MSPeak.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// --------------------------------------------------------------------------
// $Maintainer: Florian Zeller $
// $Authors: Lukas Mueller, Markus Mueller $
// --------------------------------------------------------------------------
//
//
//  PEAK DETECTION OF FOURIER TRANSFORME MS INSTRUMENT DATA
//
//  written by Markus Mueller, markus.mueller@imsb.biol.ethz.ch
//  and Lukas Mueller, Lukas.Mueller@imsb.biol.ethz.ch
//  October 2005
//
//  Ported to OpenMS by Florian Zeller, florian.zeller@bsse.ethz.ch
//  December 2010
//
//  Group of Prof. Ruedi Aebersold, IMSB, ETH Hoenggerberg, Zurich
//

#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_MSPEAK_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_MSPEAK_H

#include <string>
#include <vector>
#include <map>

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/CentroidPeak.h>

namespace OpenMS
{

//class CentroidPeak; // changed to include

  class OPENMS_DLLAPI MSPeak
  {

    // declaration of the private members:

    double precursorMZ;
    double MZ;
    float INTENSITY;
    int SCAN;
    double TR;
    unsigned int CHRG;
    unsigned int NRISOTOPES;
    float SCORE;

    std::string extraMSPeakInfo;

    // child scan options:
    bool precursorMass;
    int childScan;

    double SignalToNoise;
    std::vector<CentroidPeak> ISOPEAKS;

private:

    // declaration of the public members:

public:

    // class destructor
    ~MSPeak();

    // class constructor
    MSPeak(int, double, float);
    MSPeak();
    MSPeak(int, double, float, unsigned int, unsigned int, float, std::vector<CentroidPeak>);
    MSPeak(const MSPeak &);
    MSPeak(const MSPeak *);

    // overload operators:
    MSPeak & operator=(const MSPeak &);
    MSPeak & operator<=(const MSPeak &);
    MSPeak & operator>=(const MSPeak &);
    MSPeak & operator<(const MSPeak &);
    MSPeak & operator>(const MSPeak &);

    // show content of peak:
    void show_info();

    // store the MS/MS scan number and activate this peak as precursor peak:
    void activateAsPrecursorPeak(int);

    // check if the input mass matches one of the isotopic masses
    bool checkIsotopeBelongingAndAdjustMass(double, double);

    // start here all the get / set
    // function to access the
    // variables of the class

    std::vector<CentroidPeak> & get_isotopic_peaks()
    {
      return ISOPEAKS;
    }

    std::vector<CentroidPeak>::iterator get_isotopic_peaks_start()
    {
      return ISOPEAKS.begin();
    }

    std::vector<CentroidPeak>::iterator get_isotopic_peaks_end()
    {
      return ISOPEAKS.end();
    }

    void setExtraPeakInfo(std::string in)
    {
      extraMSPeakInfo = in;
    }

    std::string getExtraPeakInfo()
    {
      return extraMSPeakInfo;
    }

    // precursor mass of the ms2 scane:
    void setPrecursorMZ(double in)
    {
      precursorMZ = in;
    }

    double getPrecursorMZ()
    {
      return precursorMZ;
    }

    // precursor mass charge state:
    void setPrecursorCHRG(int in)
    {
      CHRG = in;
    }

    int getPrecursorCHRG()
    {
      return CHRG;
    }

    // check if this peak has been determined as precursor:
    bool getPrecursorActivation()
    {
      return precursorMass;
    }

    int get_Chrg()
    {
      return CHRG;
    }

    void set_Chrg(int z)
    {
      CHRG = z;
    }

    int get_Scan()
    {
      return SCAN;
    }

    float get_intensity()
    {
      return INTENSITY;
    }

    double get_MZ()
    {
      return MZ;
    }

    int get_scan_number()
    {
      return SCAN;
    }

    void set_retention_time(double IN)
    {
      TR = IN;
    }

    double get_retention_time()
    {
      return TR;
    }

    unsigned int get_charge_state()
    {
      return CHRG;
    }

    unsigned int get_nr_isotopes()
    {
      return NRISOTOPES;
    }

    float get_score()
    {
      return SCORE;
    }

    double getSignalToNoise()
    {
      return SignalToNoise;
    }

    void setSignalToNoise(double in)
    {
      SignalToNoise = in;
    }

  };

} // ns

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_MSPEAK_H