package Bio::DOOP::Motif;

use strict;
use warnings;

=head1 NAME

  Bio::DOOP::Motif - DOOP database motif object

=head1 VERSION

Version 0.6

=cut

our $VERSION = '0.6';

=head1 SYNOPSIS

  use Bio::DOOP::Motif;

  $db = Bio::DOOP::DBSQL->connect("user","pass","database","somewhere.where.org");
  my $motif = Bio::DOOP::Motif->new($db,"160945");
  print $motif->seq,":",$motif->start," ",$motif->end,"\n";

=head1 DESCRIPTION

  This object represents the conserved motifs.
  You should not use the constructor directly, but
  sometimes it can be useful. In most cases you
  get this object from other objects.

=head1 AUTHORS

  Tibor Nagy, Godollo, Hungary and Endre Sebestyen, Martonvasar, Hungary

=head1 METHODS

=cut

=head2 new

  $motif = Bio::DOOP::Motif->new($db,"1234");
 
  You can create the object with the new method.

  The arguments are the following : Bio::DOOP::DBSQL object, motif_primary_id

=cut

sub new {
	my $dummy          = shift;
	my $db             = shift;
	my $id             = shift;
	my $self           = {};

	my $ret = $db->query("SELECT * FROM motif_feature where motif_feature_primary_id=\"$id\";");

	if ($#$ret == -1) {
		return(-1);
	}

	my @motif = @{$$ret[0]};
	$self->{PRIMARY}   = $motif[0];
	$self->{SUBSET}    = $motif[1];
	$self->{CONSENSUS} = $motif[2];
	$self->{TYPE}      = $motif[3];
	$self->{START}     = $motif[4];
	$self->{END}       = $motif[5];
	$self->{SUBSET_ID} = $motif[6];
	$self->{DB}        = $db;
	bless $self;
	return($self);
}

=head2 type

  $motif_type = $motif->type;

  Returns the type of the motif.

  Return type : string

=cut

sub type {
  my $self                 = shift;
  return($self->{TYPE});
}

=head2 seq

  $motif_seq = $motif->seq;

  Returns the consensus sequence of the motif.

  Return type : string

=cut

sub seq {
  my $self                 = shift;
  return($self->{CONSENSUS});
}

=head2 start

  $start = $motif->start;

  Returns the start position of the motif.

  Return type : string

=cut

sub start {
  my $self                 = shift;
  return($self->{START});
}

=head2 end

  $end = $motif->end;

  Returns the end position of the motif.

  Return type : string;

=cut

sub end {
  my $self                 = shift;
  return($self->{END});
}

=head2 length

  $length = $motif->length;

  Returns the length of the motif.

  Return type : string

=cut

sub length {
  my $self                 = shift;
  return($self->{END} - $self->{START} + 1);
}

=head2 get_id

  $primary_id = $motif->get_id;

  Returns the primary ID of the motif. This is the internal ID from the MySQL database.

  Return type : string

=cut

sub get_id {
  my $self                 = shift;
  return($self->{PRIMARY});
}

=head2 get_subset_id

  $subset_id = $motif->get_subset_id;

  Returns the motif subset primary id.

  Return type : string

=cut

sub get_subset_id {
  my $self                 = shift;
  return($self->{SUBSET_ID});
}

=head2 get_seqfeats

  @feats = @{$motif->get_seqfeats}

  Returns all the sequence features, associated with the motif.

  Return type : arrayref, the array containing Bio::DOOP::SequenceFeature objects.

=cut

sub get_seqfeats {
  my $self                 = shift;
  my $db  = $self->{DB};
  my $id  = $self->{PRIMARY};
  my $ret = $db->query("SELECT sequence_feature_primary_id FROM sequence_feature WHERE motif_feature_primary_id = \"$id\";");

  if ($#$ret == -1) {
  	return(-1);
  }
  my @seqfeats;

  for my $i (@$ret){
     push @seqfeats,Bio::DOOP::SequenceFeature->new($db,$$i[0]);
  }

  return(\@seqfeats);
}

1;