def test_Edges(self):
a = MultiGraph(["a", "b", "c", "d"])
a.add_edge("a", "b", "label1")
self.assertEqual(a.child_edges("a"), [("b", "label1")])
a.add_edge("a", "b", "label2")
self.assertEqual(sorted(a.child_edges("a")), [("b", "label1"), ("b", "label2")])
a.add_edge("b", "a", "label2")
self.assertEqual(a.parent_edges("a"), [("b", "label2")])
a.add_edge("b", "c", "label3")
self.assertEqual(a.parent_edges("c"), [("b", "label3")])
children = a.children("b")
children.sort()
self.assertEqual(children, ["a", "c"], "incorrect children")
self.assertEqual(a.children("d"), [], "incorrect children for singleton")
self.assertEqual(a.parents("a"), ["b"], "incorrect parents")
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 test_Edges(self):
a = MultiGraph(['a', 'b', 'c', 'd'])
a.add_edge('a', 'b', 'label1')
self.assertEqual(a.child_edges('a'),
[('b', 'label1')]) # , "incorrect child edges")
a.add_edge('a', 'b', 'label2')
self.assertEqual(sorted(a.child_edges('a')),
[('b', 'label1'),
('b', 'label2')]) # , "incorrect child edges")
a.add_edge('b', 'a', 'label2')
self.assertEqual(a.parent_edges('a'),
[('b', 'label2')]) # , "incorrect parent edges")
a.add_edge('b', 'c', 'label3')
self.assertEqual(a.parent_edges('c'),
[('b', 'label3')]) # , "incorrect parent edges")
children = a.children('b')
children.sort()
self.assertEqual(children, ['a', 'c'], "incorrect children")
self.assertEqual(a.children('d'), [],
"incorrect children for singleton")
self.assertEqual(a.parents('a'), ['b'], "incorrect parents")