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Bio/DB/GFF/Adaptor/dbi/pg.pm  view on Meta::CPAN

}

sub min_bin {
  my $self = shift;
  return $self->meta('min_bin') || MIN_BIN;
}
sub max_bin {
  my $self = shift;
  return $self->meta('max_bin') || MAX_BIN;
}
sub straight_join_limit {
  my $self = shift;
  return $self->meta('straight_join_limit') || STRAIGHT_JOIN_LIMIT;
}


sub _feature_by_name {
  my $self = shift;
  my ($class,$name,$location,$callback) = @_;
  $callback || $self->throw('must provide a callback argument');

  my @bin_parts      = split /\s*OR/, $self->bin_query($location->[1],$location->[2]) if $location;
  my $select         = $self->make_features_select_part;
  my $from           = $self->make_features_from_part(undef,{sparse_groups=>1});
  my ($where,@args)  = $self->make_features_by_name_where_part($class,$name);
  my $join           = $self->make_features_join_part;
  my $range          = $self->pg_make_features_by_range_where_part('overlaps',
                                                                {refseq=>$location->[0],
                                                                 class =>'',
                                                                 start=>$location->[1],
                                                                 stop =>$location->[2]}) if $location;

  my @temp_args;
  my @query_pieces;
  my $query;
  if (@bin_parts) {
    foreach my $bin (@bin_parts) {
      my $temp_query = "SELECT $select FROM $from WHERE $join AND $where AND $range AND $bin\n";
      push @temp_args, @args;
      push @query_pieces, $temp_query;
    }

    @args  = @temp_args;
    $query = join("UNION\n", @query_pieces);

  } else {
    $query  = "SELECT $select FROM $from WHERE $where AND $join";
  }

  my $sth    = $self->dbh->do_query($query,@args);

  my $count = 0;
  while (my @row = $sth->fetchrow_array) {
    $callback->(@row);
    $count++;
  }
  $sth->finish;
  return $count;
}

sub update_sequences {
  my $self = shift;
  my $dbh  = $self->features_db;
 
  $dbh->do("SELECT setval('public.fdata_fid_seq', max(fid)+1) FROM fdata");
  $dbh->do("SELECT setval('public.fattribute_fattribute_id_seq', max(fattribute_id)+1) FROM fattribute");
  $dbh->do("SELECT setval('public.fgroup_gid_seq', max(gid)+1) FROM fgroup");
  $dbh->do("SELECT setval('public.ftype_ftypeid_seq', max(ftypeid)+1) FROM ftype");

  1;
}

=head2 make_features_by_name_where_part

 Title   : make_features_by_name_where_part
 Usage   : $db->make_features_by_name_where_part
 Function: Overrides a function in Bio::DB::GFF::Adaptor::dbi to insure
           that searches will be case insensitive. It creates the SQL
           fragment needed to select a feature by its group name & class
 Returns : a SQL fragment and bind arguments
 Args    : see below
 Status  : Protected

=cut

sub make_features_by_name_where_part {
  my $self = shift;
  my ($class,$name) = @_;

  if ($name !~ /\*/) {
    #allows utilization of an index on lower(gname)
    return ("fgroup.gclass=? AND lower(fgroup.gname) = lower(?)",$class,$name);
  }
  else {
    $name =~ tr/*/%/;
    return ("fgroup.gclass=? AND lower(fgroup.gname) LIKE lower(?)",$class,$name);
  }
}

#
# Methods from dbi.pm that need to be overridden to make
# searching for fref case insensitive
#
#
sub get_dna {
  my $self = shift;
  my ($ref,$start,$stop,$class) = @_;

  my ($offset_start,$offset_stop);

  my $has_start = defined $start;
  my $has_stop  = defined $stop;

  my $reversed;
  if ($has_start && $has_stop && $start > $stop) {
    $reversed++;
    ($start,$stop) = ($stop,$start);
  }

  # turn start and stop into 0-based offsets
  my $cs = $self->dna_chunk_size;