FeatureFindingMetabo.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Erhan Kenar, Holger Franken $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/MassTrace.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
#include <OpenMS/CHEMISTRY/Element.h>
 
#include <vector>
 
struct svm_model;
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI FeatureHypothesis
  {
public:
    FeatureHypothesis() = default;
 
    ~FeatureHypothesis() = default;
 
    FeatureHypothesis(const FeatureHypothesis&) = default;
 
    FeatureHypothesis& operator=(const FeatureHypothesis& rhs) = default;
 
    // getter & setter
    Size getSize() const;
 
    String getLabel() const;
 
    std::vector<String> getLabels() const;
 
    double getScore() const;
 
    void setScore(const double& score);
 
    SignedSize getCharge() const;
 
    void setCharge(const SignedSize& ch);
 
    std::vector<double> getAllIntensities(bool smoothed = false) const;
 
    std::vector<double> getAllCentroidMZ() const;
 
    std::vector<double> getAllCentroidRT() const;
 
    std::vector<double> getIsotopeDistances() const;
 
    double getCentroidMZ() const;
 
    double getCentroidRT() const;
 
    double getFWHM() const;
 
    void addMassTrace(const MassTrace&);
    double getMonoisotopicFeatureIntensity(bool) const;
    double getSummedFeatureIntensity(bool) const;
 
    double getMaxIntensity(bool smoothed = false) const;
 
    Size getNumFeatPoints() const;
    std::vector<ConvexHull2D> getConvexHulls() const;
    std::vector< OpenMS::MSChromatogram > getChromatograms(UInt64 feature_id) const;
 
private:
 
    // pointers of MassTraces contained in isotopic pattern
    std::vector<const MassTrace*> iso_pattern_;
 
    double feat_score_{};
 
    SignedSize charge_{};
  };
 
  class OPENMS_DLLAPI CmpMassTraceByMZ
  {
public:
 
    bool operator()(const MassTrace& x, const MassTrace& y) const
    {
      return x.getCentroidMZ() < y.getCentroidMZ();
    }
 
  };
 
  class OPENMS_DLLAPI CmpHypothesesByScore
  {
public:
 
    bool operator()(const FeatureHypothesis& x, const FeatureHypothesis& y) const
    {
      return x.getScore() > y.getScore();
    }
 
  };
 
  struct OPENMS_DLLAPI  Range
{
  double left_boundary;
  double right_boundary;
};
 
  class OPENMS_DLLAPI FeatureFindingMetabo :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:
    FeatureFindingMetabo();
 
    ~FeatureFindingMetabo() override;
 
    void run(std::vector<MassTrace>& input_mtraces, FeatureMap& output_featmap, std::vector<std::vector< OpenMS::MSChromatogram > >& output_chromatograms);
 
protected:
    void updateMembers_() override;
 
private:
    std::vector<const Element*> elementsFromString_(const std::string& elements_string) const;
    Range getTheoreticIsotopicMassWindow_(const std::vector<Element const *> alphabet, int peakOffset) const;
 
    double computeCosineSim_(const std::vector<double>&, const std::vector<double>&) const;
 
    int isLegalIsotopePattern_(const FeatureHypothesis& feat_hypo) const;
 
    void loadIsotopeModel_(const String&);
 
    double scoreMZ_(const MassTrace &, const MassTrace &, Size isotopic_position, Size charge, Range isotope_window) const;
 
    double scoreMZByExpectedMean_(Size iso_pos, Size charge, const double diff_mz, double mt_variances) const;
 
    double scoreMZByExpectedRange_(Size charge, const double diff_mz, double mt_variances, Range isotope_window) const;
 
    double scoreRT_(const MassTrace&, const MassTrace&) const;
 
    double computeAveragineSimScore_(const std::vector<double>& intensities, const double& molecular_weight) const;
 
    void findLocalFeatures_(const std::vector<const MassTrace*>& candidates, double total_intensity, std::vector<FeatureHypothesis>& output_hypotheses) const;
 
    svm_model* isotope_filt_svm_ = nullptr;
    std::vector<double> svm_feat_centers_;
    std::vector<double> svm_feat_scales_;
 
    //unused
    //double total_intensity_;
 
    double local_rt_range_;
    double local_mz_range_;
    Size charge_lower_bound_;
    Size charge_upper_bound_;
    double chrom_fwhm_;
 
    bool report_summed_ints_;
    bool enable_RT_filtering_;
    String isotope_filtering_model_;
    bool use_smoothed_intensities_;
    
    bool use_mz_scoring_C13_;
    bool use_mz_scoring_by_element_range_;
    bool report_convex_hulls_;
    bool report_chromatograms_;
 
    bool remove_single_traces_;
    std::vector<const Element*> elements_;
  };
 
}