mason/feature/types/polypeptide.mas

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 'WARNING: This feature is obsolete, new data is available.'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