def testHeightTable(self):
"""Make sure the height-table is calculated correctly."""
og = GreedyOutgroup()
og.importTree(self.borMcTree)
htable = og.heightTable()
self.assertEquals(htable[self.borMcTree.getNodeId('HUMAN')], 0)
self.assertEquals(htable[self.borMcTree.getNodeId('PIG')], 0)
self.assertEquals(htable[self.borMcTree.getNodeId('RAT')], 0)
self.assertEquals(htable[self.borMcTree.getNodeId('Anc7')], 1)
self.assertEquals(htable[self.borMcTree.getNodeId('Anc1')], 2)
self.assertEquals(htable[self.borMcTree.getNodeId('Anc0')], 4)
def testHeightTable(self):
"""Make sure the height-table is calculated correctly."""
og = GreedyOutgroup()
og.importTree(self.borMcTree)
htable = og.heightTable()
self.assertEquals(htable[self.borMcTree.getNodeId('HUMAN')], 0)
self.assertEquals(htable[self.borMcTree.getNodeId('PIG')], 0)
self.assertEquals(htable[self.borMcTree.getNodeId('RAT')], 0)
self.assertEquals(htable[self.borMcTree.getNodeId('Anc7')], 1)
self.assertEquals(htable[self.borMcTree.getNodeId('Anc1')], 2)
self.assertEquals(htable[self.borMcTree.getNodeId('Anc0')], 4)
def testZeroThreshold(self):
"""A threshold of 0 should produce outgroup sets that cause no additional depth in the resulting schedule."""
tree = self.backboneTree
og = GreedyOutgroup()
og.importTree(tree)
og.greedy(candidateSet=set(['Homo_sapiens', 'Mus_musculus']),threshold=0, maxNumOutgroups=3, candidateChildFrac=0.75)
og.greedy(threshold=0, maxNumOutgroups=3, candidateChildFrac=0.75)
htable = og.heightTable()
for node, outgroups in og.ogMap.items():
for outgroup, _ in outgroups:
# For the outgroup assignment to create no
# additional dependencies, each outgroup must have
# a height lower than the node it's outgroup to
# (or be a leaf)
self.assertTrue(htable[tree.getNodeId(outgroup)] < htable[tree.getNodeId(node)] \
or htable[tree.getNodeId(outgroup)] == 0)
def testZeroThreshold(self):
"""A threshold of 0 should produce outgroup sets that cause no additional depth in the resulting schedule."""
tree = self.backboneTree
og = GreedyOutgroup()
og.importTree(tree)
og.greedy(candidateSet=set(['Homo_sapiens', 'Mus_musculus']),
threshold=0,
maxNumOutgroups=3,
candidateChildFrac=0.75)
og.greedy(threshold=0, maxNumOutgroups=3, candidateChildFrac=0.75)
htable = og.heightTable()
for node, outgroups in og.ogMap.items():
for outgroup, _ in outgroups:
# For the outgroup assignment to create no
# additional dependencies, each outgroup must have
# a height lower than the node it's outgroup to
# (or be a leaf)
self.assertTrue(htable[tree.getNodeId(outgroup)] < htable[tree.getNodeId(node)] \
or htable[tree.getNodeId(outgroup)] == 0)
