lib/CXGN/CDBI/SGN/Unigene.pm

   1 package CXGN::CDBI::SGN::Unigene;
   2 use strict;
   3
   4 =head1 DATA FIELDS
   5
   6   Primary Keys:
   7       unigene_id
   8
   9   Columns:
  10       unigene_id
  11       unigene_build_id
  12       consensi_id
  13       cluster_no
  14       contig_no
  15       nr_members
  16       database_name
  17       sequence_name
  18
  19   Sequence:
  20       (sgn base schema).unigene_unigene_id_seq
  21
  22 =cut
  23
  24 use base 'CXGN::CDBI::Class::DBI';
  25 __PACKAGE__->table(__PACKAGE__->qualify_schema('sgn') . '.unigene');
  26
  27 our @primary_key_names =
  28     qw/
  29       unigene_id
  30       /;
  31
  32 our @column_names =
  33     qw/
  34       unigene_id
  35       unigene_build_id
  36       consensi_id
  37       cluster_no
  38       contig_no
  39       nr_members
  40       database_name
  41       sequence_name
  42       /;
  43
  44 __PACKAGE__->columns( Primary => @primary_key_names, );
  45 __PACKAGE__->columns( All     => @column_names,      );
  46 __PACKAGE__->SUPER::sequence( __PACKAGE__->base_schema('sgn').'.unigene_unigene_id_seq' );
  47
  48
  49 __PACKAGE__->has_a(unigene_build_id => 'CXGN::CDBI::SGN::UnigeneBuild');
  50 __PACKAGE__->has_a(consensi_id => 'CXGN::CDBI::SGN::UnigeneConsensi');
  51 __PACKAGE__->has_many(members => 'CXGN::CDBI::SGN::UnigeneMember');
  52
  53 sub build_object {
  54   shift->unigene_build_id(@_);
  55 }
  56
  57 sub consensus_object {
  58   shift->consensi_id(@_);
  59 }
  60
  61 sub seq {
  62   my $this = shift;
  63
  64   if(my $c = $this->consensi_id) {
  65     return $c->seq;
  66   } else {
  67     my @members = $this->members;
  68     @members > 1 and
  69       die 'Unigene ID ',$this->unigene_id,' has '.$this->members.' members, but no consensus sequence!';
  70     @members < 1 and
  71       die 'Unigene ID ',$this->unigene_id,' has no members!';
  72     use Data::Dumper;
  73     return $members[0]->est_object->trimmed_seq;
  74   }
  75 }
  76
  77 sub external_identifier {
  78   'SGN-U'.shift->unigene_id
  79 }
  80
  81 sub info_page_href {
  82   my $this = shift;
  83   my $infopage = '/search/unigene.pl?unigene_id='.$this->external_identifier
  84 }
  85
  86 sub species_name {
  87   my $this = shift;
  88
  89   die 'not yet implemented.  wanna do it?';
  90 }
  91
  92
  93
  94 ###
  95 1;#do not remove
  96 ###