C++ ToolKit: CAlignCollapser Class Reference

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#include <algo/gnomon/aligncollapser.hpp>

void CollapsIdentical () void CleanSelfTranscript (CAlignModel &align, const string &trans) const void CleanExonEdge (int ie, CAlignModel &align, const string &transcript, bool right_edge) const CAlignModel FillGapsInAlignmentAndAddToGenomicGaps (const CAlignModel &align, int fill) bool CheckAndInsert (const CAlignModel &align, TAlignModelClusterSet &clsset) const void ClipProteinToStartStop (CAlignModel &align) bool RemoveNotSupportedIntronsFromProt (CAlignModel &align) bool RemoveNotSupportedIntronsFromTranscript (CAlignModel &align, bool check_introns_on_both_strands) const void ClipNotSupportedFlanks (CAlignModel &align, double clip_threshold, double min_lim=0) void ClipESTorSR (CAlignModel &align, double clip_threshold, double min_lim) void AddFlexible (int status, TSignedSeqPos pos, EStrand strand, Int8 id, double weight)

Definition at line 124 of file aligncollapser.hpp.

◆ TAlignIntrons ◆ Tdata ◆ Tidpool ◆ TIntMap ◆ anonymous enum ◆ CAlignCollapser() CAlignCollapser::CAlignCollapser ( string contig = "", CScope * scope = 0, bool nofilteringcollapsing = false )

Definition at line 294 of file aligncollapser.cpp.

References CNcbiApplicationAPI::GetArgs(), COpenRange< TSignedSeqPos >::GetWhole(), InitContig(), CNcbiApplication::Instance(), m_collapsest, m_collapssr, m_fillgenomicgaps, m_filterest, m_filtermrna, m_filterprots, m_filtersr, m_minident, m_no_lr_only_introns, m_range, m_scope, and m_use_long_reads_tss.

◆ AddAlignment() void CAlignCollapser::AddAlignment ( CAlignModel & align )

Definition at line 2578 of file aligncollapser.cpp.

References a, AddFlexible(), map_checker< Container >::begin(), COLLAPS_CHUNK, CollapsIdentical(), CGeneModel::Continuous(), CGeneModel::eCap, CAlignMap::EditedSequence(), CGeneModel::eEST, CGeneModel::eGapFiller, CInDelInfo::eGenomeNotCorrect, CGeneModel::eLeftFlexible, eMinus, map_checker< Container >::empty(), COpenRange< Position >::Empty(), CGeneModel::emRNA, CGeneModel::eNotForChaining, Entropy(), ePlus, CGeneModel::ePolyA, CGeneModel::eProt, CGeneModel::eRemoveExons, CGeneModel::eReversed, CGeneModel::eRightFlexible, CGeneModel::eSR, CGeneModel::eUnknownOrientation, CGeneModel::Exons(), GetAlignParts(), COpenRange< TSignedSeqPos >::GetEmpty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), i, CGeneModel::ID(), int, ITERATE, l(), CGeneModel::Limits(), m_align_introns, m_aligns, m_aligns_for_filtering_only, SCorrectionData::m_confirmed_intervals, m_contig, m_contig_name, m_correction_data, SCorrectionData::m_correction_indels, m_count, m_fillgenomicgaps, m_filterest, m_filtermrna, m_filterprots, m_filtersr, m_genomic_gaps_len, m_long_read_count, m_minident, m_no_lr_only_introns, m_range, SCorrectionData::m_replacements, m_target_id_pool, m_use_long_reads_tss, max(), min(), NOT_ALIGNED_PHONY_CAGE, CGeneModel::ReverseComplementModel(), CRange_Base::SetFrom(), CRange_Base::SetTo(), CAlignMap::ShrinkToRealPoints(), CGeneModel::Status(), CGeneModel::Strand(), swap(), toupper(), CGeneModel::Type(), map_checker< Container >::upper_bound(), and CGeneModel::Weight().

◆ AddFlexible()

Definition at line 2559 of file aligncollapser.cpp.

References CGeneModel::AddExon(), CGeneModel::eRightFlexible, CGeneModel::eSR, CGeneModel::GetAlignMap(), CRange_Base::GetFrom(), CGeneModel::Limits(), m_special_aligns, CGeneModel::SetWeight(), SPECIAL_ALIGN_LEN, CGeneModel::Status(), and weight.

Referenced by AddAlignment().

