Module MarkovModel

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Deal with representations of Markov Models.

Classes

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MarkovModelBuilder
Interface to build up a Markov Model.

HiddenMarkovModel
Represent a hidden markov model that can be used for state estimation.

Functions

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_gen_random_array(n)
Return an array of n random numbers, where the elements of the array sum to 1.0

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_calculate_emissions(emission_probs)
Calculate which symbols can be emitted in each state

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_calculate_from_transitions(trans_probs)
Calculate which 'from transitions' are allowed for each state

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_calculate_to_transitions(trans_probs)
Calculate which 'to transitions' are allowed for each state

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Variables

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__package__ = 'Bio.HMM'

Function Details

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_calculate_from_transitions(trans_probs)

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Calculate which 'from transitions' are allowed for each state

This looks through all of the trans_probs, and uses this dictionary to determine allowed transitions. It converts this information into a dictionary, whose keys are source states and whose values are lists of destination states reachable from the source state via a transition.

_calculate_to_transitions(trans_probs)

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Calculate which 'to transitions' are allowed for each state

This looks through all of the trans_probs, and uses this dictionary to determine allowed transitions. It converts this information into a dictionary, whose keys are destination states and whose values are lists of source states from which the destination is reachable via a transition.