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 testRemoveNode(self):
a = MultiGraph(['a','b','c','d','e'])
a.add_edge('a','e','label1')
a.add_edge('b','e','label1')
a.add_edge('c','e','label2')
a.add_edge('d','e','label3')
a.add_edge('e','d','label4')
a.add_edge('a','b','label5')
a.remove_node('e')
b = MultiGraph(['a','b','c','d'])
b.add_edge('a','b','label5')
self.assertEqual(a, b)#, "incorrect node removal")
def testEdges(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')
l = a.child_edges('a')
l.sort()
self.assertEqual(l, [('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")
l = a.children('b')
l.sort()
self.assertEqual(l, ['a', 'c'], "incorrect children")
self.assertEqual(a.children('d'), [], "incorrect children for singleton")
self.assertEqual(a.parents('a'), ['b'], "incorrect parents")
def testNodes(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')
l = a.nodes()
l.sort()
self.assertEqual(l, ['a', 'b'], "second node not added")
def testEquals(self):
a = MultiGraph(['a','b','c'])
a.add_edge('a','b','label1')
a.add_edge('b','c','label1')
a.add_edge('b','a','label2')
b = MultiGraph(['a','b','c'])
self.assertNotEqual(a, b, "equal to similar nodes, no edges")
b.add_edge('a','b','label1')
self.assertNotEqual(a, b, "equal to similar nodes, edge subset")
b.add_edge('b','c','label1')
b.add_edge('b','a','label2')
self.assertEqual(a, b, "not equal to similar")
c = MultiGraph(['a','b','c'])
c.add_edge('a','b','label2')
c.add_edge('b','c','label2')
c.add_edge('b','a','label1')
self.assertNotEqual(a, c, "equal to similar with different labels")
self.assertNotEqual(c, MultiGraph(), "equal to empty graph")
self.assertEqual(MultiGraph(), MultiGraph(), "empty graph not equal to self")
def __init__(self, species=()):
"""Initializes a new Network object."""
self.__graph = MultiGraph(species)
def testRemoveNode(self):
a = MultiGraph(['a','b','c','d','e'])
a.add_edge('a','e','label1')
a.add_edge('b','e','label1')
a.add_edge('c','e','label2')
a.add_edge('d','e','label3')
a.add_edge('e','d','label4')
a.add_edge('a','b','label5')
a.remove_node('e')
b = MultiGraph(['a','b','c','d'])
b.add_edge('a','b','label5')
self.assertEqual(a, b)#, "incorrect node removal")
def testEdges(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')
l = a.child_edges('a')
l.sort()
self.assertEqual(l, [('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")
l = a.children('b')
l.sort()
self.assertEqual(l, ['a', 'c'], "incorrect children")
self.assertEqual(a.children('d'), [], "incorrect children for singleton")
self.assertEqual(a.parents('a'), ['b'], "incorrect parents")
def testNodes(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')
l = a.nodes()
l.sort()
self.assertEqual(l, ['a', 'b'], "second node not added")
def testEquals(self):
a = MultiGraph(['a','b','c'])
a.add_edge('a','b','label1')
a.add_edge('b','c','label1')
a.add_edge('b','a','label2')
b = MultiGraph(['a','b','c'])
self.assertNotEqual(a, b, "equal to similar nodes, no edges")
b.add_edge('a','b','label1')
self.assertNotEqual(a, b, "equal to similar nodes, edge subset")
b.add_edge('b','c','label1')
b.add_edge('b','a','label2')
self.assertEqual(a, b, "not equal to similar")
c = MultiGraph(['a','b','c'])
c.add_edge('a','b','label2')
c.add_edge('b','c','label2')
c.add_edge('b','a','label1')
self.assertNotEqual(a, c, "equal to similar with different labels")
self.assertNotEqual(c, MultiGraph(), "equal to empty graph")
self.assertEqual(MultiGraph(), MultiGraph(), "empty graph not equal to self")
