IsotopeDistribution.h

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// $Maintainer: Chris Bielow $
// $Authors: Clemens Groepl, Andreas Bertsch, Chris Bielow $
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#ifndef OPENMS_CHEMISTRY_ISOTOPEDISTRIBUTION_ISOTOPEDISTRIBUTION_H
#define OPENMS_CHEMISTRY_ISOTOPEDISTRIBUTION_ISOTOPEDISTRIBUTION_H


#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/KERNEL/Peak1D.h>

#include <utility>
#include <functional>

#include <vector>
#include <set>
#include <map>


namespace OpenMS
{
  class Element; 

  class OPENMS_DLLAPI IsotopeDistribution
  {
public:


    typedef Peak1D MassAbundance;
    typedef std::vector<MassAbundance> ContainerType;
    typedef ContainerType::iterator iterator;
    typedef ContainerType::iterator Iterator;
    typedef ContainerType::const_iterator const_iterator;
    typedef ContainerType::const_iterator ConstIterator;

    typedef ContainerType::reverse_iterator reverse_iterator;
    typedef ContainerType::reverse_iterator ReverseIterator;
    typedef ContainerType::const_reverse_iterator const_reverse_iterator;
    typedef ContainerType::const_reverse_iterator ConstReverseIterator;


    enum Sorted {INTENSITY, MASS, UNDEFINED};




    IsotopeDistribution();

    IsotopeDistribution(const IsotopeDistribution & isotope_distribution);

    virtual ~IsotopeDistribution();



    void set(const ContainerType & distribution);

    const ContainerType & getContainer() const;

    Peak1D::CoordinateType getMax() const;

    Peak1D::CoordinateType getMin() const;

    Peak1D getMostAbundant() const;

    Size size() const;

    void clear();

    // resizes distribution container
    void resize(UInt size);

    void trimIntensities(double cutoff);

    void sortByIntensity();

    void sortByMass();

    void renormalize();

    void merge(double resolution, double min_prob);


    void trimRight(double cutoff);

    void trimLeft(double cutoff);

    
    
    bool isNormalized() const;


    double averageMass() const;

    bool isConvolutionUnit() const;


    IsotopeDistribution & operator=(const IsotopeDistribution & isotope_distribution);

    bool operator==(const IsotopeDistribution & isotope_distribution) const;

    bool operator!=(const IsotopeDistribution & isotope_distribution) const;

    bool operator<(const IsotopeDistribution & isotope_distribution) const;


    inline Iterator begin() { return distribution_.begin(); }

    inline Iterator end()   { return distribution_.end(); }

    inline ConstIterator begin() const { return distribution_.begin(); }

    inline ConstIterator end() const { return distribution_.end(); }

    inline ReverseIterator rbegin() { return distribution_.rbegin(); }

    inline ReverseIterator rend()   { return distribution_.rend(); }

    inline ConstReverseIterator rbegin() const { return distribution_.rbegin(); }

    inline ConstReverseIterator rend() const { return distribution_.rend(); }

    inline void insert(const Peak1D::CoordinateType& mass, const Peak1D::IntensityType& intensity)
    {
      distribution_.push_back(Peak1D(mass, intensity));
    }


    Peak1D& operator[](const Size& index){ return distribution_[index];}



protected:   

    void sort_(std::function<bool(const MassAbundance& p1, const MassAbundance& p2)> sorter);
    void transform_(std::function<void(MassAbundance&)> lambda);

    ContainerType distribution_;
  };


} // namespace OpenMS

#endif // OPENMS_CHEMISTRY_ISOTOPEDISTRIBUTION_ISOTOPEDISTRIBUTION_H