NAME
Bio::DOOP::ClusterSubset - One element of the cluster
VERSION
Version 0.07
SYNOPSIS
@cluster_subsets = @{$cluster->get_all_subsets};
DESCRIPTION
This object is represents one subset from the cluster. A subset is a set of homologous sequences
those are groupped by evolution distance.
AUTHOR
Tibor Nagy, Godollo, Hungary
METHODS
new
This is the object creation process. Most of the cases you do 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.
Return type: string
get_type
print $cluster_subset->get_type;
Print out the subset type.
Return type: string
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.
Return type: string
get_featno
if ($cluster_subset->get_featno > 4){
print "Lots of features have\n";
}
get_featno is the number of the contained features.
Return type: string
get_motifno
get_motifno is the number of the contained motifs.
Return type: string
get_orig
if ($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.
Return type: string
get_cluster
$cluster_id = $cluster_subset->get_cluster;
The variable is equal with the cluster id, that is contain the subset.
Return type: string
get_dialign
print $cluster_subset->get_dialign;
Print out the dialign alignment of the subset.
Return type: string
get_fasta_align
print $cluster_subset->get_fasta_align;
Print out the fasta alignment of the subset.
Return type: string
get_all_motifs
@motifs = @{$cluster_subset->get_all_motifs};
Returns the arrayref of all the motifs that contained by the subset.
Return type: listref of Bio::DOOP::Motif
get_all_seqs
@seq = @{$cluster_subset->get_all_seqs};
Return the arrayref of all the sequences that contained by the subset.
Return type: listref of Bio::DOOP::Sequence