def __init__(self, **kwargs):
"""Initializes a model.
kwargs:
`r_mat` must be a square matrix (list of lists of floats). Diagonal
elements will be ignored. The columns of this matrix will be
multiplied by their corresponding equilibirium frequencies.
`r_upper` can be used instead of `r_mat.` It should correspond to the
upper triangle of the R-matrix.
`equil_freq` must be None a list of the equilibrium frequencies.
"""
r_upper = kwargs.get('r_upper')
r_mat = kwargs.get('r_mat')
sf = kwargs.get('state_freq')
self.normalize_rates = kwargs.get('normalize_rates', True) # adjust the qmat such that the mean flux is 1.0
if r_upper:
if r_mat:
raise ValueError("r_mat or r_upper cannot both be specified")
r_mat = _r_upper_to_r_mat(r_upper)
_LOG.debug('r_mat from r_upper (%s) is %s' % (str(r_upper), str(r_mat)))
elif not r_mat:
raise ValueError("Either r_mat or r_upper must be given")
priv_mat = []
param_set = set()
for row in r_mat:
priv_row = list(row)
for n, cell in enumerate(row):
try:
param_set.update(cell.parameters())
except:
priv_row[n] = MutableFloatParameter(cell)
priv_mat.append(tuple(priv_row))
if sf is None:
raise ValueError("State frequencies must be specified for a RevDiscStateContTimeModel")
if isinstance(sf, ProbabilityVectorParameter):
self._state_freq = sf
else:
priv_sf = list(sf)
for cell in sf:
try:
param_set.update(cell.parameters())
priv_sf.append(cell)
except:
priv_sf.append(FloatParameter(cell))
self._state_freq = ProbabilityVectorParameter(priv_sf)
param_set.update(set(self._state_freq.parameters()))
DiscStateContTimeModel.__init__(self, param_list=param_set, **kwargs)
if r_mat:
if self.num_states is None:
self._num_states = len(r_mat)
self._verify_r_mat(r_mat)
else:
raise ValueError("Either r_mat or r_upper must be specified")
self._r_mat = tuple(priv_mat)
class RevDiscStateContTimeModel(DiscStateContTimeModel):
def __init__(self, **kwargs):
"""Initializes a model.
kwargs:
`r_mat` must be a square matrix (list of lists of floats). Diagonal
elements will be ignored. The columns of this matrix will be
multiplied by their corresponding equilibirium frequencies.
`r_upper` can be used instead of `r_mat.` It should correspond to the
upper triangle of the R-matrix.
`equil_freq` must be None a list of the equilibrium frequencies.
"""
r_upper = kwargs.get('r_upper')
r_mat = kwargs.get('r_mat')
sf = kwargs.get('state_freq')
self.normalize_rates = kwargs.get('normalize_rates', True) # adjust the qmat such that the mean flux is 1.0
if r_upper:
if r_mat:
raise ValueError("r_mat or r_upper cannot both be specified")
r_mat = _r_upper_to_r_mat(r_upper)
_LOG.debug('r_mat from r_upper (%s) is %s' % (str(r_upper), str(r_mat)))
elif not r_mat:
raise ValueError("Either r_mat or r_upper must be given")
priv_mat = []
param_set = set()
for row in r_mat:
priv_row = list(row)
for n, cell in enumerate(row):
try:
param_set.update(cell.parameters())
except:
priv_row[n] = MutableFloatParameter(cell)
priv_mat.append(tuple(priv_row))
if sf is None:
raise ValueError("State frequencies must be specified for a RevDiscStateContTimeModel")
if isinstance(sf, ProbabilityVectorParameter):
self._state_freq = sf
else:
priv_sf = list(sf)
for cell in sf:
try:
param_set.update(cell.parameters())
priv_sf.append(cell)
except:
priv_sf.append(FloatParameter(cell))
self._state_freq = ProbabilityVectorParameter(priv_sf)
param_set.update(set(self._state_freq.parameters()))
DiscStateContTimeModel.__init__(self, param_list=param_set, **kwargs)
if r_mat:
if self.num_states is None:
self._num_states = len(r_mat)
self._verify_r_mat(r_mat)
else:
raise ValueError("Either r_mat or r_upper must be specified")
self._r_mat = tuple(priv_mat)
def get_r_mat(self):
"Accessor for R-matrix."
