FeatureFinder.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: Clemens Groepl $
// $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();

    template <class PeakType, class FeatureType>
    void run(const String & algorithm_name, MSExperiment<PeakType> & input_map, FeatureMap<FeatureType> & features, const Param & param, const FeatureMap<FeatureType> & 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