| OpenMS 2.5.0

HiddenMarkovModel Member List

This is the complete list of members for HiddenMarkovModel, including all inherited members.

addNewState(HMMState *state) | HiddenMarkovModel |
addNewState(const String &name) | HiddenMarkovModel |
addSynonymTransition(const String &name1, const String &name2, const String &synonym1, const String &synonym2) | HiddenMarkovModel |
backward_ | HiddenMarkovModel | private
calculateBackwardPart_() | HiddenMarkovModel | protected
calculateEmissionProbabilities(Map< HMMState *, double > &emission_probs) | HiddenMarkovModel |
calculateForwardPart_() | HiddenMarkovModel | protected
clear() | HiddenMarkovModel |
clearInitialTransitionProbabilities() | HiddenMarkovModel |
clearTrainingEmissionProbabilities() | HiddenMarkovModel |
copy_(const HiddenMarkovModel &source) | HiddenMarkovModel | private
count_trans_ | HiddenMarkovModel | private
count_trans_all_ | HiddenMarkovModel | private
disableTransition(const String &s1, const String &s2) | HiddenMarkovModel |
disableTransition_(HMMState *s1, HMMState *s2) | HiddenMarkovModel | protected
disableTransitions() | HiddenMarkovModel |
dump() | HiddenMarkovModel |
enabled_trans_ | HiddenMarkovModel | private
enableTransition(const String &s1, const String &s2) | HiddenMarkovModel |
enableTransition_(HMMState *s1, HMMState *s2) | HiddenMarkovModel | protected
estimateUntrainedTransitions() | HiddenMarkovModel |
evaluate() | HiddenMarkovModel |
forward_ | HiddenMarkovModel | private
forwardDump() | HiddenMarkovModel |
getBackwardVariable_(HMMState *) | HiddenMarkovModel | protected
getForwardVariable_(HMMState *) | HiddenMarkovModel | protected
getNumberOfStates() const | HiddenMarkovModel |
getPseudoCounts() const | HiddenMarkovModel |
getState(const String &name) | HiddenMarkovModel |
getState(const String &name) const | HiddenMarkovModel |
getTransitionProbability(const String &s1, const String &s2) const | HiddenMarkovModel |
getTransitionProbability_(HMMState *s1, HMMState *s2) const | HiddenMarkovModel | protected
HiddenMarkovModel() | HiddenMarkovModel |
HiddenMarkovModel(const HiddenMarkovModel &hmm_new) | HiddenMarkovModel |
init_prob_ | HiddenMarkovModel | private
name_to_state_ | HiddenMarkovModel | private
operator=(const HiddenMarkovModel &) | HiddenMarkovModel |
pseudo_counts_ | HiddenMarkovModel | private
setInitialTransitionProbability(const String &state, double prob) | HiddenMarkovModel |
setPseudoCounts(double pseudo_counts) | HiddenMarkovModel |
setTrainingEmissionProbability(const String &state, double prob) | HiddenMarkovModel |
setTrainingEmissionProbability_(HMMState *state, double prob) | HiddenMarkovModel | protected
setTransitionProbability(const String &s1, const String &s2, double prob) | HiddenMarkovModel |
setTransitionProbability_(HMMState *s1, HMMState *s2, double prob) | HiddenMarkovModel | protected
setVariableModifications(const StringList &modifications) | HiddenMarkovModel |
states_ | HiddenMarkovModel | private
synonym_trans_ | HiddenMarkovModel | private
synonym_trans_names_ | HiddenMarkovModel | private
train() | HiddenMarkovModel |
train_count_trans_all_ | HiddenMarkovModel | private
train_emission_prob_ | HiddenMarkovModel | private
trained_trans_ | HiddenMarkovModel | private
training_steps_count_ | HiddenMarkovModel | private
trans_ | HiddenMarkovModel | private
var_modifications_ | HiddenMarkovModel | private
write(std::ostream &out) const | HiddenMarkovModel |
writeGraphMLFile(const String &filename) | HiddenMarkovModel |
~HiddenMarkovModel() | HiddenMarkovModel | virtual