removed unreliable fetch_grouped function

modules/Bio/EnsEMBL/Map/DBSQL/DitagFeatureAdaptor.pm

@@ -237,82 +237,6 @@ sub fetch_all_by_Slice {
 }
 
 
-=head2 fetch_grouped
-
-  Arg [1]    : (optional) ditag id
-  Arg [2]    : (optional) ditag type
-  Arg [3]    : (optional) Bio::EnsEMBL::Slice
-  Example    : $gouped_tags = $ditagfeature_adaptor->fetch_grouped(undef, "ZZ11", undef);
-  Description: Retrieves Features from the database in their start-end groups;
-               The start will be the lower seq_region_start, the end the higher seq_region_end.
-               In context this should refer to potential transcript start and end locations.
-               This is a convinience method for analysing the ditag mappings, in general
-               fetch_grouped_ditagFeatures should be used to fetch proper objects.
-  Returntype : listref of hashes similar to DitagFeatures:
-                 %grouped_tag( -slice         => $slice,
-                               -start         => $seqstart,
-			       -end           => $seqend,
-			       -strand        => $strand,
-			       -tag_count     => $tagcount,
-			       -hit_strand    => $hit_strand,
-			       -ditag_id      => $ditag_id,
-			       -ditag_pair_id => $ditag_pair_id,
-			     );
-  Caller     : general
-
-=cut
-
-sub fetch_grouped {
-  my ($self, $ditagid, $tagtype, $slice) = @_;
-
-  my (@grouped_tags, @querywords);
-  my $sql = "SELECT df.seq_region_id, MIN(df.seq_region_start) AS minstart, 
-             MAX(df.seq_region_end) AS maxend, df.seq_region_strand, 
-             df.hit_strand, df.ditag_id, df.ditag_pair_id, d.tag_count 
-             FROM ditag_feature df, ditag d 
-             WHERE df.ditag_id=d.ditag_id ";
-
-  if($tagtype){
-    $sql .= " AND d.type = \"".$tagtype."\"";
-  }
-  if($ditagid){
-    $sql .= " AND df.ditag_id = ".$ditagid;
-  }
-  if($slice){
-    $sql .= " AND df.seq_region_id     = ".$slice->get_seq_region_id.
-            " AND df.seq_region_start >= ".$slice->start.
-	    " AND df.seq_region_end   <= ".$slice->end;
-  }
-  $sql .= " GROUP BY df.ditag_id, df.ditag_pair_id".
-          " ORDER BY df.seq_region_id, minstart, maxend";
-
-  my $sth = $self->prepare($sql);
-  $sth->execute();
-
-  my ( $seqreg, $seqstart, $seqend, $strand, $hit_strand, $ditag_id, $ditag_pair_id, $tagcount );
-  $sth->bind_columns( \$seqreg,        \$seqstart,    \$seqend,
-                      \$strand,        \$hit_strand,  \$ditag_id,
-                      \$ditag_pair_id, \$tagcount );
-
-  while ( $sth->fetch ) {
-    my $alt_slice = $self->db->get_SliceAdaptor->fetch_by_seq_region_id($seqreg);
-
-    my %grouped_tag = ( slice         => $alt_slice,
-			start         => $seqstart,
-			end           => $seqend,
-			strand        => $strand,
-			tag_count     => $tagcount,
-			hit_strand    => $hit_strand,
-			ditag_id      => $ditag_id,
-			ditag_pair_id => $ditag_pair_id,
-		      );
-    push @grouped_tags, \%grouped_tag;
-  }
-
-  return \@grouped_tags;
-}
-
-
 =head2 _fetch
 
   Arg [1]    : statement handler

modules/t/ditagFeatureAdaptor.t

@@ -2,7 +2,7 @@ use strict;
 
 BEGIN { $| = 1;  
 	use Test ;
-	plan tests => 14;
+	plan tests => 12;
 }
 
 use Bio::EnsEMBL::Test::MultiTestDB;
@@ -84,7 +84,7 @@ ok($testfeature && $testfeature->isa('Bio::EnsEMBL::Map::DitagFeature'));
 $multi->restore('core', 'ditag_feature');
 
 ########
-# 5-13 #
+# 5-11 #
 ########
 
 #test fetch methods
@@ -120,15 +120,10 @@ ok(scalar(@$dfs) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature'));
 
 #use logic-name
 $dfs = $dfa->fetch_all_by_Slice($slice, '', $logic_name);
-ok(1);#scalar(@$dfs) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature'));
-
-#test fetch_grouped
-$dfs = $dfa->fetch_grouped('', $tag_library);
-ok(scalar @$dfs);
-ok($dfs->[0]->{'ditag_id'} && $dfs->[0]->{'start'} && $dfs->[0]->{'end'});
+ok(scalar(@$dfs) && $dfs->[0]->isa('Bio::EnsEMBL::Map::DitagFeature'));
 
 ######
-# 14 #
+# 12 #
 ######
 
 #test list_dbIDs