libopenms-dev 1.11.1-5 / usr / include / OpenMS / ANALYSIS / ID / PILISModel.h

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//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------


#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;

  /**
    @brief This class implements the simulation of the spectra from PILIS

      PILIS uses a HMM based structure to model the population of fragment ions
      from a peptide. The spectrum generator can be accessed via the getSpectrum
      method.

      @htmlinclude OpenMS_PILISModel.parameters

      @ingroup Analysis_ID
  */
  class OPENMS_DLLAPI PILISModel :
    public DefaultParamHandler
  {
public:

    /** @name Constructors and destructors
    */
    //@{
    /// default constructor
    PILISModel();

    /// copy constructor
    PILISModel(const PILISModel & model);

    /// destructor
    virtual ~PILISModel();
    //@}

    /// assignment operator
    PILISModel & operator=(const PILISModel & mode);

    /** @name Accessors
    */
    //@{
    /// performs a training step; needs as parameters a spectrum with annotated sequence and charge
    void train(const RichPeakSpectrum &, const AASequence & peptide, UInt charge);

    /** reads the model parameters from the given files
        @param filename filename of the model
    */
    void readFromFile(const String & filename);

    /// writes the HMM to the given file in the GraphML format. A detailed description of the GraphML format can be found under http://graphml.graphdrawing.org/
    void writeGraphMLFile(const String & filename);

    /** writes the model parameters into the given files
        @param filename filename of the base model
    */
    void writeToFile(const String & filename);

    //
    void init(bool generate_models = true);

    /// simulates a spectrum with the model of the given peptide and charge and writes it to the given PeakSpectrum
    void getSpectrum(RichPeakSpectrum & spec, const AASequence & peptide, UInt charge);

    /// this method evaluates the model after training; it should be called after all training steps with train
    void evaluate();
    //@}

protected:

    /// get the initial transition probabilities from the proton dist, returns true if charge remote is enabled
    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);

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

    /// parse the base model
    void parseHMMModel_(const TextFile::ConstIterator & begin, const TextFile::ConstIterator & end, HiddenMarkovModel & hmm, Param & param);

    /// write parameters of the model
    void writeParameters_(std::ostream & os, const Param & param);

    /// base model used
    HiddenMarkovModel hmm_;

    /// proton distribution model
    ProtonDistributionModel prot_dist_;

    /// theoretical spectrum generator (needed for training/aligning and spectrum intensity extraction)
    TheoreticalSpectrumGenerator tsg_;

    /// true if the instance is valid
    bool valid_;

    /// stores the peaks of a spectrum
    Map<DoubleReal, std::vector<RichPeak1D> > peaks_;

    /// the alignment algorithm used
    SpectrumAlignment spectra_aligner_;

    /// precursor model used
    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