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Searched refs:Exons (Results 1 – 25 of 77) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dselect_alignments_alt.cpp65 if(a.Exons()[i-1].GetTo() == b.Exons()[j-1].GetTo()) in CountCommonSplices()
67 if(a.Exons()[i].GetFrom() == b.Exons()[j].GetFrom() ) in CountCommonSplices()
99 while(amin < (int)a.Exons().size() && a.Exons()[amin].GetTo() < mutual_min) ++amin; in AreSimilar()
102 int amax = (int)a.Exons().size()-1; in AreSimilar()
107 while(bmin < (int)b.Exons().size() && b.Exons()[bmin].GetTo() < mutual_min) ++bmin; in AreSimilar()
117 …if (amin != 0 || size_t(amax) != a.Exons().size()-1 || bmin != 0 || size_t(bmax) != b.Exons().size… in AreSimilar()
143 if(check_in_holes || (algn.Exons()[i-1].m_ssplice && algn.Exons()[i].m_fsplice)) { in RangeNestedInIntron()
144 TSignedSeqRange intron(algn.Exons()[i-1].GetTo()+1,algn.Exons()[i].GetFrom()-1); in RangeNestedInIntron()
158 if(a.Exons()[i] == b.Exons()[j]) in HaveCommonExonOrIntron()
164 TSignedSeqRange introna(a.Exons()[i-1].GetTo()+1,a.Exons()[i].GetFrom()-1); in HaveCommonExonOrIntron()
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H A Dgnomon_model.cpp125 _ASSERT(Exons().size() > 1 && Exons()[1].Limits().NotEmpty()); in TranscriptLimits()
131 _ASSERT(Exons().size() > 1 && Exons()[Exons().size()-2].Limits().NotEmpty()); in TranscriptLimits()
132 … r = amap.MapOrigToEdited(Exons()[Exons().size()-2].GetTo()) + Exons().back().m_seq.length(); in TranscriptLimits()
138 _ASSERT(Exons().size() > 1 && Exons()[1].Limits().NotEmpty()); in TranscriptLimits()
144 _ASSERT(Exons().size() > 1 && Exons()[Exons().size()-2].Limits().NotEmpty()); in TranscriptLimits()
145 … l = amap.MapOrigToEdited(Exons()[Exons().size()-2].GetTo()) - Exons().back().m_seq.length(); in TranscriptLimits()
166 …if(Exons()[i].m_fsplice && Exons()[i-1].m_ssplice && Exons()[i].m_fsplice_sig != "XX" && Exons()[i… in isNMD()
173 …if(Exons()[i].m_ssplice && Exons()[i+1].m_fsplice && Exons()[i].m_ssplice_sig != "XX" && Exons()[i… in isNMD()
669 bool hole = !Exons()[i-1].m_ssplice || !Exons()[i].m_fsplice; in RemoveShortHolesAndRescore()
670 int intron = Exons()[i].GetFrom()-Exons()[i-1].GetTo()-1; in RemoveShortHolesAndRescore()
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H A Daligncollapser.cpp462 … for( ; piece_end < (int)align.Exons().size() && align.Exons()[piece_end].m_ssplice; ++piece_end); in ClipNotSupportedFlanks()
573 for(int k = (int)a.Exons().size()-1; k > 0 && a.Exons()[k-1].GetTo() > new_left; --k) { in RemoveNotSupportedIntronsFromTranscript()
1376 if(reversed.Exons().size() > align.Exons().size()) { in FilterAlignments()
1383 if(!align.Exons().empty()) in FilterAlignments()
1465 if(editedalign.Exons().size() > align.Exons().size()) { in FilterAlignments()
1486 … l.SetTo(min(a.Exons()[ie+1].GetTo(),a.Exons()[ie+1].GetFrom()+DESIRED_CHUNK-len-1)); in FilterAlignments()
1494 if(editedalign.Exons().size() > a.Exons().size()) { in FilterAlignments()
1501 if((!align.Exons()[ie].m_ssplice || !align.Exons()[ie+1].m_fsplice) && in FilterAlignments()
1539 if(editedalign.Exons().size() > a.Exons().size()) { in FilterAlignments()
1569 if(editedalign.Exons().size() > a.Exons().size()) { in FilterAlignments()
