Package Bio :: Package HMM :: Module MarkovModel
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Module MarkovModel

source code

Deal with representations of Markov Models.

Classes [hide private]
  MarkovModelBuilder
Interface to build up a Markov Model.
  HiddenMarkovModel
Represent a hidden markov model that can be used for state estimation.
Functions [hide private]
 
_gen_random_array(n)
Return an array of n random numbers, where the elements of the array sum...
source code
 
_calculate_emissions(emission_probs)
Calculate which symbols can be emitted in each state...
source code
 
_calculate_from_transitions(trans_probs)
Calculate which 'from transitions' are allowed for each state
source code
 
_calculate_to_transitions(trans_probs)
Calculate which 'to transitions' are allowed for each state
source code
Variables [hide private]
  __package__ = 'Bio.HMM'
Function Details [hide private]

_gen_random_array(n)

source code 
Return an array of n random numbers, where the elements of the array sum
to 1.0

_calculate_emissions(emission_probs)

source code 
Calculate which symbols can be emitted in each state
    

_calculate_from_transitions(trans_probs)

source code 
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)

source code 
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.