FeatureFinderAlgorithm.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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// $Maintainer: Timo Sachsenberg $
// $Authors: $
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#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinder.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>

namespace OpenMS
{

  // forward declaration
  class FeatureFinder;
  class FeatureMap;

  struct OPENMS_DLLAPI Summary
  {
    std::map<String, UInt> exception; //count exceptions
    UInt no_exceptions;
    std::map<String, UInt> mz_model; //count used mz models
    std::map<float, UInt> mz_stdev; //count used mz standard deviations
    std::vector<UInt> charge; //count used charges
    double corr_mean, corr_max, corr_min; //boxplot for correlation

    Summary() :
      no_exceptions(0),
      corr_mean(0),
      corr_max(0),
      corr_min(1)
    {}

  };

  class FeatureFinderAlgorithm :
    public DefaultParamHandler
  {
public:
    typedef PeakMap MapType;
    typedef MapType::CoordinateType CoordinateType;
    typedef MapType::IntensityType IntensityType;

    FeatureFinderAlgorithm() :
      DefaultParamHandler("FeatureFinderAlgorithm"),
      map_(nullptr),
      features_(nullptr),
      ff_(nullptr)
    {
    }

    ~FeatureFinderAlgorithm() override
    {
    }

    static void registerChildren();

    virtual void run() = 0;

    virtual Param getDefaultParameters() const
    {
      return this->defaults_;
    }

    void setData(const MapType& map, FeatureMap& features, FeatureFinder& ff)
    {
      map_ = &map;
      features_ = &features;
      ff_ = &ff;
    }

    virtual void setSeeds(const FeatureMap& seeds)
    {
      if (seeds.size() != 0)
      {
        throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "The used feature detection algorithm does not support user-specified seed lists!");
      }
    }

protected:

    const MapType* map_;

    FeatureMap* features_;

    FeatureFinder* ff_;

private:

    FeatureFinderAlgorithm& operator=(const FeatureFinderAlgorithm&);

    FeatureFinderAlgorithm(const FeatureFinderAlgorithm&);

  };
}