◆ CheckAndInsert() ◆ CleanExonEdge() ◆ CleanSelfTranscript()

Definition at line 716 of file aligncollapser.cpp.

References _ASSERT, CGeneModel::AddExon(), CGeneModel::AddHole(), map_checker< Container >::begin(), BIG_NOT_ALIGNED, CGeneModel::ClearExons(), count, eMinus, map_checker< Container >::end(), ePlus, CGeneModel::eUnknownOrientation, CGeneModel::Exons(), EXTRA_CUT, CGeneModel::FrameShifts(), CAlignCollapser::CPartialString::FullLength(), g(), CRange_Base::GetFrom(), CGeneModel::GetInDels(), COpenRange< Position >::GetLength(), CAlignModel::GetTargetId(), CRange_Base::GetTo(), i, Include(), INDEL_PENALTY, int, ITERATE, len, CModelExon::Limits(), map_checker< Container >::lower_bound(), m_contig, CModelExon::m_fsplice, CModelExon::m_fsplice_sig, m_genomic_gaps_len, CModelExon::m_ident, CModelExon::m_ssplice, CModelExon::m_ssplice_sig, CAlignMap::MapRangeEditedToOrig(), max(), min(), MISM_PENALTY, COpenRange< Position >::NotEmpty(), CGeneModel::Orientation(), pb, ReverseComplement(), CRange_Base::SetFrom(), CAlignModel::SetTargetId(), CRange_Base::SetTo(), CGeneModel::Status(), CGeneModel::Strand(), CAlignCollapser::CPartialString::substr(), t, CAlignModel::TargetLen(), and CGeneModel::TranscriptExon().

Referenced by FilterAlignments().

◆ ClipESTorSR() void CAlignCollapser::ClipESTorSR ( CAlignModel & align, double clip_threshold, double min_lim ) private

Definition at line 359 of file aligncollapser.cpp.

References _ASSERT, CGeneModel::AlignLen(), CGeneModel::ClearExons(), CAlignModel::Clip(), END_PART_LENGTH, CGeneModel::eRemoveExons, EXON_TO_SKIP, CGeneModel::Exons(), CRange_Base::GetFrom(), CRange_Base::GetTo(), i, int, ITERATE, CGeneModel::Limits(), m_coverage, m_left_end, and max().

Referenced by FilterAlignments().

◆ ClipNotSupportedFlanks() void CAlignCollapser::ClipNotSupportedFlanks ( CAlignModel & align, double clip_threshold, double min_lim = 0 ) private

Definition at line 403 of file aligncollapser.cpp.

References a, b, CGeneModel::ClearExons(), CAlignModel::Clip(), CAlignModel::CutExons(), CGeneModel::eCap, eMinus, COpenRange< Position >::Empty(), END_PART_LENGTH, CGeneModel::eNotForChaining, ePlus, CGeneModel::ePolyA, CGeneModel::eProt, CGeneModel::eRemoveExons, CGeneModel::Exons(), CAlignMap::FShiftedLen(), CAlignModel::GetAlignMap(), CModelExon::GetFrom(), CRange_Base::GetFrom(), CModelExon::GetTo(), CRange_Base::GetTo(), i, int, ITERATE, l(), CGeneModel::Limits(), m_coverage, CModelExon::m_fsplice, m_left_end, CModelExon::m_ssplice, max(), min(), CGeneModel::Orientation(), r(), CAlignMap::ShrinkToRealPoints(), CGeneModel::Status(), CGeneModel::Strand(), swap(), CAlignModel::TargetLen(), CGeneModel::TranscriptLimits(), and CGeneModel::Type().

Referenced by FilterAlignments().

◆ ClipProteinToStartStop() void CAlignCollapser::ClipProteinToStartStop ( CAlignModel & align ) private ◆ CollapsIdentical() void CAlignCollapser::CollapsIdentical ( ) private ◆ FillGapsInAlignmentAndAddToGenomicGaps()

Definition at line 2454 of file aligncollapser.cpp.

