DIAPrescoring.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Witold Wolski $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/OPENSWATHALGO/DATAACCESS/DataFrameWriter.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DIAHelper.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI DiaPrescore :
    public DefaultParamHandler
  {
    double dia_extract_window_; //done
    int nr_isotopes_;
    int nr_charges_;
public:
    struct OPENMS_DLLAPI TransitionGroupTheoreticalSpectrumCache
    {
      std::vector<double> mz_theor;
      std::vector<double> int_theor;
      std::vector<double> int_theor_neg;
      double neg_val = 0.0;
      double pos_val = 0.0;
 
      void clear();
    };
 
    DiaPrescore();
 
    DiaPrescore(double dia_extract_window, int nr_isotopes = 4, int nr_charges = 4);
 
    void defineDefaults();
 
    void updateMembers_() override;
 
    void score(const SpectrumSequence& spec,
               const std::vector<OpenSwath::LightTransition>& lt,
               const RangeMobility& im_range,
               double& dotprod,
               double& manhattan) const;
 
    void buildTheoreticalSpectrum(const std::vector<OpenSwath::LightTransition>& lt,
                                  TransitionGroupTheoreticalSpectrumCache& theoretical_spectrum_cache) const;
 
    static void scorePrepared(const SpectrumSequence& spec,
                              const TransitionGroupTheoreticalSpectrumCache& theoretical_spectrum_cache,
                              double dia_extract_window,
                              const RangeMobility& im_range,
                              double& dotprod,
                              double& manhattan);
 
    void operator()(const OpenSwath::SpectrumAccessPtr& swath_ptr,
                    OpenSwath::LightTargetedExperiment& transition_exp_used, const RangeMobility& range_im,
                    OpenSwath::IDataFrameWriter* ivw) const;
  };
 
 
}