Added supporting feature store

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -676,6 +676,41 @@ sub store {
      $sth->finish();
    }
 
+
+  # Now the supporting evidence
+  # should be stored from featureAdaptor
+  my $sql = "insert into transcript_supporting_feature (transcript_id, feature_id, feature_type)
+             values(?, ?, ?)";
+
+  my $sf_sth = $self->prepare($sql);
+
+  my $anaAdaptor = $self->db->get_AnalysisAdaptor();
+  my $dna_adaptor = $self->db->get_DnaAlignFeatureAdaptor();
+  my $pep_adaptor = $self->db->get_ProteinAlignFeatureAdaptor();
+  my $type;
+
+  foreach my $sf (@{$transcript->get_all_supporting_features}) {
+    if(!$sf->isa("Bio::EnsEMBL::BaseAlignFeature")){
+      throw("$sf must be an align feature otherwise" .
+            "it can't be stored");
+    }
+
+    if($sf->isa("Bio::EnsEMBL::DnaDnaAlignFeature")){
+      $dna_adaptor->store($sf);
+      $type = 'dna_align_feature';
+    }elsif($sf->isa("Bio::EnsEMBL::DnaPepAlignFeature")){
+      $pep_adaptor->store($sf);
+      $type = 'protein_align_feature';
+    } else {
+      warning("Supporting feature of unknown type. Skipping : [$sf]\n");
+      next;
+    }
+
+    $sf_sth->execute($transc_dbID, $sf->dbID, $type);
+  }
+
+
+
    #update the original transcript object - not the transfered copy that
    #we might have created
    $original->dbID( $transc_dbID );