PILISNeutralLossModel.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
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#ifndef OPENMS_ANALYSIS_ID_PILISNEUTRALLOSSMODEL_H
#define OPENMS_ANALYSIS_ID_PILISNEUTRALLOSSMODEL_H

#include <vector>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/ANALYSIS/ID/HiddenMarkovModel.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

namespace OpenMS
{
  class AASequence;

  class OPENMS_DLLAPI PILISNeutralLossModel :
    public DefaultParamHandler
  {
    friend class PILISNeutralLossModelGenerator;

public:


    PILISNeutralLossModel();

    PILISNeutralLossModel(const PILISNeutralLossModel & model);

    virtual ~PILISNeutralLossModel();

    PILISNeutralLossModel & operator=(const PILISNeutralLossModel & mode);


    DoubleReal train(const RichPeakSpectrum & spec, const AASequence & peptide, DoubleReal ion_weight, UInt charge, DoubleReal peptide_weight);

    void getIons(std::vector<RichPeak1D> & peaks, const AASequence & peptide, DoubleReal initial_prob);

    void setHMM(const HiddenMarkovModel & model);

    const HiddenMarkovModel & getHMM() const;

    void generateModel();

    void evaluate();

protected:

    DoubleReal getIntensitiesFromSpectrum_(const RichPeakSpectrum & train_spec, Map<String, DoubleReal> & pre_ints, DoubleReal ion_weight, const AASequence & peptide, UInt charge);

    void trainIons_(DoubleReal initial_probability, const Map<String, DoubleReal> & intensities, const AASequence & peptide);

    void getIons_(Map<String, DoubleReal> & intensities, DoubleReal initial_probability, const AASequence & precursor);

    void enableIonStates_(const AASequence & peptide);

    HiddenMarkovModel hmm_precursor_;

    UInt num_explicit_;

    void updateMembers_();
  };
}
#endif