Only do block retrieval of repeats when we are caching our hits. Otherwise...

Only do block retrieval of repeats when we are caching our hits. Otherwise we're bringing back more data for no reason

modules/Bio/EnsEMBL/RepeatMaskedSlice.pm

@@ -217,10 +217,10 @@ sub seq {
   my $soft_mask   = $self->soft_mask();
   my $not_default_masking_cases = $self->not_default_masking_cases;
 
-  my $repeats = [];
+  my @repeats;
 
   foreach my $l (@$logic_names) {
-    push @{$repeats}, @{$self->get_all_RepeatFeatures($l)};
+    push @repeats, @{$self->get_all_RepeatFeatures($l)};
   }
 
   #
@@ -231,12 +231,10 @@ sub seq {
   #
   # mask the dna
   #
-  $self->_mask_features(\$dna,$repeats,$soft_mask,$not_default_masking_cases);
+  $self->_mask_features(\$dna,\@repeats,$soft_mask,$not_default_masking_cases);
   return $dna;
 }
 
-
-
 =head2 subseq
 
   Arg [1]    : none
@@ -251,58 +249,58 @@ sub seq {
 
 =cut
 
-
 sub subseq {
   my $self   = shift;
   my $start  = shift;
   my $end    = shift;
   my $strand = shift;
 
-  #
-  # get all the features
-  #
-  my $logic_names = $self->repeat_mask_logic_names();
-  my $soft_mask   = $self->soft_mask();
-  my $not_default_masking_cases = $self->not_default_masking_cases;
-
+  my $subsequence_slice = $self->sub_Slice($start, $end, $strand);
 
   # If frequent subseqs happen on repeatMasked sequence this results in
   # a lot of feature retrieval from the database. To avoid this, features
   # are only retrieved from subslices with fixed space boundaries. 
   # The access happens in block to make cache hits more likely
-
-  # The blocksize can be defined on the top of this module.
-
-  my $seq_region_slice = $self->seq_region_Slice();
-  my $block_min = ($self->start()-1) >> $BLOCK_PWR;
-  my $block_max = ($self->end()-1) >> $BLOCK_PWR;
-
-  my $repeats = [];
-
-  my $sub_start = ($block_min << $BLOCK_PWR)+1;
-  my $sub_end = ($block_max+1)<<$BLOCK_PWR;
-  if ($sub_end > $seq_region_slice->length) {
-    $sub_end =  $seq_region_slice->length ;
+  # ONLY DO IF WE ARE CACHING
+  
+  my $subslice;
+  if(! $self->adaptor()->db()->no_cache()) {
+    
+    my $seq_region_slice = $self->seq_region_Slice();
+    # The blocksize can be defined on the top of this module.
+    my $block_min = ($self->start()-1) >> $BLOCK_PWR;
+    my $block_max = ($self->end()-1) >> $BLOCK_PWR;
+    
+    my $sub_start = ($block_min << $BLOCK_PWR)+1;
+    my $sub_end = ($block_max+1)<<$BLOCK_PWR;
+    if ($sub_end > $seq_region_slice->length) {
+      $sub_end =  $seq_region_slice->length ;
+    }
+    $subslice = $seq_region_slice->sub_Slice($sub_start, $sub_end);
   }
-
-  my $subslice = $seq_region_slice->sub_Slice( $sub_start, $sub_end);
-
-  foreach my $l (@$logic_names) {
-    push @{$repeats}, @{$subslice->get_all_RepeatFeatures($l)};
+  else {
+    $subslice = $subsequence_slice;
   }
-
+  
   #
-  # get the dna
+  # get all the features
   #
-  my $subsequence_slice = $self->sub_Slice( $start, $end, $strand );
-  my $dna = $subsequence_slice->seq();
+  my $logic_names = $self->repeat_mask_logic_names();
+  my $soft_mask   = $self->soft_mask();
+  my $not_default_masking_cases = $self->not_default_masking_cases;
+  
+  my @repeats;
+
+  foreach my $l (@$logic_names) {
+    push @repeats, @{$subslice->get_all_RepeatFeatures($l)};
+  }
+  
   #
   # mask the dna
   #
-  $subsequence_slice->_mask_features(\$dna,$repeats,$soft_mask,$not_default_masking_cases);
-
+  my $dna = $subsequence_slice->seq();
+  $subsequence_slice->_mask_features(\$dna,\@repeats,$soft_mask,$not_default_masking_cases);
   return $dna;
 }
 
-
 1;