DIAScoring.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 2002-2022.
//
// 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: Hannes Roest $
// $Authors: Hannes Roest, Witold Wolski $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
namespace OpenMS
{
  class TheoreticalSpectrumGenerator;
 
  class OPENMS_DLLAPI DIAScoring :
    public DefaultParamHandler
  {
 
    typedef OpenSwath::SpectrumPtr SpectrumPtrType;
    typedef OpenSwath::LightTransition TransitionType;
 
public:
 
 
    DIAScoring();
 
    ~DIAScoring() override;
 
    // DIA / SWATH scoring
 
 
    void dia_isotope_scores(const std::vector<TransitionType>& transitions,
                            SpectrumPtrType spectrum,
                            OpenSwath::IMRMFeature* mrmfeature,
                            double& isotope_corr,
                            double& isotope_overlap) const;
 
    void dia_massdiff_score(const std::vector<TransitionType>& transitions,
                            SpectrumPtrType spectrum,
                            const std::vector<double>& normalized_library_intensity,
                            double& ppm_score,
                            double& ppm_score_weighted,
                            std::vector<double>& diff_ppm) const;
 
    bool dia_ms1_massdiff_score(double precursor_mz, SpectrumPtrType spectrum,
                                double& ppm_score) const;
 
    void dia_ms1_isotope_scores_averagine(double precursor_mz, SpectrumPtrType spectrum,
                                          double& isotope_corr, double& isotope_overlap, int charge_state) const;
    void dia_ms1_isotope_scores(double precursor_mz, SpectrumPtrType spectrum,
                                double& isotope_corr, double& isotope_overlap, const EmpiricalFormula& sum_formula) const;
 
 
    void dia_by_ion_score(SpectrumPtrType spectrum, AASequence& sequence,
                          int charge, double& bseries_score, double& yseries_score) const;
 
    void score_with_isotopes(SpectrumPtrType spectrum,
                             const std::vector<TransitionType>& transitions,
                             double& dotprod,
                             double& manhattan) const;
 
private:
 
    DIAScoring(const DIAScoring& rhs);
 
    DIAScoring& operator=(const DIAScoring& rhs);
 
    void updateMembers_() override;
 
    void diaIsotopeScoresSub_(const std::vector<TransitionType>& transitions,
                              SpectrumPtrType spectrum,
                              std::map<std::string, double>& intensities,
                              double& isotope_corr,
                              double& isotope_overlap) const;
 
    void getFirstIsotopeRelativeIntensities_(const std::vector<TransitionType>& transitions,
                                            OpenSwath::IMRMFeature* mrmfeature,
                                            std::map<std::string, double>& intensities //experimental intensities of transitions
                                            ) const;
 
private:
 
    void largePeaksBeforeFirstIsotope_(SpectrumPtrType spectrum, double mono_mz, double mono_int, int& nr_occurrences, double& max_ratio) const;
 
    double scoreIsotopePattern_(const std::vector<double>& isotopes_int,
                                double product_mz,
                                int putative_fragment_charge) const;
 
    double scoreIsotopePattern_(const std::vector<double>& isotopes_int,
                                const EmpiricalFormula& sum_formula) const;
 
    double scoreIsotopePattern_(const std::vector<double>& isotopes_int,
                                const IsotopeDistribution& isotope_dist) const;
 
    void getIsotopeIntysFromExpSpec_(double precursor_mz, SpectrumPtrType spectrum,
                                     std::vector<double>& isotopes_int,
                                     int charge_state) const;
 
    // Parameters
    double dia_extract_window_;
    double dia_byseries_intensity_min_;
    double dia_byseries_ppm_diff_;
    double dia_nr_isotopes_;
    double dia_nr_charges_;
    double peak_before_mono_max_ppm_diff_;
    bool dia_extraction_ppm_;
    bool dia_centroided_;
 
    TheoreticalSpectrumGenerator * generator;
  };
}