DIAPrescoring.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Witold Wolski $
// $Authors: Witold Wolski $
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#ifndef OPENMS_ANALYSIS_OPENSWATH_DIAPRESCORING_H
#define OPENMS_ANALYSIS_OPENSWATH_DIAPRESCORING_H

#include <algorithm>
#include <iterator>
#include <boost/bind.hpp>
#include <boost/lexical_cast.hpp>

#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataFrameWriter.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
#include <OpenMS/ANALYSIS/OPENSWATH/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_();


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

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


}

#endif