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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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//    may be used to endorse or promote products derived from this software
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Markus Mueller $
// --------------------------------------------------------------------------
//
/*
 *  CentroidPeak.h
 *  PeakDetection
 *
 *  Created by Markus Mueller on 10/19/06.
 *
 *  Ported to OpenMS by Florian Zeller, florian.zeller@bsse.ethz.ch
 *  December 2010
 *
 */

#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_CENTROIDPEAK_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_CENTROIDPEAK_H

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.h>

#include <OpenMS/CONCEPT/Types.h>

#include <ostream>
#include <cmath>
#include <vector>

namespace OpenMS
{

  class SUPERHIRN_DLLAPI CentroidPeak
  {
public:

//static int sfCentroidWindowWidth;

    CentroidPeak();
    CentroidPeak(double, double);
    CentroidPeak(double, double, double);
    CentroidPeak(const CentroidPeak &);
    // Copy constructor
    CentroidPeak(const CentroidPeak *);

    CentroidPeak & operator=(const CentroidPeak &);

    bool operator<(const CentroidPeak &);

    virtual ~CentroidPeak();

    // getters and setters
    double getMass();
    double getIntensity();
    int getIsotopIdx();
    double getSignalToNoise();
    double getFittedIntensity();
    double getOrgIntensity();
    std::string getExtraPeakInfo();
    double getRetentionTime();

    void setMass(double pMass);
    void setIntensity(double pIntensity);
    void setIsotopIdx(double pIsotopIdx);
    void setSignalToNoise(double in);
    void setFittedIntensity(double pFittedIntensity);
    void setOrgIntensity(double pOrgIntensity);
    void setExtraPeakInfo(std::string in);
    void setRetentionTime(double in);

    void show_info();
    void subtractIntensity(double);

protected:

    int isotopIdx_;
    double mass_;
    double intensity_;
    double fittedIntensity_;
    double orgIntensity_;
    double tr_;
    double signalToNoise_;
    std::string extraPeakInfo_;
  };

  // Class for deconvoluted isotopic patterns
  class DeconvPeak :
    public CentroidPeak
  {
public:

    DeconvPeak();
    DeconvPeak(double, double, int, int, double, double);
    DeconvPeak(const DeconvPeak &);
    DeconvPeak(const DeconvPeak *);

    DeconvPeak & operator=(const DeconvPeak &);

    virtual ~DeconvPeak();

    // shows the info of the peak:
    void show_info();

    // getters and setters
    int getCharge();
    int getNrIsotopes();
    double getC13MassError();
    double getScore();
    std::vector<CentroidPeak> getIsotopicPeaks();

    void setCharge(int pCharge);
    void setNrIsotopes(int pNrIsotopes);
    void setC13MassError(double pC13MassError);
    void setScore(double pScore);
    void setIsotopicPeaks(std::vector<CentroidPeak> pIsotopicPeaks);

protected:

    int charge_;
    int nrIsotopes_;
    double c13MassError_;
    double score_;
    std::vector<CentroidPeak> isotopicPeaks_;
  };

  // stream operators
  std::ostream & operator<<(std::ostream &, CentroidPeak &);
  std::ostream & operator<<(std::ostream &, DeconvPeak &);

  // inline implementation of getters and setters

  inline double CentroidPeak::getMass()
  {
    return mass_;
  }

  inline double CentroidPeak::getIntensity()
  {
    return intensity_;
  }

  inline int CentroidPeak::getIsotopIdx()
  {
    return isotopIdx_;
  }

  inline double CentroidPeak::getSignalToNoise()
  {
    return signalToNoise_;
  }

  inline double CentroidPeak::getFittedIntensity()
  {
    return fittedIntensity_;
  }

  inline double CentroidPeak::getOrgIntensity()
  {
    return orgIntensity_;
  }

  inline std::string CentroidPeak::getExtraPeakInfo()
  {
    return extraPeakInfo_;
  }

  inline double CentroidPeak::getRetentionTime()
  {
    return tr_;
  }

  inline void CentroidPeak::setMass(double pMass)
  {
    mass_ = pMass;
  }

  inline void CentroidPeak::setIntensity(double pIntensity)
  {
    intensity_ = pIntensity;
  }

  inline void CentroidPeak::setIsotopIdx(double pIsotopIdx)
  {
    isotopIdx_ = (int) pIsotopIdx;
  }

  inline void CentroidPeak::setSignalToNoise(double in)
  {
    signalToNoise_ = in;
  }

  inline void CentroidPeak::setFittedIntensity(double pFittedIntensity)
  {
    fittedIntensity_ = pFittedIntensity;
  }

  inline void CentroidPeak::setOrgIntensity(double pOrgIntensity)
  {
    orgIntensity_ = pOrgIntensity;
  }

  inline void CentroidPeak::setExtraPeakInfo(std::string in)
  {
    extraPeakInfo_ = in;
  }

  inline void CentroidPeak::setRetentionTime(double in)
  {
    tr_ = in;
  }

  //

  inline int DeconvPeak::getCharge()
  {
    return charge_;
  }

  inline int DeconvPeak::getNrIsotopes()
  {
    return nrIsotopes_;
  }

  inline double DeconvPeak::getC13MassError()
  {
    return c13MassError_;
  }

  inline double DeconvPeak::getScore()
  {
    return score_;
  }

  inline std::vector<CentroidPeak> DeconvPeak::getIsotopicPeaks()
  {
    return isotopicPeaks_;
  }

  inline void DeconvPeak::setCharge(int pCharge)
  {
    charge_ = pCharge;
  }

  inline void DeconvPeak::setC13MassError(double pC13MassError)
  {
    c13MassError_ = pC13MassError;
  }

  inline void DeconvPeak::setNrIsotopes(int pNrIsotopes)
  {
    nrIsotopes_ = pNrIsotopes;
  }

  inline void DeconvPeak::setScore(double pScore)
  {
    score_ = pScore;
  }

  inline void DeconvPeak::setIsotopicPeaks(std::vector<CentroidPeak> pIsotopicPeaks)
  {
    isotopicPeaks_ = pIsotopicPeaks;
  }

} // ns

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_CENTROIDPEAK_H
