NAME

  Bio::DOOP::Cluster - Doop cluster object

VERSION

Version 0.07

SYNOPSIS

  This object represent a cluster. You can access properties through the methods.
  Usage:

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

AUTHOR

  Tibor Nagy, Godollo, Hungary

METHODS

new

  $cluster = Bio::DOOP::Cluster->new($db,"8010110","500");
  Create a new cluster object from cluster id and promoter type. Every promoter sequence has an uniq number. 
  This number is the cluster id. We have three promoter size (500,1000,3000 bps), so the uniq sequence is
  identified by two parameter: cluster id and promoter type.
  Return type: Bio::DOOP::Cluster

new_by_id

  Bio::DOOP::Cluster->new_by_id($db,"2453");
  Used by internal MySQL querys
  Return type: Bio::DOOP::Cluster

get_id

  $cluster_id = $cluster->get_id;

  Returns with the MySQL id.
  Return type: string

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 bps). This is the maximum number.
  Return type: string

get_type

  print $cluster->get_type;

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

get_date

  $date = $cluster->get_date;

  Returns the cluster time when we add to the database.
  Return type: string

get_version

  print $cluster->get_version;

  Returns the version number.

get_all_subsets

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

  Returns all the subsets that is linked to this cluster.
  Return type: Bio::DOOP::ClusterSubset

get_all_seqs

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

  Return all the sequences that are linked to the cluster
  Return type: Bio::DOOP::Sequence

get_orig_subset

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

  Return the original subset, that is contain the whole cluster.
  Return type: Bio::DOOP::ClusterSubset

get_ref_seq

  $refseq = $cluster->get_ref_seq;

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

cpanm Bio::DOOP::DOOP

perl -MCPAN -e shell
install Bio::DOOP::DOOP