// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Sandro Andreotti $
// --------------------------------------------------------------------------

#ifndef OPENMS_CHEMISTRY_SVMTHEORETICALSPECTRUMGENERATORTRAINER_H
#define OPENMS_CHEMISTRY_SVMTHEORETICALSPECTRUMGENERATORTRAINER_H

#include <OpenMS/KERNEL/StandardDeclarations.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/RichPeak1D.h>

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CHEMISTRY/SvmTheoreticalSpectrumGenerator.h>
#include <OpenMS/FORMAT/TextFile.h>

namespace OpenMS
{
  /**
   @brief Train SVM models that are used by SvmTheoreticalSpectrumGenerator

   @htmlinclude OpenMS_SvmTheoreticalSpectrumGeneratorTrainer.parameters

   This class implements the algorithm used by the homonymous tool which can be
   used to train models for MS/MS spectrum simulation.\n
   For the primary ion types (y, b) a SVM is trained using the libSVM library.\n
   All important libSVM parameters are accessible as parameters.\n
   Please refer to the libSVM manuals for detailed description of the parameters.
   Default values are chosen as in the svm-training tool delivered with libSVM.\n

   For the secondary types (a, c, x, z, losses, b2, y2) a simple Bayesian model is used.

   @ingroup Chemistry
   */

  class OPENMS_DLLAPI SvmTheoreticalSpectrumGeneratorTrainer :
    public DefaultParamHandler
  {
    typedef SvmTheoreticalSpectrumGenerator::IonType IonType;
    typedef SvmTheoreticalSpectrumGenerator::DescriptorSet DescriptorSet;
    typedef std::map<std::pair<IonType, Size>, std::vector<double> > ObservedIntensMap;

    /// stores the observed intensities for each sector-type combination in a vector
    void countIntensities_(const PeakSpectrum & spectrum,
                           const AASequence & annotation,
                           IonType type,
                           std::map<std::pair<IonType, Size>, std::vector<double> > & observed_intensities,
                           double tolerance,
                           Size number_of_regions
                           );

    /// trains the Bayesian secondary peak types models
    void trainSecondaryTypes_(TextFile & info_outfile,
                              Size number_of_regions,
                              Size number_of_intensity_levels,
                              ObservedIntensMap & observed_intensities,
                              const std::vector<IonType> & ion_types,
                              const std::vector<bool> & is_primary
                              );
public:

    /** @name Constructors and Destructors
     */
    //@{
    /// Default constructor
    SvmTheoreticalSpectrumGeneratorTrainer();

    /// Copy constructor
    SvmTheoreticalSpectrumGeneratorTrainer(const SvmTheoreticalSpectrumGeneratorTrainer & source);

    /// Destructor
    virtual ~SvmTheoreticalSpectrumGeneratorTrainer();
    //@}

    /// Assignment operator
    SvmTheoreticalSpectrumGeneratorTrainer & operator=(const SvmTheoreticalSpectrumGeneratorTrainer & tsg);

    /// trains an SVM for each ion_type and stores them in files \<filename\>_residue_loss_charge.svm
    void trainModel(const PeakMap & spectra, const std::vector<AASequence> & annotations, String filename, Int precursor_charge);

    /// Normalizes the intensity of the peaks in the input data
    void normalizeIntensity(PeakSpectrum & S) const;

protected:

    /// Write a training file that can be passed to libsvm command line tools
    void writeTrainingFile_(std::vector<DescriptorSet> & training_input, std::vector<double> & training_output, String filename);

  };
}

#endif // SvmTheoreticalSpectrumGeneratorTrainer_H
