def __init__(self, codon_table = None, *args, **kwargs):
self.mCodonTable = codon_table
self.mDefaultRates = {}
Transitions.__init__( self,
rate_generator = RatesDictionary( self.mDefaultRates ),
*args,
**kwargs )
def __init__(self, codon_table=None, *args, **kwargs):
self.mCodonTable = codon_table
self.mDefaultRates = {}
Transitions.__init__(self,
rate_generator=RatesDictionary(
self.mDefaultRates),
*args,
**kwargs)
def __init__(self,
generator_initial_states=None,
generator_transitions=None,
*args,
**kwargs):
if not generator_transitions:
generator_transitions = Transitions(*args, **kwargs)
# the alphabet is given by the codon table, but the states
# are separated.
alphabet = ('a', 'c', 'g', 't')
Chain.__init__(
self,
alphabet=alphabet,
generator_initial_states=generator_initial_states,
generator_transitions=generator_transitions,
)
self.mName = "dna"
def __init__(self, *args, **kwargs):
Transitions.__init__( self, *args, **kwargs )
def __init__(self, *args, **kwargs):
Transitions.__init__(self, *args, **kwargs)
def __init__(self, fix_frequencies = False, *args,**kwargs):
Transitions.__init__(self,*args,**kwargs)
self.mFixFrequencies = fix_frequencies
def __init__(self, fix_frequencies=False, *args, **kwargs):
Transitions.__init__(self, *args, **kwargs)
self.mFixFrequencies = fix_frequencies