NAME
Bio::Network::Node - describe a Node, either a protein or protein complex
SYNOPSIS
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;
}
}
DESCRIPTION
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.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
http://bugzilla.open-bio.org/
AUTHORS
Brian Osborne bosborne at alum.mit.edu
Maintained by Brian Osborne
new
Name : new
Purpose : Constructor for an Node object
Usage : my $node = Bio::Network::Node->new(-protein => $seqobj)
or
my $node = Bio::Network::Node->new(-protein => [($seqobj1,$seqobj2)])
or
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
or
-protein => Reference to an array containing 1 or more
Sequence objects
or
-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 :
proteins
Name : proteins
Purpose : Get the proteins in a Node or get a count of proteins in the Node
Usage : my $count = $node->proteins
or
my @proteins = $node->proteins
Returns : Gets an array of Sequence objects or a count of
the number of Sequence objects
Arguments : None
next_protein
Name :
Purpose :
Usage :
Returns :
Arguments :
is_complex
Name : is_complex
Purpose : Get or set whether a node is a protein or a protein complex
Usage : if ($node->is_complex){ ... }
or
$node->is_complex(1)
Returns : 1 if the Node has more than 1 proteins, 0 if not
Arguments : None
subunit_number
Name : subunit_number
Purpose : Get or set the number of a given protein in a protein
complex.
Usage : $num = $node->subunit_number($protein)
or
$node->subunit_number($protein,$number)
Returns : A number, whether get or set
Arguments : None or a Sequence object in a given Node