/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
H A D | select_alignments_alt.cpp | 65 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() [all …]
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H A D | gnomon_model.cpp | 125 _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() [all …]
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H A D | aligncollapser.cpp | 462 … 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() [all …]
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H A D | chainer.cpp | 481 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() [all …]
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H A D | score.cpp | 243 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() [all …]
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H A D | annot.cpp | 460 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()
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H A D | asn1.cpp | 361 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() [all …]
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H A D | gnomon_objmgr.cpp | 358 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()
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H A D | parse.cpp | 516 if (!support.Exons().empty()) { in AddSupport() 600 CAlignMap localmap(local_gene.Exons(), local_gene.FrameShifts(), local_gene.Strand()); in GetGenes()
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H A D | variations.cpp | 200 for(int i = 0; i < (int)align.Exons().size(); ++i) { in AddAlignment() 201 TSignedSeqRange exon_lim = align.Exons()[i].Limits(); in AddAlignment()
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/dports/biology/sim4/sim4.2003-09-21/ |
H A D | sim4.init.c | 130 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() [all …]
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H A D | poly.c | 97 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() [all …]
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/dports/biology/emboss/EMBOSS-6.6.0/ajax/ensembl/ |
H A D | enstranscript.c | 516 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() [all …]
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H A D | ensdata.h | 1697 AjPList Exons; member
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
H A D | gnomon_model.hpp | 406 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()
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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/PerlLib/ |
H A D | GTF.pm | 25 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;
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/dports/biology/bedtools/bedtools2-2.30.0/docs/content/tools/ |
H A D | bamtobed.rst | 155 Exons *************** **********
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/dports/textproc/link-grammar/link-grammar-5.8.0/data/en/ |
H A D | corpus-biolg.batch | 59 Exons 40 to 50 were examined 85 Exons 40 -- 50 were examined
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/dports/biology/bedtools/bedtools2-2.30.0/docs/content/ |
H A D | example-usage.rst | 218 Remove introns from gene features. Exons will (should) be reported.
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/dports/databases/tile38/tile38-1.12.0/vendor/google.golang.org/genproto/googleapis/genomics/v1/ |
H A D | annotations.pb.go | 805 Exons []*Transcript_Exon `protobuf:"bytes,2,rep,name=exons" json:"exons,omitempty"` member 836 return m.Exons
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/dports/biology/wise/wise2.4.1/src/models/ |
H A D | geneutil.dy | 604 * Exons can start in INSERTs (yuk). In which case we don't 988 while( alc != NULL ) { /* while loop goes over all coding Exons */
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/dports/databases/prometheus-postgresql-adapter/prometheus-postgresql-adapter-0.6.0/vendor/google.golang.org/genproto/googleapis/genomics/v1/ |
H A D | annotations.pb.go | 735 Exons []*Transcript_Exon `protobuf:"bytes,2,rep,name=exons,proto3" json:"exons,omitempty"` member 789 return m.Exons
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/dports/audio/murmur-cli/murmur-cli-8f83169/vendor/google.golang.org/genproto/googleapis/genomics/v1/ |
H A D | annotations.pb.go | 735 Exons []*Transcript_Exon `protobuf:"bytes,2,rep,name=exons,proto3" json:"exons,omitempty"` member 789 return m.Exons
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/dports/databases/cayley/cayley-0.7.5-2-gcf576ba/vendor/google.golang.org/genproto/googleapis/genomics/v1/ |
H A D | annotations.pb.go | 735 Exons []*Transcript_Exon `protobuf:"bytes,2,rep,name=exons,proto3" json:"exons,omitempty"` member 789 return m.Exons
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/dports/sysutils/go-wtf/wtf-0.21.0/vendor/google.golang.org/genproto/go-genproto-eb59cef1c072/googleapis/genomics/v1/ |
H A D | annotations.pb.go | 735 Exons []*Transcript_Exon `protobuf:"bytes,2,rep,name=exons,proto3" json:"exons,omitempty"` member 789 return m.Exons
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