def __init__(self, *p):
PairRepeatState.__init__(self, *p)
self.maxK = 0
self.time = self.mathType(0.0)
self.backgroundProb = []
self.indelProb = self.mathType(0.0)
self.indelExtProb = self.mathType(0.0)
self.repeatProb = self.mathType(0.0)
self.endProb = self.mathType(0.0)
self.model = None
self.memoize = dict()
def load(self, dictionary):
PairRepeatState.load(self, dictionary)
if 'maxK' not in dictionary:
raise ParseException('maxK was not found in state')
self.maxK = int(dictionary['maxK'])
if 'time' not in dictionary:
raise ParseException('time was not found in state')
self.time = float(dictionary['time'])
if 'backgroundprob' not in dictionary:
raise ParseException('backgroundprob was not found in state')
self.backgroundProb = dictionary['backgroundprob']
if 'indelprob' not in dictionary:
raise ParseException('indelprob was not found in state')
self.indelProb = dictionary['indelprob']
if 'indelextprob' not in dictionary:
raise ParseException('indelextprob was not found in state')
self.indelExtProb = dictionary['indelextprob']
if 'repeatprob' not in dictionary:
raise ParseException('repeatprob was not found in state')
self.repeatProb = dictionary['repeatprob']
if 'endprob' not in dictionary:
raise ParseException('endprob was not found in state')
self.endProb = dictionary['endprob']
if 'silendprob' not in dictionary:
self.silEndProb = self.endProb
else:
self.silEndProb = dictionary['silendprob']
if 'initendprob' not in dictionary:
self.initEndProb = self.endProb
else:
self.initEndProb = dictionary['initendprob']
self.model = createKRepeatHMM(
self.mathType,
self.maxK,
self.time,
self.backgroundProb,
self.indelProb,
self.indelExtProb,
self.repeatProb,
self.endProb,
self.initEndProb,
self.silEndProb,
)
def toJSON(self):
ret = PairRepeatState.toJSON(self)
del ret['consensusdistribution']
ret['maxK'] = self.maxK
ret['time'] = self.time
ret['backgroundprob'] = dist_to_json(self.backgroundProb)
ret['indelprob'] = self.indelProb
ret['indelextprob'] = self.indelExtProb
ret['repeatprob'] = self.repeatProb
ret['endprob'] = self.endProb
ret['silendprob'] = self.silEndProb
ret['initendprob'] = self.initEndProb
return ret