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H A Dchainer.cpp481 if(b.Exons()[i-1].m_ssplice && b.Exons()[i].m_fsplice) { in IsAllowedAlternative()
489 …if(a.Exons()[i-1].m_ssplice && a.Exons()[i].m_fsplice && a.Exons()[i-1].m_ssplice_sig != "XX" && a… in IsAllowedAlternative()
2380 …if(aj.Exons()[j].GetTo() != ai.Exons()[fex+j].GetTo() || aj.Exons()[j+1].GetFrom() != ai.Exons()[f… in CanIncludeJinI()
2630 if(ai.Exons()[i-1].m_ssplice && ai.Exons()[i].m_fsplice) { in LRIinit()
4423 if(Exons()[i-1].m_ssplice && Exons()[i].m_fsplice) in CalculateSupportAndWeightFromMembers()
4478 if(!Exons()[i-1].m_ssplice || !Exons()[i].m_fsplice) { in CalculateSupportAndWeightFromMembers()
4707 if(!Exons()[i-1].m_ssplice || !Exons()[i].m_fsplice) in RestoreReasonableConfirmedStart()
5491 …if(align.Exons()[i-1].m_ssplice && align.Exons()[i].m_fsplice && align.Exons()[i-1].m_ssplice_sig … in ClipLowCoverageUTR()
5541 if(Exons()[i-1].m_ssplice && Exons()[i].m_fsplice) { in ClipLowCoverageUTR()
8207 if(!m.Exons()[i-1].m_ssplice || !m.Exons()[i].m_fsplice) in model_predicate()
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H A Dscore.cpp243 if (!align.Exons()[i-1].m_ssplice || !align.Exons()[i].m_fsplice) { in CSeqScores()
244 int hole_len = align.Exons()[i].GetFrom()-align.Exons()[i-1].GetTo()-1; in CSeqScores()
256 … a.AddExon(TSignedSeqRange(align.Exons()[i-1].GetTo(),align.Exons()[i].GetFrom())); in CSeqScores()
638 if(algn.Exons()[k-1].m_ssplice) in Init()
644 if(algn.Exons()[k].m_fsplice) in Init()
665 if(algn.Exons()[k].m_fsplice) in Init()
673 if(algn.Exons()[k-1].m_ssplice && algn.Exons()[k].m_fsplice) in Init()
946 … if(algn.Exons().front().m_fsplice_sig == "XX" || algn.Exons().front().m_ssplice_sig == "XX") { in Init()
957 if(algn.Exons().back().m_fsplice_sig == "XX" || algn.Exons().back().m_ssplice_sig == "XX") { in Init()
980 if(algn.Exons()[k-1].m_ssplice && algn.Exons()[k].m_fsplice) continue; in Init()
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H A Dannot.cpp460 for(int i = 0; i < (int)ai.Exons().size(); ++i) { in Predict()
461 TSignedSeqRange overlap = (model_lim_for_nested & ai.Exons()[i].Limits()); in Predict()
466 for(int i = 1; i < (int)ai.Exons().size(); ++i) { in Predict()
467 if(!ai.Exons()[i-1].m_ssplice || !ai.Exons()[i].m_fsplice) { in Predict()
468 … TSignedSeqRange hole(ai.Exons()[i-1].Limits().GetTo()+1,ai.Exons()[i].Limits().GetFrom()-1); in Predict()
619 ITERATE(CGeneModel::TExons, ie, model.Exons()) { in Predict()
748 _ASSERT(m.Exons().front().Limits().GetLength() > left); in transform_model()
752 _ASSERT(m.Exons().back().Limits().GetLength() > right); in transform_model()
H A Dasn1.cpp361 for (size_t i=0; i < model.Exons().size(); ++i) { in create_packed_int_seqloc()
362 const CModelExon* e = &model.Exons()[i]; in create_packed_int_seqloc()
381 …if (i < model.Exons().size()-1 && (!e->m_ssplice || (model.Exons()[i+1].Limits().Empty() && extend… in create_packed_int_seqloc()
469 for(int i = 1; i < (int)model.Exons().size() && !ggap; ++i) { in ModelMethod()
470 ggap = model.Exons()[i-1].m_ssplice_sig == "XX" || model.Exons()[i].m_fsplice_sig == "XX"; in ModelMethod()
788 for (size_t i=0; i < model.Exons().size(); ++i) { in AlignModelToSeqalign()
789 const CModelExon *e = &model.Exons()[i]; in AlignModelToSeqalign()
