MS2Fragment.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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//    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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// --------------------------------------------------------------------------
// $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_MS2FRAGMENT_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_MS2FRAGMENT_H

#include <OpenMS/CONCEPT/Types.h>

namespace OpenMS
{

  class OPENMS_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 hte averaged precurso mass:
    double getPrecursorMZ(){ return precursorMZ; }
    void setPrecursorMZ(double iMZ){ precursorMZ = iMZ; }
    // get hte averaged precurso chrg:
    int getPrecursorCHRG(){ return precursorCHRG; }
    // retention time:
    double getTR(){return TR; }
    // start TR:
    double getStartTR(){return trStart; }
    // end TR:
    double getEndTR(){return trEnd; }
    // get the Fragment MZ:
    double getFragmentMz(){return fragmentMZ; }
    void setFragmentMz(double iMz){fragmentMZ = iMz; }
    // get teh charge state:
    int getCHRG(){return z; }
    // get the apex scan:
    int getApexScan(){return scan; }
    // get the apex scan:
    int getStartScan(){return scanStart; }
    // get the apex scan:
    int getEndScan(){return scanEnd; }

    // get the integrated peak area:
    double getFragmentPeakArea(){return intensityArea; }
    void setFragmentPeakArea(double iIntens){intensityArea = iIntens; }


  };

} // ns

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_MS2FRAGMENT_H