Implement Transcript::get_all_RNAProducts() + its tests

The optional argument allows the user to only retrieve RNA products of
specific type, e.g. microRNAs. At the moment the type has to be
specified by a numerical ID, in the future this will be changed to allow
the passing of string codes.

modules/Bio/EnsEMBL/Transcript.pm

@@ -3003,6 +3003,43 @@ sub get_all_DAS_Features {
 }
 
 
+=head2 get_all_RNAProducts
+
+  Arg [1]    : optional int $type_id
+               The numerical ID of the rnaproduct type to retrieve values for.
+               FIXME: this should definitely take string codes instead.
+  Example    : @transc_mirnas = @{$transcript->get_all_RNAProducts(1)};
+               @transc_rnaproducts = @{$transcript->get_all_RNAProducts()};
+  Description: Gets a list of RNAProducts of this transcript.
+               Optionally just get RNAProducts for given type ID.
+  Returntype : listref Bio::EnsEMBL::RNAProduct
+  Exceptions : none
+  Caller     : general
+  Status     : In Development
+
+=cut
+
+sub get_all_RNAProducts {
+  my ($self, $type_id) = @_;
+
+  if (!exists $self->{'rnaproducts'}) {
+    if (!$self->adaptor()) {
+      return [];
+    }
+
+    my $rnaproduct_adaptor = $self->adaptor->db->get_RNAProductAdaptor();
+    $self->{'rnaproducts'} = $rnaproduct_adaptor->fetch_all_by_Transcript($self);
+  }
+
+  if (defined $type_id) {
+    my @results = grep { $_->type_id() == $type_id } @{$self->{'rnaproducts'}};
+    return \@results;
+  } else {
+    return $self->{'rnaproducts'};
+  }
+}
+
+
 
 =head2 _compare_xrefs
 

modules/t/transcript.t

@@ -1028,6 +1028,18 @@ for (my $i = 0; $i < scalar(@absolute_coords); $i++) {
   }
 }
 
+## Test retrieval of mature RNA products
+{
+  $tr = $ta->fetch_by_stable_id('ENST00000278995');
+  my $rps_all = $tr->get_all_RNAProducts();
+  my $rps_micro = $tr->get_all_RNAProducts(1);
+  my $rps_circ = $tr->get_all_RNAProducts(2);
+
+  cmp_ok(scalar @{$rps_all}, '>', 0, 'Have RNA products');
+  is_deeply($rps_all, $rps_micro, 'All RNA products are microRNAs');
+  cmp_ok(scalar @{$rps_circ}, '==', 0, 'Have no circRNAs');
+}
+
 done_testing();
 
 #