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Searched refs:get_Annotations (Results 1 – 25 of 54) sorted by relevance

123

/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/AlignIO/
H A Darp.t34 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');
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Annotation/
H A DCollection.pm160 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');
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/dports/biology/p5-Bio-FeatureIO/Bio-FeatureIO-1.6.905/lib/Bio/SeqFeature/
H A DAnnotated.pm313 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 = $self->annotation->get_Annotations(@_);
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/SeqIO/
H A Dkegg.t29 is(($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…
H A Dbsml.t23 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');
H A Dlocuslink.t36 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)) {
H A Dswiss.t25 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");
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H A Dbsml_sax.t24 my @refs = $seq->annotation->get_Annotations('reference');
37 is($seq->annotation->get_Annotations('reference'),2);
38 is($seq->annotation->get_Annotations('dblink'),2);
H A Dtable.t133 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");
H A DHandler.t63 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) = $seq->annotation->get_Annotations('gene_name');
[all …]
H A Dseqxml.t60 my ($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();
H A DSeqBuilder.t27 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);
H A Dgenbank.t63 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];
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H A Dscf.t130 $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');
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/TreeIO/
H A Dphyloxml.pm401 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();
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Annotation/
H A DAnnotationAdaptor.t35 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");
H A DAnnotation.t89 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');
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Tree/
H A DAnnotatableNode.pm176 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);
/dports/biology/p5-Bio-FeatureIO/Bio-FeatureIO-1.6.905/lib/Bio/FeatureIO/
H A Dgff.pm226 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'))){
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/dports/biology/p5-Bio-FeatureIO/Bio-FeatureIO-1.6.905/t/release-SeqFeature/
H A DAnnotated.t65 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 $sfa3->get_Annotations('new')->value,1;
/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Tree/TreeIO/
H A Dphyloxml.t172 my ($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) = $distribution->get_Annotations('desc');
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/dports/biology/p5-Bio-ASN1-EntrezGene/Bio-ASN1-EntrezGene-1.73/t/
H A Dentrezgene.t191 my @egstatus=$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')) {
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqFeature/
H A DAnnotationAdaptor.pm286 sub get_Annotations{ subroutine
315 push(@anns, $self->annotation->get_Annotations(@keys));
452 my @anns = $self->get_Annotations(@keys);
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SeqIO/
H A Dgenbank.pm1028 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');
/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Tools/
H A DMatch.t33 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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