SvmTheoreticalSpectrumGeneratorTrainer.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Sandro Andreotti $
// --------------------------------------------------------------------------

#pragma once

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

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

namespace OpenMS
{
  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;

    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
                           );

    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:

    SvmTheoreticalSpectrumGeneratorTrainer();

    SvmTheoreticalSpectrumGeneratorTrainer(const SvmTheoreticalSpectrumGeneratorTrainer & source);

    ~SvmTheoreticalSpectrumGeneratorTrainer() override;

    SvmTheoreticalSpectrumGeneratorTrainer & operator=(const SvmTheoreticalSpectrumGeneratorTrainer & tsg);

    void trainModel(const PeakMap & spectra, const std::vector<AASequence> & annotations, String filename, Int precursor_charge);

    void normalizeIntensity(PeakSpectrum & S) const;

protected:

    void writeTrainingFile_(std::vector<DescriptorSet> & training_input, std::vector<double> & training_output, String filename);

  };
}