def expand(self, _=None):
json = self.model.toJSON()
prefix = self.stateName + '_'
states = map(deepcopy, self.model.states)
for i in range(len(states)):
states[i].stateName = prefix + states[i].stateName
transitions = map(
lambda x: {
'from': prefix + x['from'],
'to': prefix + x['to'],
'prob': x['prob'],
},
json['transitions'],
)
return double_track_hmm(states, transitions, prefix + 'I1', prefix + 'End', self.mathType)
def expand(self, params=None):
if params == None:
raise "Houston, we have a problem"
consensuses = params['consensus']
prefix_t = self.stateName + '_{}_'
prefix_i = 0
states = list()
transitions = list()
init = self.stateName + '_Init'
end = self.stateName + '_End'
total = 0.0
for consensus in consensuses:
prefix = prefix_t.format(prefix_i)
prefix_i += 1
model = self.factory.getHMM(consensus)
probability = self.consensusDistribution[consensus]
total += probability
json = model.toJSON()
new_init = prefix + 'Init'
new_end = prefix + 'End'
st = map(deepcopy, model.states)
for i in range(len(st)):
st[i].stateName = prefix + st[i].stateName
tr = map(
lambda x: {
'from': prefix + x['from'],
'to': prefix + x['to'],
'prob': x['prob'],
},
json['transitions'],
)
st, tr, new_init, new_end = double_track_hmm(
st, tr, new_init, new_end, self.mathType
)
transitions.extend(tr)
states.extend(st)
transitions.extend([
{
'from': init,
'to': new_init,
'prob': probability,
},
{
'from': new_end,
'to': end,
'prob': 1.0,
},
])
#transitions.append({
# 'from': init,
# 'to': init,
# 'prob': 1.0 - total,
#})
template = {
'__name__': 'GeneralizedPairState',
'name': init,
'startprob': 1.0,
'endprob': 0.0,
'emission': [(('', ''), self.mathType(1.0))],
'durations': [((0, 0), self.mathType(1.0))],
}
st = GeneralizedPairState(self.mathType)
st.load(template)
states.append(st)
template['name'] = end
template['startprob'] = 0.0
template['endprob'] = 1.0
st = GeneralizedPairState(self.mathType)
st.load(template)
states.append(st)
return states, transitions, init, end
