The Compara API can deal with Slice objects directly

Created by: muffato

Description

I'm deprecating fetch_all_by_GenomeDB_region and was going to update the call here in Slice.pm when I realised that the code could be simplified since the Compara API understand slices.

Benefits

Less code to maintain.

Possible Drawbacks

Coverage percentage will decrease, if you pay attention to that.

Testing

Have you added/modified unit tests to test the changes?

No.

Have you run the entire test suite and no regression was detected?

Yes.

modules/Bio/EnsEMBL/Slice.pm

@@ -2834,7 +2834,6 @@ sub get_all_compara_Syntenies {
   }
   my $gdba = $compara_db->get_GenomeDBAdaptor();
   my $mlssa = $compara_db->get_MethodLinkSpeciesSetAdaptor();
-  my $dfa = $compara_db->get_DnaFragAdaptor();
   my $sra = $compara_db->get_SyntenyRegionAdaptor();
 
   my $this_gdb = $gdba->fetch_by_core_DBAdaptor($self->adaptor()->db());
@@ -2846,10 +2845,7 @@ sub get_all_compara_Syntenies {
     $mlss = $mlssa->fetch_by_method_link_type_GenomeDBs($method_link_type, [$this_gdb, $query_gdb]);
   }
 
-  my $cs = $self->coord_system()->name();
-  my $sr = $self->seq_region_name();
-  my ($dnafrag) = @{$dfa->fetch_all_by_GenomeDB_region($this_gdb, $cs, $sr)};
-  return $sra->fetch_all_by_MethodLinkSpeciesSet_DnaFrag($mlss, $dnafrag, $self->start, $self->end);
+  return $sra->fetch_all_by_MethodLinkSpeciesSet_Slice($mlss, $self);
 }
 
 =head2 get_all_Haplotypes