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,
codon_table = Bio.Data.CodonTable.standard_dna_table,
generator_initial_states = None,
generator_transitions = None ):
if not generator_transitions:
generator_transitions = TransitionsCodons( codon_table = codon_table )
self.mCodonTable = codon_table
# the alphabet is given by the codon table, but the states
# are separated.
alphabet = map( lambda x: tuple(x.lower()), codon_table.forward_table.keys())
Chain.__init__(self,
alphabet = alphabet,
generator_initial_states = generator_initial_states,
generator_transitions = generator_transitions,
)
self.mName = "codons"
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,
codon_table=Bio.Data.CodonTable.standard_dna_table,
generator_initial_states=None,
generator_transitions=None):
if not generator_transitions:
generator_transitions = TransitionsCodons(codon_table=codon_table)
self.mCodonTable = codon_table
# the alphabet is given by the codon table, but the states
# are separated.
alphabet = map(lambda x: tuple(x.lower()),
codon_table.forward_table.keys())
Chain.__init__(
self,
alphabet=alphabet,
generator_initial_states=generator_initial_states,
generator_transitions=generator_transitions,
)
self.mName = "codons"
