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Searched refs:utrs (Results 1 – 18 of 18) sorted by relevance

/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/codecs/gtf/
H A DGencodeGtfTranscriptFeature.java38 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()
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/genebuilder/
H A DGeneComponentTree.java173 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()
H A DBasicGeneViewerPanel.java672 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()
H A DGeneViewerPanel.java878 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()
/dports/biology/p5-Bio-Graphics/Bio-Graphics-2.40/lib/Bio/Graphics/Glyph/
H A Dprocessed_transcript.pm17 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 && $utrs;
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqIO/
H A Dtigr.pm1168 my($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 …]
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/io/
H A DChadoCanonicalGene.java727 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()
H A DPublicDBDocumentEntry.java350 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()
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqFeature/Gene/
H A DGeneStructure.pm344 sub utrs { subroutine
350 push(@feas, $tr->utrs(@args));
H A DTranscript.pm362 sub utrs { subroutine
582 foreach $elem ($self->utrs('utr5prime')) {
587 foreach $elem ($self->utrs('utr3prime')) {
H A DGeneStructureI.pm197 sub utrs { subroutine
H A DTranscriptI.pm174 sub utrs { subroutine
/dports/biology/wise/wise2.4.1/src/models/
H A Dgeneoutput.dy116 fprintf(ofp," -[no]geneutr show gene structure with utrs (default no)\n");
/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/SeqFeature/
H A DGene.t114 is($gene->utrs, 2, 'has 2 UTRs');
/dports/www/mediawiki136/mediawiki-1.36.3/vendor/wikimedia/parsoid/tests/phpunit/Parsoid/Config/Api/data/
H A Dsiteinfo.reqdata2 …//usability.wikimedia.org/wiki/$1","protorel":false},{"prefix":"utrs","url":"https://utrs.wmflabs.…
/dports/www/mediawiki135/mediawiki-1.35.5/vendor/wikimedia/parsoid/tests/phpunit/Parsoid/Config/Api/data/
H A Dsiteinfo.reqdata2 …//usability.wikimedia.org/wiki/$1","protorel":false},{"prefix":"utrs","url":"https://utrs.wmflabs.…
/dports/www/mediawiki137/mediawiki-1.37.1/vendor/wikimedia/parsoid/tests/phpunit/Parsoid/Config/Api/data/
H A Dsiteinfo.reqdata2 …//usability.wikimedia.org/wiki/$1","protorel":false},{"prefix":"utrs","url":"https://utrs.wmflabs.…
/dports/biology/bedtools/bedtools2-2.30.0/docs/content/
H A Dhistory.rst461 $ tagBam -i aln.bam -files exons.bed introns.bed cpg.bed utrs.bed \