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Searched refs:TSignedSeqRange (Results 1 – 25 of 32) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp74 inline bool Precede(TSignedSeqRange l, TSignedSeqRange r) { return l.GetTo() < r.GetFrom(); } in Precede()
106 TSignedSeqRange m_range;
180 virtual TSignedSeqRange operator()(TSignedSeqRange r, bool withextras = true) const = 0;
218 TSignedSeqRange m_range;
260 void Cut(TSignedSeqRange hole);
267 SPStop(TSignedSeqRange r, EStatus s) : TSignedSeqRange(r), m_status(s) {}; in SPStop()
342 TSignedSeqRange m_start, m_stop;
343 TSignedSeqRange m_reading_frame;
598 TSignedSeqRange m_range;
660 TSignedSeqRange ShrinkToRealPointsOnEdited(TSignedSeqRange edited_range) const;
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H A Dvariations.hpp52 …CLiteAlign(TSignedSeqRange range, const TLiteInDels& indels, set<CLiteIndel>& indel_holder, double…
57 TSignedSeqRange Limits() const { return m_range; } in Limits()
66 TSignedSeqRange m_range;
109 … void Variations(map<TSignedSeqRange,TSIMap>& variations, list<TSignedSeqRange>& confirmed_ranges);
123 TSignedSeqRange LegitRange(int ir);
124 string EmitSequenceFromRead(int ir, const TSignedSeqRange& word_range);
125 string EmitSequenceFromBase(const TSignedSeqRange& word_range);
126 bool CheckWord(const TSignedSeqRange& word_range, const string& word);
127 …ongWord(int nextp, const string& maximal_bases, string& strong_word, TSignedSeqRange& strong_word_…
128 …sBetweenTwoStrongWords(const TSignedSeqRange& prev_strong_word_range, const string& prev_strong_wo…
H A Dgnomon.hpp73 …CHMMParameters> hmm_params, const CResidueVec& sequence, TSignedSeqRange range = TSignedSeqRange::…
74 …tRef<CHMMParameters> hmm_params, CResidueVec&& sequence, TSignedSeqRange range = TSignedSeqRange::…
77 void ResetRange(TSignedSeqRange range);
78 void ResetRange(TSignedSeqPos from, TSignedSeqPos to) { ResetRange(TSignedSeqRange(from,to)); } in ResetRange()
H A Dglb_align.hpp57 TSignedSeqRange QueryRange() const { return TSignedSeqRange(m_qfrom, m_qto); } in QueryRange()
58 TSignedSeqRange SubjectRange() const { return TSignedSeqRange(m_sfrom, m_sto); } in SubjectRange()
79 …jectlen, int gopen, int gapextend, const char delta[256][256], const TSignedSeqRange* subject_limi…
H A Daligncollapser.hpp53 TSignedSeqRange m_range;
71 TSignedSeqRange m_range;
118 …list<TSignedSeqRange> m_confirmed_intervals; // include all "confirmed" or "corrected" positions
224 TSignedSeqRange m_range;
H A Dchainer.hpp122 …::CScope& scope, const SCorrectionData& correction_data, TSignedSeqRange range = TSignedSeqRange::…
164 TSignedSeqRange m_limits; // limits on contig
182 map<string,TSignedSeqRange>& SetMrnaCDS();
H A Dannot.hpp112 TSignedSeqRange& tested_range);
143 …static bool RangeNestedInIntron(TSignedSeqRange r, const CGeneModel& algn, bool check_in_holes = t…
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dgnomon_seq.cpp682 TSignedSeqRange CAlignMap::ShrinkToRealPointsOnEdited(TSignedSeqRange edited_range) const { in ShrinkToRealPointsOnEdited()
712 return TSignedSeqRange::GetEmpty(); in ShrinkToRealPointsOnEdited()
744 return TSignedSeqRange(a, b); in ShrinkToRealPointsOnEdited()
748 TSignedSeqRange CAlignMap::ShrinkToRealPoints(TSignedSeqRange orig_range, bool snap_to_codons) cons… in ShrinkToRealPoints()
810 return TSignedSeqRange(a, b); in ShrinkToRealPoints()
910 right = TSignedSeqRange::GetWholeTo(); in MapRangeAtoB()
919 return TSignedSeqRange(left, right); in MapRangeAtoB()
922 TSignedSeqRange CAlignMap::MapRangeOrigToEdited(TSignedSeqRange orig_range, ERangeEnd lend, ERangeE… in MapRangeOrigToEdited()
942 right = TSignedSeqRange::GetWholeTo(); in MapRangeOrigToEdited()
947 return TSignedSeqRange(left, right); in MapRangeOrigToEdited()
