def __init__(self,
distance=None,
moltype=None,
fast_calc=None,
slow_calc=None):
super(fast_slow_dist, self).__init__(
input_types=ALIGNED_TYPE,
output_types=(PAIRWISE_DISTANCE_TYPE, SERIALISABLE_TYPE),
data_types=("ArrayAlignment", "Alignment"),
)
self._formatted_params()
self._moltype = moltype if moltype is None else get_moltype(moltype)
self._sm = None
if (fast_calc or slow_calc) and distance:
raise ValueError("cannot combine distance and fast/slow")
if distance:
fast_calc = distance
slow_calc = distance
d = set(["hamming", "paralinear", "logdet"]) & set(
[slow_calc, fast_calc])
if d and not self._moltype:
raise ValueError(f"you must provide a moltype for {d}")
try:
fast_calc = get_distance_calculator(fast_calc,
moltype=self._moltype)
except (ValueError, AttributeError):
fast_calc = None
try:
slow_calc = get_model(slow_calc)
except ValueError:
slow_calc = None
if not (fast_calc or slow_calc):
raise ValueError(f"invalid values for {slow_calc} or {fast_calc}")
self.fast_calc = fast_calc
if fast_calc and self._moltype and fast_calc.moltype != self._moltype:
raise ValueError(
f"{self._moltype} incompatible moltype with fast calculator {fast_calc.moltype}"
)
elif fast_calc:
self._moltype = fast_calc.moltype
if slow_calc and self._moltype and slow_calc.moltype != self._moltype:
raise ValueError("incompatible moltype with slow calculator")
elif slow_calc:
self._moltype = slow_calc.moltype
self._sm = slow_calc
def test_get_calculator(self):
"""exercising getting specified calculator"""
for key in _calculators:
get_distance_calculator(key)
get_distance_calculator(key.upper())
with self.assertRaises(ValueError):
get_distance_calculator("blahblah")
def __init__(self,
distance=None,
moltype=None,
fast_calc=None,
slow_calc=None):
"""
Parameters
----------
moltype : str
cogent3 moltype
distance : str
Name of a distance method available as both fast and slow calculator.
fast_calc
Name of a fast distance calculator. See cogent3.available_distances().
slow_calc
Name of a slow distance calculator. See cogent3.available_models().
Notes
-----
If you provide fast_calc or slow_calc, you must specify the moltype.
"""
super(fast_slow_dist, self).__init__(
input_types=self._input_types,
output_types=self._output_types,
data_types=self._data_types,
)
self._formatted_params()
self._moltype = moltype if moltype is None else get_moltype(moltype)
self._sm = None
if (fast_calc or slow_calc) and distance:
raise ValueError("cannot combine distance and fast/slow")
if distance:
fast_calc = distance
slow_calc = distance
d = {"hamming", "percent", "paralinear", "logdet"
} & {slow_calc, fast_calc}
if d and not self._moltype:
raise ValueError(f"you must provide a moltype for {d}")
try:
fast_calc = get_distance_calculator(fast_calc,
moltype=self._moltype)
except (ValueError, AttributeError):
fast_calc = None
try:
slow_calc = get_model(slow_calc)
except ValueError:
slow_calc = None
if not (fast_calc or slow_calc):
raise ValueError(f"invalid values for {slow_calc} or {fast_calc}")
self.fast_calc = fast_calc
if fast_calc and self._moltype and fast_calc.moltype != self._moltype:
raise ValueError(
f"{self._moltype} incompatible moltype with fast calculator {fast_calc.moltype}"
)
elif fast_calc:
self._moltype = fast_calc.moltype
if slow_calc and self._moltype and slow_calc.moltype != self._moltype:
raise ValueError("incompatible moltype with slow calculator")
elif slow_calc:
self._moltype = slow_calc.moltype
self._sm = slow_calc
self.func = self.calc_distance
