// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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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_PROCESSDATA_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_PROCESSDATA_H

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

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

namespace OpenMS
{

  class CentroidData;
  class LCMSCData;

  class SUPERHIRN_DLLAPI ProcessData
  {


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

public:
    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<double, MZ_series> main_data_structure;
    typedef main_data_structure::iterator main_iterator;


protected:

    ////////////////////////////////////////////////
    // declaration of the public members:
    // map that tracts all observed masses in keys


    // clustering of ms peak along time axis:
//  bool TIME_CLUSTERING_BY_RETENTION_TIME;

    // max_distance from next elution peak member in scan numbers:
    int max_inter_scan_distance;

    // cluster data structure:
    LCMSCData * data_;

    // and stores as contents vectors of type
    main_data_structure pMZ_LIST;

    // tracks the number of observed mz cluster
    // elements:
    std::map<double, int> MZ_CLUSTER;
    unsigned int LC_elution_peak_counter;


    ///////////////////////////////////////////////
    // data processing classes:
    BackgroundControl * backgroundController;

public:

    /*
  // minimal intensity level:
  static float INTENSITY_THRESHOLD;

  // m/z tolerance value:
  static double MZ_TOLERANCE;

  // max_distance from next elution peak member in min.:
  static double max_inter_scan_retention_time_distance;

  // define minimal number of members in LC elution peaks cluster
  static int min_nb_cluster_members;

  static std::map<int, float> scan_TR_index;

  // to track detected monoisotopic mass for debugging:
  static bool MonoIsoDebugging;
  static double DebugMonoIsoMassMin;
  static double DebugMonoIsoMassMax;
  static double MS1_intensity_apex_percentil_cutoff;
  static double MS1_TR_RESOLUTION;
  // if data are in centroid form or not:
  static bool CENTROID_DATA_MODUS;
    */

    // class destructor
    ~ProcessData();

    // class constructor
    ProcessData();
    // class copy constructor
    ProcessData(const ProcessData &);


    ///////////////////////////////////////////////////////////////////////////////
    // inputs raw /centroided  data into the object:
    void add_scan_raw_data(int, double, CentroidData *);
    // inputs raw data into the object:
    void add_scan_raw_data(std::vector<MSPeak>);

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

    // insert an already observed mz into the data structure, checks
    // if it belongs to an existing LC elution peak or starts a new one:
    void insert_observed_mz(main_iterator, MSPeak *);
    // insert a newly observed mz into the data structure
    void insert_new_observed_mz(MSPeak *);


    // converts DeconvPeak list to ms_peak vector
    void convert_ms_peaks(int, double, std::list<DeconvPeak> &, std::vector<MSPeak> &);

    // check if the ms peak is in the selected mz, z, int range
    bool filterDeisotopicMSPeak(MSPeak *);

    //////////////////////////////////////////////////////////////////
    // function which check if a data structure iterator is similar
    // to a peak and should be considered
    // returns 1 if ok
    // returns 0 if not
    // returns -1 if scan range exceeded
    int compareIteratorToPeak(MSPeak *, main_iterator);
    // checks if a mz value has already been seen,
    // also look for very close ones and cluster them
    main_iterator check_MZ_occurence(MSPeak *);


    ///////////////////////////////////////////////////////////////////////////////
    // process a series of MS peaks
    // set the signal to noise level:
    void processMSPeaks(std::multimap<int, MSPeak> *);


    ///////////////////////////////////////////////////////////////////////////////
    // get the  full summed up intensity
    double getPeakIntensitySum(double);


    // check if a peak with this scan number belong to this elution cluster:
    bool check_elution_peak_belong(MZ_series_ITERATOR, MSPeak *);
    // returns the distance to this elution peak:
    int getElutionPeakDistance(MZ_series_ITERATOR, int);

    // runs through the whole data structure and puts the elution_peaks into
    // a proper LC_elution peak object
    void extract_elution_peaks();

    // check if this elution peak is accepted as a really LC-elution peak:
    bool check_elution_peak(MZ_series_ITERATOR);

    // convert the MZ_series elution peak element into a LC_elution_peak object
    void convert_to_LC_elution_peak(MZ_series_ITERATOR, double);

    // find a retention time by the scan number:
    double find_retention_time(double);

    // find closest match mz mass in the main structure
    main_iterator find_closest_mz_match(double);

    // go back to the MS1 level and
    // find the correct precursor mass by mz and z:
    void adjustCorrectToMS1Precursor(double *, int, int, int);


    ///////////////////////////////////////////////////////////
    // access methods to the object variables:

    // get an observed MZ mass, otherwise end of list iterator
    main_iterator get_MZ(double);
    // get an observed MZ mass, otherwise end of list iterator
    main_iterator get_MZ_lower_bound(double);
    // get end of MZ list:
    main_iterator get_MZ_LIST_end();
    // get start of MZ list:
    main_iterator get_MZ_LIST_start();
    // erase element in MZ list:
    void erase_MZ_LIST_element(main_iterator);
    int getNbMSTraces();

    double getMinimalIntensityLevel();

    // access the MZ_CLUSTER:
    // find element numbers:
    std::map<double, int>::iterator get_nb_MZ_cluster_elements(double);
    // erase an element:
    void erase_MZ_cluster_element(std::map<double, int>::iterator);
    // insert an element:
    void insert_MZ_cluster_element(double, int);

    // add the scan vs TR index to the data structure:
    // void add_scan_TR_index(std::map<int, float> IN){scan_TR_index = IN;};

    // get the processed data:
    LCMSCData * getProcessedData();

    // increase the LC_elution_profile counter:
    void increase_LC_elution_peak_counter();
    unsigned int get_LC_elution_peak_counter();

    // get the maximal scan distance between two same monoisotopic masses
    int getMaxScanDistance();
    void setMaxScanDistance(int in);


    // build up an index scan vs retention time:
    //  static void insert_into_scan_TR_index(int IN, float TR){scan_TR_index.insert(std::pair<int, float>(IN,TR));};

  };

} // ns

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_SUPERHIRN_PROCESSDATA_H
