// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_ITRANSITION_H
#define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_ITRANSITION_H

#include <vector>
#include <boost/shared_ptr.hpp>

#include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/OpenSwathAlgoConfig.h>

namespace OpenSwath
{
  // Datastructures for Scoring
  class OPENSWATHALGO_DLLAPI IFeature
  {
public:
    virtual ~IFeature(){}
    virtual void getRT(std::vector<double>& rt) = 0;
    virtual void getIntensity(std::vector<double>& intens) = 0;
    virtual float getIntensity() = 0;
    virtual double getRT() = 0;
  };

  class OPENSWATHALGO_DLLAPI IMRMFeature
  {
public:
    virtual ~IMRMFeature(){}
    virtual boost::shared_ptr<OpenSwath::IFeature> getFeature(std::string nativeID) = 0;
    virtual boost::shared_ptr<OpenSwath::IFeature> getPrecursorFeature(std::string nativeID) = 0;
    virtual std::vector<std::string> getNativeIDs() const = 0;
    virtual std::vector<std::string> getPrecursorIDs() const = 0;
    virtual float getIntensity() = 0;
    virtual double getRT() = 0;
    virtual size_t size() = 0;
  };

  struct OPENSWATHALGO_DLLAPI ITransitionGroup
  {
    virtual ~ITransitionGroup() {}
    virtual std::size_t size() = 0;
    virtual std::vector<std::string> getNativeIDs() = 0;
    virtual void getLibraryIntensities(std::vector<double>& intensities) = 0;
  };

  struct OPENSWATHALGO_DLLAPI ISignalToNoise
  {
    virtual ~ISignalToNoise() {}
    virtual double getValueAtRT(double RT) = 0;
  };
  typedef boost::shared_ptr<ISignalToNoise> ISignalToNoisePtr;


} //end Namespace OpenSwath

#endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_ITRANSITION_H
