95                                                           TSignedSeqRange& tested_range)  in TryWithoutObviouslyBadAlignments()
97     bool already_tested = Include(tested_range, TSignedSeqRange(left,right));  in TryWithoutObviouslyBadAlignments()
105         tested_range = TSignedSeqRange(left,right);  in TryWithoutObviouslyBadAlignments()
207     TSignedSeqRange tested_range;  in Predict()
320 TSignedSeqRange WalledCdsLimits(const CGeneModel& a)  in WalledCdsLimits()
325 TSignedSeqRange GetWallLimits(const CGeneModel& m)  in GetWallLimits()
332     TSignedSeqRange a = GetWallLimits(ap);  in s_AlignSeqOrder()
333     TSignedSeqRange b = GetWallLimits(bp);  in s_AlignSeqOrder()
368         TSignedSeqRange limits = GetWallLimits(*ir);  in FindPartials()
429         set<TSignedSeqRange> hosting_intervals;  in Predict()
439             TSignedSeqRange gene_lim_for_nested;  in Predict()
444                 TSignedSeqRange model_lim_for_nested = ai.Limits();  in Predict()
456                 TSignedSeqRange model_lim_for_nested = ai.Limits();  in Predict()
461                     TSignedSeqRange overlap = (model_lim_for_nested & ai.Exons()[i].Limits());  in Predict()
468 …       TSignedSeqRange hole(ai.Exons()[i-1].Limits().GetTo()+1,ai.Exons()[i].Limits().GetFrom()-1);  in Predict()
488 …  TSignedSeqRange interval(left+gene_lim_for_nested.GetFrom(),right+gene_lim_for_nested.GetFrom());  in Predict()
495         typedef map<TSignedSeqRange,TIterList> TRangeModels;  in Predict()
501 …TSignedSeqRange lim_for_nested = nested_modeli->RealCdsLimits().Empty() ? nested_modeli->Limits() …  in Predict()
503                 TSignedSeqRange hosting_interval;  in Predict()
504                 ITERATE(set<TSignedSeqRange>, ii, hosting_intervals) {  in Predict()
505                     TSignedSeqRange interval = *ii;  in Predict()
529                         TSignedSeqRange finished_interval;  in Predict()
561             TSignedSeqRange hosting_interval = i->first;  in Predict()
613         TSignedSeqRange cds = model.RealCdsLimits();  in Predict()
681         TSignedSeqRange fullcds = cds_info.Cds();  in Predict()
746             TSignedSeqRange new_lim(m.Limits());  in transform_model()