NAME

  Bio::DOOP::Cluster - DoOP cluster object

VERSION

Version 0.11

SYNOPSIS

  This object represents a cluster. You can access the properties through the methods.

  Usage:

  $cluster = Bio::DOOP::Cluster->new($db,"81007400","500");
  print $cluster->get_cluster_id;

DESCRIPTION

AUTHORS

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

METHODS

new

  $cluster = Bio::DOOP::Cluster->new($db,"8010110","500");

  Create a new cluster object from the cluster id and promoter type. Every promoter cluster has a unique
  identifier. This is the cluster id. There are three promoter sizes (500,1000,3000 bp), so the unique
  cluster is identified by two parameters : cluster id and promoter type.

  Return type :

  Bio::DOOP::Cluster object

new_by_id

  Bio::DOOP::Cluster->new_by_id($db,"2453");

  Used by internal MySQL queries.
  Return type :

  Bio::DOOP::Cluster object

get_id

  $cluster_id = $cluster->get_id;

  Returns the MySQL id.

  Return type :

  string

get_cluster_id

  $cluster_id = $cluster->get_cluster_id;

  Returns the cluster id.
  Return type: string

get_promo_type

  $pt = $cluster->get_promo_type;

  Returns the size of the promoter (500,1000,3000 bp).
  Return type: string

get_type

  print $cluster->get_type;

  Returns the type of the promoter (The available return types are the following: 1,2,3,4,5n,6n). 
  See http://doop.abc.hu for more details.
  Return type: string

get_date

  $date = $cluster->get_date;

  Returns the date when the cluster was last modified.
  Return type: string

get_version

  print $cluster->get_version;

  Returns the version of the cluster.
  Return type: string

get_all_subsets

  @subsets = @{$cluster->get_all_subsets};

  Returns the arrayref of all subsets associated with the cluster.
  Return type: arrayref, the array containing Bio::DOOP::ClusterSubset objects

get_subset_by_type

  $subset = $cluster->get_subset_by_type("B");
  if ($subset == -1){
     print"No subset! Try another subset type\n";
  }

  Returns the subset specified by type.
  Return type: Bio::DOOP::ClusterSubset object

get_available_types

  @types = @{$cluster->get_available_types};

  Returns all available cluster subset types.
  Return type: arrayref of string

get_all_seqs

  @seqs = @{$cluster->get_all_seqs};

  Returns the arrayref of all sequences associated with the cluster.
  Return type: arrayref, the array containig Bio::DOOP::Sequence objects

get_orig_subset

  @subsets = @{$cluster->get_orig_subset};

  Returns the original subset, containing the whole cluster.
  Return type: Bio::DOOP::ClusterSubset object

get_ref_seq

  $refseq = $cluster->get_ref_seq;

  Returns the cluster reference sequence (human or arabidopsis).
  Return type: Bio::DOOP::Sequence object