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H A Dgnomon_model.cpp149 return TSignedSeqRange(l,r); in TranscriptLimits()
754 TSignedSeqRange cds_hole = hole; in CutExons()
1113 TSignedSeqRange exon_range(TSignedSeqRange::GetEmpty()); in AddGgapExon()
1759 TSignedSeqRange rf = cds; in CollectAttributes()
1946 TSignedSeqRange start, stop; in ParseAttributes()
2201 struct Precedence : public binary_function<TSignedSeqRange, TSignedSeqRange, bool>
2203 bool operator()(const TSignedSeqRange& __x, const TSignedSeqRange& __y) const in operator ()()
2207 TSignedSeqRange operator- (TSignedSeqRange a, TSignedSeqRange b) in operator -()
2248 TSignedSeqRange cds; in readGFF3()
2368 TSignedSeqRange reading_frame; in readGFF3()
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H A Dchainer.cpp137 const TSignedSeqRange& m_limits;
2908 …map<TSignedSeqRange,int>& mrna_count, map<TSignedSeqRange,int>& est_count, map<TSignedSeqRange,int… in GoodSupportForIntrons() argument
2922 …map<TSignedSeqRange,int>& mrna_count, map<TSignedSeqRange,int>& est_count, map<TSignedSeqRange,int… in MarkUnwantedLowSupportIntrons() argument
4284 TSignedSeqRange m_range;
4299 bool operator()(const TSignedSeqRange& a, const TSignedSeqRange& b) const { in operator ()()
4668 TSignedSeqRange conf_start; in RestoreReasonableConfirmedStart()
6487 TSignedSeqRange m_limits;
6686 TSignedSeqRange start = cdsmap.MapRangeEditedToOrig(TSignedSeqRange(0,2)); in transform_align()
6687 TSignedSeqRange stop = cdsmap.MapRangeEditedToOrig(TSignedSeqRange(length-3,length-1)); in transform_align()
6840 TSignedSeqRange newlimits = alignmap.ShrinkToRealPoints(TSignedSeqRange(a,b),false); in TrimTranscript()
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H A Dvariations.cpp137 m_range = TSignedSeqRange(gstart,gstop-1); in CLiteAlign()
254 map<TSignedSeqRange,TSIMap> variations; in GetVariationAlignList()
255 list<TSignedSeqRange> confirmed_ranges; in GetVariationAlignList()
261 TSignedSeqRange range = *i; in GetVariationAlignList()
271 TSignedSeqRange range = i->first; in GetVariationAlignList()
478 TSignedSeqRange legit_range = LegitRange(ir); in GetCounts()
523 TSignedSeqRange CMultAlign::LegitRange(int ir) { in LegitRange()
547 void CMultAlign::Variations(map<TSignedSeqRange,TSIMap>& variations, list<TSignedSeqRange>& confirm… in Variations() argument
581 TSignedSeqRange prev_strong_word_range; in Variations()
589 TSignedSeqRange strong_word_range; in Variations()
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H A Dannot.cpp105 tested_range = TSignedSeqRange(left,right); in TryWithoutObviouslyBadAlignments()
207 TSignedSeqRange tested_range; in Predict()
325 TSignedSeqRange GetWallLimits(const CGeneModel& m) in GetWallLimits()
332 TSignedSeqRange a = GetWallLimits(ap); in s_AlignSeqOrder()
333 TSignedSeqRange b = GetWallLimits(bp); in s_AlignSeqOrder()
429 set<TSignedSeqRange> hosting_intervals; in Predict()
439 TSignedSeqRange gene_lim_for_nested; in Predict()
503 TSignedSeqRange hosting_interval; in Predict()
505 TSignedSeqRange interval = *ii; in Predict()
681 TSignedSeqRange fullcds = cds_info.Cds(); in Predict()
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H A Daligncollapser.cpp312 m_range = TSignedSeqRange::GetWhole(); in CAlignCollapser()
384 … TSignedSeqRange seg = amap.ShrinkToRealPoints(TSignedSeqRange(l,align.Limits().GetTo()), false); in ClipNotSupportedFlanks()
404 … TSignedSeqRange seg = amap.ShrinkToRealPoints(TSignedSeqRange(align.Limits().GetFrom(),r), false); in ClipNotSupportedFlanks()
476 TSignedSeqRange seg(a, b); in ClipNotSupportedFlanks()
512 TSignedSeqRange segl; in RemoveNotSupportedIntronsFromProt()
516 TSignedSeqRange segr; in RemoveNotSupportedIntronsFromProt()
629 vector<TSignedSeqRange> transcript_exons; in RemoveNotSupportedIntronsFromTranscript()
674 vector<TSignedSeqRange> transcript_exons; in CleanSelfTranscript()
