mason/feature/types/mrna.mas

   1 <%args>
   2     $feature
   3     $featurelocs
   4     $blast_url => undef
   5     $xrefs     => []
   6 </%args>
   7 <%once>
   8     use SGN::View::Feature qw/ type_name /;
   9 </%once>
  10
  11 <& /feature/page_title.mas, feature => $feature &>
  12
  13 <&| /page/info_section.mas,
  14     title       => type_name($feature,'caps').' details',
  15     subtitle    => $feature->is_obsolete ? 'WARNING: This feature is obsolete, new data is available.' : '',
  16     collapsible => 1,
  17 &>
  18    <& /feature/feature_data.mas,
  19       feature     => $feature,
  20       featurelocs => $featurelocs,
  21     &>
  22     <& /feature/properties.mas,
  23        feature => $feature,
  24     &>
  25 </&>
  26
  27 %    for my $seqs ( mrna_cds_protein_sequence( $feature ) ) {
  28 %       if( $seqs->[0] ) {
  29         <&| /page/info_section.mas,
  30                 title         => 'mRNA sequence',
  31                 subtitle      => 'spliced mRNA sequence, including UTRs',
  32                 collapsible   => 1,
  33                 collapsed     => 0,
  34         &>
  35           <div style="margin-left: 3em">
  36             <& /sequence/with_markup.mas,
  37                seq       => $seqs->[0],
  38                width     => 80,
  39                subdiv    => 10,
  40                blast_url => $blast_url,
  41              &>
  42           </div>
  43           <div style="margin-top: 1em">
  44             <& /feature/sequence_download.mas,
  45                  feature => $feature,
  46              &>
  47           </div>
  48         </&>
  49 %       }
  50 %    }
  51
  52 <&| /page/info_section.mas,
  53      title         => 'Genomic sequence(s)',
  54      subtitle      => "unprocessed genomic sequence underlying each location of this mRNA",
  55      collapsible   => 1,
  56      collapsed     => 1,
  57      hide_if_empty => 1,
  58  &>
  59     <& /feature/region_sequence.mas,
  60             feature   => $feature,
  61             blast_url => $blast_url,
  62     &>
  63 </&>
  64
  65 <&| /page/info_section.mas,
  66    title => 'Related features',
  67    collapsible => 1,
  68    hide_if_empty => 1,
  69 &>
  70
  71   <& /feature/related_features.mas,
  72       feature   => $feature,
  73       omit_columns => ['organism'],
  74   &>
  75
  76 </&>
  77
  78 <&| /page/info_section.mas,
  79      title => 'Related views',
  80      empty_message => 'None found',
  81      collapsible => 1,
  82      is_empty => ! scalar @$xrefs,
  83  &>
  84      <& /sitefeatures/mixed/xref_set/link.mas,
  85         xrefs => $xrefs,
  86       &>
  87 </&>
  88
  89
  90 <%once>
  91    use SGN::View::Feature qw/ mrna_cds_protein_sequence /;
  92 </%once>