class Network(object):
"""A set of species that are explicitly linked by interactions.
The network is a directed multigraph with labeled edges. The nodes in the graph
are the biochemical species involved. The edges represent an interaction between
two species, and the edge label is a reference to the associated Interaction
object.
Attributes:
None
"""
def __init__(self, species = []):
"""Initializes a new Network object."""
self.__graph = MultiGraph(species)
def __repr__(self):
"""Returns a debugging string representation of this network."""
return "<Network: __graph: " + repr(self.__graph) + ">"
def __str__(self):
"""Returns a string representation of this network."""
return "Network of " + str(len(self.species())) + " species and " + \
str(len(self.interactions())) + " interactions."
def add_species(self, species):
"""Adds species to this network."""
self.__graph.add_node(species)
def add_interaction(self, source, sink, interaction):
"""Adds interaction to this network."""
self.__graph.add_edge(source, sink, interaction)
def source(self, species):
"""Returns list of unique sources for species."""
return self.__graph.parents(species)
def source_interactions(self, species):
"""Returns list of (source, interaction) pairs for species."""
return self.__graph.parent_edges(species)
def sink(self, species):
"""Returns list of unique sinks for species."""
return self.__graph.children(species)
def sink_interactions(self, species):
"""Returns list of (sink, interaction) pairs for species."""
return self.__graph.child_edges(species)
def species(self):
"""Returns list of the species in this network."""
return self.__graph.nodes()
def interactions(self):
"""Returns list of the unique interactions in this network."""
return self.__graph.labels()
class Network(object):
"""A set of species that are explicitly linked by interactions.
The network is a directed multigraph with labeled edges. The nodes in the graph
are the biochemical species involved. The edges represent an interaction between
two species, and the edge label is a reference to the associated Interaction
object.
Attributes:
None
"""
def __init__(self, species=[]):
"""Initializes a new Network object."""
self.__graph = MultiGraph(species)
def __repr__(self):
"""Returns a debugging string representation of this network."""
return "<Network: __graph: " + repr(self.__graph) + ">"
def __str__(self):
"""Returns a string representation of this network."""
return "Network of " + str(len(self.species())) + " species and " + \
str(len(self.interactions())) + " interactions."
def add_species(self, species):
"""Adds species to this network."""
self.__graph.add_node(species)
def add_interaction(self, source, sink, interaction):
"""Adds interaction to this network."""
self.__graph.add_edge(source, sink, interaction)
def source(self, species):
"""Returns list of unique sources for species."""
return self.__graph.parents(species)
def source_interactions(self, species):
"""Returns list of (source, interaction) pairs for species."""
return self.__graph.parent_edges(species)
def sink(self, species):
"""Returns list of unique sinks for species."""
return self.__graph.children(species)
def sink_interactions(self, species):
"""Returns list of (sink, interaction) pairs for species."""
return self.__graph.child_edges(species)
def species(self):
"""Returns list of the species in this network."""
return self.__graph.nodes()
def interactions(self):
"""Returns list of the unique interactions in this network."""
return self.__graph.labels()
def __init__(self, species=[]):
"""Initializes a new Network object."""
self.__graph = MultiGraph(species)
def __init__(self, species = []):
"""Initializes a new Network object."""
self.__graph = MultiGraph(species)
