HiddenMarkovModel.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
 
#pragma once
 
#include <vector>
#include <set>
 
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/StringListUtils.h>
#include <OpenMS/DATASTRUCTURES/String.h>
 
#include <utility>
 
namespace OpenMS
{
  class OPENMS_DLLAPI HMMState
  {
public:
 
    HMMState();
 
    HMMState(const HMMState & state);
 
    HMMState(const String & name, bool hidden = true);
 
    virtual ~HMMState();
 
    HMMState & operator=(const HMMState &);
 
    void setName(const String & name);
 
    const String & getName() const;
 
    void setHidden(bool hidden);
 
    bool isHidden() const;
 
    void addPredecessorState(HMMState * state);
 
    void deletePredecessorState(HMMState * state);
 
    void addSuccessorState(HMMState * state);
 
    void deleteSuccessorState(HMMState * state);
 
    const std::set<HMMState *> & getPredecessorStates() const;
 
    const std::set<HMMState *> & getSuccessorStates() const;
 
protected:
 
    bool hidden_;
 
    String name_;
 
    std::set<HMMState *> pre_states_;
 
    std::set<HMMState *> succ_states_;
  };
 
 
  class OPENMS_DLLAPI HiddenMarkovModel
  {
public:
 
    HiddenMarkovModel();
 
    HiddenMarkovModel(const HiddenMarkovModel & hmm_new);
 
    virtual ~HiddenMarkovModel();
 
    HiddenMarkovModel & operator=(const HiddenMarkovModel &);
 
    void writeGraphMLFile(const String & filename);
 
    void write(std::ostream & out) const;
 
    double getTransitionProbability(const String & s1, const String & s2) const;
 
    void setTransitionProbability(const String & s1, const String & s2, double prob);
 
    Size getNumberOfStates() const;
 
    void addNewState(HMMState * state);
 
    void addNewState(const String & name);
 
    void addSynonymTransition(const String & name1, const String & name2, const String & synonym1, const String & synonym2);
 
    void evaluate();
 
    void train();
 
    void setInitialTransitionProbability(const String & state, double prob);
 
    void clearInitialTransitionProbabilities();
 
    void setTrainingEmissionProbability(const String & state, double prob);
 
    void clearTrainingEmissionProbabilities();
 
    void enableTransition(const String & s1, const String & s2);
 
    void disableTransition(const String & s1, const String & s2);
 
    void disableTransitions();
 
    void calculateEmissionProbabilities(Map<HMMState *, double> & emission_probs);
 
    void dump();
 
    void forwardDump();
 
    //void buildSynonyms();
 
    void estimateUntrainedTransitions();
 
    HMMState * getState(const String & name);
 
    const HMMState * getState(const String & name) const;
 
    void clear();
 
    void setPseudoCounts(double pseudo_counts);
 
    double getPseudoCounts() const;
 
    void setVariableModifications(const StringList & modifications);
 
protected:
 
    void disableTransition_(HMMState * s1, HMMState * s2);
 
    void enableTransition_(HMMState * s1, HMMState * s2);
 
    void setTrainingEmissionProbability_(HMMState * state, double prob);
 
    void setTransitionProbability_(HMMState * s1, HMMState * s2, double prob);
 
    double getTransitionProbability_(HMMState * s1, HMMState * s2) const;
 
 
    void calculateForwardPart_();
 
    void calculateBackwardPart_();
 
    double getForwardVariable_(HMMState *);
 
    double getBackwardVariable_(HMMState *);
 
private:
 
    // transition probs
    Map<HMMState *, Map<HMMState *, double> > trans_;
 
    // transition prob counts
    Map<HMMState *, Map<HMMState *, double> > count_trans_;
 
    Map<HMMState *, Map<HMMState *, std::vector<double> > > count_trans_all_;
 
    // all transition probs of all training steps (for model checking)
    Map<HMMState *, Map<HMMState *, std::vector<double> > > train_count_trans_all_;
 
    // number of training steps of the transitions
    Map<HMMState *, Map<HMMState *, Size> > training_steps_count_;
 
    // forward variables
    Map<HMMState *, double> forward_;
 
    // backward variables
    Map<HMMState *, double> backward_;
 
    // name to state Mapping
    Map<String, HMMState *> name_to_state_;
 
    // emission probabilities
    Map<HMMState *, double> train_emission_prob_;
 
    // initial transition probabilities
    Map<HMMState *, double> init_prob_;
 
    // all states of the HMM
    std::set<HMMState *> states_;
 
    // trained transitions
    std::set<std::pair<HMMState *, HMMState *> > trained_trans_;
 
    // synonym transitions Mapping
    Map<String, Map<String, std::pair<String, String> > > synonym_trans_names_;
 
    // synonym transitions
    Map<HMMState *, Map<HMMState *, std::pair<HMMState *, HMMState *> > > synonym_trans_;
 
    // transitions which are enabled
    Map<HMMState *, std::set<HMMState *> > enabled_trans_;
 
    // pseudocounts used in this instance
    double pseudo_counts_;
 
    // copy all the stuff from one HMM to this
    void copy_(const HiddenMarkovModel & source);
 
    StringList var_modifications_;
  };
}