def __init__(self, rate_generator=None, expression_generator=None, *args, **kwargs):
"""prefix: prefix all rate variables with this prefix."""
ChainComponent.__init__(self, *args, **kwargs)
if not rate_generator:
self.mRateGenerator = Rates()
else:
self.mRateGenerator = rate_generator
if not expression_generator:
self.mExpressionGenerator = Expressions()
else:
self.mExpressionGenerator = expression_generator
def buildGrammar(self, chain):
"""build grammar.
This stub generically iterates over the alphabet and
calls self.addTransitions for each pair of letters.
"""
ChainComponent.buildGrammar(self, chain)
alphabet = self.mChainGenerator.getAlphabet()
l = len(alphabet)
for l1 in range(0, l - 1):
a = alphabet[l1]
for l2 in range(l1 + 1, l):
self.addTransitions(chain, a, alphabet[l2])
def buildGrammar(self, chain):
"""build grammar.
This stub generically iterates over the alphabet and
calls self.addTransitions for each pair of letters.
"""
ChainComponent.buildGrammar(self, chain)
alphabet = self.mChainGenerator.getAlphabet()
l = len(alphabet)
for l1 in range(0, l - 1):
a = alphabet[l1]
for l2 in range(l1 + 1, l):
self.addTransitions(chain, a, alphabet[l2])
def __init__(self,
rate_generator=None,
expression_generator=None,
*args,
**kwargs):
"""prefix: prefix all rate variables with this prefix."""
ChainComponent.__init__(self, *args, **kwargs)
if not rate_generator:
self.mRateGenerator = Rates()
else:
self.mRateGenerator = rate_generator
if not expression_generator:
self.mExpressionGenerator = Expressions()
else:
self.mExpressionGenerator = expression_generator
def buildGrammar(self, chain):
"""build grammar for chain by adding initial states."""
ChainComponent.buildGrammar(self, chain)
def __init__(self, *args, **kwargs):
ChainComponent.__init__(self, *args, **kwargs)
def buildGrammar(self, chain):
"""build grammar for chain by adding initial states."""
ChainComponent.buildGrammar(self,chain)
def __init__(self, *args, **kwargs):
ChainComponent.__init__(self, *args, **kwargs )