887 for(int e = 0; e < (int)model.Exons().size(); ++e) { in AlignModelToSeqalign()
888 if(model.Exons()[e].Limits().Empty()) in AlignModelToSeqalign()
890 if(e > 0 && !model.Exons()[e].m_fsplice) { in AlignModelToSeqalign()
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H A Dgnomon_objmgr.cpp358 m_alignmap = CAlignMap(Exons(), transcript_exons, indels, orientation, target_len ); in CAlignModel()
366 …for (CGeneModel::TExons::const_iterator piece_begin = Exons().begin(); piece_begin != Exons().end(… in CAlignModel()
376 … for (piece_end = piece_begin; piece_end != Exons().end() && piece_end->m_ssplice; ++piece_end) ; in CAlignModel()
377 _ASSERT( piece_end != Exons().end() ); in CAlignModel()
598 copy(igene.Exons().begin(), igene.Exons().end(), back_inserter(mrna_vec)); in GetAnnot()
H A Dparse.cpp516 if (!support.Exons().empty()) { in AddSupport()
600 CAlignMap localmap(local_gene.Exons(), local_gene.FrameShifts(), local_gene.Strand()); in GetGenes()
H A Dvariations.cpp200 for(int i = 0; i < (int)align.Exons().size(); ++i) { in AddAlignment()
201 TSignedSeqRange exon_lim = align.Exons()[i].Limits(); in AddAlignment()
/dports/biology/sim4/sim4.2003-09-21/
H A Dsim4.init.c130 Exon *Exons=NULL, *rev_Exons=NULL; in main() local
258 in_H,&dist,&xpT,&xpA,&Exons,&st): in main()
260 in_H,&dist,&xpT,&xpA,&Exons,&st); in main()
274 in_H,&dist,&xpT,&xpA,&Exons,&st): in main()
301 if (Exons) { free_list(Exons); Exons = NULL; } in main()
307 add_offset_exons(Exons, pT); in main()
323 if (Exons) (void)printf("\n"); in main()
324 print_exons(Exons); in main()
375 if (Exons) (void)printf("\n"); in main()
399 if (Exons) (void)printf("\n"); in main()
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H A Dpoly.c97 void remove_poly(struct edit_script_list **Script, Exon *Exons, uchar *s1, uchar *s2, int len2, int… in remove_poly() argument
99 remove_polyT_front(Script, Exons, s1, s2, pT); in remove_poly()
100 remove_polyA_back(Script, Exons, s1, s2, len2, pA); in remove_poly()
113 if (!Exons || ! Exons->next_exon || ! Exons->next_exon->to1) return; in remove_polyA_back()
122 exons_tail = Exons->next_exon; prev = Exons; in remove_polyA_back()
135 trim_polyA_align(Sptr,Exons,&exons_tail,t->from2,lastA,s1,s2); in remove_polyA_back()
145 trim_polyA_align(Sptr,Exons,&exons_tail,ct_pA,lastA,s1,s2); in remove_polyA_back()
269 static void remove_polyT_front(struct edit_script_list **Sptr, Exon *Exons, uchar *s1, uchar *s2, i… in remove_polyT_front() argument
276 if (!Exons || !Exons->next_exon || !Exons->next_exon->to1) return; in remove_polyT_front()
284 exons_head = Exons->next_exon; trim_p = TRUE; in remove_polyT_front()
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/dports/biology/emboss/EMBOSS-6.6.0/ajax/ensembl/
H A Denstranscript.c516 if (transcript->Exons && ajListGetLength(transcript->Exons)) in ensTranscriptNewCpy()
532 pthis->Exons = NULL; in ensTranscriptNewCpy()
840 if (newtranscript->Exons) in transcriptNewCpyFeatures()
1094 ajListFree(&pthis->Exons); in ensTranscriptDel()
1835 if (transcript->Exons) in ensTranscriptLoadExons()
1856 return transcript->Exons; in ensTranscriptLoadExons()
2395 if (transcript->Exons) in ensTranscriptSetFeature()
2977 if (!transcript->Exons) in ensTranscriptAddExon()
3437 if (transcript->Exons) in ensTranscriptTrace()
