make use of meta_coord.max_length to further optomize generated feature queries

modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm

@@ -491,6 +491,10 @@ sub _slice_fetch {
 
     if($feat_cs->equals($slice_cs)) {
       # no mapping is required if this is the same coord system
+
+      my $max_len =
+        $mcc->fetch_max_length_by_CoordSystem_feature_type($feat_cs,$tab_name);
+
       my $constraint = $orig_constraint;
 
       my $sr_id = $self->db->get_SliceAdaptor->get_seq_region_id($slice);
@@ -499,6 +503,13 @@ sub _slice_fetch {
           "${tab_syn}.seq_region_id = $sr_id AND " .
           "${tab_syn}.seq_region_start <= $slice_end AND " .
           "${tab_syn}.seq_region_end >= $slice_start";
+
+      if($max_len) {
+        my $min_start = $slice_start - $max_len;
+        $constraint .=
+          " AND ${tab_syn}.seq_region_start >= $min_start";
+      }
+
       my $fs = $self->generic_fetch($constraint,undef,$slice);
 
       # features may still have to have coordinates made relative to slice
@@ -540,6 +551,10 @@ sub _slice_fetch {
 
       } else {
         # do multiple split queries using start / end constraints
+
+        my $max_len =
+          $mcc->fetch_max_length_by_CoordSystem_feature_type($feat_cs,
+                                                             $tab_name);
         my $len = @coords;
         for(my $i = 0; $i < $len; $i++) {
           my $constraint = $orig_constraint;
@@ -548,6 +563,13 @@ sub _slice_fetch {
               "${tab_syn}.seq_region_id = "     . $ids[$i] . " AND " .
               "${tab_syn}.seq_region_start <= " . $coords[$i]->end() . " AND ".
               "${tab_syn}.seq_region_end >= "   . $coords[$i]->start();
+
+          if($max_len) {
+            my $min_start = $coords[$i]->start() - $max_len;
+            $constraint .=
+              " AND ${tab_syn}.seq_region_start >= $min_start";
+          }
+
           my $fs = $self->generic_fetch($constraint,$mapper,$slice);
 
           $fs = _remap($fs, $mapper, $slice);

modules/Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm

@@ -24,12 +24,13 @@ sub new {
   # and cache them
   #
   my $sth = $self->prepare
-    ('SELECT table_name, coord_system_id  FROM meta_coord');
+    ('SELECT table_name, coord_system_id, max_length  FROM meta_coord');
   $sth->execute();
 
-  while(my ($table_name, $cs_id) = $sth->fetchrow_array()) {
+  while(my ($table_name, $cs_id, $max_length) = $sth->fetchrow_array()) {
     $self->{'_feature_cache'}->{lc($table_name)} ||= [];
     push @{$self->{'_feature_cache'}->{lc($table_name)}}, $cs_id;
+    $self->{'_max_len_cache'}->{$cs_id}->{lc($table_name)} = $max_length;
   }
   $sth->finish();
 
@@ -49,7 +50,7 @@ sub new {
                the API to perform queries to these tables and to ensure that
                features are only stored in appropriate coordinate systems.
   Returntype : listref of Bio::EnsEMBL::CoordSystem objects
-  Exceptions : none
+  Exceptions : throw if name argument not provided
   Caller     : BaseFeatureAdaptor
 
 =cut
@@ -84,6 +85,36 @@ sub fetch_all_CoordSystems_by_feature_type {
 
 
 
+=head2 fetch_max_length_by_CoordSystem_feature_type
+
+  Arg [1]    : Bio::EnsEMBL::CoordSystem $cs
+  Arg [2]    : string $table
+  Example    : $max_len = 
+                $mcc->fetch_max_length_by_CoordSystem_feature_type($cs,'gene');
+  Description: Returns the maximum length of features of a given type in
+               a given coordinate system.
+  Returntype : int or undef
+  Exceptions : throw on incorrect argument
+  Caller     : BaseFeatureAdaptor
+
+=cut
+
+
+sub fetch_max_length_by_CoordSystem_feature_type {
+  my $self = shift;
+  my $cs = shift;
+  my $table = shift;
+
+  if(!ref($cs) || !$cs->isa('Bio::EnsEMBL::CoordSystem')) {
+    throw('Bio::EnsEMBL::CoordSystem argument expected');
+  }
+
+  throw("Table name argument is required") unless $table;
+
+  return $self->{'_max_len_cache'}->{$cs->dbID()}->{lc($table)};
+}
+
+
 
 =head2 add_feature_type