References CGeneModel::AddExon(), CGeneModel::AddHole(), map_checker< Container >::begin(), CGeneModel::ClearExons(), CInDelInfo::eDel, efill_left, efill_middle, efill_right, eMinus, map_checker< Container >::end(), ePlus, CGeneModel::ePolyA, CGeneModel::eReversed, CGeneModel::Exons(), CGeneModel::FrameShifts(), CAlignModel::GetAlignMap(), GetDNASequence(), COpenRange< TSignedSeqPos >::GetEmpty(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CAlignModel::GetTargetId(), CModelExon::GetTo(), CRange_Base::GetTo(), i, int, CModelExon::Limits(), CGeneModel::Limits(), map_checker< Container >::lower_bound(), CInDelInfo::SSource::m_acc, m_correction_data, SCorrectionData::m_correction_indels, CModelExon::m_fsplice_sig, m_genomic_gaps_len, CModelExon::m_ident, CInDelInfo::SSource::m_range, m_scope, CModelExon::m_ssplice, CModelExon::m_ssplice_sig, CInDelInfo::SSource::m_strand, CAlignMap::MapRangeOrigToEdited(), max(), MAX_DIST_TO_FLANK_GAP, CGeneModel::Orientation(), ReverseComplement(), CRange_Base::SetFrom(), CAlignModel::SetTargetId(), CRange_Base::SetTo(), CGeneModel::Status(), swap(), CAlignModel::TargetAccession(), CAlignMap::TargetLen(), CAlignModel::TargetLen(), CGeneModel::TranscriptExon(), CGeneModel::TranscriptLimits(), and map_checker< Container >::upper_bound().

Referenced by FilterAlignments().

◆ FilterAlignments() void CAlignCollapser::FilterAlignments ( )

Definition at line 1027 of file aligncollapser.cpp.

References _ASSERT, a, AlignmentIsSupportedBySR(), AlignmentMarkedForDeletion(), b, map_checker< Container >::begin(), CleanSelfTranscript(), CAlignModel::Clip(), ClipESTorSR(), ClipNotSupportedFlanks(), close(), COVERAGE_WINDOW, CAlignModel::CutExons(), data, delta(), DESIRED_CHUNK, CGeneModel::eCap, CGeneModel::eChangedByFilter, CGeneModel::eEST, efill_left, efill_middle, efill_right, CGeneModel::eGapFiller, CInDelInfo::eGenomeNotCorrect, eMinus, set< Key, Compare >::empty(), COpenRange< Position >::Empty(), CGeneModel::emRNA, map_checker< Container >::end(), END_PART_LENGTH, CGeneModel::eNotForChaining, ePlus, CGeneModel::ePolyA, CGeneModel::eProt, map_checker< Container >::erase(), CGeneModel::eRemoveExons, eUnknown, CGeneModel::eUnknownOrientation, CGeneModel::eUnmodifiedAlign, CGeneModel::Exons(), FillGapsInAlignmentAndAddToGenomicGaps(), map_checker< Container >::find(), FS_FUZZ, CAlignMap::FShiftedLen(), CAlignModel::GetAlignMap(), CAlignCommon::GetAlignment(), GetAlignParts(), CNcbiApplicationAPI::GetArgs(), GetDNASequence(), CModelExon::GetFrom(), CRange_Base::GetFrom(), CGeneModel::GetInDels(), CAlignCommon::GetIntrons(), COpenRange< Position >::GetLength(), CAlignModel::GetTargetId(), CModelExon::GetTo(), CRange_Base::GetTo(), CGeneModel::HasStart(), CGeneModel::HasStop(), i, in(), Include(), set< Key, Compare >::insert(), CNcbiApplication::Instance(), int, ip, CAlignCommon::isCap(), CAlignCommon::isEST(), CAlignCommon::isMinus(), CAlignCommon::isPlus(), CAlignCommon::isPolyA(), CAlignCommon::isSR(), CAlignCommon::isUnknown(), ITERATE, l(), len, CModelExon::Limits(), CGeneModel::Limits(), Loc, m_align_introns, m_aligns, m_aligns_for_filtering_only, m_contig, m_correction_data, SCorrectionData::m_correction_indels, m_count, m_coverage, m_filterest, m_filtermrna, m_filterprots, m_filtersr, CModelExon::m_fsplice, m_left_end, m_long_read_count, m_minident, SIntron::m_oriented, SIntron::m_range, m_range, m_scope, CModelExon::m_ssplice, SIntron::m_strand, m_target_id_pool, max(), MAX_CLIP, min(), MIN_EXON, n, NON_CONST_ITERATE, number, r(), remove_if(), RemoveNotSupportedIntronsFromProt(), RemoveNotSupportedIntronsFromTranscript(), CGeneModel::ReverseComplementModel(), CRange_Base::SetFrom(), CRange_Base::SetTo(), CAlignMap::ShrinkToRealPoints(), map_checker< Container >::size(), SMALL_CLIP, ct::sort(), CGeneModel::Status(), CGeneModel::Strand(), tolower(), TotalFrameShift(), CAlignCollapser::CPartialString::ToUpper(), CGeneModel::Type(), map_checker< Container >::upper_bound(), and weight.

