MS1FeatureMerger.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Lukas Mueller, Markus Mueller $
// --------------------------------------------------------------------------
//
//
//  written by Lukas N Mueller, 30.3.05
//  Lukas.Mueller@imsb.biol.ethz.ch
//  Group of Prof. Ruedi Aebersold, IMSB, ETH Hoenggerberg, Zurich
//
//  Ported to OpenMS by Florian Zeller, florian.zeller@bsse.ethz.ch
//  December 2010
//
// **********************************************************************//
// CLASS Spec MERGER:
// merges 2 spectra which have been preprocessed
// by spec_merge-> common lc_peaks are marked!!!!
//

#pragma once

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

#include <vector>
#include <map>

namespace OpenMS
{
  class LCMS;
  class SHFeature;

  class SUPERHIRN_DLLAPI MS1FeatureMerger
  {


    // declaration of the private members:

private:

    // the common lc-ms spectrum,
    // created from the overlap of A and B
    LCMS * lcmsMap;

    std::vector<int> idsToRemove;
    std::map<double, std::vector<SHFeature *> > mzClusters;


    // declaration of the public members:

public:

    /*
    static double INTENSITY_APEX_THRESHOLD;
    static double MS1_PEAK_AREA_TR_RESOLUTION;

    static double INITIAL_TR_TOLERANCE;
    static double MS1_FEATURE_MERGING_TR_TOLERANCE;
    static double PERCENTAGE_INTENSITY_ELUTION_BORDER_VARIATION;
    static double PPM_TOLERANCE_FOR_MZ_CLUSTERING;
    static bool MS1_FEATURE_CLUSTERING;
  */

    // class destructor
    ~MS1FeatureMerger();
    // class constructor
    MS1FeatureMerger(LCMS *);


    // start the merging process
    void startFeatureMerging();
    // create a distribution of delta Tr for the split features
    void createMZFeatureClusters();
    // process a vector of m/z features
    void processMZFeatureVector(std::vector<SHFeature *> *);
    // find to this feature the features which should be merged
    std::vector<SHFeature *>::iterator findFeaturesToMerge(SHFeature *, std::vector<SHFeature *>::iterator, std::vector<SHFeature *> *);
    // compare if a feature belongs to another feature
    bool compareMZFeatureBeloning(SHFeature *, SHFeature *);
    // merge the target to the search feature
    void mergeFeatures(SHFeature *, SHFeature *);
    // compute new parameters for the merged MS1 feature
    void computeNewMS1FeatureParameters(SHFeature *);
    // computes the area of between 2 peaks:
    double computeDeltaArea(double, double, double, double);


    // this structure provides the function to compare
    // in the sorting algorithm:
    struct OPERATOR_FEATURE_TR
    {
      // provide the compare function for sort:
      bool operator()(const SHFeature A, const SHFeature B) const;
    };
  };

} // ns