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Searched refs:transcript_exons (Results 1 – 6 of 6) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dgnomon_objmgr.cpp106 vector<TSignedSeqRange> transcript_exons; in CAlignModel() local
224 …transcript_exons.push_back(TSignedSeqRange(exon.GetProduct_start().AsSeqPos(), exon.GetProduct_end… in CAlignModel()
226 _ASSERT(transcript_exons.back().NotEmpty()); in CAlignModel()
299 sort(transcript_exons.begin(),transcript_exons.end()); in CAlignModel()
303 reverse(transcript_exons.begin(),transcript_exons.end()); in CAlignModel()
313 _ASSERT((transcript_exons.back().GetTo()+1)%3 == 0); in CAlignModel()
314 transcript_exons.back().SetTo(transcript_exons.back().GetTo()+3); in CAlignModel()
317 _ASSERT((transcript_exons.front().GetTo()+1)%3 == 0); in CAlignModel()
318 transcript_exons.front().SetTo(transcript_exons.front().GetTo()+3); in CAlignModel()
358 m_alignmap = CAlignMap(Exons(), transcript_exons, indels, orientation, target_len ); in CAlignModel()
H A Dgnomon_seq.cpp504 …Map(const CGeneModel::TExons& exons, const vector<TSignedSeqRange>& transcript_exons, const TInDel… in CAlignMap() argument
507 _ASSERT(transcript_exons.size() == exons.size()); in CAlignMap()
508 …_ASSERT(transcript_exons.size() == 1 || (orientation == ePlus && transcript_exons.front().GetFrom(… in CAlignMap()
509 …(orientation == eMinus && transcript_exons.front().GetFrom() > transcript_exons.back().GetFrom())); in CAlignMap()
513 diff += exonlen-(transcript_exons[i].GetTo()-transcript_exons[i].GetFrom()+1); in CAlignMap()
525 …TSignedSeqPos estart = (m_orientation == ePlus) ? transcript_exons.front().GetFrom() : transcript_… in CAlignMap()
553 estart += transcript_exons[i+1].GetFrom()-transcript_exons[i].GetTo()-1; in CAlignMap()
555 estart += transcript_exons[i].GetFrom()-transcript_exons[i+1].GetTo()-1; in CAlignMap()
H A Daligncollapser.cpp629 vector<TSignedSeqRange> transcript_exons; in RemoveNotSupportedIntronsFromTranscript() local
633 transcript_exons.push_back(te); in RemoveNotSupportedIntronsFromTranscript()
674 vector<TSignedSeqRange> transcript_exons; in CleanSelfTranscript() local
675 transcript_exons.reserve(exons.size()); in CleanSelfTranscript()
690 int t = transcript_exons[ie].GetFrom(); in CleanSelfTranscript()
698 transcript_exons[ie].SetFrom(t); in CleanSelfTranscript()
705 int t = transcript_exons[ie].GetTo(); in CleanSelfTranscript()
713 transcript_exons[ie].SetTo(t); in CleanSelfTranscript()
2134 vector<TSignedSeqRange> transcript_exons; in FillGapsInAlignmentAndAddToGenomicGaps() local
2168 transcript_exons.push_back(left_texon); in FillGapsInAlignmentAndAddToGenomicGaps()
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H A Dgnomon_model.cpp236 vector<TSignedSeqRange> transcript_exons; in RecalculateAlignMap() local
240 transcript_exons.push_back(TranscriptExon(ie)); in RecalculateAlignMap()
245 transcript_exons.push_back(texon); in RecalculateAlignMap()
248 …m_alignmap = CAlignMap(Exons(), transcript_exons, FrameShifts(), Orientation(), m_alignmap.TargetL… in RecalculateAlignMap()
2253 vector<TSignedSeqRange> transcript_exons; in readGFF3() local
2318 transcript_exons.push_back(texon); in readGFF3()
2360 if(!transcript_exons.empty()) in readGFF3()
2361 …amap = CAlignMap(a.Exons(), transcript_exons, indels, a.Orientation(), NStr::StringToNumeric<int>(… in readGFF3()
H A Dchainer.cpp7671 vector<TSignedSeqRange> transcript_exons; in MapOneModelToEditedContig() local
7798 transcript_exons.push_back(texon); in MapOneModelToEditedContig()
7813 transcript_exons.push_back(align.TranscriptExon(i)); in MapOneModelToEditedContig()
7851 …CAlignMap editedamap(editedmodel.Exons(), transcript_exons, editedindels, align.Orientation(), ama… in MapOneModelToEditedContig()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp646 …CAlignMap(const CGeneModel::TExons& exons, const vector<TSignedSeqRange>& transcript_exons, const …