lib/SGN/Feature/LocusPages.pm

   1 package SGN::Feature::LocusPages;
   2 use Moose;
   3 use namespace::autoclean;
   4
   5 use URI;
   6
   7 use CXGN::Phenome;
   8
   9 use SGN::SiteFeatures::CrossReference;
  10
  11 extends 'SGN::Feature';
  12
  13 has '+description' => (
  14     default    => 'Genetic loci',
  15    );
  16
  17 sub xrefs {
  18     my ( $self, $query ) = @_;
  19
  20     return if ref $query;
  21
  22     return ( $self->_name_xrefs( $query ),
  23              #$self->_phenotype_xrefs( $query ),
  24            );
  25 }
  26
  27 sub _name_xrefs {
  28     my ( $self, $q ) = @_;
  29
  30     my $search = CXGN::Phenome->new;
  31     my $query = $search->new_query;
  32     $query->locus_obsolete(" = 'f' ");
  33     $query->any_name("lower(&t) = ? ", lc $q );
  34     my $result = $search->do_search($query);
  35
  36     # fetch at most 5 results, hashing by locus name
  37     my %results = map { $_->[1] => $_ } reverse grep $_, map { $result->next_result } 1..5;
  38
  39     # make xrefs out of them
  40     my @xrefs;
  41     for my $locus_name ( sort keys %results ) {
  42         my $r = $results{$locus_name};
  43
  44         my $text = qq|$r->[14] locus $r->[2]|;
  45         $text .= " ($locus_name)" unless $locus_name eq $r->[2];
  46
  47         push @xrefs, SGN::SiteFeatures::CrossReference->new({
  48             feature => $self,
  49             text    => $text,
  50             url     => URI->new( '/phenome/locus_display.pl?locus_id='.$r->[0] ),
  51         });
  52     }
  53
  54     return @xrefs;
  55 }
  56
  57
  58 1;