3897 if (transcript->Exons) in ensTranscriptCalculateMemsize()
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H A Densdata.h1697 AjPList Exons; member
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp406 const TExons& Exons() const { return m_exons; } in Exons() function in CGeneModel
496 for(unsigned int i = 1; i < Exons().size(); ++i) in Continuous()
497 if (!Exons()[i-1].m_ssplice || !Exons()[i].m_fsplice) in Continuous()
560 …{ return Strand()==a.Strand() && Limits()==a.Limits() && Exons() == a.Exons() && FrameShifts()==a.… in IdenticalAlign()
897 for(unsigned int i = 1; i < algn.Exons().size(); ++i) { in GetAlignParts()
898 if (!algn.Exons()[i-1].m_ssplice || !algn.Exons()[i].m_fsplice) { in GetAlignParts()
902 m.Clip(TSignedSeqRange(left,algn.Exons()[i-1].GetTo()),CGeneModel::eRemoveExons); in GetAlignParts()
908 left = algn.Exons()[i].GetFrom(); in GetAlignParts()
/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/PerlLib/
H A DGTF.pm25 my $gtf = bless {Genes => [], Transcripts => [], Exons => [], CDS => [],
443 $_->{Exons} = [] for (@{$gtf->transcripts});
2938 $tx->{Exons} = [];
2988 push @{$tx->{Exons}}, $feature;
2989 $tx->{Exons} = [sort {$a->start <=> $b->start} @{$tx->{Exons}}];
3095 return $tx->{Exons};
3204 foreach my $exon (@{$tx->{Exons}}){
3212 $tx->{Exons} = $new_exons;
/dports/biology/bedtools/bedtools2-2.30.0/docs/content/tools/
H A Dbamtobed.rst155 Exons *************** **********
/dports/textproc/link-grammar/link-grammar-5.8.0/data/en/
H A Dcorpus-biolg.batch59 Exons 40 to 50 were examined
85 Exons 40 -- 50 were examined
/dports/biology/bedtools/bedtools2-2.30.0/docs/content/
H A Dexample-usage.rst218 Remove introns from gene features. Exons will (should) be reported.
/dports/databases/tile38/tile38-1.12.0/vendor/google.golang.org/genproto/googleapis/genomics/v1/
H A Dannotations.pb.go805 Exons []*Transcript_Exon `protobuf:"bytes,2,rep,name=exons" json:"exons,omitempty"` member
836 return m.Exons
/dports/biology/wise/wise2.4.1/src/models/
H A Dgeneutil.dy604 * Exons can start in INSERTs (yuk). In which case we don't
988 while( alc != NULL ) { /* while loop goes over all coding Exons */
/dports/databases/prometheus-postgresql-adapter/prometheus-postgresql-adapter-0.6.0/vendor/google.golang.org/genproto/googleapis/genomics/v1/
H A Dannotations.pb.go735 Exons []*Transcript_Exon `protobuf:"bytes,2,rep,name=exons,proto3" json:"exons,omitempty"` member
789 return m.Exons
/dports/audio/murmur-cli/murmur-cli-8f83169/vendor/google.golang.org/genproto/googleapis/genomics/v1/
H A Dannotations.pb.go735 Exons []*Transcript_Exon `protobuf:"bytes,2,rep,name=exons,proto3" json:"exons,omitempty"` member
789 return m.Exons
/dports/databases/cayley/cayley-0.7.5-2-gcf576ba/vendor/google.golang.org/genproto/googleapis/genomics/v1/
H A Dannotations.pb.go735 Exons []*Transcript_Exon `protobuf:"bytes,2,rep,name=exons,proto3" json:"exons,omitempty"` member
789 return m.Exons
/dports/sysutils/go-wtf/wtf-0.21.0/vendor/google.golang.org/genproto/go-genproto-eb59cef1c072/googleapis/genomics/v1/
H A Dannotations.pb.go735 Exons []*Transcript_Exon `protobuf:"bytes,2,rep,name=exons,proto3" json:"exons,omitempty"` member
789 return m.Exons

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