Added get_all_VariationFeatures_by_Population method

modules/Bio/EnsEMBL/Slice.pm

@@ -1552,6 +1552,7 @@ sub get_all_VariationFeatures{
                  If $annotation_source is set only variations whose annotations come from
                  $annotation_source will be retrieved.
                  If $annotation_name is set only variations with that annotation will be retrieved.
+                 $annotation_name can be a phenotype's internal dbID.
     ReturnType : listref of Bio::EnsEMBL::Variation::VariationFeature
     Exceptions : none
     Caller     : contigview, snpview
@@ -1665,6 +1666,46 @@ sub get_all_StructuralVariations{
 }
 
 
+=head2 get_all_VariationFeatures_by_Population
+
+  Arg [1]    : Bio::EnsEMBL::Variation::Population
+  Arg [2]	 : $minimum_frequency (optional)
+  Example    : $pop = $pop_adaptor->fetch_by_dbID(659);
+               @vfs = @{$slice->get_all_VariationFeatures_by_Population(
+                 $pop,$slice)};
+  Description: Retrieves all variation features in a slice which are stored for
+			   a specified population. If $minimum_frequency is supplied, only
+			   variations with a minor allele frequency (MAF) greater than
+			   $minimum_frequency will be returned.
+  Returntype : listref of Bio::EnsEMBL::Variation::VariationFeature
+  Exceptions : throw on incorrect argument
+  Caller     : general
+  Status     : At Risk
+
+=cut
+
+sub get_all_VariationFeatures_by_Population {
+ my $self = shift;
+
+ if(!$self->adaptor()) {
+  warning('Cannot get variation features without attached adaptor');
+  return [];
+ }
+
+ my $vf_adaptor = Bio::EnsEMBL::DBSQL::MergedAdaptor->new(-species => $self->adaptor()->db()->species, -type => "VariationFeature");
+ if( $vf_adaptor ) {
+    return $vf_adaptor->fetch_all_by_Slice_Population($self, @_);
+ }
+ else {
+     warning("Variation database must be attached to core database to " .
+       "retrieve variation information" );
+  return [];
+ }
+}
+
+
+
+
 =head2 get_all_IndividualSlice
 
     Args        : none