NAME
Bio::DOOP::Cluster - DoOP cluster object
VERSION
Version 0.10
SYNOPSIS
This object represents a cluster. You can access properties through the methods.
Usage:
$cluster = Bio::DOOP::Cluster->new($db,"81007400","500");
print $cluster->get_cluster_id;
DESCRIPTION
AUTHOR
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
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 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