FeatureFinderAlgorithm.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Clemens Groepl $
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#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHM_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHM_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;

  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
    DoubleReal corr_mean, corr_max, corr_min;       //boxplot for correlation

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

  };

  template <class PeakType, class FeatureType>
  class FeatureFinderAlgorithm :
    public DefaultParamHandler
  {
public:
    typedef MSExperiment<PeakType> MapType;
    typedef typename MapType::CoordinateType CoordinateType;
    typedef typename MapType::IntensityType IntensityType;
    typedef FeatureMap<FeatureType> FeatureMapType;

    FeatureFinderAlgorithm() :
      DefaultParamHandler("FeatureFinderAlgorithm"),
      map_(0),
      features_(0),
      ff_(0)
    {
    }

    virtual ~FeatureFinderAlgorithm()
    {
    }

    static void registerChildren();

    virtual void run() = 0;

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

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

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

protected:

    const MapType * map_;

    FeatureMapType * features_;

    FeatureFinder * ff_;

private:

    FeatureFinderAlgorithm & operator=(const FeatureFinderAlgorithm &);

    FeatureFinderAlgorithm(const FeatureFinderAlgorithm &);

  };
}

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHM_H