def test_Nodes(self): a = MultiGraph() self.assertEqual(a.nodes(), [], "default graph not empty") a.add_node('a') self.assertEqual(a.nodes(), ['a'], "one node not added") a.add_node('a') self.assertEqual(a.nodes(), ['a'], "duplicate node added") a.add_node('b') self.assertEqual(sorted(a.nodes()), ['a', 'b'], "second node not added")
def test_Nodes(self): a = MultiGraph() self.assertEqual(a.nodes(), [], "default graph not empty") a.add_node("a") self.assertEqual(a.nodes(), ["a"], "one node not added") a.add_node("a") self.assertEqual(a.nodes(), ["a"], "duplicate node added") a.add_node("b") self.assertEqual(sorted(a.nodes()), ["a", "b"], "second node not added")
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()
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()