/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/AlignIO/ |
H A D | arp.t | 34 my ($ann) = $coll->get_Annotations('Samples'); 39 is(($coll->get_Annotations('DataType'))[0]->value,'DNA'); 40 is(($coll->get_Annotations('MissingData'))[0]->value,'?'); 54 ($ann) = $coll->get_Annotations('Samples'); 59 is(($coll->get_Annotations('DataType'))[0]->value, 'DNA'); 60 is(($coll->get_Annotations('SampleSize'))[0]->value, 6); 70 ($ann) = $coll->get_Annotations('Samples'); 75 is(($coll->get_Annotations('DataType'))[0]->value, 'DNA'); 76 is(($coll->get_Annotations('SampleSize'))[0]->value, 8); 86 ($ann) = $coll->get_Annotations('Samples'); [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Annotation/ |
H A D | Collection.pm | 160 sub get_Annotations{ subroutine 277 } $self->get_Annotations(@keys); 405 my @anns = $self->get_Annotations(@keys); 469 foreach my $ann ($self->get_Annotations()) { 502 foreach my $ann ($obj->get_Annotations()) { 536 $tree->{$key} = [$self->get_Annotations($key)]; 599 my ($desc) = $self->get_Annotations('description'); 646 my @gene = $self->get_Annotations('gene_name'); 695 return $self->get_Annotations('reference'); 737 return $self->get_Annotations('comment'); [all …]
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/dports/biology/p5-Bio-FeatureIO/Bio-FeatureIO-1.6.905/lib/Bio/SeqFeature/ |
H A D | Annotated.pm | 313 my @values = $adaptor->get_Annotations($key); 405 return ($self->get_Annotations('seq_id'))[0]->value; 454 return $self->get_Annotations('type'); 485 unless ($self->get_Annotations('source')) { 488 return $self->get_Annotations('source'); 523 return ($self->get_Annotations('score'))[0]->display_text; 557 return ($self->get_Annotations('phase'))[0]->value; 592 return ($self->get_Annotations('frame'))[0]->value; 1068 sub get_Annotations { subroutine 1071 my @annotations = $self->annotation->get_Annotations(@_); [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/SeqIO/ |
H A D | kegg.t | 29 is(($kegg->annotation->get_Annotations('description'))[0]->text, 32 is(($kegg->annotation->get_Annotations('pathway'))[0]->text, 36 $kegg->annotation->get_Annotations('dblink'))[0]->comment, 40 $kegg->annotation->get_Annotations('dblink'))[0]->primary_id, 43 is( ($kegg->annotation->get_Annotations('aa_seq'))[0]->text, 46 is( ($kegg->annotation->get_Annotations('position'))[0]->text, '1:join(26813..26932,50794..50905,52…
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H A D | bsml.t | 23 my @refs = $seq->annotation->get_Annotations('reference'); 36 is($seq->annotation->get_Annotations('reference'), 2, 'get_Annotations reference'); 37 is($seq->annotation->get_Annotations('dblink'), 2, 'get_Annotations dblink');
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H A D | locuslink.t | 36 foreach my $ann ($seq->annotation->get_Annotations($k)) { 54 my @dblinks = $seqs[0]->annotation->get_Annotations('dblink'); 74 my ($cmt) = $ac->get_Annotations('comment'); 78 foreach ($ac->get_Annotations('PRODUCT')) { 86 foreach my $ann ($ac->get_Annotations($k)) {
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H A D | swiss.t | 25 my @gns = $seq->annotation->get_Annotations('gene_name'); 45 my ($ann) = $seq->annotation->get_Annotations('seq_update'); 60 my @gns2 = $seq->annotation->get_Annotations('gene_name'); 68 my @refs = $seq->annotation->get_Annotations('reference'); 74 ($ann) = $seq->annotation->get_Annotations('seq_update'); 98 ($ann) = $as->annotation->get_Annotations('seq_update'); 105 ($ann) = $as->annotation->get_Annotations('evidence'); 131 ($ann) = $seq->annotation->get_Annotations('seq_update'); 140 ($ann) = $seq->annotation->get_Annotations('gene_name'); 193 ($ann) = $seq->annotation->get_Annotations("gene_name"); [all …]
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H A D | bsml_sax.t | 24 my @refs = $seq->annotation->get_Annotations('reference'); 37 is($seq->annotation->get_Annotations('reference'),2); 38 is($seq->annotation->get_Annotations('dblink'),2);
