Searched refs:ReadingFrame (Results 1 – 10 of 10) sorted by relevance
81 if(a.ReadingFrame().NotEmpty() && b.ReadingFrame().NotEmpty()) { in AreSimilar()82 …if(!a.ReadingFrame().IntersectingWith(b.ReadingFrame()) || a.GetCdsInfo().PStops() != b.GetCdsInfo… in AreSimilar()182 if(cds_info.ReadingFrame().Empty()) in FilterGenes()
265 if(ReadingFrame().NotEmpty()) in Remap()297 if(ReadingFrame().NotEmpty()) { in MapFromEditedToOrig()343 if(ReadingFrame().NotEmpty()) { in MapFromOrigToEdited()432 if (Precede(ReadingFrame(),Stop())) in Clear5PrimeCdsLimit()558 if (ReadingFrame().Empty()) in Clip()694 if (ReadingFrame().Empty()) in CdsInvariant()742 _ASSERT( cds_info.ReadingFrame().Empty() || Include(Limits(),cds_info.ReadingFrame()) ); in CombineCdsInfo()753 if (ReadingFrame().NotEmpty()) { in CutExons()801 if (ReadingFrame().NotEmpty()) { in Clip()1279 if(align.ReadingFrame().NotEmpty()) in Extend()[all …]
185 … TSignedSeqPos x = a.ReadingFrame().NotEmpty() ? a.ReadingFrame().GetFrom() : a.Limits().GetFrom(); in operator ()()186 … TSignedSeqPos y = b.ReadingFrame().NotEmpty() ? b.ReadingFrame().GetFrom() : b.Limits().GetFrom(); in operator ()()572 pnt = align.ReadingFrame().GetFrom()-1; in Init()574 pnt = align.ReadingFrame().GetTo()+1; in Init()710 if(algn.ReadingFrame().NotEmpty()) { in Init()711 … for(TSignedSeqPos i = algn.ReadingFrame().GetFrom(); i <= algn.ReadingFrame().GetTo(); ++i) in Init()787 TSignedSeqRange cds_lim = algn.ReadingFrame(); in Init()942 if(algn.ReadingFrame().Empty()) in Init()947 int p = algn.ReadingFrame().GetFrom()-1; in Init()958 int p = algn.ReadingFrame().GetTo(); in Init()[all …]
289 left = genes.back().ReadingFrame().GetTo()+1; in Predict()433 if((*im)->ReadingFrame().NotEmpty()) { in Predict()442 if(coding_gene && ai.ReadingFrame().Empty()) in Predict()445 if(ai.ReadingFrame().NotEmpty()) in Predict()453 if(coding_gene && ai.ReadingFrame().Empty()) in Predict()457 if(ai.ReadingFrame().NotEmpty()) in Predict()523 if((*im)->ReadingFrame().NotEmpty()) { in Predict()532 if(coding_gene && ai.ReadingFrame().Empty()) in Predict()
607 …} else if(a.ReadingFrame().NotEmpty() && b.ReadingFrame().Empty()) { // coding is always bet… in DescendingModelOrder()609 } else if(b.ReadingFrame().NotEmpty() && a.ReadingFrame().Empty()) { in DescendingModelOrder()725 …} else if(algn.ReadingFrame().Empty() || gene.front()->ReadingFrame().Empty()) { // one noncoding in CheckCompatibility()2220 if(cds_info.ReadingFrame() != algn.ReadingFrame()) { in Duplicate5pendsAndShortCDSes()2266 … if(mbr.m_copy->front()->m_cds_info->ReadingFrame() == cdsinfo.ReadingFrame()) in Duplicate5pendsAndShortCDSes()2268 … } else if((*mbr.m_copy)[1]->m_cds_info->ReadingFrame() == cdsinfo.ReadingFrame()) { in Duplicate5pendsAndShortCDSes()4665 if(ReadingFrame().Empty()) in RestoreReasonableConfirmedStart()5441 if(ReadingFrame().NotEmpty()) { in ClipLowCoverageUTR()5658 if(ReadingFrame().NotEmpty()) { in CalculateDropLimits()5980 if(!ReadingFrame().Empty()) in HarborsNested()[all …]
440 if(cds_info_g.ReadingFrame().NotEmpty()) // successful projection in CAlignModel()476 if(ReadingFrame().Empty()) in GetCdsDnaSequence()637 …TFrame(1+(strand == ePlus?(igene.ReadingFrame().GetFrom()-cds_limits.GetFrom())%3:(cds_limits.GetT… in GetAnnot()
498 …if ((algn.ReadingFrame().Empty()?algn.Limits():algn.ReadingFrame()).IntersectingWith(reading_frame… in AddSupport()539 …if ((algn.ReadingFrame().Empty()?algn.Limits():algn.ReadingFrame()).IntersectingWith(reading_frame… in AddSupport()
99 is_ncrna = m.ReadingFrame().Empty(); in SModelData()678 …if (cds_info.ReadingFrame().NotEmpty() && model.GetAlignMap().MapRangeOrigToEdited(model.Limits(),… in create_internal_feature()942 TSignedSeqRange lim = GetCdsInfo().Start()+GetCdsInfo().ReadingFrame(); in MakeSeqAlign()1070 if(model.GetCdsInfo().ReadingFrame().NotEmpty()) { in RestoreModelAttributes()1073 if(cds_info_g.ReadingFrame().NotEmpty()) // successful projection in RestoreModelAttributes()
191 if (!model.ReadingFrame().Empty()) { in FindStartsStops()202 TSignedSeqRange rf = mrnamap.MapRangeOrigToEdited(model.ReadingFrame(),true); in FindStartsStops()
235 TSignedSeqRange ReadingFrame() const { return m_reading_frame; } in ReadingFrame() function in CCDSInfo237 TSignedSeqRange Cds() const { return Start()+ReadingFrame()+Stop(); } in Cds()291 if (ReadingFrame().Empty()) { in Invariant()302 _ASSERT( !Start().IntersectingWith(ReadingFrame()) ); in Invariant()303 _ASSERT( !Stop().IntersectingWith(ReadingFrame()) ); in Invariant()304 _ASSERT( ProtReadingFrame().Empty() || Include(ReadingFrame(), ProtReadingFrame()) ); in Invariant()310 if (Precede(Start(), ReadingFrame())) { in Invariant()316 _ASSERT( Include(Start()+Stop(),ReadingFrame()) ); in Invariant()319 if (Precede(ReadingFrame(),Stop())) { in Invariant()435 TSignedSeqRange ReadingFrame() const { return m_cds_info.ReadingFrame(); } in ReadingFrame() function in CGeneModel[all …]