moving logic for slice projection filtering into sliceadaptor so compara have...

moving logic for slice projection filtering into sliceadaptor so compara have an easier time using it and getting better patch support in

modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm

@@ -662,9 +662,8 @@ sub count_by_Slice_constraint {
 =head2 _get_and_filter_Slice_projections
 
     Arg [1]     : Bio::EnsEMBL::Slice
-    Description : Finds all features with at least partial overlap to the given
-                  slice and sums them up
-    Example     : my $proj= $self->_get_and_filter_Slice_projections($slice);
+    Description : Delegates onto SliceAdaptor::fetch_normalized_slice_projection() 
+                  with filtering on
     Returntype  : ArrayRef Bio::EnsEMBL::ProjectionSegment; Returns an array
                   of projected segments
 =cut
@@ -672,27 +671,8 @@ sub count_by_Slice_constraint {
 sub _get_and_filter_Slice_projections {
   my ($self, $slice) = @_;
   my $sa = $slice->adaptor();
-  my @proj = @{ $sa->fetch_normalized_slice_projection($slice) };
-  if ( !@proj ) {
-    throw( 'Could not retrieve normalized Slices. '
-         . 'Database contains incorrect assembly_exception information.'
-    );
-  }
-  
-  # Want to get features on the FULL original slice as well as any
-  # symlinked slices.
-  
-  # Filter out partial slices from projection that are on same
-  # seq_region as original slice.
-
-  my $sr_id = $slice->get_seq_region_id();
-
-  @proj = grep { $_->to_Slice->get_seq_region_id() != $sr_id } @proj;
-
-  my $segment = bless( [ 1, $slice->length(), $slice ],
-                       'Bio::EnsEMBL::ProjectionSegment' );
-  push( @proj, $segment );
-  return \@proj;
+  my $filter_projections = 1;
+  return $sa->fetch_normalized_slice_projection($slice, $filter_projections);
 }
 
 =head2 _generate_feature_bounds

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -101,6 +101,7 @@ use Bio::EnsEMBL::CircularSlice;
 use Bio::EnsEMBL::Mapper;
 use Bio::EnsEMBL::LRGSlice;
 use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning stack_trace_dump);
+use Bio::EnsEMBL::ProjectionSegment;
 use Scalar::Util qw/looks_like_number/;
 
 @ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
@@ -1668,6 +1669,9 @@ sub fetch_by_misc_feature_attribute {
 =head2 fetch_normalized_slice_projection
 
   Arg [1]    : Bio::EnsEMBL::Slice $slice
+  Arg [2]    : boolean $filter_projections 
+               Optionally filter the projections to remove anything 
+               which is the same sequence region as the given slice
   Example    :  ( optional )
   Description: gives back a project style result. The returned slices 
                represent the areas to which there are symlinks for the 
@@ -1684,6 +1688,7 @@ sub fetch_by_misc_feature_attribute {
 sub fetch_normalized_slice_projection {
   my $self = shift;
   my $slice = shift;
+  my $filter_projections = shift;
 
   my $slice_seq_region_id = $self->get_seq_region_id( $slice );
 
@@ -1824,11 +1829,45 @@ sub fetch_normalized_slice_projection {
     }
     $rel_start += $coord->length();
   }
-
+  
+  if($filter_projections) {
+    return $self->_filter_Slice_projections($slice, \@out);
+  }
   return \@out;
 }
 
+=head2 _filter_Slice_projections
+
+    Arg [1]     : Bio::EnsEMBL::Slice The slice the projections were made from
+    Arg [2]     : Array The projections which were fetched from the previous slice
+    Description : Removes any projections which occur within the same sequence 
+                  region as the given Slice object
+    Returntype  : ArrayRef Bio::EnsEMBL::ProjectionSegment; Returns an array
+                  of projected segments
+=cut
+
+sub _filter_Slice_projections {
+  my ($self, $slice, $projections) = @_;
+  my @proj = @{ $projections };
+  if ( !@proj ) {
+    throw('Was not given any projections to filter. Database may have incorrect assembly_exception information loaded');
+  }
+  
+  # Want to get features on the FULL original slice as well as any
+  # symlinked slices.
+  
+  # Filter out partial slices from projection that are on same
+  # seq_region as original slice.
 
+  my $sr_id = $slice->get_seq_region_id();
+
+  @proj = grep { $_->to_Slice->get_seq_region_id() != $sr_id } @proj;
+
+  my $segment = bless( [ 1, $slice->length(), $slice ],
+                       'Bio::EnsEMBL::ProjectionSegment' );
+  push( @proj, $segment );
+  return \@proj;
+}
 
 
 =head2 store