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H A D | table.t | 133 my @anns = $seq->annotation->get_Annotations(); 136 } $seq->annotation->get_Annotations("Pseudogene?"); 155 my ($protann) = $seq->annotation->get_Annotations("Protein"); 161 } $seq->annotation->get_Annotations("Novelty"); 163 @anns = $seq->annotation->get_Annotations("Subfamily"); 165 @anns = $seq->annotation->get_Annotations("Family");
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H A D | Handler.t | 63 my @dblinks = $ac->get_Annotations('dblink'); 144 my @refs = $seq->annotation->get_Annotations('reference'); 276 my $reference = ($ac->get_Annotations('reference') )[0]; 308 $reference = ($ac->get_Annotations('reference') )[0]; 447 my @values = $ac->get_Annotations($key); 664 $reference = ($ac->get_Annotations('reference') )[1]; 667 my $cmmnt = ($ac->get_Annotations('comment') )[0]; 752 @refs = $seq->annotation->get_Annotations('reference'); 782 ($ann) = $as->annotation->get_Annotations('seq_update'); 821 ($ann) = $seq->annotation->get_Annotations('gene_name'); [all …]
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H A D | seqxml.t | 60 my ($source) = $seq_obj->get_Annotations('source'); 69 my @dblinks = $seq_obj->get_Annotations('dblink'); 76 my @annotations = $seq_obj->get_Annotations(); 134 my ($new_source) = $new_seqobj->get_Annotations('source'); 144 my @dblinks = $new_seqobj->get_Annotations('dblink'); 151 my @annotations = $new_seqobj->get_Annotations();
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H A D | SeqBuilder.t | 27 ok $seq->annotation->get_Annotations; 53 $seq->annotation->get_Annotations), 0; 82 ok scalar($seq->annotation->get_Annotations); 127 ok scalar($seq->annotation->get_Annotations);
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H A D | genbank.t | 63 my @dblinks = $ac->get_Annotations('dblink'); 144 my @refs = $seq->annotation->get_Annotations('reference'); 278 my $reference = ($ac->get_Annotations('reference') )[0]; 310 $reference = ($ac->get_Annotations('reference') )[0]; 457 my @values = $ac->get_Annotations($key); 563 @dblinks = $ac->get_Annotations('dblink'); 576 ok my @ctg = $seq->annotation->get_Annotations('contig'); 650 my @anns = $seq->annotation->get_Annotations('contig'); 672 @anns = $seq->annotation->get_Annotations('contig'); 697 my $comment = ($seq->get_Annotations('comment') )[0]; [all …]
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H A D | scf.t | 130 $ac->get_Annotations('comment'); 140 $ac->get_Annotations('comment'); 145 $ac->get_Annotations('comment'); 154 my @ann = $st_ac->get_Annotations(); 185 $ac->get_Annotations('comment'); 190 $ac->get_Annotations('comment');
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/TreeIO/ |
H A D | phyloxml.pm | 401 my @relations = $ac->get_Annotations('clade_relation'); 524 my @id_source = $attr[0]->get_Annotations('id_source'); 602 foreach my $ann ($ac->get_Annotations($key)) { 627 foreach my $ann ($ac->get_Annotations($key)) { 633 my @sv = map {$_->get_Annotations($attrname)} @nextacs; 1095 my ($strac) = $molseq->get_Annotations('_text'); 1364 my @all_anns = $ac->get_Annotations(); 1381 my @attrs = $ann->get_Annotations('_attr'); 1420 my @all_attrs = $ac->get_Annotations(); 1469 my @all_anns = $seq->annotation->get_Annotations(); [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Annotation/ |
H A D | AnnotationAdaptor.t | 35 my @anns = $anncoll->get_Annotations("tag1"); 43 @anns = $anncoll->get_Annotations("tag2"); 44 my @fanns = $feat->annotation->get_Annotations("tag2"); 57 @fanns = $feat->annotation->get_Annotations("comment"); 65 @anns = $anncoll->get_Annotations("tag2"); 66 @fanns = $feat->annotation->get_Annotations("tag2");
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H A D | Annotation.t | 89 foreach my $link ( $ac->get_Annotations('dblink') ) { 99 foreach my $ann ( $ac->get_Annotations() ) { 109 foreach my $link ( $ac->get_Annotations('dblink') ) { 142 is (scalar($nested_ac->get_Annotations()), 1); 143 ($ac) = $nested_ac->get_Annotations(); 147 is (scalar($nested_ac->get_Annotations()), 2); 149 is (scalar($nested_ac->get_Annotations('dblink')), 0); 150 my @anns = $nested_ac->get_Annotations('gene names'); 152 @anns = map { $_->get_Annotations('dblink'); 153 } $nested_ac->get_Annotations('nested'); [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Tree/ |