Referenced by GetCollapsedAlgnments(), and GetOnlyOtherAlignments().

◆ GetCollapsedAlgnments()

Definition at line 2230 of file aligncollapser.cpp.

References _ASSERT, a, b, map_checker< Container >::begin(), set< Key, Compare >::begin(), CheckAndInsert(), CollapsIdentical(), CGeneModel::eCap, CGeneModel::eEST, eMinus, map_checker< Container >::empty(), CGeneModel::emRNA, set< Key, Compare >::end(), ePlus, CGeneModel::ePolyA, CGeneModel::eSR, CMolInfo_Base::eTech_tsa, CGeneModel::eTSA, CGeneModel::eUnknownOrientation, CGeneModel::Exons(), FilterAlignments(), CAlignCollapser::CPartialString::FullLength(), CAlignCommon::GetAlignment(), CNcbiApplicationAPI::GetArgs(), CScope::GetBioseqHandle(), COpenRange< TSignedSeqPos >::GetEmpty(), CRange_Base::GetFrom(), CAlignCommon::GetIntrons(), COpenRange< Position >::GetLength(), GetMolInfo(), CMolInfo_Base::GetTech(), CRange_Base::GetTo(), i, set< Key, Compare >::insert(), CNcbiApplication::Instance(), CAlignCommon::isCap(), CAlignCommon::isEST(), CAlignCommon::isMinus(), CAlignCommon::isPlus(), CAlignCommon::isPolyA(), CMolInfo_Base::IsSetTech(), CAlignCommon::isSR(), ITERATE, CGeneModel::Limits(), map_checker< Container >::lower_bound(), set< Key, Compare >::lower_bound(), m_align_introns, m_aligns, m_aligns_for_filtering_only, m_collapsest, m_collapssr, m_contig, m_contig_name, m_count, m_fillgenomicgaps, SAlignIndividual::m_range, SIntron::m_range, m_scope, m_special_aligns, m_target_id_pool, SAlignIndividual::m_weight, max(), min(), minus(), NON_CONST_ITERATE, plus(), CGeneModel::SetStrand(), CRange_Base::SetTo(), CGeneModel::SetWeight(), ct::sort(), CGeneModel::Status(), CGeneModel::Strand(), CGeneModel::Type(), set< Key, Compare >::upper_bound(), and CGeneModel::Weight().

◆ GetContigGaps() TIntMap CAlignCollapser::GetContigGaps ( ) const inline ◆ GetGenomicCorrections() ◆ GetGenomicGaps() TInDels CAlignCollapser::GetGenomicGaps ( ) const inline ◆ GetOnlyOtherAlignments()

Definition at line 2213 of file aligncollapser.cpp.

References CheckAndInsert(), CGeneModel::emRNA, CMolInfo_Base::eTech_tsa, CGeneModel::eTSA, FilterAlignments(), CScope::GetBioseqHandle(), GetMolInfo(), CMolInfo_Base::GetTech(), i, CMolInfo_Base::IsSetTech(), m_aligns_for_filtering_only, m_count, m_scope, and NON_CONST_ITERATE.

◆ InitContig() void CAlignCollapser::InitContig ( string contig, CScope * scope )

Definition at line 250 of file aligncollapser.cpp.

References CSeq_id::Assign(), CSeq_id_Base::e_Local, CBioseq_Handle::eCoding_Iupac, map_checker< Container >::end(), eUnknown, CScope::GetBioseqHandle(), CRange_Base::GetFrom(), CBioseq_Handle::GetSeqVector(), CRange_Base::GetTo(), COpenRange< TSignedSeqPos >::GetWhole(), i, CAlignCollapser::CPartialString::Init(), map_checker< Container >::insert(), CSeqVector::IsInGap(), m_contig, m_contig_name, m_genomic_gaps_len, m_range, m_scope, max(), MAX_DIST_TO_FLANK_GAP, min(), NCBI_THROW, COpenRange< Position >::NotEmpty(), CSeqVector::size(), and CIdHandler::ToSeq_id().

