class Network:
"""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=()):
"""Initialize a new Network object."""
self.__graph = MultiGraph(species)
def __repr__(self):
"""Return a debugging string representation of this network."""
return "<Network: __graph: " + repr(self.__graph) + ">"
def __str__(self):
"""Return a string representation of this network."""
return "Network of %i species and %i interactions." % (
len(self.species()),
len(self.interactions()),
)
def add_species(self, species):
"""Add species to this network."""
self.__graph.add_node(species)
def add_interaction(self, source, sink, interaction):
"""Add interaction to this network."""
self.__graph.add_edge(source, sink, interaction)
def source(self, species):
"""Return list of unique sources for species."""
return self.__graph.parents(species)
def source_interactions(self, species):
"""Return list of (source, interaction) pairs for species."""
return self.__graph.parent_edges(species)
def sink(self, species):
"""Return list of unique sinks for species."""
return self.__graph.children(species)
def sink_interactions(self, species):
"""Return list of (sink, interaction) pairs for species."""
return self.__graph.child_edges(species)
def species(self):
"""Return list of the species in this network."""
return self.__graph.nodes()
def interactions(self):
"""Return list of the unique interactions in this network."""
return self.__graph.labels()
def testAdditionalFunctions(self):
a = MultiGraph(['a', 'b', 'c'])
a.add_edge('a', 'b', 'label1')
a.add_edge('b', 'c', 'label1')
a.add_edge('b', 'a', 'label2')
self.assertTrue(
str(a) == "<MultiGraph: 3 node(s), 3 edge(s), 2 unique label(s)>")
self.assertListEqual(a.edges('label1'), [('a', 'b'), ('b', 'c')])
self.assertListEqual(a.labels(), ['label1', 'label2'])
def testAdditionalFunctions(self):
a = MultiGraph(["a", "b", "c"])
a.add_edge("a", "b", "label1")
a.add_edge("b", "c", "label1")
a.add_edge("b", "a", "label2")
self.assertEqual(
str(a), "<MultiGraph: 3 node(s), 3 edge(s), 2 unique label(s)>")
self.assertListEqual(a.edges("label1"), [("a", "b"), ("b", "c")])
self.assertListEqual(a.labels(), ["label1", "label2"])
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=()):
"""Initialize a new Network object."""
self.__graph = MultiGraph(species)
def __repr__(self):
"""Return a debugging string representation of this network."""
return "<Network: __graph: " + repr(self.__graph) + ">"
def __str__(self):
"""Return 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):
"""Add species to this network."""
self.__graph.add_node(species)
def add_interaction(self, source, sink, interaction):
"""Add interaction to this network."""
self.__graph.add_edge(source, sink, interaction)
def source(self, species):
"""Return list of unique sources for species."""
return self.__graph.parents(species)
def source_interactions(self, species):
"""Return list of (source, interaction) pairs for species."""
return self.__graph.parent_edges(species)
def sink(self, species):
"""Return list of unique sinks for species."""
return self.__graph.children(species)
def sink_interactions(self, species):
"""Return list of (sink, interaction) pairs for species."""
return self.__graph.child_edges(species)
def species(self):
"""Return list of the species in this network."""
return self.__graph.nodes()
def interactions(self):
"""Return list of the unique interactions in this network."""
return self.__graph.labels()
def testAdditionalFunctions(self):
a = MultiGraph(['a', 'b', 'c'])
a.add_edge('a', 'b', 'label1')
a.add_edge('b', 'c', 'label1')
a.add_edge('b', 'a', 'label2')
self.assertTrue(
str(a) == "<MultiGraph: 3 node(s), 3 edge(s), 2 unique label(s)>")
self.assertListEqual(a.edges('label1'), [('a', 'b'), ('b', 'c')])
self.assertListEqual(a.labels(), ['label1', 'label2'])
