NAME
Bio::DOOP::ClusterSubset - One element of the cluster
SYNOPSIS
@cluster_subsets = @{$cluster->get_all_subsets};
DESCRIPTION
This object is represents one element from the cluster.
AUTHOR
Tibor Nagy, Godollo, Hungary
METHODS
new
This is the object creation process. Most of the cases you not need to use.
$db = Bio::DOOP::DBSQL->connect("doopuser","dooppasswd","localhost");
$cluster_subset = Bio::DOOP::ClusterSubset->new($db,"123");
get_id
print $cluster_subset->get_id;
Print out the subset primary id. It is the MySQL field id.
get_type
print $cluster_subset->get_type;
print out the subset type.
get_seqno
for(i = 0; i < $cluster_subset->get_seqno; i++){
print $seq[$i];
}
print out all of the sequences that linked to the subset.
get_seqno is the number of the sequences.
get_featno
if ($cluster_subset->get_featno > 4){
print "Lots of features have\n";
}
get_featno is the number of the features that linked to the subset
get_motifno
get_motifno is the number of the motifs that linked to the subset
get_orig
if ($cluster_subset->get_orig eq "y") {
print"The subset is original\n";
}
elsif ($cluster_subset->get_orig eq "n"){
print"The subset is not original\n";
}
if the subset is original, then print: The subset is original
otherwise print: The subset is not original
get_cluster
$cluster_id = $cluster_subset->get_cluster;
the variable is equal with the cluster id, that is contain the subset
get_dialign
print $cluster_subset->get_dialign;
Print out the dialign alignment of the subset
get_fasta_align
print $cluster_subset->get_fasta_align;
Print out the fasta alignment of the subset
get_all_motifs
@motifs = @{$cluster_subset->get_all_motifs};
return the arrayref of all the motifs that contained by the subset
get_all_seqs
@seq = @{$cluster_subset->get_all_seqs};
Return the arrayref of all the sequences that contained by the subset