Tibor Nagy > Bio-DOOP-DOOP-1.02 > Bio::DOOP::ClusterSubset

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Bio-DOOP-DOOP-1.02.tar.gz

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Module Version: 0.12   Source   Latest Release: Bio-DOOP-DOOP-1.04

NAME ^

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

VERSION ^

Version 0.12

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).

AUTHORS ^

  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.
  
  Arguments :

  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.

  The get_seqno method 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";
  }

  The get_featno method returns the total number of features in the subset.

  Return type :

  string

get_motifno

  $motifs = $cluster_subset->get_motifno;

  The get_motifno method 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
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