/ 
Bio-DOOP-DOOP-0.08
/ Bio::DOOP::ClusterSubset

NAME

Bio::DOOP::ClusterSubset - One subset of a cluster

VERSION

Version 0.08

SYNOPSIS

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

DESCRIPTION

This object represents one subset of a cluster. A subset is a set of homologous sequences,
hopefully monophyletic, grouped by evolutionary distance from the reference species (Arabidopsis
or human).

AUTHOR

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

METHODS

new

$cluster_subset = Bio::DOOP::ClusterSubset->new($db,"123");

You can create the object with the new method.
The arguments are the following : Bio::DOOP::DBSQL object, subset_primary_id

get_id

print $cluster_subset->get_id;

Prints out the subset primary id. This is the internal ID from the MySQL database.
Return type: string.

get_type

print $cluster_subset->get_type;

Prints out the subset type.
Return type: string.

get_seqno

for(i = 0; i < $cluster_subset->get_seqno; i++){
    print $seq[$i];
}

Prints out all sequences linked to the subset.

get_seqno returns the number of sequences in the
subset.
Return type: string

get_featno

if ($cluster_subset->get_featno > 4){
    print "We have lots of features!!!\n";
}

get_featno returns the total number of features in the
subset.
Return type: string

get_motifno

get_motifno returns the number of motifs in the
subset.
Return type: string

get_orig

if ($cluster_subset->get_orig eq "y") {
    print "This is the original cluster!\n";
}
elsif ($cluster_subset->get_orig eq "n"){
    print "This is some smaller subset!\n";
}

Return type: string ('y' or 'n')

get_cluster

$cluster_id = $cluster_subset->get_cluster;

Returns the ID of the cluster, from which the subset originates.
Return type: string

get_dialign

print $cluster_subset->get_dialign;

Prints out the dialign format alignment of the subset.
Return type: string

get_fasta_align

print $cluster_subset->get_fasta_align;

Prints out the fasta format alignment of the subset.
Return type: string

get_all_motifs

@motifs = @{$cluster_subset->get_all_motifs};

Returns the arrayref of all motifs associated with the subset.
Return type: arrayref, the array containig Bio::DOOP::Motif objects

get_all_seqs

@seq = @{$cluster_subset->get_all_seqs};

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