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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest, Witold Wolski $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_SPECTRUMHELPERS_H
#define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_SPECTRUMHELPERS_H

#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/OpenSwathAlgoConfig.h>

namespace OpenSwath
{


  /**
    @brief Integrate intensity in a spectrum from start to end

    This function will integrate the intensity in a spectrum between mz_start
    and mz_end, returning the total intensity and an intensity-weighted m/z
    value.

    @note If there is no signal, mz will be set to -1 and intensity to 0
    @return Returns true if a signal was found (and false if no signal was found)

  */
//integrate Window
  OPENSWATHALGO_DLLAPI bool integrateWindow(const OpenSwath::SpectrumPtr spectrum, double mz_start,
                                            double mz_end, double& mz, double& intensity, bool centroided = false);

/**
  @brief Integrate intensities in a spectrum from start to end
*/
//integrate Window
  OPENSWATHALGO_DLLAPI void integrateWindows(const OpenSwath::SpectrumPtr spectrum, //!< [in] Spectrum
                                             const std::vector<double>& windowsCenter, //!< [in] center location
                                             double width,
                                             std::vector<double>& integratedWindowsIntensity,
                                             std::vector<double>& integratedWindowsMZ, bool remZero = false);

}

#endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_SPECTRUMHELPERS_H
