FeatureFinder.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm, Clemens Groepl $
// --------------------------------------------------------------------------

#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_H

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderDefs.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>

namespace OpenMS
{

  class OPENMS_DLLAPI FeatureFinder :
    public ProgressLogger,
    public FeatureFinderDefs
  {

public:
    FeatureFinder();

    virtual ~FeatureFinder();

    void run(const String& algorithm_name, PeakMap& input_map, FeatureMap& features, const Param& param, const FeatureMap& seeds);

    const Flag& getPeakFlag(const IndexPair& index) const
    {
      return flags_[index.first][index.second];
    }

    Flag& getPeakFlag(const IndexPair& index)
    {
      return flags_[index.first][index.second];
    }

    Param getParameters(const String& algorithm_name) const;

protected:

    std::vector<std::vector<Flag> > flags_;

  }; // class FeatureFinder

} // namespace OpenMS

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDER_H