FeatureFindingMetabo.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// 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,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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 <vector>
#include <svm.h>

namespace OpenMS
{

  class OPENMS_DLLAPI FeatureHypothesis
  {
public:
    FeatureHypothesis();

    ~FeatureHypothesis();

    FeatureHypothesis(const FeatureHypothesis&);

    FeatureHypothesis& operator=(const FeatureHypothesis& rhs);

    // 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;

    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();
    }

  };

  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:
    double computeCosineSim_(const std::vector<double>&, const std::vector<double>&) const;

    double computeOLSCoeff_(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) 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, const double total_intensity, std::vector<FeatureHypothesis>& output_hypotheses) const;

    svm_model* isotope_filt_svm_;
    std::vector<double> svm_feat_centers_;
    std::vector<double> svm_feat_scales_;

    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 report_convex_hulls_;
    bool report_chromatograms_;

    bool remove_single_traces_;
  };

}