36 #ifndef OPENMS_ANALYSIS_ID_HIDDENMARKOVMODEL_H 
   37 #define OPENMS_ANALYSIS_ID_HIDDENMARKOVMODEL_H 
   80     void setName(
const String & name);
 
   84     const String & getName() 
const;
 
   87     void setHidden(
bool hidden);
 
   90     bool isHidden() 
const;
 
   93     void addPredecessorState(
HMMState * state);
 
   96     void deletePredecessorState(
HMMState * state);
 
   99     void addSuccessorState(
HMMState * state);
 
  102     void deleteSuccessorState(
HMMState * state);
 
  105     const std::set<HMMState *> & getPredecessorStates() 
const;
 
  108     const std::set<HMMState *> & getSuccessorStates() 
const;
 
  162     void writeGraphMLFile(
const String & filename);
 
  165     void write(std::ostream & out) 
const;
 
  174     Size getNumberOfStates() 
const;
 
  180     void addNewState(
const String & name);
 
  183     void addSynonymTransition(
const String & name1, 
const String & name2, 
const String & synonym1, 
const String & synonym2);
 
  192     void setInitialTransitionProbability(
const String & state, 
DoubleReal prob);
 
  195     void clearInitialTransitionProbabilities();
 
  201     void clearTrainingEmissionProbabilities();
 
  204     void enableTransition(
const String & s1, 
const String & s2);
 
  207     void disableTransition(
const String & s1, 
const String & s2);
 
  210     void disableTransitions();
 
  225     void estimateUntrainedTransitions();
 
  237     void setPseudoCounts(
DoubleReal pseudo_counts);
 
  242     void setVariableModifications(
const StringList & modifications);
 
  264     void calculateForwardPart_();
 
  267     void calculateBackwardPart_();
 
StringList var_modifications_
Definition: HiddenMarkovModel.h:327
A more convenient string class. 
Definition: String.h:56
bool hidden_
Definition: HiddenMarkovModel.h:114
std::set< HMMState * > succ_states_
Definition: HiddenMarkovModel.h:123
std::set< HMMState * > pre_states_
Definition: HiddenMarkovModel.h:120
Map< HMMState *, Map< HMMState *, std::pair< HMMState *, HMMState * > > > synonym_trans_
Definition: HiddenMarkovModel.h:316
std::set< HMMState * > states_
Definition: HiddenMarkovModel.h:307
Map< HMMState *, Map< HMMState *, std::vector< DoubleReal > > > train_count_trans_all_
Definition: HiddenMarkovModel.h:286
Map< HMMState *, DoubleReal > init_prob_
Definition: HiddenMarkovModel.h:304
Map< HMMState *, Map< HMMState *, DoubleReal > > trans_
Definition: HiddenMarkovModel.h:278
Map< String, Map< String, std::pair< String, String > > > synonym_trans_names_
Definition: HiddenMarkovModel.h:313
String name_
Definition: HiddenMarkovModel.h:117
std::set< std::pair< HMMState *, HMMState * > > trained_trans_
Definition: HiddenMarkovModel.h:310
Hidden Markov Model State class for the Hidden Markov Model. 
Definition: HiddenMarkovModel.h:54
Map< String, HMMState * > name_to_state_
Definition: HiddenMarkovModel.h:298
int evaluate(const gsl_vector *x, void *params, gsl_vector *f, gsl_matrix *J)
Driver function for the evaluation of function and jacobian. 
Map< HMMState *, Map< HMMState *, DoubleReal > > count_trans_
Definition: HiddenMarkovModel.h:281
Map< HMMState *, DoubleReal > forward_
Definition: HiddenMarkovModel.h:292
Map< HMMState *, std::set< HMMState * > > enabled_trans_
Definition: HiddenMarkovModel.h:319
String list. 
Definition: StringList.h:56
size_t Size
Size type e.g. used as variable which can hold result of size() 
Definition: Types.h:144
DoubleReal pseudo_counts_
Definition: HiddenMarkovModel.h:322
Map< HMMState *, DoubleReal > backward_
Definition: HiddenMarkovModel.h:295
Hidden Markov Model implementation of PILIS. 
Definition: HiddenMarkovModel.h:134
Map< HMMState *, DoubleReal > train_emission_prob_
Definition: HiddenMarkovModel.h:301
Map class based on the STL map (containing serveral convenience functions) 
Definition: Map.h:50
Map< HMMState *, Map< HMMState *, Size > > training_steps_count_
Definition: HiddenMarkovModel.h:289
Map< HMMState *, Map< HMMState *, std::vector< DoubleReal > > > count_trans_all_
Definition: HiddenMarkovModel.h:283