def test_is_generator_unique(self):
""" is_generator_unique should identify non-unique primary roots or
raise a NotImplementedError for non-primary roots"""
q_fail = array(
[
[-9.08955989, 4.50419008, 2.93729567, 1.64807414],
[3.0820101213, -11.867582855, 3.0196380713, 5.7659346624],
[3.1293061336, 0.6470353007, -4.340134955, 0.5637935206],
[9.95494662, 0.63789574, 1.39069539, -11.98353775],
]
)
self.assertFalse(is_generator_unique(q_fail))
q_pass = array(
[
[-3.764760594, 1.1273556812, 1.3310122018, 1.3063927109],
[0.920950736, -2.6797373188, 0.4269374722, 1.3318491106],
[1.1327752022, 1.1606494551, -2.7789984239, 0.4855737666],
[1.2387180594, 0.1873997167, 0.9202488686, -2.3463666447],
]
)
self.assertTrue(is_generator_unique(q_pass))
q_raise = array(
[
[-2.77453845e-03, 2.77453817e-03, 1.00809110e-10, 1.74200370e-10],
[6.81595242e-11, -3.43166912e-10, 1.00810050e-10, 1.74197338e-10],
[6.81605094e-11, 2.77453817e-03, -2.77453841e-03, 1.74198726e-10],
[6.81594144e-11, 1.38727059e-10, 1.00808021e-04, -1.00808228e-04],
]
)
self.assertRaises(NotImplementedError, is_generator_unique, q_raise)
def allRateMatricesUnique(self):
"""Returns True if every rate matrix is unique for its Psub matrix"""
for edge in self.tree.getEdgeVector(include_root=False):
Q = self.getRateMatrixForEdge(edge.Name).asarray()
t = self.getParamValue("length", edge=edge.Name)
if not is_generator_unique(Q * t):
return False
return True
def allRateMatricesUnique(self):
"""Returns True if every rate matrix is unique for its Psub matrix"""
for edge in self.tree.getEdgeVector(include_root=False):
Q = self.getRateMatrixForEdge(edge.Name).asarray()
t = self.getParamValue('length', edge=edge.Name)
if not is_generator_unique(Q * t):
return False
return True
def test_is_generator_unique(self):
""" is_generator_unique should identify non-unique primary roots or
raise a NotImplementedError for non-primary roots"""
q_fail = array([[ -9.08955989, 4.50419008, 2.93729567, 1.64807414 ],
[ 3.0820101213, -11.867582855 , 3.0196380713, 5.7659346624],
[ 3.1293061336, 0.6470353007, -4.340134955 , 0.5637935206],
[ 9.95494662 , 0.63789574 , 1.39069539 , -11.98353775 ]])
self.assertFalse(is_generator_unique(q_fail))
q_pass = array([[-3.764760594, 1.1273556812, 1.3310122018, 1.3063927109],
[0.920950736 , -2.6797373188, 0.4269374722, 1.3318491106],
[1.1327752022, 1.1606494551, -2.7789984239, 0.4855737666],
[1.2387180594, 0.1873997167, 0.9202488686, -2.3463666447]])
self.assertTrue(is_generator_unique(q_pass))
q_raise = array([
[-2.77453845e-03, 2.77453817e-03, 1.00809110e-10, 1.74200370e-10],
[6.81595242e-11, -3.43166912e-10, 1.00810050e-10, 1.74197338e-10],
[6.81605094e-11, 2.77453817e-03, -2.77453841e-03, 1.74198726e-10],
[6.81594144e-11, 1.38727059e-10, 1.00808021e-04, -1.00808228e-04]])
self.assertRaises(NotImplementedError, is_generator_unique, q_raise)
