80 …    a.AddExon(TSignedSeqRange(ali.m_range.GetFrom(), m_introns.front().m_range.GetFrom()), fs, ss);  in GetAlignment()
91 …a.AddExon(TSignedSeqRange(m_introns[i].m_range.GetTo(), m_introns[i+1].m_range.GetFrom()), fs, ss);  in GetAlignment()
100         a.AddExon(TSignedSeqRange(m_introns.back().m_range.GetTo(), ali.m_range.GetTo()), fs, ss);  in GetAlignment()
265         if(m_range !=  TSignedSeqRange::GetWhole()) {              in InitContig()
312         m_range = TSignedSeqRange::GetWhole();  in CAlignCollapser()
365     TSignedSeqRange old_limits = align.Limits();  in ClipNotSupportedFlanks()
368         TSignedSeqRange tlim = align.TranscriptLimits();  in ClipNotSupportedFlanks()
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()
424                 TSignedSeqRange segl(align.Limits().GetFrom(),l);  in ClipNotSupportedFlanks()
427 …segl = amap.ShrinkToRealPoints(TSignedSeqRange(align.Limits().GetFrom(),max(align.Limits().GetFrom…  in ClipNotSupportedFlanks()
430                 TSignedSeqRange segr(r,align.Limits().GetTo());  in ClipNotSupportedFlanks()
433 …segr = amap.ShrinkToRealPoints(TSignedSeqRange(min(align.Limits().GetTo(),r),align.Limits().GetTo(…  in ClipNotSupportedFlanks()
449                     align.CutExons(TSignedSeqRange(segl.GetTo()+1,segr.GetFrom()-1));  in ClipNotSupportedFlanks()
470                 TSignedSeqRange seg(align.Exons()[piece_end+1].GetFrom(),align.Limits().GetTo());  in ClipNotSupportedFlanks()
473                 TSignedSeqRange seg(align.Limits().GetFrom(),align.Exons()[piece_begin-1].GetTo());  in ClipNotSupportedFlanks()
476                 TSignedSeqRange seg(a, b);  in ClipNotSupportedFlanks()
512             TSignedSeqRange segl;  in RemoveNotSupportedIntronsFromProt()
514 …segl = amap.ShrinkToRealPoints(TSignedSeqRange(align.Limits().GetFrom(),exonl.GetTo()-CUT_MARGIN),…  in RemoveNotSupportedIntronsFromProt()
516             TSignedSeqRange segr;  in RemoveNotSupportedIntronsFromProt()
518 …segr = amap.ShrinkToRealPoints(TSignedSeqRange(exonr.GetFrom()+CUT_MARGIN,align.Limits().GetTo()),…  in RemoveNotSupportedIntronsFromProt()
534                 align.CutExons(TSignedSeqRange(segl.GetTo()+1,segr.GetFrom()-1));  in RemoveNotSupportedIntronsFromProt()
560 …a.Clip(TSignedSeqRange(piece_begin->Limits().GetFrom(),piece_end->Limits().GetTo()),CGeneModel::eR…  in RemoveNotSupportedIntronsFromTranscript()
582             TSignedSeqRange new_lim(new_left,new_right);  in RemoveNotSupportedIntronsFromTranscript()
615 …TSignedSeqRange segl =  amap.ShrinkToRealPoints(TSignedSeqRange(editedmodel.Limits().GetFrom(),exo…  in RemoveNotSupportedIntronsFromTranscript()
616 …TSignedSeqRange segr = amap.ShrinkToRealPoints(TSignedSeqRange(exonr.GetFrom()+1,editedmodel.Limit…  in RemoveNotSupportedIntronsFromTranscript()
618                         editedmodel.CutExons(TSignedSeqRange(segl.GetTo()+1,segr.GetFrom()-1));   in RemoveNotSupportedIntronsFromTranscript()
629     vector<TSignedSeqRange> transcript_exons;  in RemoveNotSupportedIntronsFromTranscript()
631 …TSignedSeqRange te = amap.MapRangeOrigToEdited(e->Limits(),e->m_fsplice ? CAlignMap::eLeftEnd : CA…  in RemoveNotSupportedIntronsFromTranscript()
636     TSignedSeqRange old_limits = align.Limits();  in RemoveNotSupportedIntronsFromTranscript()
674     vector<TSignedSeqRange> transcript_exons;  in CleanSelfTranscript()
681             TSignedSeqRange& te = transcript_exons[ie];  in CleanSelfTranscript()
682             te = TSignedSeqRange(tlen-1-te.GetTo(),tlen-1-te.GetFrom());  in CleanSelfTranscript()
721     vector<TSignedSeqRange> edited_transcript_exons;  in CleanSelfTranscript()
787 …TSignedSeqRange trange(transcript_exons[piece_begin].GetFrom()+align_left-agaps, transcript_exons[…  in CleanSelfTranscript()
789             TSignedSeqRange grange = amap.MapRangeEditedToOrig(trange, false);  in CleanSelfTranscript()
820                 TSignedSeqRange t = transcript_exons[ie];  in CleanSelfTranscript()
856             TSignedSeqRange& elim = edited_exons[piece_begin].Limits();  in CleanSelfTranscript()
