def __init__(self):
self.mGrammar = Grammar()
self.mAlphabet = Alphabet()
class Model:
def __init__(self):
self.mGrammar = Grammar()
self.mAlphabet = Alphabet()
def __str__(self):
return 'grammar:\n%s\nalphabet:\n%s' % (self.mGrammar, self.mAlphabet)
def setAlphabet(self, alphabet):
self.mAlphabet = alphabet
def setGrammar(self, grammar):
self.mGrammar = grammar
def getGrammar(self):
s = "\n".join( self.getGrammarLines())
return IndentString( s )
def getGrammarLines(self):
"""write the grammar for this chain."""
lines = []
lines += self.mGrammar.getGrammarLines()
lines += self.mAlphabet.getGrammarLines()
return lines
def renameParameter(self, old, new):
"""rename a parameter in the model."""
self.mGrammar.renameParameter( old, new )
def evaluateRateMatrix(self, terminals = None):
"""returns the evaluated rate Matrix for the given terminals.
This method uses the parameter section of the grammar to evaluate
the expressions in the rate matrix.
"""
if terminals == None:
tt = self.mGrammar.getTerminals()
else:
tt = [terminals,]
results = {}
for terminals in tt:
chain = self.mGrammar.getChain( terminals )
lines = self.mGrammar.getParameterCode()
transitions = chain.getTransitions()
for start, ends in transitions.items():
for end, rate in ends.items():
if type(rate[1]) == StringType:
expr = rate[1]
else:
n = []
for x in rate[1]:
if x[:2] == "# ":
n.append( x[2:])
else:
n.append( x )
expr = " ".join( tuple(n) )
lines.append( "matrix[%s][%s] = %s" % ( (str(start), str(end), expr) ))
# build the full rate matrix
matrix = {}
states = chain.getInitialStates().keys()
for x in states:
s = {}
for y in states:
s[y] = 0
matrix[x] = s
## fill the matrix with values
try:
exec("\n".join(lines))
except SyntaxError, msg:
raise Exceptions.ProgrammingError( 'error "%s" while computing rate matrix:\n%s\n' % \
(msg,"\n".join(lines)))
## set the diagonal elements
for x in states:
matrix[x][x] = 0
s = sum( matrix[x].values() )
matrix[x][x] = -s
results[terminals] = matrix
return results