/ 
Bio-DOOP-DOOP-0.28
/ Bio::DOOP::Cluster

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 uniq
identifier. This is the cluster id. There are three promoter sizes (500,1000,3000 bp), so the uniq
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