예제 #1
0
 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")
예제 #2
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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()
예제 #3
0
 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")