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Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
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17 | 2 | 4 | 0.967 | compound_stmt |

Clone Abstraction | Parameter Bindings |

Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
---|---|---|---|

1 | 11 | 213 | Bio/HMM/MarkovModel.py |

2 | 17 | 225 | Bio/HMM/MarkovModel.py |

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def set_transition_score(self,from_state,to_state,probability): """Set the probability of a transition between two states. Raises: KeyError if the transition is not allowed. """ if self.transition_prob.has_key((from_state,to_state)): self.transition_prob[(from_state,to_state)] = probability else: raise KeyError("Transition from %s to %s is not allowed."%(from_state,to_state)) |

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def set_transition_pseudocount(self,from_state,to_state,count): """Set the default pseudocount for a transition. 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 transitions have a pseudocount of 1. Raises: KeyError if the transition is not allowed. """ if self.transition_pseudo.has_key((from_state,to_state)): self.transition_pseudo[(from_state,to_state)] = count else: raise KeyError("Transition from %s to %s is not allowed."%(from_state,to_state)) # --- functions to deal with emissions from the sequence |

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def [[#variable2e0968c0]](self,from_state,to_state, [[#variable2e096840]]): [[#variable2e0967a0]] if self. [[#variable2e096740]].has_key((from_state,to_state)): self. [[#variable2e096740]][(from_state,to_state)] = [[#variable2e096840]] else: raise KeyError("Transition from %s to %s is not allowed."%(from_state,to_state)) # --- functions to deal with emissions from the sequence |

CloneAbstraction |

Parameter Index | Clone Instance | Parameter Name | Value |
---|---|---|---|

1 | 1 | [[#2e0968c0]] | set_transition_pseudocount |

1 | 2 | [[#2e0968c0]] | set_transition_score |

2 | 1 | [[#2e096840]] | count |

2 | 2 | [[#2e096840]] | probability |

3 | 1 | [[#2e0967a0]] | """Set the default pseudocount for a transition. 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 transitions have a pseudocount of 1. Raises: KeyError if the transition is not allowed. """ |

3 | 2 | [[#2e0967a0]] | """Set the probability of a transition between two states. Raises: KeyError if the transition is not allowed. """ |

4 | 1 | [[#2e096740]] | transition_pseudo |

4 | 2 | [[#2e096740]] | transition_prob |