DIAPrescoring.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Timo Sachsenberg $
// $Authors: Witold Wolski $
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#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>

namespace OpenMS
{
  class OPENMS_DLLAPI DiaPrescore :
    public DefaultParamHandler
  {
    double dia_extract_window_; //done
    int nr_isotopes_;
    int nr_charges_;
public:

    DiaPrescore();

    DiaPrescore(double dia_extract_window, int nr_isotopes = 4, int nr_charges = 4);

    void defineDefaults();

    void updateMembers_() override;

    void score(OpenSwath::SpectrumPtr spec,
               const std::vector<OpenSwath::LightTransition>& lt,
               double& dotprod,
               double& manhattan) const;

    void operator()(const OpenSwath::SpectrumAccessPtr& swath_ptr,
                    OpenSwath::LightTargetedExperiment& transition_exp_used,
                    OpenSwath::IDataFrameWriter* ivw) const;
  };


}