def test_sampleLabelings(self):
tree = Tree("(A:1,(B:1,(C:1,(E:1,D:1)Int_1:0.5[&&NHX:ancient=1])Int_2:0.5[&&NHX:ancient=0])Int_3:1)Root;", format=1)
chrom = {}
chrom["one"] = ["3","4"]
species = {}
species["C"] = chrom
chrom = {}
chrom["one"] = ["3","4"]
species["D"] = chrom
chrom = {}
chrom["one"] = []
species["E"] = chrom
chrom = {}
chrom["one"] = []
species["A"] = chrom
chrom = {}
chrom["one"] = []
species["B"] = chrom
adj = getAdjacencies.findAdjacencies(species)
paths = getAdjacencies.findTreePaths(tree)
internal,adjacenciesAncestral = getAdjacencies.assignAncestralAdjacencies(paths,adj,tree)
graphs = globalAdjacencyGraph.createGraph(adj,adjacenciesAncestral)
jointLabels, first = SR.enumJointLabelings(graphs)
probs={"Int_1":{(6, 7):0.1},"Int_2":{(6, 7):0.1},"Int_3":{(6, 7):0.1},"Root":{(6, 7):0.1}}
for i in range(0,10):
validLabels, validAtNode = SR.validLabels(jointLabels,first)
resolvedCCs = SR.sampleLabelings(tree, graphs, validAtNode, adj,probs, alpha=0)
reconstructedAdj = SR.reconstructedAdjacencies(resolvedCCs)
print reconstructedAdj
def test_assignAncestralAdjacencies(self):
internal, adjacenciesAncestral = getAdjacencies.assignAncestralAdjacencies(self.paths, self.adj, self.tree)
internal1 = internal[self.int1]
unittest.TestCase.assertEqual(self, internal1, set([]))
internal2 = internal[self.int2]
internal3 = internal[self.int3]
unittest.TestCase.assertEqual(self, internal2, internal3)
shared = set([(2, 3)])
unittest.TestCase.assertEqual(self, internal2, shared)
shared = set([(7, 9)])
unittest.TestCase.assertNotEqual(self, internal2, shared)
