minor changes, formatting

modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm

@@ -129,7 +129,7 @@ sub register_region{
   $self->throw("$assmapper is not a Bio::EnsEMBL::AssemblyMapper")
     unless $assmapper->isa("Bio::EnsEMBL::AssemblyMapper");
 
-  my $chr = $self->db->get_ChromosomeAdaptor()->fetch_by_name( $chr_name );
+  my $chr = $self->db->get_ChromosomeAdaptor()->fetch_by_chr_name( $chr_name );
   my $chr_id = $chr->dbID();
   my $max_assembly_contig = $self->db()->get_MetaContainer->get_max_assembly_contig();
 
@@ -142,7 +142,7 @@ sub register_region{
          ass.chr_start,
          ass.chr_end
       from
-         assembly ass,
+         assembly ass
       where
          ass.chromosome_id = $chr_id and
          ? <= ass.chr_end  and

modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm

@@ -1124,7 +1124,8 @@ sub set_adaptor() {
   Arg [1]    : List of names of feature adaptors to get. If no adaptor names are given, all the defined adaptors are returned.
   Example    : $db->get_GenericFeature("SomeFeature", "SomeOtherFeature")
   Description: Returns a hash containing the named feature adaptors (or all feature adaptors).
-  Returntype : Hash containing the named feature adaptors (or all feature adaptors).
+  Returntype : reference to a Hash containing the named 
+               feature adaptors (or all feature adaptors).
   Exceptions : If any of the the named generic feature adaptors do not exist.
   Caller     : external
 
@@ -1132,22 +1133,22 @@ sub set_adaptor() {
 
 sub get_GenericFeatureAdaptors() {
 
-	my ($self, @names) = @_;
+  my ($self, @names) = @_;
 
-  my %adaptors = {};
+  my %adaptors = ();
 
-	if (!@names) {
-		%adaptors = %{$self->{'generic_feature_adaptors'}};
-	} else {
-		foreach my $name (@names) {
-			if (!exists($self->{'generic_feature_adaptors'}->{$name})) {
-				$self->throw("No generic feature adaptor has been defined for $name" );
-			}
-			%adaptors->{$name} = $self->{'generic_feature_adaptors'}->{$name};
-		}
-	}
+  if (!@names) {
+    %adaptors = %{$self->{'generic_feature_adaptors'}};
+  } else {
+    foreach my $name (@names) {
+      if (!exists($self->{'generic_feature_adaptors'}->{$name})) {
+	$self->throw("No generic feature adaptor has been defined for $name" );
+      }
+      $adaptors{$name} = $self->{'generic_feature_adaptors'}->{$name};
+    }
+  }
 
-	return %adaptors;
+  return \%adaptors;
 
 }
 

modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm

@@ -70,6 +70,8 @@ sub fetch_by_RawContig_start_end_strand {
   my ( $self, $contig, $start, $end, $strand, $compressed ) = @_;
   my $sth;
   
+  $compressed ||= 0;
+
   if( $start < 1 ) {
     $self->throw( "Wrong parameters" );
   }

modules/Bio/EnsEMBL/Slice.pm

@@ -1496,25 +1496,25 @@ sub get_generic_features() {
 
   my ($self, @names) = @_;
 
-	my $db = $self->adaptor()->db();
+  my $db = $self->adaptor()->db();
 
-	my %features = {};   # this will hold the results
+  my %features = ();   # this will hold the results
 
-	# get the adaptors for each feature
-	my %adaptors = $db->get_GenericFeatureAdaptors(@names);
+  # get the adaptors for each feature
+  my %adaptors = %{$db->get_GenericFeatureAdaptors(@names)};
 
-	foreach my $adaptor_name (keys(%adaptors)) {
+  foreach my $adaptor_name (keys(%adaptors)) {
 		
-		my $adaptor_obj = %adaptors->{$adaptor_name};
-		# get the features and add them to the hash
-		my $features_ref = $adaptor_obj->fetch_all_by_Slice($self);
-		# add each feature to the hash to be returned
-		foreach my $feature (@$features_ref) {
-			%features->{$adaptor_name} = $feature;
-		}
-	}
-
-	return %features;
+    my $adaptor_obj = %adaptors->{$adaptor_name};
+    # get the features and add them to the hash
+    my $features_ref = $adaptor_obj->fetch_all_by_Slice($self);
+    # add each feature to the hash to be returned
+    foreach my $feature (@$features_ref) {
+      $features{$adaptor_name} = $feature;
+    }
+  }
+
+  return \%features;
 
 }
 

modules/t/canonicalDBAdaptor.t

@@ -119,11 +119,11 @@ ok($db->add_GenericFeatureAdaptor("Simple", $sfa));
 
 # Check get-ing the above
 # by name ...
-my %generic_adaptors = $db->get_GenericFeatureAdaptors("Simple", "Repeat");
+my %generic_adaptors = %{$db->get_GenericFeatureAdaptors("Simple", "Repeat")};
 ok(%generic_adaptors);
 
 # no arg should return all
-%generic_adaptors = $db->get_GenericFeatureAdaptors();
+%generic_adaptors = %{$db->get_GenericFeatureAdaptors()};
 my $size = keys(%generic_adaptors);
 ok($size == 2);
 
@@ -135,5 +135,5 @@ ok($@);
 my $slice = $db->get_SliceAdaptor()->fetch_by_chr_start_end('X', 1, 10000);
 ok($slice);
 
-my %features = $slice->get_generic_features();
-ok(%features);
+my %features = %{$slice->get_generic_features()};
+ok(!%features);