MSPeak.h

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// $Maintainer: Timo Sachsenberg $
// $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
//
 
#pragma once
 
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.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 SUPERHIRN_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();
 
    std::vector<CentroidPeak>::iterator get_isotopic_peaks_start();
 
    std::vector<CentroidPeak>::iterator get_isotopic_peaks_end();
 
    void setExtraPeakInfo(std::string in);
 
    std::string getExtraPeakInfo();
 
    // precursor mass of the MS2 scan:
    void setPrecursorMZ(double in);
 
    double getPrecursorMZ();
 
    // precursor mass charge state:
    void setPrecursorCHRG(int in);
 
    int getPrecursorCHRG();
 
    // check if this peak has been determined as precursor:
    bool getPrecursorActivation();
 
    int get_Chrg();
 
    void set_Chrg(int z);
 
    int get_Scan();
 
    float get_intensity();
 
    double get_MZ();
 
    int get_scan_number();
 
    void set_retention_time(double in);
 
    double get_retention_time();
 
    unsigned int get_charge_state();
 
    unsigned int get_nr_isotopes();
 
    float get_score();
 
    double getSignalToNoise();
 
    void setSignalToNoise(double in);
 
  };
 
} // ns