Author image Christopher Fields
and 1 contributors


Bio::Network::Node - describe a Node, either a protein or protein complex


  use Bio::Network::Node;

  my $node = Bio::Network::Node->new(-protein => [($seq1,$seq2)]);

  # or get nodes from a network:
  my @nodes = $graph->nodes;
  for my $node (@nodes) {
     my @proteins = $node->proteins
     for my $protein (@proteins) {
        print "Sequence is ", $protein->seq;


This class describes nodes in a network of interactions. A node is either a protein, a Sequence object, or a protein complex, which is a collection of Sequence objects.


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Brian Osborne bosborne at

Maintained by Brian Osborne


 Name       : new
 Purpose    : Constructor for an Node object
 Usage      : my $node = Bio::Network::Node->new(-protein => $seqobj)   
              my $node = Bio::Network::Node->new(-protein => [($seqobj1,$seqobj2)])  
              my $node = Bio::Network::Node->new(-protein => 
                                               [ [(2, $seqobj1)],
                                                                                                                                 [(1, $seqobj2)],
                                                 [(3, $seqobj3)] ];
 Returns    : A new Bio::Network::Node object 
 Arguments  : -protein => 1 Sequence object    
                                  -protein => Reference to an array containing 1 or more
                          Sequence objects       
              -protein => Reference to an array of arrays where the elements are 
                          arrays containing a number denoting the number of subunits of 
                          a protein in the protein complex and a Sequence object
 Notes      :


 Name       : proteins
 Purpose    : Get the proteins in a Node or get a count of proteins in the Node
 Usage      : my $count = $node->proteins   
              my @proteins = $node->proteins 
 Returns    : Gets an array of Sequence objects or a count of 
              the number of Sequence objects
 Arguments  : None


 Name       :
 Purpose    :
 Usage      :
 Returns    :
 Arguments  :


 Name       : is_complex
 Purpose    : Get or set whether a node is a protein or a protein complex
 Usage      : if ($node->is_complex){ ... }
 Returns    : 1 if the Node has more than 1 proteins, 0 if not
 Arguments  : None


 Name       : subunit_number
 Purpose    : Get or set the number of a given protein in a protein
 Usage      : $num = $node->subunit_number($protein)    
 Returns    : A number, whether get or set
 Arguments  : None or a Sequence object in a given Node