OpenSwathScoring.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// 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,
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// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
// data access
#include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
 
// scoring
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DIAScoring.h>
 
#include <vector>
#include <boost/shared_ptr.hpp>
#include <boost/make_shared.hpp>
 
namespace OpenMS
{
  class OPENMS_DLLAPI OpenSwathScoring 
  {
    typedef OpenSwath::LightCompound CompoundType;
    typedef OpenSwath::LightTransition TransitionType;
 
    double rt_normalization_factor_;
    double spacing_for_spectra_resampling_;
    int add_up_spectra_;
    std::string spectra_addition_method_;
    double im_drift_extra_pcnt_;
    OpenSwath_Scores_Usage su_;
 
  public:
 
    OpenSwathScoring();
 
    ~OpenSwathScoring();
 
    void initialize(double rt_normalization_factor,
                    int add_up_spectra,
                    double spacing_for_spectra_resampling,
                    const double drift_extra,
                    const OpenSwath_Scores_Usage & su,
                    const std::string& spectrum_addition_method);
 
    void calculateChromatographicScores(OpenSwath::IMRMFeature* imrmfeature,
                                        const std::vector<std::string>& native_ids,
                                        const std::vector<std::string>& precursor_ids,
                                        const std::vector<double>& normalized_library_intensity,
                                        std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators,
                                        OpenSwath_Scores & scores);
 
    void calculateChromatographicIdScores(OpenSwath::IMRMFeature* imrmfeature,
                                          const std::vector<std::string>& native_ids_identification,
                                          const std::vector<std::string>& native_ids_detection,
                                          std::vector<OpenSwath::ISignalToNoisePtr>& signal_noise_estimators,
                                          OpenSwath_Ind_Scores & scores);
 
    void calculateLibraryScores(OpenSwath::IMRMFeature* imrmfeature,
                                const std::vector<TransitionType> & transitions,
                                const CompoundType& compound,
                                const double normalized_feature_rt,
                                OpenSwath_Scores & scores);
 
    void calculateDIAScores(OpenSwath::IMRMFeature* imrmfeature,
                            const std::vector<TransitionType>& transitions,
                            const std::vector<OpenSwath::SwathMap>& swath_maps,
                            OpenSwath::SpectrumAccessPtr ms1_map,
                            OpenMS::DIAScoring& diascoring,
                            const CompoundType& compound,
                            OpenSwath_Scores& scores,
                            std::vector<double>& mzerror_ppm,
                            const double drift_lower,
                            const double drift_upper,
                            const double drift_target);
 
    void calculatePrecursorDIAScores(OpenSwath::SpectrumAccessPtr ms1_map, 
                                     OpenMS::DIAScoring& diascoring, 
                                     double precursor_mz, 
                                     double rt, 
                                     const CompoundType& compound, 
                                     OpenSwath_Scores& scores,
                                     double drift_lower,
                                     double drift_upper);
 
    void calculateDIAIdScores(OpenSwath::IMRMFeature* imrmfeature,
                              const TransitionType & transition,
                              const std::vector<OpenSwath::SwathMap> swath_maps,
                              OpenMS::DIAScoring & diascoring,
                              OpenSwath_Scores & scores,
                              double drift_lower,
                              double drift_upper);
 
    void getNormalized_library_intensities_(const std::vector<TransitionType> & transitions,
                                            std::vector<double>& normalized_library_intensity);
 
    OpenSwath::SpectrumPtr fetchSpectrumSwath(std::vector<OpenSwath::SwathMap> swath_maps,
                                              double RT,
                                              int nr_spectra_to_add,
                                              const double drift_lower,
                                              const double drift_upper);
    
    OpenSwath::SpectrumPtr fetchSpectrumSwath(OpenSwath::SpectrumAccessPtr swath_map,
                                              double RT,
                                              int nr_spectra_to_add,
                                              const double drift_lower,
                                              const double drift_upper);
 
  protected:
 
    OpenSwath::SpectrumPtr getAddedSpectra_(OpenSwath::SpectrumAccessPtr swath_map,
                                            double RT,
                                            int nr_spectra_to_add,
                                            const double drift_lower,
                                            const double drift_upper);
 
  };
}