MassExplainer.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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//  * Redistributions in binary form must reproduce the above copyright
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// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/Adduct.h>

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/OpenMSConfig.h>

namespace OpenMS
{
  class Compomer;

  class OPENMS_DLLAPI MassExplainer
  {

public:

    typedef Adduct::AdductsType AdductsType; //vector<Adduct>
    typedef std::vector<Compomer>::const_iterator CompomerIterator;


    MassExplainer();

    MassExplainer(AdductsType adduct_base);

    MassExplainer(Int q_min, Int q_max, Int max_span, double thresh_logp);

    MassExplainer(AdductsType adduct_base, Int q_min, Int q_max, Int max_span, double thresh_logp, Size max_neutrals);


private:
    void init_(bool init_thresh_p);
public:
    MassExplainer& operator=(const MassExplainer& rhs);

    virtual ~MassExplainer();


    void compute();


    //@name Accessors

    void setAdductBase(AdductsType adduct_base);
    AdductsType getAdductBase() const;

    const Compomer& getCompomerById(Size id) const;


    SignedSize query(const Int net_charge,
                     const float mass_to_explain,
                     const float mass_delta,
                     const float thresh_log_p,
                     std::vector<Compomer>::const_iterator& firstExplanation,
                     std::vector<Compomer>::const_iterator& lastExplanation) const;
protected:

    bool compomerValid_(const Compomer& cmp);

    Adduct createAdduct_(const String& formula, const Int charge, const double p) const;

    std::vector<Compomer> explanations_;
    AdductsType adduct_base_;
    Int q_min_;
    Int q_max_;
    Int max_span_;
    double thresh_p_;
    Size max_neutrals_;

  };


} // namespace OpenMS