allow for undef returned as mapper from AssemblyMapperAdaptor

modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm

@@ -127,7 +127,7 @@ sub new {
                $mapper = $asma->fetch_by_CoordSystems($cs1,$cs2);
                $mapper = $asma->fetch_by_CoordSystems($cs2,$cs1);
   Returntype : Bio::EnsEMBL::AssemblyMapper
-  Exceptions : none
+  Exceptions : wrong argument types
   Caller     : general
 
 =cut
@@ -162,9 +162,10 @@ sub fetch_by_CoordSystems {
   my @mapping_path = @{$csa->get_mapping_path($cs1,$cs2)};
 
   if(!@mapping_path) {
-    throw("There is no mapping defined between these coord systems:\n" .
+    warn("There is no mapping defined between these coord systems:\n" .
           $cs1->name() . " " . $cs1->version() . " and " . $cs2->name() . " " .
           $cs2->version());
+    return undef;
   }
 
   my $key = join(':', map({defined($_)?$_->dbID():"-"} @mapping_path));

modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm

@@ -316,6 +316,8 @@ sub _slice_fetch {
     } else {
       $mapper = $asma->fetch_by_CoordSystems($slice_cs, $feat_cs);
 
+      next unless defined $mapper;
+
       # Get list of coordinates and corresponding internal ids for
       # regions the slice spans
       @coords = $mapper->map($slice_seq_region, $slice_start, $slice_end,

modules/Bio/EnsEMBL/Slice.pm

@@ -693,11 +693,18 @@ sub project {
     my $asm_mapper = $asma->fetch_by_CoordSystems($slice_cs, $cs);
 
     # perform the mapping between this slice and the requested system
-    my @coords = $asm_mapper->map($normal_slice->seq_region_name(),
-				  $normal_slice->start(),
-				  $normal_slice->end(),
-				  $normal_slice->strand(),
-				  $slice_cs);
+    my @coords;
+
+    if( defined $asm_mapper ) {
+      @coords = $asm_mapper->map($normal_slice->seq_region_name(),
+				 $normal_slice->start(),
+				 $normal_slice->end(),
+				 $normal_slice->strand(),
+				 $slice_cs);
+    } else {
+      $coords[0] = Bio::EnsEMBL::Mapper::Gap->new( $normal_slice->start(),
+						   $normal_slice->end());
+    }
 
     #construct a projection from the mapping results and return it