PILISModel.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
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#ifndef OPENMS_ANALYSIS_ID_PILISMODEL_H
#define OPENMS_ANALYSIS_ID_PILISMODEL_H

#include <vector>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/ANALYSIS/ID/HiddenMarkovModel.h>
#include <OpenMS/ANALYSIS/ID/ProtonDistributionModel.h>
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
#include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h>
#include <OpenMS/FORMAT/TextFile.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/ANALYSIS/ID/PILISNeutralLossModel.h>


namespace OpenMS
{
  class AASequence;

  class OPENMS_DLLAPI PILISModel :
    public DefaultParamHandler
  {
public:


    PILISModel();

    PILISModel(const PILISModel & model);

    virtual ~PILISModel();

    PILISModel & operator=(const PILISModel & mode);


    void train(const RichPeakSpectrum &, const AASequence & peptide, UInt charge);

    void readFromFile(const String & filename);

    void writeGraphMLFile(const String & filename);

    void writeToFile(const String & filename);

    //
    void init(bool generate_models = true);

    void getSpectrum(RichPeakSpectrum & spec, const AASequence & peptide, UInt charge);

    void evaluate();

protected:

    bool getInitialTransitionProbabilities_(std::vector<DoubleReal> & bb_init,
                                            std::vector<DoubleReal> & cr_init,
                                            std::vector<DoubleReal> & sc_init,
                                            DoubleReal & precursor_init,
                                            const std::vector<DoubleReal> & bb_charges,
                                            const std::vector<DoubleReal> & sc_charges,
                                            const AASequence & peptide);

    DoubleReal getAvailableBackboneCharge_(const AASequence & ion, Residue::ResidueType res_type, int charge);

    void addPeaks_(DoubleReal mz, int charge, DoubleReal mz_offset, DoubleReal intensity, RichPeakSpectrum & spectrum, const IsotopeDistribution & id, const String & name);

    void parseHMMModel_(const TextFile::ConstIterator & begin, const TextFile::ConstIterator & end, HiddenMarkovModel & hmm, Param & param);

    void writeParameters_(std::ostream & os, const Param & param);

    HiddenMarkovModel hmm_;

    ProtonDistributionModel prot_dist_;

    TheoreticalSpectrumGenerator tsg_;

    bool valid_;

    Map<DoubleReal, std::vector<RichPeak1D> > peaks_;

    SpectrumAlignment spectra_aligner_;

    PILISNeutralLossModel precursor_model_cr_;

    PILISNeutralLossModel precursor_model_cd_;

    PILISNeutralLossModel a_ion_losses_cr_;
    PILISNeutralLossModel a_ion_losses_cd_;

    PILISNeutralLossModel b_ion_losses_cr_;
    PILISNeutralLossModel b_ion_losses_cd_;

    PILISNeutralLossModel b2_ion_losses_cr_;
    PILISNeutralLossModel b2_ion_losses_cd_;

    PILISNeutralLossModel y_ion_losses_cr_;
    PILISNeutralLossModel y_ion_losses_cd_;

    void updateMembers_();
  };
}
#endif