967 int TotalFrameShift(const TInDels& indels, TSignedSeqRange range = TSignedSeqRange::GetWhole()) { in TotalFrameShift()
2134 vector<TSignedSeqRange> transcript_exons; in FillGapsInAlignmentAndAddToGenomicGaps()
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H A Dgnomon_engine.cpp48 (CConstRef<CHMMParameters> hmm_params, CResidueVec&& sequence, TSignedSeqRange range) : m_seq(move(… in BEGIN_SCOPE()
51 (CConstRef<CHMMParameters> hmm_params, const CResidueVec& sequence, TSignedSeqRange range) : m_seq(… in SGnomonEngineImplData()
55 …:CGnomonEngine(CConstRef<CHMMParameters> hmm_params, CResidueVec&& sequence, TSignedSeqRange range) in CGnomonEngine()
64 …monEngine(CConstRef<CHMMParameters> hmm_params, const CResidueVec& sequence, TSignedSeqRange range) in CGnomonEngine()
98 m_data->m_range.IntersectWith(TSignedSeqRange(0,m_data->m_seq.size()-1)); in CheckRange()
103 void CGnomonEngine::ResetRange(TSignedSeqRange range) in ResetRange()
113 TSignedSeqRange gc_range(middle-GC_RANGE_SIZE/2, middle+GC_RANGE_SIZE/2); in ResetRange()
114 gc_range &= TSignedSeqRange(0,m_data->m_seq.size()-1); in ResetRange()
H A Dselect_alignments_alt.cpp86 TSignedSeqRange acds = a.GetCdsInfo().Cds(); in AreSimilar()
87 TSignedSeqRange bcds = b.GetCdsInfo().Cds(); in AreSimilar()
94 TSignedSeqRange intersection = a.Limits() & b.Limits(); in AreSimilar()
141 bool CModelCompare::RangeNestedInIntron(TSignedSeqRange r, const CGeneModel& algn, bool check_in_ho… in RangeNestedInIntron()
144 TSignedSeqRange intron(algn.Exons()[i-1].GetTo()+1,algn.Exons()[i].GetFrom()-1); in RangeNestedInIntron()
164 TSignedSeqRange introna(a.Exons()[i-1].GetTo()+1,a.Exons()[i].GetFrom()-1); in HaveCommonExonOrIntron()
166 TSignedSeqRange intronb(b.Exons()[j-1].GetTo()+1,b.Exons()[j].GetFrom()-1); in HaveCommonExonOrIntron()
187 TSignedSeqRange cds = cds_info.Cds(); in FilterGenes()
H A Dgnomon_engine.hpp49 …ngineImplData(CConstRef<CHMMParameters> hmm_params, CResidueVec&& sequence, TSignedSeqRange range);
50 …ImplData(CConstRef<CHMMParameters> hmm_params, const CResidueVec& sequence, TSignedSeqRange range);
55 TSignedSeqRange m_range;
H A Dgnomon_objmgr.cpp106 vector<TSignedSeqRange> transcript_exons; in CAlignModel()
212 fill_src.m_range = TSignedSeqRange(nuc_cur_start, nuc_cur_end); in CAlignModel()
361 TSignedSeqRange newlimits = m_alignmap.ShrinkToRealPoints(Limits(),is_protein); in CAlignModel()
386 TSignedSeqRange piece_range(piece_begin->GetFrom(),piece_end_g->GetTo()); in CAlignModel()
418 TSignedSeqRange start, stop; in CAlignModel()
553 CRef<CSeq_loc> s_ExonDataToLoc(const vector<TSignedSeqRange>& vec, in s_ExonDataToLoc()
559 ITERATE (vector<TSignedSeqRange>, iter, vec) { in s_ExonDataToLoc()
595 TSignedSeqRange cds_limits = igene.RealCdsLimits(); in GetAnnot()
597 vector<TSignedSeqRange> mrna_vec; in GetAnnot()
599 vector<TSignedSeqRange> cds_vec; in GetAnnot()
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H A Dparse.cpp486 …AddSupport(const TGeneModelList& align_list, TSignedSeqRange inside_range, CGeneModel& gene, TSign… in AddSupport()
578 TSignedSeqRange local_exon(pe->Start(),pe->Stop()); in GetGenes()
580 TSignedSeqRange exon = seq_map.MapRangeEditedToOrig(local_exon); in GetGenes()
645 TSignedSeqRange(m_seqscr.From(),m_seqscr.To()), in GetGenes()
648 TSignedSeqRange start, stop; in GetGenes()
658 TSignedSeqRange rf = gene_map.MapRangeOrigToEdited(reading_frame, true); in GetGenes()
659 TSignedSeqRange stt(rf.GetFrom()-3,rf.GetFrom()-1); in GetGenes()
660 TSignedSeqRange stp(rf.GetTo()+1,rf.GetTo()+3); in GetGenes()
675 TSignedSeqRange rf = gene_map.MapRangeOrigToEdited(reading_frame, true); in GetGenes()
676 TSignedSeqRange stt(rf.GetFrom()-3,rf.GetFrom()-1); in GetGenes()
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H A Dscore.cpp164 TSignedSeqRange chunk(m_chunk_start, m_chunk_stop); in ConstructSequenceAndMaps()
