2.5.0/html/MS2Fragment_8h_source.html

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// $Maintainer: Timo Sachsenberg $

// $Authors: Lukas Mueller, Markus Mueller $

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//

//

//  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 <OpenMS/CONCEPT/Types.h>


namespace OpenMS

{


  class SUPERHIRN_DLLAPI MS2Fragment

  {


    // declaration of the private members:


private:


    // declaration of the public members:


    // AMRT tag

    double precursorMZ;

    int precursorCHRG;

    double TR;

    int scan;

    int z;


    double fragmentMZ;

    double intensityArea;


    // scan and TR ranges:

    int scanStart;

    int scanEnd;

    double trStart;

    double trEnd;


public:


    static int OutlierAttribute;


    // class destructor

    ~MS2Fragment();


    // constructor for the object MS2Fragment:

    MS2Fragment(double iPrecursorMZ, int iPrecursorCHRG, double iTR, int iScan, int iZ, double iFragmentMZ, double iIntensityArea,

                int iScanStart, int iScanEnd, double iTrStart, double iTrEnd);

    MS2Fragment(double iPrecursorMZ, int iPrecursorCHRG, double iTR, int iScan, int iZ, double iFragmentMZ, double iIntensityArea);


    // class constructor

    MS2Fragment();

    // class copy constructor

    MS2Fragment(const MS2Fragment &);

    // class copy constructor

    MS2Fragment(const MS2Fragment *);


    // show info of the MS2 fragment

    void show_info();


    // get the attribute of the fragment

    // according to which outliers are removed

    double getOutlierDetectionAttribute();


    // overload operators:

    MS2Fragment & operator=(const MS2Fragment &);

    bool operator==(const MS2Fragment &);

    MS2Fragment & operator<=(const MS2Fragment &);

    MS2Fragment & operator>=(const MS2Fragment &);

    MS2Fragment & operator<(const MS2Fragment &);

    MS2Fragment & operator>(const MS2Fragment &);


    // start here all the get / set

    // function to access the

    // variables of the class


    // get the averaged precursor mass:

    double getPrecursorMZ();

    void setPrecursorMZ(double iMZ);

    // get the averaged precursor charge:

    int getPrecursorCHRG();

    // retention time:

    double getTR();

    // start TR:

    double getStartTR();

    // end TR:

    double getEndTR();

    // get the Fragment MZ:

    double getFragmentMz();

    void setFragmentMz(double iMz);

    // get the charge state:

    int getCHRG();

    // get the apex scan:

    int getApexScan();

    // get the apex scan:

    int getStartScan();

    // get the apex scan:

    int getEndScan();


    // get the integrated peak area:

    double getFragmentPeakArea();

    void setFragmentPeakArea(double iIntens);


  };


} // ns