CentroidData.h

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// $Maintainer: Timo Sachsenberg $
// $Authors: Markus Mueller $
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//
/*
 *  CentroidData.h
 *  PeakDetection
 *
 *  Created by Markus Mueller on 10/19/06.
 *
 *  Ported to OpenMS by Florian Zeller, florian.zeller@bsse.ethz.ch
 *  December 2010
 *
 */
 
#pragma once
 
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/SuperHirnConfig.h>
 
#include <OpenMS/CONCEPT/Types.h>
 
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/CentroidPeak.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SUPERHIRN/RawData.h>
 
#include <list>
#include <vector>
 
#include <boost/shared_ptr.hpp>
 
namespace OpenMS
{
 
  class SUPERHIRN_DLLAPI CentroidData
  {
public:
 
    /*
     static double sfMassTolPpm;
     static double sfMassTolDa;
     static double sfMinIntensity;
     static double sfIntensityFloor;
     */
    // debugging parameters => used by other classes :( :( :(
    /*
     static bool MonoIsoDebugging;
     static double DebugMonoIsoMassMin;
     static double DebugMonoIsoMassMax;
     */
 
    CentroidData(int, boost::shared_ptr<RawData>, bool);
    CentroidData(int, boost::shared_ptr<RawData>, double, bool);
    virtual ~CentroidData();
 
    void get(std::list<CentroidPeak> &);
    void set(boost::shared_ptr<RawData>);
    void set(std::vector<double> &, std::vector<double> &);
 
    void setWidth(int pWidth);
 
    int getWidth();
 
    void setNoise(double);
    double getNoise();
 
    void removeNoise();
 
    bool getNextPeakGroup(std::list<CentroidPeak>::iterator &, std::list<CentroidPeak>::iterator &);
    void resetPeakGroupIter();
 
    bool centroidDataModus_;
 
protected:
 
    void calcCentroids(boost::shared_ptr<RawData>);
 
    int fWindowWidth;
    double fNoise;
    double fScanRetentionTime;
    std::list<CentroidPeak> fCentroidPeaks;
    std::list<CentroidPeak>::iterator fPeakGroupStart;
  };
 
  std::ostream & operator<<(std::ostream &, CentroidData &);
 
} // ns