H A D | AnnotatableNode.pm | 176 return scalar $ac->get_Annotations($tag); 194 if( @{$ac->get_Annotations($tag)} ) { 250 my @values = map {$_->value()} $ac->get_Annotations($tag); 267 return ( scalar $ac->get_Annotations($tag) > 0);
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/dports/biology/p5-Bio-FeatureIO/Bio-FeatureIO-1.6.905/lib/Bio/FeatureIO/ |
H A D | gff.pm | 226 my $anno_ID = $feat->get_Annotations('ID'); 238 my @parents = $feat->get_Annotations('Parent'); 873 …my ($transcript_id, $gene_id) = (($feature->get_Annotations('transcript_id'))[0], ($feature->get_A… 875 $group = ($feature->get_Annotations('ID'))[0]; 931 if(my @v = ($feature->get_Annotations('Name'))){ 935 if(my @v = ($feature->get_Annotations('ID'))){ 940 if(my @v = ($feature->get_Annotations('Parent'))){ 944 if(my @v = ($feature->get_Annotations('dblink'))){ 948 if(my @v = ($feature->get_Annotations('ontology_term'))){ 952 if(my @v = ($feature->get_Annotations('comment'))){ [all …]
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/dports/biology/p5-Bio-FeatureIO/Bio-FeatureIO-1.6.905/t/release-SeqFeature/ |
H A D | Annotated.t | 65 is $sfa2->get_Annotations('silly')->value,20; 66 is $sfa2->get_Annotations('new')->value,1; 94 is $sfa3->get_Annotations('silly')->value,20; 95 is $sfa3->get_Annotations('new')->value,1;
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Tree/TreeIO/ |
H A D | phyloxml.t | 172 my ($ac) = $C->annotation->get_Annotations('taxonomy'); 174 my ($ac2) = $ac->get_Annotations('scientific_name'); 176 my ($scientificname) = $ac2->get_Annotations('_text'); 183 ($scientificname) = $ac2->get_Annotations('_text'); 193 my ($desc) = $descac->get_Annotations('_text'); 410 my (@annotations) = $ac->get_Annotations('property'); 456 my @annotations = $ac->get_Annotations('property'); 458 my @value = $annotations[0]->get_Annotations('_text'); 510 my ($rank_text) = $rank->get_Annotations('_text'); 517 my ($desc) = $distribution->get_Annotations('desc'); [all …]
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/dports/biology/p5-Bio-ASN1-EntrezGene/Bio-ASN1-EntrezGene-1.73/t/ |
H A D | entrezgene.t | 191 my @egstatus=$ann->get_Annotations('Entrez Gene Status'); 209 my @refstatus=$ann->get_Annotations('RefSeq status'); 228 my @ofname=$ann->get_Annotations('Official Full Name'); 245 my @chr=$ann->get_Annotations('chromosome'); 262 my @sym=$ann->get_Annotations('ALIAS_SYMBOL'); 273 my @map=$ann->get_Annotations('cyto'); 290 my @refs=$ann->get_Annotations('Reference'); 294 my @dblinks=$ann->get_Annotations('dblink'); 360 my @all=$ann->get_Annotations($key); 398 foreach my $ot ($ann->get_Annotations('OntologyTerm')) { [all …]
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqFeature/ |
H A D | AnnotationAdaptor.pm | 286 sub get_Annotations{ subroutine 315 push(@anns, $self->annotation->get_Annotations(@keys)); 452 my @anns = $self->get_Annotations(@keys);
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqIO/ |
H A D | genbank.pm | 1028 for my $proj ( $seq->annotation->get_Annotations('project') ) { 1033 foreach my $ref ( $seq->annotation->get_Annotations('dblink') ) { 1054 foreach my $ref ( $seq->annotation->get_Annotations('segment') ) { 1093 foreach my $ref ( $seq->annotation->get_Annotations('reference') ) { 1133 foreach my $comment ( $seq->annotation->get_Annotations('comment') ) { 1171 if ($seq->annotation->get_Annotations('wgs')) { 1172 foreach my $wgs (map {$seq->annotation->get_Annotations($_)} 1181 if ($seq->annotation->get_Annotations('contig')) { 1184 foreach my $contig ($seq->annotation->get_Annotations('contig')) { 1208 my ($o) = $seq->annotation->get_Annotations('origin');
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Tools/ |
H A D | Match.t | 33 my $matrix_score = ($feat->annotation->get_Annotations('matrix_score'))[0]->value; 34 my $matrix_id = ($feat->annotation->get_Annotations('matrix_id'))[0]->value;
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