202 TSignedSeqRange operator() (TSignedSeqRange r, bool withextras = true) const in operator ()()
393 TSignedSeqRange chunk(m_chunk_start, m_chunk_stop); in Init()
787 TSignedSeqRange cds_lim = algn.ReadingFrame(); in Init()
976 TSignedSeqRange lim = algn.Limits(); in Init()
1157 TSignedSeqRange cds_lim = algn.ReadingFrame(); in Init()
1410 TSignedSeqRange pstop = TSignedSeqRange(*pstp,*pstp+2); in GetScore()
1532 TSignedSeqRange best_reading_frame = TSignedSeqRange(best_start+3,best_stop-1); in GetScore()
1535 cds_info.SetStart(TSignedSeqRange::GetEmpty()); in GetScore()
1537 cds_info.SetStop(TSignedSeqRange::GetEmpty()); in GetScore()
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H A Dgnomon_seq.hpp101 …(TIVec codons[], const CEResidueVec& mrna, const CAlignMap& mrnamap, TSignedSeqRange search_region…
102 …(TIVec codons[], const CEResidueVec& mrna, const CAlignMap& mrnamap, TSignedSeqRange search_region…
H A Dasn1.cpp117 …> create_packed_int_seqloc(const CGeneModel& model, TSignedSeqRange limits_on_mrna = TSignedSeqRan…
318 TSignedSeqRange tlim = model.TranscriptLimits(); in create_cdregion_feature()
353 …mplementationData::create_packed_int_seqloc(const CGeneModel& model, TSignedSeqRange limits_on_mrn… in create_packed_int_seqloc()
365 … TSignedSeqRange interval_range_on_mrna = amap.MapRangeOrigToEdited(e->Limits()) & limits_on_mrna; in create_packed_int_seqloc()
374 TSignedSeqRange interval_range = amap.MapRangeEditedToOrig(interval_range_on_mrna); in create_packed_int_seqloc()
671 TSignedSeqRange rcds_on_mrna = cds_info.MaxCdsLimits() & model.TranscriptLimits(); in create_internal_feature()
793 TSignedSeqRange transcript_exon = model.TranscriptExon(i); in AlignModelToSeqalign()
878 TSignedSeqRange tlim = model.TranscriptLimits(); in AlignModelToSeqalign()
942 TSignedSeqRange lim = GetCdsInfo().Start()+GetCdsInfo().ReadingFrame(); in MakeSeqAlign()
1082 TSignedSeqRange rf = TSignedSeqRange(cds_range.GetFrom(), cds_range.GetTo()); in RestoreModelReadingFrame()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dinternal_stops.cpp70 set<TSignedSeqRange>* gaps) in FindStartStopRanges()
223 gaps->insert(TSignedSeqRange(mapped_pos, mapped_pos2)); in FindStartStopRanges()
237 gaps->insert(TSignedSeqRange(gap_stop -9, gap_stop)); in FindStartStopRanges()
243 gaps->insert(TSignedSeqRange(gap_stop, gap_stop -9)); in FindStartStopRanges()
253 gaps->insert(TSignedSeqRange(gap_start, gap_start +9)); in FindStartStopRanges()
259 gaps->insert(TSignedSeqRange(gap_start +9, gap_start)); in FindStartStopRanges()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/
H A Dinternal_stops.hpp68 … set<TSignedSeqRange>* gaps = nullptr);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/seqalign/
H A DDense_seg.cpp318 list<TSignedSeqRange> delete_ranges; in TrimEndGaps()
343 delete_ranges.push_back(TSignedSeqRange(0, i)); in TrimEndGaps()
363 delete_ranges.push_back(TSignedSeqRange(i + 1, GetNumseg())); in TrimEndGaps()
366 list<TSignedSeqRange>::reverse_iterator iter = delete_ranges.rbegin(); in TrimEndGaps()
367 list<TSignedSeqRange>::reverse_iterator end = delete_ranges.rend(); in TrimEndGaps()
369 TSignedSeqRange r = *iter; in TrimEndGaps()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/seqalign/
H A DDense_seg.cpp318 list<TSignedSeqRange> delete_ranges; in TrimEndGaps()
343 delete_ranges.push_back(TSignedSeqRange(0, i)); in TrimEndGaps()
363 delete_ranges.push_back(TSignedSeqRange(i + 1, GetNumseg())); in TrimEndGaps()
366 list<TSignedSeqRange>::reverse_iterator iter = delete_ranges.rbegin(); in TrimEndGaps()
367 list<TSignedSeqRange>::reverse_iterator end = delete_ranges.rend(); in TrimEndGaps()
369 TSignedSeqRange r = *iter; in TrimEndGaps()

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