return self._r_mat
r_mat = property(get_r_mat)
def get_r_upper(self):
"Accessor for R-matrix."
return _r_mat_to_r_upper(self._r_mat)
r_upper = property(get_r_upper)
def get_state_freq(self):
"Accessor for state frequencies."
return self._state_freq
def set_state_freq(self, v):
"Accessor for state frequencies."
_LOG.debug("In RevDiscStateContTimeModel.set_state_freq")
if isinstance(v, ProbabilityVectorParameter):
self.substitute_parameter_instance(self._state_freq, v)
self._state_freq = v
else:
self._state_freq.value = v
state_freq = property(get_state_freq, set_state_freq)
q_mat = property(DiscStateContTimeModel.get_q_mat)
def calc_q_mat(self):
"""Uses self._state_freq and self._r_mat to refresh self._q_mat.
As required by the current version of cdsctm_set_q_mat, the Q-matrix
is rescaled such that each row sums to 0.0 and the weighted
average of the diagonal elements is -1.0 (with the weight being the
associated equilibrium frequency)."""
assert(self._state_freq is not None)
_LOG.debug("in self.calc_q_mat: _r_mat = %s _state_freq = %s" % (repr(self._r_mat), str(self._state_freq)))
ns = self.num_states
qr = [0.0] * ns
qm = [list(qr) for i in range(ns)]
w_mat_sum = 0.0
for i, rows in enumerate(izip(self._r_mat, self._state_freq)):
r_row, sf = rows
q_row = qm[i]
row_sum = 0.0
for j, to_state in enumerate(izip(r_row, self._state_freq)):
r_val, stf = [float(p) for p in to_state]
if i != j:
v = r_val * stf
assert(r_val >= 0.0)
assert(stf >= 0.0)
q_row[j] = v
row_sum += v
q_row[i] = -row_sum
w_mat_sum += row_sum*self._state_freq[i]
if self.normalize_rates:
for q_row in qm:
for i in xrange(len(q_row)):
q_row[i] /= w_mat_sum
self._q_mat = tuple([tuple(row) for row in qm])
_LOG.debug("_q_mat = %s" % str(qm))
return self._q_mat
def _verify_eq_freq_len(self, equil_freq):
"Raises a ValueError if `equil_freq` is not the correct length"
nef = len(equil_freq)
if nef != self._num_states:
if nef != (1 + self._num_states):
raise ValueError("The number of states in the r_mat and "\
"equil_freq must agree.")
def _verify_r_mat(self, r_mat):
"""Raises a ValueError if `r_mat` is not the correct shape or has
negative values (other than on the diagonal).
"""
for i, row in enumerate(r_mat):
if len(row) != self.num_states:
raise ValueError("The R-matrix must be square.")
for j, val in enumerate(row):
if i != j:
if val < 0.0:
raise ValueError("Off-diagonal elements of the "\
"R-matrix cannot be negative.")
if abs(val - float(r_mat[j][i])) > 1.0e-6:
raise ValueError("R-matrix must be symmetric")
def get_num_states(self):
"Returns the number of states"
return self._num_states
def get_adjusted_brlens_list(self, b):
return [b]
def get_model_list(self):
return [self]
def get_model_probs(self):
return (1.0,)
def get_parameters(self):
return self._parameters
model_probs = property(get_model_probs)
r_mat = property(get_r_mat)
r_upper = property(get_r_upper)
def get_state_freq_value(self):
return self._state_freq.value
def set_state_freq_value(self, v):
self._state_freq.value = v
state_freq_value = property(get_state_freq_value, set_state_freq_value)