NAME

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

VERSION

Version 0.6

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";

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.

AUTHORS

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

METHODS

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

type

  $motif_type = $motif->type;

  Returns the type of the motif.

  Return type : string

seq

  $motif_seq = $motif->seq;

  Returns the consensus sequence of the motif.

  Return type : string

start

  $start = $motif->start;

  Returns the start position of the motif.

  Return type : string

end

  $end = $motif->end;

  Returns the end position of the motif.

  Return type : string;

length

  $length = $motif->length;

  Returns the length of the motif.

  Return type : string

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

get_subset_id

  $subset_id = $motif->get_subset_id;

  Returns the motif subset primary id.

  Return type : string

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.