Referenced by CAlignCollapser().

◆ RemoveNotSupportedIntronsFromProt() bool CAlignCollapser::RemoveNotSupportedIntronsFromProt ( CAlignModel & align ) private

Definition at line 552 of file aligncollapser.cpp.

References CGeneModel::ClearExons(), CAlignModel::Clip(), CUT_MARGIN, CAlignModel::CutExons(), COpenRange< Position >::Empty(), END_PART_LENGTH, CGeneModel::eRemoveExons, CGeneModel::Exons(), CAlignMap::FShiftedLen(), CAlignModel::GetAlignMap(), CModelExon::GetFrom(), CRange_Base::GetFrom(), CModelExon::GetTo(), CRange_Base::GetTo(), int, isGoodIntron(), CGeneModel::Limits(), m_align_introns, CModelExon::m_fsplice, CModelExon::m_ssplice, CAlignMap::ShrinkToRealPoints(), and CGeneModel::Strand().

Referenced by FilterAlignments().

◆ RemoveNotSupportedIntronsFromTranscript() bool CAlignCollapser::RemoveNotSupportedIntronsFromTranscript ( CAlignModel & align, bool check_introns_on_both_strands ) const private

Definition at line 597 of file aligncollapser.cpp.

References _ASSERT, a, CGeneModel::AddExon(), CGeneModel::AddHole(), CGeneModel::ClearExons(), CGeneModel::CutExons(), CGeneModel::eCap, CGeneModel::eEST, CGeneModel::eGapFiller, CAlignMap::eLeftEnd, eMinus, ePlus, CGeneModel::ePolyA, CGeneModel::eRemoveExons, CAlignMap::eRightEnd, CAlignMap::eSinglePoint, CGeneModel::Exons(), CGeneModel::FrameShifts(), CAlignModel::GetAlignMap(), CModelExon::GetFrom(), CRange_Base::GetFrom(), CAlignModel::GetTargetId(), CModelExon::GetTo(), CRange_Base::GetTo(), int, isGoodIntron(), ITERATE, CGeneModel::Limits(), m_align_introns, CModelExon::m_fsplice, CModelExon::m_ssplice, CAlignMap::MapRangeOrigToEdited(), COpenRange< Position >::NotEmpty(), CGeneModel::Orientation(), CAlignModel::SetTargetId(), CAlignMap::ShrinkToRealPoints(), CGeneModel::Status(), CGeneModel::Strand(), CAlignMap::TargetLen(), and CGeneModel::Type().

Referenced by FilterAlignments().

◆ SetGenomicCorrections() ◆ SetupArgDescriptions() ◆ m_align_introns ◆ m_aligns Tdata CAlignCollapser::m_aligns private ◆ m_aligns_for_filtering_only ◆ m_collapsest bool CAlignCollapser::m_collapsest private ◆ m_collapssr bool CAlignCollapser::m_collapssr private ◆ m_contig ◆ m_contig_name string CAlignCollapser::m_contig_name private ◆ m_correction_data ◆ m_count int CAlignCollapser::m_count private ◆ m_coverage vector<double> CAlignCollapser::m_coverage private ◆ m_fillgenomicgaps bool CAlignCollapser::m_fillgenomicgaps private ◆ m_filterest bool CAlignCollapser::m_filterest private ◆ m_filtermrna bool CAlignCollapser::m_filtermrna private ◆ m_filterprots bool CAlignCollapser::m_filterprots private ◆ m_filtersr bool CAlignCollapser::m_filtersr private ◆ m_genomic_gaps_len TIntMap CAlignCollapser::m_genomic_gaps_len private ◆ m_left_end int CAlignCollapser::m_left_end private ◆ m_long_read_count int CAlignCollapser::m_long_read_count private ◆ m_minident double CAlignCollapser::m_minident private ◆ m_no_lr_only_introns bool CAlignCollapser::m_no_lr_only_introns private ◆ m_range ◆ m_scope CScope* CAlignCollapser::m_scope private ◆ m_special_aligns ◆ m_target_id_pool Tidpool CAlignCollapser::m_target_id_pool private ◆ m_use_long_reads_tss bool CAlignCollapser::m_use_long_reads_tss private

The documentation for this class was generated from the following files:

include/algo/gnomon/aligncollapser.hpp
src/algo/gnomon/aligncollapser.cpp

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