Add _lightweight() method and use it to (temporarily) set the

lightweight flag when creating objects for binning.

modules/Bio/EnsEMBL/Collection.pm

@@ -22,8 +22,10 @@ sub fetch_bins_by_Slice {
   my ( $slice, $method, $nbins, $logic_name ) =
     rearrange( [ 'SLICE', 'METHOD', 'NBINS', 'LOGIC_NAME' ], @_ );
 
-  # FIXME: Set lightweight
-  return
+  my $old_value = $this->_lightweight();
+  $this->_lightweight(1);
+
+  my $bins =
     $this->_bin_features(
         -slice  => $slice,
         -nbins  => $nbins,
@@ -31,7 +33,10 @@ sub fetch_bins_by_Slice {
         -features =>
           $this->fetch_by_Slice_constraint( $slice, undef, $logic_name )
     );
-  # FIXME: Unset lightweight
+
+  $this->_lightweight($old_value);
+
+  return $bins;
 }
 
 # ----------------------------------------------------------------------
@@ -87,6 +92,16 @@ sub _create_feature_fast {
 # ----------------------------------------------------------------------
 # Private methods
 
+sub _lightweight {
+  my ( $this, $value ) = @_;
+
+  if ( defined($value) ) {
+    $self->{'lightweight'} = ( $value != 0 );
+  }
+
+  return $self->{'lightweight'} || 0;
+}
+
 our %VALID_BINNING_METHODS = (
                'count'            => 0,
                'density'          => 0,    # Same as 'count'.

modules/Bio/EnsEMBL/Collection/Exon.pm

@@ -16,10 +16,12 @@ sub _create_feature {
 
   my $feature = $this->SUPER::_create_feature( $feature_type, $args );
 
-  my ( $analysis, $stable_id, $version ) =
-    rearrange( [ 'STABLE_ID', 'VERSION', ], %{$args} );
+  if ( !$this->_lightweight() ) {
+    my ( $analysis, $stable_id, $version ) =
+      rearrange( [ 'STABLE_ID', 'VERSION', ], %{$args} );
 
-  push( @{$feature}, $stable_id, $version );
+    push( @{$feature}, $stable_id, $version );
+  }
 
   return $feature;
 }

modules/Bio/EnsEMBL/Collection/RepeatFeature.pm

@@ -16,16 +16,18 @@ sub _create_feature {
 
   my $feature = $this->SUPER::_create_feature( $feature_type, $args );
 
-  my ( $hstart, $hend, $score, $repeat_consensus, $analysis ) =
-    rearrange( [ 'HSTART', 'HEND',
-                 'SCORE',  'REPEAT_CONSENSUS',
-                 'ANALYSIS'
-               ],
-               @{$args} );
-
-  push( @{$feature},
-        $hstart, $hend, $score, $repeat_consensus->dbID(),
-        $analysis->dbID() );
+  if ( !$this->_lightweight() ) {
+    my ( $hstart, $hend, $score, $repeat_consensus, $analysis ) =
+      rearrange( [ 'HSTART', 'HEND',
+                   'SCORE',  'REPEAT_CONSENSUS',
+                   'ANALYSIS'
+                 ],
+                 @{$args} );
+
+    push( @{$feature},
+          $hstart, $hend, $score, $repeat_consensus->dbID(),
+          $analysis->dbID() );
+  }
 
   return $feature;
 }
@@ -36,10 +38,12 @@ sub _create_feature_fast {
   my $feature =
     $this->SUPER::_create_feature_fast( $feature_type, $args );
 
-  push( @{$feature},
-        $args->{'hstart'}, $args->{'hend'}, $args->{'score'},
-        $args->{'repeat_consensus'}->dbID(),
-        $args->{'analysis'}->dbID() );
+  if ( !$this->_lightweight() ) {
+    push( @{$feature},
+          $args->{'hstart'}, $args->{'hend'}, $args->{'score'},
+          $args->{'repeat_consensus'}->dbID(),
+          $args->{'analysis'}->dbID() );
+  }
 
   return $feature;
 }