ConsensusIsotopePattern.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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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
//

#pragma once

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

#include <map>
#include <vector>

namespace OpenMS
{

  class SUPERHIRN_DLLAPI ConsensusIsotopePattern
  {

    // declaration of the private members:

private:

    // stores the consensus pattern:
    std::map<double, double> isotopesTrace_;
    std::vector<double> mzIsotopesStDev_;
    std::vector<double> intensIsotopesStDev_;

    // stores the detected patterns by retention time
    std::map<double, std::pair<std::vector<double>, std::vector<double> > > rawIsotopes_;

    // declaration of the public members:

public:

    // class destructor
    ~ConsensusIsotopePattern();

    // class constructor
    ConsensusIsotopePattern();
    // class copy constructor
    ConsensusIsotopePattern(const ConsensusIsotopePattern &);
    // class copy constructor
    ConsensusIsotopePattern(const ConsensusIsotopePattern *);

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

    // constructs the consensus pattern:
    void constructConsusPattern();
    // order an isotope trace in the correct cluster:
    void addIsotopeTrace(double, double);
    // condenses the pattern, make average peaks from the traces:
    void condensIsotopePattern(std::pair<std::vector<double>, std::vector<double> > *);

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

    std::map<double, double>::iterator getConsensIsotopeIteratorStart();
    std::map<double, double>::iterator getConsensIsotopeIteratorEnd();

  };

  inline std::map<double, double>::iterator ConsensusIsotopePattern::getConsensIsotopeIteratorStart()
  {
    return isotopesTrace_.begin();
  }

  inline std::map<double, double>::iterator ConsensusIsotopePattern::getConsensIsotopeIteratorEnd()
  {
    return isotopesTrace_.end();
  }

} // ns