CloneSet273


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Clone
Mass
Clones in
CloneSet
Parameter
Count
Clone
Similarity
Syntax Category
[Sequence Length]
17240.967compound_stmt
Clone AbstractionParameter Bindings
Clone Instance
(Click to see clone)
Line CountSource Line
Source File
111245
Bio/HMM/MarkovModel.py
217257
Bio/HMM/MarkovModel.py
Clone Instance
1
Line Count
11
Source Line
245
Source File
Bio/HMM/MarkovModel.py

    def set_emission_score(self,seq_state,emission_state,probability):   
        """Set the probability of a emission from a particular state.

        Raises:
        KeyError if the emission from the given state is not allowed.
        """ 
        if self.emission_prob.has_key((seq_state,emission_state)): 
            self.emission_prob[(seq_state,emission_state)] =  probability 
        else: 
             raise KeyError("Emission of %s from %s is not allowed."%(emission_state,seq_state)) 
        


Clone Instance
2
Line Count
17
Source Line
257
Source File
Bio/HMM/MarkovModel.py

    def set_emission_pseudocount(self,seq_state,emission_state,count):   
        """Set the default pseudocount for an emission.

        To avoid computational problems, it is helpful to be able to
        set a 'default' pseudocount to start with for estimating
        transition and emission probabilities (see p62 in Durbin et al
        for more discussion on this. By default, all emissions have
        a pseudocount of 1.

        Raises:
        KeyError if the emission from the given state is not allowed.
        """ 
        if self.emission_pseudo.has_key((seq_state,emission_state)): 
            self.emission_pseudo[(seq_state,emission_state)] =  count 
        else: 
             raise KeyError("Emission of %s from %s is not allowed."%(emission_state,seq_state)) 
        


Clone AbstractionParameter Count: 4Parameter Bindings

def [[#variable76bb04c0]](self,seq_state,emission_state, [[#variable76bb0080]]):
   [[#variable76bb0420]]
  if self. [[#variable76bb0480]].has_key((seq_state,emission_state)):
  
    self. [[#variable76bb0480]][(seq_state,emission_state)] = [[#variable76bb0080]]
  else:
  
    raise KeyError("Emission of %s from %s is not allowed."%(emission_state,seq_state)) 
  
 

CloneAbstraction
Parameter Bindings
Parameter
Index
Clone
Instance
Parameter
Name
Value
11[[#76bb04c0]]
set_emission_pseudocount 
12[[#76bb04c0]]
set_emission_score 
21[[#76bb0080]]
count 
22[[#76bb0080]]
probability 
31[[#76bb0420]]
"""Set the default pseudocount for an emission.

        To avoid computational problems, it is helpful to be able to
        set a 'default' pseudocount to start with for estimating
        transition and emission probabilities (see p62 in Durbin et al
        for more discussion on this. By default, all emissions have
        a pseudocount of 1.

        Raises:
        KeyError if the emission from the given state is not allowed.
        """ 
32[[#76bb0420]]
"""Set the probability of a emission from a particular state.

        Raises:
        KeyError if the emission from the given state is not allowed.
        """ 
41[[#76bb0480]]
emission_pseudo 
42[[#76bb0480]]
emission_prob