mason/markers/polymorphisms.mas

   1
   2 <%doc>
   3
   4 =head1 NAME
   5
   6 /markers/polymorphisms.mas - a Mason component displaying information about map polymorphisms of marker product lengths
   7
   8 =head1 DESCRIPTION
   9
  10 parameters
  11
  12 =over 5
  13
  14 =item *
  15
  16 $marker - a CXGN::Marker object.
  17
  18
  19 =back
  20
  21 =head1 AUTHOR
  22
  23 Lukas Mueller <lam87@cornell.edu>
  24
  25 =cut
  26
  27 </%doc>
  28
  29 <%args>
  30 $marker
  31 </%args>
  32
  33 <%perl>
  34   my $polymorphisms_html='';
  35 my $dbh = $marker->{dbh};
  36 my @displayed_pcr=();
  37 my $experiments=$marker->experiments();
  38 if($experiments and @{$experiments}) {
  39   for my $experiment(@{$experiments}) {
  40     my $pcr=$experiment->{pcr_experiment};
  41     my $rflp=$experiment->{rflp_experiment};
  42     if($pcr and !grep {$_==$pcr->pcr_experiment_id()} @displayed_pcr) {
  43       my $pcr_bands=$pcr->pcr_bands_hash_of_strings();
  44       my $digest_bands=$pcr->pcr_digest_bands_hash_of_strings();
  45       my $pcr_bands_html='';
  46       my $digest_bands_html='';
  47       for my $accession_id(keys(%{$pcr_bands})) {
  48         my $accession_name=CXGN::Accession->new($dbh,$accession_id)->verbose_name();
  49         $pcr_bands_html.="<b>$accession_name:</b> $pcr_bands->{$accession_id}<br />";
  50       }
  51       for my $accession_id(keys(%{$digest_bands})) {
  52         my $accession_name=CXGN::Accession->new($dbh,$accession_id)->verbose_name();
  53         $digest_bands_html.="<b>$accession_name:</b> $digest_bands->{$accession_id}<br />";
  54       }
  55       my $mg='';
  56       if($pcr->mg_conc()) {
  57         $mg=$pcr->mg_conc().'mM';
  58       }
  59       my $temp='';
  60       if($pcr->temp()) {
  61         $temp=$pcr->temp().'&deg;C';
  62       }
  63       $polymorphisms_html.='<tr><td width="100%">';
  64       my $fwd=$pcr->fwd_primer();
  65       my $rev=$pcr->rev_primer();
  66       if($fwd) {
  67         $fwd='<span class="sequence">'.$fwd.'</span>';
  68       }
  69       else {
  70         $fwd='<span class="ghosted">Unknown</span>';
  71       }
  72       if($rev) {
  73         $rev='<span class="sequence">'.$rev.'</span>';
  74       }
  75       else {
  76         $rev='<span class="ghosted">Unknown</span>';
  77       }
  78       my $enz=$pcr->enzyme()||'unknown enzyme';
  79       $temp||='<span class="ghosted">Unknown</span>';
  80       $mg||='<span class="ghosted">Unknown</span>';
  81       my $digest_title="Digested band sizes (using $enz)";
  82       unless($digest_bands_html) {
  83         $digest_title='&nbsp;';
  84         $digest_bands_html='&nbsp;';
  85       }
  86       $polymorphisms_html.=CXGN::Page::FormattingHelpers::info_table_html
  87         (
  88          '__title'=>"PCR data&nbsp;&nbsp;&nbsp;<span class=\"tinytype\">Exp. ID ".$pcr->pcr_experiment_id."</span>",
  89          "Forward primer (5'-3')"=>"<span class=\"sequence\">$fwd</span>",
  90          "Reverse primer (5'-3')"=>"<span class=\"sequence\">$rev</span>",
  91          'Accessions and product sizes'=>$pcr_bands_html,
  92          $digest_title=>$digest_bands_html,
  93          'Approximate temperature'=>$temp,
  94          'Mg<sup>+2</sup> concentration'=>$mg,
  95          '__multicol'=>3,
  96          '__tableattrs'=>"width=\"100%\"",
  97         );
  98       $polymorphisms_html.='</td></tr>';
  99     }
 100   }
 101 }
 102 if($polymorphisms_html) {
 103  print  info_section_html(title=>'Other PCR data',contents=>'<table width="100%" cellspacing="0" cellpadding="0" border="0">'.$polymorphisms_html.'</table>');
 104 }
 105 else {
 106   return '';
 107 }
 108
 109 </%perl>