857             TSignedSeqRange& tlim = edited_transcript_exons[piece_begin];  in CleanSelfTranscript()
891             TSignedSeqRange& elim = edited_exons[piece_end].Limits();  in CleanSelfTranscript()
892             TSignedSeqRange& tlim = edited_transcript_exons[piece_end];  in CleanSelfTranscript()
939             TSignedSeqRange& te = edited_transcript_exons[ie];  in CleanSelfTranscript()
940             te = TSignedSeqRange(tlen-1-te.GetTo(),tlen-1-te.GetFrom());  in CleanSelfTranscript()
967 int TotalFrameShift(const TInDels& indels, TSignedSeqRange range = TSignedSeqRange::GetWhole()) {  in TotalFrameShift()
1026                 TSignedSeqRange range = k->m_range;  in FilterAlignments()
1196                 align.Clip(TSignedSeqRange(new_left,new_right),CGeneModel::eRemoveExons);  in FilterAlignments()
1279                     TSignedSeqRange new_lim = align.Limits();  in FilterAlignments()
1439     typedef pair<TSignedSeqRange,TInDels> TGapEnd;  in FilterAlignments()
1475                 TSignedSeqRange l = a.Exons().front().Limits();  in FilterAlignments()
1534                         TSignedSeqRange l(left, right);  in FilterAlignments()
1550                 TSignedSeqRange l = a.Exons().back().Limits();  in FilterAlignments()
1711 …TSignedSeqRange seg = amap.ShrinkToRealPoints(TSignedSeqRange(new_l,align.Limits().GetTo()),snap_t…  in FilterAlignments()
1713 …if(ie == 0 || amap.FShiftedLen(TSignedSeqRange(align.Limits().GetFrom(),align.Exons()[ie-1].GetTo(…  in FilterAlignments()
1716 …align.Clip(TSignedSeqRange(align.Limits().GetFrom(),align.Exons()[ie-1].GetTo()),CGeneModel::eRemo…  in FilterAlignments()
1723 …align.CutExons(TSignedSeqRange(align.Limits().GetFrom(),seg.GetFrom()-1));   // Clip() is not frie…  in FilterAlignments()
1725 …                    align.CutExons(TSignedSeqRange(align.Exons()[ie-1].GetTo()+1,seg.GetFrom()-1));  in FilterAlignments()
1783 …TSignedSeqRange seg = amap.ShrinkToRealPoints(TSignedSeqRange(align.Limits().GetFrom(),new_r),snap…  in FilterAlignments()
1785 …if(ie == (int)align.Exons().size()-1 || amap.FShiftedLen(TSignedSeqRange(align.Exons()[ie+1].GetFr…  in FilterAlignments()
1788 …align.Clip(TSignedSeqRange(align.Exons()[ie+1].GetFrom(),align.Limits().GetTo()),CGeneModel::eRemo…  in FilterAlignments()
1795 …align.CutExons(TSignedSeqRange(seg.GetTo()+1, align.Limits().GetTo()));   // Clip() is not friendl…  in FilterAlignments()
1797 …                    align.CutExons(TSignedSeqRange(seg.GetTo()+1,align.Exons()[ie+1].GetFrom()-1));  in FilterAlignments()
2044                     exons.front().Limits() = TSignedSeqRange::GetEmpty();  in GetCollapsedAlgnments()
2134     vector<TSignedSeqRange> transcript_exons;  in FillGapsInAlignmentAndAddToGenomicGaps()
2142     TSignedSeqRange left_texon, right_texon;  in FillGapsInAlignmentAndAddToGenomicGaps()
2143     TSignedSeqRange tlim = align.TranscriptLimits();  in FillGapsInAlignmentAndAddToGenomicGaps()
2147         left_texon = TSignedSeqRange(0,tlim.GetFrom()-1);  in FillGapsInAlignmentAndAddToGenomicGaps()
2154         right_texon = TSignedSeqRange(tlim.GetTo()+1,align.TargetLen()-1);  in FillGapsInAlignmentAndAddToGenomicGaps()
2169             editedmodel.AddExon(TSignedSeqRange::GetEmpty(), "XX", "XX", 1, left_seq, left_src);  in FillGapsInAlignmentAndAddToGenomicGaps()
2186 …TSignedSeqRange texon = align.GetAlignMap().MapRangeOrigToEdited(TSignedSeqRange(e.GetTo(),align.E…  in FillGapsInAlignmentAndAddToGenomicGaps()
2197                     editedmodel.AddExon(TSignedSeqRange::GetEmpty(), "XX", "XX", 1, seq, src);  in FillGapsInAlignmentAndAddToGenomicGaps()
2217             editedmodel.AddExon(TSignedSeqRange::GetEmpty(), "XX", "XX", 1, right_seq, right_src);  in FillGapsInAlignmentAndAddToGenomicGaps()
2296         TSignedSeqRange tlim = a.TranscriptLimits();  in AddAlignment()
2312                 galign.AddExon(TSignedSeqRange(pos, pos+spec_extend));  in AddAlignment()
2316                 galign.AddExon(TSignedSeqRange(pos-spec_extend, pos));  in AddAlignment()