HiddenMarkovModel#

class pyopenms.HiddenMarkovModel#

Bases: object

Cython implementation of _HiddenMarkovModel

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1HiddenMarkovModel.html

__init__()#

Cython signature: void HiddenMarkovModel() Hidden Markov Model implementation of PILIS
Cython signature: void HiddenMarkovModel(HiddenMarkovModel &)

Methods

`__init__`	Cython signature: void HiddenMarkovModel()
`addNewState`	Cython signature: void addNewState(HMMState * state)
`addSynonymTransition`	Cython signature: void addSynonymTransition(const String & name1, const String & name2, const String & synonym1, const String & synonym2) Add a new synonym transition to the given state names
`clear`	Cython signature: void clear() Clears all data
`clearInitialTransitionProbabilities`	Cython signature: void clearInitialTransitionProbabilities() Clears the initial probabilities
`clearTrainingEmissionProbabilities`	Cython signature: void clearTrainingEmissionProbabilities() Clear the emission probabilities
`disableTransition`	Cython signature: void disableTransition(const String & s1, const String & s2) Disables the transition; deletes the nodes from the predecessor/successor list respectively
`disableTransitions`	Cython signature: void disableTransitions() Disables all transitions
`dump`	Cython signature: void dump() Writes some stats to cerr
`enableTransition`	Cython signature: void enableTransition(const String & s1, const String & s2) Enables a transition; adds s1 to the predecessor list of s2 and s2 to the successor list of s1
`estimateUntrainedTransitions`	Cython signature: void estimateUntrainedTransitions() Estimates the transition probabilities of not trained transitions by averages similar trained ones
`evaluate`	Cython signature: void evaluate() Evaluate the HMM, estimates the transition probabilities from the training
`forwardDump`	Cython signature: void forwardDump() Writes some info of the forward "matrix" to cerr
`getNumberOfStates`	Cython signature: size_t getNumberOfStates() Returns the number of states
`getPseudoCounts`	Cython signature: double getPseudoCounts() Returns the pseudo counts
`getState`	Cython signature: HMMState * getState(const String & name) Returns the state with the given name
`getTransitionProbability`	Cython signature: double getTransitionProbability(const String & s1, const String & s2) Returns the transition probability of the given state names
`setInitialTransitionProbability`	Cython signature: void setInitialTransitionProbability(const String & state, double prob) Sets the initial transition probability of the given state to prob
`setPseudoCounts`	Cython signature: void setPseudoCounts(double pseudo_counts) Sets the pseudo count that are added instead of zero
`setTrainingEmissionProbability`	Cython signature: void setTrainingEmissionProbability(const String & state, double prob) Sets the emission probability of the given state to prob
`setTransitionProbability`	Cython signature: void setTransitionProbability(const String & s1, const String & s2, double prob) Sets the transition probability of the given state names to prob
`setVariableModifications`	Cython signature: void setVariableModifications(StringList & modifications)
`train`	Cython signature: void train() Trains the HMM.
`writeGraphMLFile`	Cython signature: void writeGraphMLFile(const String & filename) Writes the HMM into a file in GraphML format

addNewState()#

Cython signature: void addNewState(HMMState * state) Registers a new state to the HMM
Cython signature: void addNewState(const String & name) Registers a new state to the HMM

addSynonymTransition()#: Cython signature: void addSynonymTransition(const String & name1, const String & name2, const String & synonym1, const String & synonym2) Add a new synonym transition to the given state names

clear()#: Cython signature: void clear() Clears all data

clearInitialTransitionProbabilities()#: Cython signature: void clearInitialTransitionProbabilities() Clears the initial probabilities

clearTrainingEmissionProbabilities()#: Cython signature: void clearTrainingEmissionProbabilities() Clear the emission probabilities

disableTransition()#: Cython signature: void disableTransition(const String & s1, const String & s2) Disables the transition; deletes the nodes from the predecessor/successor list respectively

disableTransitions()#: Cython signature: void disableTransitions() Disables all transitions

dump()#: Cython signature: void dump() Writes some stats to cerr

enableTransition()#: Cython signature: void enableTransition(const String & s1, const String & s2) Enables a transition; adds s1 to the predecessor list of s2 and s2 to the successor list of s1

estimateUntrainedTransitions()#: Cython signature: void estimateUntrainedTransitions() Estimates the transition probabilities of not trained transitions by averages similar trained ones

evaluate()#: Cython signature: void evaluate() Evaluate the HMM, estimates the transition probabilities from the training

forwardDump()#: Cython signature: void forwardDump() Writes some info of the forward “matrix” to cerr

getNumberOfStates()#: Cython signature: size_t getNumberOfStates() Returns the number of states

getPseudoCounts()#: Cython signature: double getPseudoCounts() Returns the pseudo counts

getState()#: Cython signature: HMMState * getState(const String & name) Returns the state with the given name

getTransitionProbability()#: Cython signature: double getTransitionProbability(const String & s1, const String & s2) Returns the transition probability of the given state names

setInitialTransitionProbability()#: Cython signature: void setInitialTransitionProbability(const String & state, double prob) Sets the initial transition probability of the given state to prob

setPseudoCounts()#: Cython signature: void setPseudoCounts(double pseudo_counts) Sets the pseudo count that are added instead of zero

setTrainingEmissionProbability()#: Cython signature: void setTrainingEmissionProbability(const String & state, double prob) Sets the emission probability of the given state to prob

setTransitionProbability()#: Cython signature: void setTransitionProbability(const String & s1, const String & s2, double prob) Sets the transition probability of the given state names to prob

setVariableModifications()#: Cython signature: void setVariableModifications(StringList & modifications)

train()#: Cython signature: void train() Trains the HMM. Initial probabilities and emission probabilities of the emitting states should be set

writeGraphMLFile()#: Cython signature: void writeGraphMLFile(const String & filename) Writes the HMM into a file in GraphML format