def __init__(
self,
masses,
probs,
atomCnt,
tabSize = 1000,
hashSize = 1000,
burnIn = 1000
):
self.clib = isoFFI.clib #because you can't use global vars in destructor, which is UTTERLY STUPID
self.masses = masses
self.probs = probs
self.isotopeNo = len(masses)
self.atomCnt = atomCnt
self.tabSize = tabSize
self.hashSize = hashSize
self.marginal = isoFFI.clib.setupMarginal(
masses,
probs,
self.isotopeNo,
atomCnt,
tabSize,
hashSize)
self.cconf_mass = isoFFI.ffi.new("double[1]")
self.cconf_lProb = isoFFI.ffi.new("double[1]")
self.cconf = isoFFI.ffi.new("int[{0}]".format(self.isotopeNo))
self.cprobs = []
self.summator = Summator()
class MarginalDistribution:
def __init__(
self,
masses,
probs,
atomCnt,
tabSize = 1000,
hashSize = 1000,
burnIn = 1000
):
self.clib = isoFFI.clib #because you can't use global vars in destructor, which is UTTERLY STUPID
self.masses = masses
self.probs = probs
self.isotopeNo = len(masses)
self.atomCnt = atomCnt
self.tabSize = tabSize
self.hashSize = hashSize
self.marginal = isoFFI.clib.setupMarginal(
masses,
probs,
self.isotopeNo,
atomCnt,
tabSize,
hashSize)
self.cconf_mass = isoFFI.ffi.new("double[1]")
self.cconf_lProb = isoFFI.ffi.new("double[1]")
self.cconf = isoFFI.ffi.new("int[{0}]".format(self.isotopeNo))
self.cprobs = []
self.summator = Summator()
def __del__(self):
self.clib.destroyConf(self.marginal)
def getConfsRaw(self):
masses = isoFFI.ffi.new("double[{0}]".format(len(self)))
logProbs = isoFFI.ffi.new("double[{0}]".format(len(self)))
confs = isoFFI.ffi.new("int[{0}]".format(len(self)*self.isotopeNo))
isoFFI.clib.getConfs(len(self), self.marginal, masses, logProbs, confs)
return (masses, logProbs, confs)
def getConfs(self):
ret = []
masses, logProbs, confs = self.getConfsRaw()
for i in xrange(len(masses)):
ret.append((masses[i], logProbs[i], list(confs[self.isotopeNo*i:(i+1)*self.isotopeNo])))
return ret
def getConf(self, idx):
if isoFFI.clib.getConfMT(self.marginal, idx, self.cconf_mass, self.cconf_lProb, self.cconf) == 1:
return (self.cconf_mass[0], self.cconf_lProb[0], tuple(self.cconf))
else:
raise IndexError
def probeConf(self, idx):
return self.clib.probeConfigurationIdx(self.marginal, idx) > 0
def CumulativeProb(self, idx):
if len(self.cprobs) > idx:
return self.cprobs[idx]
else:
for i in xrange(len(self.cprobs), idx+1):
self.summator.add(math.exp(self.getConf(i)[1]))
self.cprobs.append(self.summator.get())
return self.cprobs[idx]
