/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/ |
H A D | GencodeGtfTranscriptFeature.java | 38 private final List<GencodeGtfUTRFeature> utrs = new ArrayList<>(); field in GencodeGtfTranscriptFeature 59 return utrs; in getUtrs() 62 public void addUtr( final GencodeGtfUTRFeature utr ) { utrs.add(utr); } in addUtr() 77 for ( final GencodeGtfUTRFeature feature : utrs ) { in getAllFeatures() 105 (!Objects.equals(utrs, otherTranscript.utrs)) ) { in equals() 117 result = 31 * result + (utrs != null ? utrs.hashCode() : 0); in hashCode()
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/genebuilder/ |
H A D | GeneComponentTree.java | 173 List utrs = new Vector(); in createNodes() local 175 utrs.addAll(utrs3); in createNodes() 177 utrs.addAll(utrs5); in createNodes() 179 utrs.addAll(others); in createNodes() 181 for(int j=0; j<utrs.size(); j++) in createNodes() 183 Feature utr = (Feature)utrs.get(j); in createNodes()
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H A D | BasicGeneViewerPanel.java | 672 final List<Feature> utrs = new Vector<Feature>(); in getFeatureAt() local 674 utrs.addAll(utr_3); in getFeatureAt() 676 utrs.addAll(utr_5); in getFeatureAt() 678 for (int j = 0; j < utrs.size(); j++) in getFeatureAt() 680 Feature utr = (Feature) utrs.get(j); in getFeatureAt()
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H A D | GeneViewerPanel.java | 878 final List utrs = new Vector(); in getFeatureAt() local 880 utrs.addAll(utr_3); in getFeatureAt() 882 utrs.addAll(utr_5); in getFeatureAt() 884 for(int j = 0; j < utrs.size(); j++) in getFeatureAt() 886 Feature utr = (Feature) utrs.get(j); in getFeatureAt()
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/dports/biology/p5-Bio-Graphics/Bio-Graphics-2.40/lib/Bio/Graphics/Glyph/ |
H A D | processed_transcript.pm | 17 my ($exons,$utrs,$cds); 20 $utrs++ if $_->feature->type =~ /utr$/i; 22 $self->configure(implied_utrs=>1) if $exons && $cds && !$utrs; 23 $self->configure(adjust_exons=>1) if $exons && $utrs;
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqIO/ |
H A D | tigr.pm | 1168 my($self, $tu, $end5, $end3, $utrs) = @_; 1180 $self->_process_left_utr($tu, $end5, $end3, $utrs); 1182 $self->_process_right_utr($tu, $end5, $end3, $utrs); 1184 $self->_process_ext_utr($tu, $end5, $end3, $utrs); 1193 return $utrs; 1200 my($self, $tu, $end5, $end3, $utrs) = @_; 1215 push(@$utrs, Bio::SeqFeature::Generic->new( 1236 my($self, $tu, $end5, $end3, $utrs) = @_; 1253 push(@$utrs, Bio::SeqFeature::Generic->new( 1274 my($self, $tu, $end5, $end3, $utrs) = @_; [all …]
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/io/ |
H A D | ChadoCanonicalGene.java | 727 List<Feature> utrs = get5UtrOfTranscript(transcript_name); in isFirstUtr() local 728 if (utrs.size() == 1) in isFirstUtr() 731 for (Feature utr : utrs) in isFirstUtr() 746 List<Feature> utrs = get3UtrOfTranscript(transcript_name); in isFirstUtr() local 747 if (utrs.size() == 1) in isFirstUtr() 750 for (Feature utr : utrs) in isFirstUtr() 1212 List<Feature> utrs = enum_utr.nextElement(); in getFeatureFromHash() local 1214 for(int i=0; i<utrs.size(); i++) in getFeatureFromHash() 1216 Feature utr = utrs.get(i); in getFeatureFromHash()
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H A D | PublicDBDocumentEntry.java | 350 List<Feature> utrs; in joinUtrs() local 353 utrs = gene.get5UtrOfTranscript(transcriptName); in joinUtrs() 355 utrs = gene.get3UtrOfTranscript(transcriptName); in joinUtrs() 357 if(utrs.size() > 1) in joinUtrs() 361 for(int i=0; i<utrs.size(); i++) in joinUtrs() 363 Feature utr = utrs.get(i); in joinUtrs()
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqFeature/Gene/ |
H A D | GeneStructure.pm | 344 sub utrs { subroutine 350 push(@feas, $tr->utrs(@args));
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H A D | Transcript.pm | 362 sub utrs { subroutine 582 foreach $elem ($self->utrs('utr5prime')) { 587 foreach $elem ($self->utrs('utr3prime')) {
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H A D | GeneStructureI.pm | 197 sub utrs { subroutine
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H A D | TranscriptI.pm | 174 sub utrs { subroutine
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/dports/biology/wise/wise2.4.1/src/models/ |
H A D | geneoutput.dy | 116 fprintf(ofp," -[no]geneutr show gene structure with utrs (default no)\n");
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/SeqFeature/ |
H A D | Gene.t | 114 is($gene->utrs, 2, 'has 2 UTRs');
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/dports/www/mediawiki136/mediawiki-1.36.3/vendor/wikimedia/parsoid/tests/phpunit/Parsoid/Config/Api/data/ |
H A D | siteinfo.reqdata | 2 …//usability.wikimedia.org/wiki/$1","protorel":false},{"prefix":"utrs","url":"https://utrs.wmflabs.…
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/dports/www/mediawiki135/mediawiki-1.35.5/vendor/wikimedia/parsoid/tests/phpunit/Parsoid/Config/Api/data/ |
H A D | siteinfo.reqdata | 2 …//usability.wikimedia.org/wiki/$1","protorel":false},{"prefix":"utrs","url":"https://utrs.wmflabs.…
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/dports/www/mediawiki137/mediawiki-1.37.1/vendor/wikimedia/parsoid/tests/phpunit/Parsoid/Config/Api/data/ |
H A D | siteinfo.reqdata | 2 …//usability.wikimedia.org/wiki/$1","protorel":false},{"prefix":"utrs","url":"https://utrs.wmflabs.…
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/dports/biology/bedtools/bedtools2-2.30.0/docs/content/ |
H A D | history.rst | 461 $ tagBam -i aln.bam -files exons.bed introns.bed cpg.bed utrs.bed \
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