def load(self, dictionary):
ConfigObject.load(self, dictionary)
#Detect if user provides the data or not
start = 0
if 'start' in dictionary:
start = float(dictionary['start'])
if 'data' not in dictionary:
if 'p' not in dictionary:
raise ParseException(
'Probability is missing in RepeatLengthDistribution'
)
p = float(dictionary['p'])
if 'fractions' not in dictionary:
raise ParseException(
'Fractions are missing in RepeatLengthDistribution'
)
fractions = dictionary['fractions']
self.setParams(p, start, fractions)
else:
data = dictionary['data']
if 'fractionssize' not in dictionary:
raise ParseException(
'Number of fractions is missing in RepeatLengthDistribution'
)
self.train(data, int(dictionary['fractionssize']), start)
def load(self, dictionary):
ConfigObject.load(self, dictionary)
if "emission" not in dictionary:
raise ParseException("Emission not found in state")
if "name" not in dictionary:
raise ParseException("Name not found in state")
if "startprob" not in dictionary:
raise ParseException("startprob not found in state")
if "endprob" not in dictionary:
raise ParseException("endprob not found in state")
if "serialize" in dictionary:
self.serialize = dictionary["serialize"]
self.stateName = dictionary["name"]
if "onechar" in dictionary:
if len(dictionary['onechar']) != 1:
raise ParseException('onechar has wrong length')
self.onechar = dictionary["onechar"]
else:
if len(self.stateName) > 0:
self.onechar = self.stateName[0]
else:
self.onechar = "?"
self.startProbability = self.mathType(dictionary["startprob"])
self.endProbability = self.mathType(dictionary["endprob"])
self.emissions = dict()
for [key, prob] in dictionary["emission"]:
if key.__class__.__name__ == "list":
key = tuple(key)
try:
self.emissions[key] = self.mathType(prob)
except ValueError:
self.emissions[key] = prob
def load(self, dictionary):
ConfigObject.load(self, dictionary)
if "sequences" not in dictionary:
raise ParseException("Sequences not in AnnotationConfig")
self.annotations = dictionary['annotations']
self.sequences = dict()
for i in dictionary["sequences"]:
self.sequences[i['name']] = dict()
for a in i['annotations']:
if a['id'] in self.annotations:
if 'offset' in a:
offset = a['offset']
else:
offset = 0
self.sequences[i['name']][a['id']] = (a['file'], offset)
def load(self, dictionary):
ConfigObject.load(self, dictionary)
if "sequences" not in dictionary:
raise ParseException("Sequences not in AnnotationConfig")
self.annotations = dictionary['annotations']
self.sequences = dict()
for i in dictionary["sequences"]:
self.sequences[i['name']] = dict()
for a in i['annotations']:
if a['id'] in self.annotations:
if 'offset' in a:
offset = a['offset']
else:
offset = 0
self.sequences[i['name']][a['id']] = (a['file'], offset)
def toJSON(self):
ret = ConfigObject.toJSON(self)
ret["annotations"] = self.annotations
ret["sequences"] = list()
for key, value in self.sequences.iteritems():
ann = list()
for akey, avalue in value.iteritems():
ann.append({'id': akey, 'file': avalue[0], 'offset': avalue[1]})
ret["sequences"].append({"name": key, "annotations": ann})
return ret
def toJSON(self):
ret = ConfigObject.toJSON(self)
ret["name"] = self.stateName
ret["onechar"] = self.onechar
ret["emission"] = list()
ret["startprob"] = self.startProbability
ret["endprob"] = self.endProbability
for (key, prob) in self.emissions.iteritems():
ret["emission"].append((key, prob))
return ret
def toJSON(self):
ret = ConfigObject.toJSON(self)
ret["annotations"] = self.annotations
ret["sequences"] = list()
for key, value in self.sequences.iteritems():
ann = list()
for akey, avalue in value.iteritems():
ann.append({
'id': akey,
'file': avalue[0],
'offset': avalue[1]
})
ret["sequences"].append({"name": key, "annotations": ann})
return ret
def load(self, dictionary):
ConfigObject.load(self, dictionary)
#Detect if user provides the data or not
start = 0
if 'start' in dictionary:
start = float(dictionary['start'])
if 'data' not in dictionary:
if 'p' not in dictionary:
raise ParseException(
'Probability is missing in RepeatLengthDistribution')
p = float(dictionary['p'])
if 'fractions' not in dictionary:
raise ParseException(
'Fractions are missing in RepeatLengthDistribution')
fractions = dictionary['fractions']
self.setParams(p, start, fractions)
else:
data = dictionary['data']
if 'fractionssize' not in dictionary:
raise ParseException(
'Number of fractions is missing in RepeatLengthDistribution'
)
self.train(data, int(dictionary['fractionssize']), start)
def test_configLoadingAndSaving(self):
input_file = "data/test_data/ConfigFactoryTestData.js"
a = ConfigFactory()
a.addObject(ConfigObject)
X = a.load(input_file)
self.assertEqual(type(X[1]), type(ConfigObject()),
"objectHook does not work")
X[1] = X[1].toJSON()
Y = [{
'1': 2,
'lol': 1.4
}, {
'__name__': 'ConfigObject'
}, [1, 2, 3, 4, {
'1': 2
}]]
self.assertEqual(X[0], Y[0], "loading of json does not work")
self.assertEqual(X[2], Y[2], "loading of json does not work")
self.assertEqual(X[1], Y[1], "saving to \"json\" is not working: " + \
str(X) + " != " + str(Y))
self.assertEqual(X, Y, "this should not happened")
def toJSON(self):
ret = ConfigObject.toJSON(self)
ret['val'] = self.value
return ret
def toJSON(self):
ret = ConfigObject.toJSON(self)
ret = self.statesToJSON(ret)
ret = self.transitionsToJSON(ret)
return ret
def toJSON(self):
ret = ConfigObject.toJSON(self)
ret['p'] = self.p
ret['start'] = self.start
ret['fractions'] = self.fractions
return ret
def toJSON(self):
ret = ConfigObject.toJSON(self)
ret['val'] = self.value
return ret
def load(self, dictionary):
ConfigObject.load(self, dictionary)
if 'val' not in dictionary:
raise ParseException("Value ('val') not found in state")
self.value = float(dictionary['val'])
def toJSON(self):
ret = ConfigObject.toJSON(self)
ret['p'] = self.p
ret['start'] = self.start
ret['fractions'] = self.fractions
return ret
def load(self, dictionary):
ConfigObject.load(self, dictionary)
self.loadStates(dictionary)
self.loadTransitions(dictionary)
def load(self, dictionary):
ConfigObject.load(self, dictionary)
if 'val' not in dictionary:
raise ParseException("Value ('val') not found in state")
self.value = float(dictionary['val'])