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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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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
//
//

#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCELUTIONPEAK_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCELUTIONPEAK_H

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

#include <vector>
#include <map>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/ConsensusIsotopePattern.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/MSPeak.h>

namespace OpenMS
{

  typedef std::multimap<int, MSPeak> elution_peak;
  typedef std::vector<elution_peak> MZ_series;
  typedef std::vector<elution_peak>::iterator MZ_series_ITERATOR;
  typedef std::multimap<int, MSPeak>::iterator SIGNAL_iterator;

  class SUPERHIRN_DLLAPI LCElutionPeak
  {

    ////////////////////////////////////////////////
    // declaration of the private members:

private:

    // isotopic pattern:
    ConsensusIsotopePattern * isotopePattern;
    int fNrIsotopes;
    double f_observed_Mass;
    double fIsotopMass;

protected:

    double fMonoMass;
    double fVolume;
    int fCharge;
    int fScanNumberStart;
    int fScanNumberApex;
    int fScanNumberEnd;
    double fapex_intensity;
    double fRT;
    double fStartTR;
    double fEndTR;
    double fpeak_area;
    double fSignalToNoise;
    double fSNIntensityThreshold;
    MSPeak * APEX;

    std::string elutionPeakExtraInfo;

    // the raw signals assigned to this peak
    std::multimap<int, MSPeak> intens_signals;
    //multimap<int, MSPeak> raw_intens_signals;
    std::multimap<int, int> CHRG_MAP;

    ////////////////////////////////////////////////
    // declaration of the public members:

public:

    // parameters to debug a certain mass range
    static double DEBUG_MASS_START;
    static double DEBUG_MASS_END;

    // cut off, where everything small than this percentile of the
    // apex is discarded
    // static float intensity_apex_percentil_cutoff;

    // resolution of the retention time, for peak area computing:
    //  static float TR_RESOLUTION;

    // class destructor
    ~LCElutionPeak();

    // class constructor
    LCElutionPeak();
    // class constructor
    LCElutionPeak(MZ_series_ITERATOR, double);
    // class copy constructor
    LCElutionPeak(const LCElutionPeak &);
    // constructor for the object feature:
    LCElutionPeak(const LCElutionPeak *);

    //////////////////////////////////////////////////////
    // Analyze the LC elution peak
    void analyzeLCElutionPeak();

    //////////////////////////////////////////////////////
    // determine the intensity background baseline based on S/N
    // value:
    void setSNIntensityThreshold();

    //////////////////////////////////////////////////////
    // Compute a variety of parameters for the LC elution peak
    void computeLCElutionPeakParameters();

    // removes background peaks and computes the total peak area:
    // void compute_LC_peak_area();
    // computes the area of between 2 peaks:
    double compute_delta_area(double, double, double, double);
    // define the apex into the elution profile::
    // void define_apex();
    // removes peaks which have lower intensity than x percentile
    // of the apex:
    void remove_background_peak();
    // compute the charge state of the LC peak
    void compute_CHRG();
    // compute the score of the LC peak:
    //void compute_SCORE_and_SN();
    // define all required peak parameters from a single MS peak:
    void defineLCElutionPeakParametersFromMSPeak();
    //////////////////////////////////////////////////////

    //////////////////////////////////////////////////////
    // print all monoisotopic peak cluster along the LC profile:
    void createConsensIsotopPattern();

    // print the elution profile from a peak:
    void print_profile(std::ofstream *);
    // find the closest existing mz peak in the elution profile:
    MSPeak * find_true_peak(float);
    // print the elution profile from a peak:
    void show_info();

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

    ////////////////////////////////////////////////////////////////////////////////
    // print all monoisotopic peak cluster along the LC profile:
    //void printIsotopClusters();
    // print the consensus isotope pattern:
    //void printConsensIsotopPattern();

    void setElutionPeakExtraInfo(std::string in);

    std::string getElutionPeakExtraInfo();

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

    ////////////////////////////
    // access signal_intens map:
    SIGNAL_iterator get_signal_list_start();

    SIGNAL_iterator get_signal_list_end();

    ////////////////////////////
    // access the raw signal intens map:
    //SIGNAL_iterator get_raw_signal_list_start(){return raw_intens_signals.begin();};
    //SIGNAL_iterator get_raw_signal_list_end(){return raw_intens_signals.end();};

    // update the retention time by the current tmp_scan_apex:
    void set_apex_retention_time(double in);

    // to update the list of score and charge state:
    void update_CHRGMAP(MSPeak * in);

    ///////////////////
    // get scan apex:
    int get_scan_apex();

    double get_apex_intensity();

    double get_apex_retention_time();

    double get_apex_MZ();

    //////////////////
    // get an intensity of a ms_peak
    float get_intensity(int in);

    // get the original M/Z of a ms_peak
    double get_MZ(int);

    /////////////////
    // get the total peak area:
    double get_total_peak_area();

    ////////////////
    // get start / end scan:
    int get_start_scan();

    int get_end_scan();

    void set_start_retention_time(double in);

    double get_start_retention_time();

    void set_end_retention_time(double in);

    double get_end_retention_time();

    ////////////////
    // get number of peaks in the elution profile:
    int get_nb_ms_peaks();

    //////////////
    // access the charge state of the LC elution peak:
    int get_charge_state();

    ////////////
    // get signal to noise ratio:
    double getSignalToNoise();

    double getSignalToNoiseBackground();

  };

} // ns

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_LCELUTIONPEAK_H
