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

cpanm Bio::DOOP::DOOP

perl -MCPAN -e shell
install Bio::DOOP::DOOP