New adaptor for transcript supporting features

modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm

+# EnsEMBL Adaptor for retrieving SupportingFeatures
+#
+# Author: Graham McVicker
+# 
+# Date : 11-Oct-2002
+#
+
+=head1 NAME
+
+Bio::EnsEMBL::DBSQL::TranscriptSupportingFeatureAdaptor - Retrieves supporting features 
+                                                from the database.
+
+=head1 SYNOPSIS
+
+$supporting_feature_adaptor = $database_adaptor->get_TranscriptSupportingFeatureAdaptor;
+@supporting_feats = @{$supporting_feat_adaptor->fetch_all_by_Transcript($transcript)};
+
+=head1 CONTACT
+
+Post questions to ensembl developer mailing list : <ensembl-dev@ebi.ac.uk>
+
+=cut
+
+
+use strict;
+
+package Bio::EnsEMBL::DBSQL::TranscriptSupportingFeatureAdaptor;
+
+use Bio::EnsEMBL::DBSQL::BaseAdaptor;
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+use vars qw(@ISA);
+
+#inherits from BaseAdaptor
+@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
+
+
+
+=head2 fetch_all_by_Transcript
+
+  Arg [1]    : Bio::EnsEMBL::Transcript $transcript 
+               The transcript to fetch supporting features for
+  Example    : @sfs = @{$supporting_feat_adaptor->fetch_all_by_Transcript($transcript)};
+  Description: Retrieves supporting features (evidence) for a given transcript. 
+  Returntype : list of Bio::EnsEMBL::BaseAlignFeatures in the same coordinate
+               system as the $transcript argument
+  Exceptions : warning if $transcript is not in the database (i.e. dbID not defined)
+               throw if a retrieved supporting feature is of unknown type 
+  Caller     : Bio::EnsEMBL::Transcript
+
+=cut
+
+sub fetch_all_by_Transcript {
+  my ( $self, $transcript )  = @_;
+
+  my $out = [];
+
+  unless($transcript->dbID) {
+    warning("Cannot retrieve evidence for transcript without dbID");
+    return [];
+  }
+
+  return $out;
+  my $sth = $self->prepare("SELECT tsf.feature_type, tsf.feature_id
+                            FROM   transcript_supporting_feature tsf
+                            WHERE  transcript_id = ?");
+
+  $sth->execute($transcript->dbID());
+
+  my $prot_adp = $self->db->get_ProteinAlignFeatureAdaptor;
+  my $dna_adp  = $self->db->get_DnaAlignFeatureAdaptor;
+
+  my $feature;
+  while(my ($type, $feature_id) = $sth->fetchrow){
+    if($type eq 'protein_align_feature'){
+      $feature = $prot_adp->fetch_by_dbID($feature_id);
+    } elsif($type eq 'dna_align_feature'){
+      $feature = $dna_adp->fetch_by_dbID($feature_id);
+    } else {
+      warning("Unknown feature type [$type]\n");
+    }
+
+    if(!$feature) {
+      warning("Supporting feature $type $feature_id does not exist in DB");
+    }
+
+    my $new_feature = $feature->transfer($transcript->slice());
+
+    push @$out, $new_feature if( $new_feature );
+  }
+
+  $sth->finish();
+
+  return $out;
+}
+
+1;
+