my ($self) = @_;
  my @query = @{$self->query};
  my @target = @{$self->target};
  my @q_not_matched;
  @query = @{$self->fast_sort(\@query)};
  @target = @{$self->fast_sort(\@target)};
  print "\nThere are ".@query." query features\n";
  print "There are ".@target." target features\n\n";
  my $num_t_feats = scalar(@target);
  my $start_ind = 0;
 QUERY:foreach my $feat(@query){
    if($start_ind > $num_t_feats){   #as the query features and target feature have been
      push(@q_not_matched, $feat);   #sorted, if there are more query features than target
      next QUERY;                    #features, the query will surely fail to find a match.
    }
  TARGET:for (my $i = $start_ind; $i< $num_t_feats; $i++){
      my $t_feat = $target[$i];
      next TARGET if(!$t_feat);
      if($t_feat->start == $feat->start &&
         $t_feat->end == $feat->end &&
         $t_feat->strand == $feat->strand){
        if($self->verbosity){                                              
          print "Got match\n";
          print "t_feat = " . $t_feat->start . " " . $t_feat->end . " ".
            $t_feat->strand."\n";
          print "feat   = " . $feat->start . " " . $feat->end . " ".
            $feat->strand."\n";
        }
        $target[$i] = undef;   #those targets which have been matched with query were "wiped out"
        next QUERY;
      }elsif($t_feat->start > $feat->start){
        push(@q_not_matched, $feat);
        next QUERY;
      }elsif($t_feat->end < $feat->start){
        $start_ind++;
      }
    }
  }
     if (scalar(@q_not_matched)>0) {  
       print "Unmatched query features\n";
       $self->feature_info(\@q_not_matched);
     }
     else {   
       print "No unmatched query features were found.\n";
       print "If the analysis has run successfully, this indicates that ".
      "all query features had matching target features.\n";
    }
 
     my @unmatched_targets;
     for (my $i = 0; $i < scalar(@target); $i++) {
        if (defined $target[$i]) {
          push (@unmatched_targets, $target[$i]);
        }
     }
  
     if (scalar(@unmatched_targets) > 0) {    
       print "\nUnmatched target features\n";
       $self->feature_info(\@target);
     }
     else {
       print "All target features had matching query features.\n";
     }

  my ($self, $db) = @_;
  if(!$db->isa('Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor')){
    throw("Can't run the RuleManager with $db you need a ".
          "Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor");
  }
  return;

  my ($self, $array) = @_;
  my @array = map { $_->[1] } sort { $a->[0] <=> $b->[0] } 
    map { [$_->start, $_] } @$array;
  return\@ array;

  my ($self, $array) = @_;
  my $name;
  foreach my $f(@$array){
    if(!$f){
      next;
    }
    $name = $f->analysis->logic_name if(!$name);
    print $name." ".$f->slice->seq_region_name." ".$f->start." ".$f->end.
      " ".$f->strand."\n";
  }

  my ($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  &verbose('WARNING');
  my ($query, $target, $verbose) = rearrange( ['QUERY', 'TARGET',
                                               'VERBOSE'], @args);
  $self->query($query);
  $self->target($target);
  $self->verbosity($verbose);
  return $self;

  my($self, $table_names, $query_db, $ref_db) = @_;
  if(!$table_names){
    $table_names = $self->tables_to_compare;
  }
  $self->db_type_check($query_db);
  $self->db_type_check($ref_db);
  if(@$table_names == 0){
    print "FeatureComparison:pipeline_compare --- you passed in no tables ".
      "so we can't make any comparisons\n";
    return;
  }
  my $query_numbers = {};
  my $ref_numbers = {};
  foreach my $table(@$table_names){
    my $sql = "select logic_name, count(*) from analysis, ";
    $sql .= $table." where analysis.analysis_id=".$table.".analysis_id ".
      "group by logic_name\n";
    $query_numbers = $self->run_query($sql, $query_db, $query_numbers);
    $ref_numbers = $self->run_query($sql, $ref_db, $ref_numbers);
  }
  print "\nThere are ".keys(%$query_numbers)." analysis in the query database ".
    $query_db->dbname." and ".keys(%$ref_numbers)." analysis in the reference ".
      "database ".$ref_db->dbname.", all from ".@$table_names." tables\n\n";
  printf("%-15s %-15s %-15s\n", 'logic_name', 'query_count', 'ref_count');
  printf("%-15s %-15s %-15s\n", '----------', '-----------', '---------');
  foreach my $logic_name(keys(%$query_numbers)){
    printf("%-15s %-15s %-15s\n", $logic_name, $query_numbers->{$logic_name},
           $ref_numbers->{$logic_name});
  }
  print "\n";

  my ($self, $query) = @_;
  if($query){
    throw("query must be an array ref not a ".$query) 
      unless(ref($query) eq 'ARRAY'); 
    $self->{'query'} = $query;
  }
  return $self->{'query'};

  my ($self, $sql, $db, $hash) = @_;
  my $sth = $db->prepare($sql);
  $sth->execute;
  while(my($logic_name, $count) = $sth->fetchrow){
    if(!$hash->{$logic_name}){
      $hash->{$logic_name} = $count;
    }else{
      warning($logic_name." already appears in ".$hash." with count ".
            $hash->{$logic_name}." from database ".$db->dbname);
    }
  }
  return $hash;

  my ($self, $target) = @_;
  if($target){
    throw("tables to compare must be an array ref not a ".$target) 
      unless(ref($target) eq 'ARRAY');
    $self->{'tables'} = $target;
  }
  return $self->{'tables'};

  my ($self, $target) = @_;
  if($target){
    throw("target must be an array ref not a ".$target) 
      unless(ref($target) eq 'ARRAY');
    $self->{'target'} = $target;
  }
  return $self->{'target'};

  my $self = shift;
  $self->{'verbose'} = shift if(@_);
  return $self->{'verbose'};