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 2002-2023.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm, Clemens Groepl $
// --------------------------------------------------------------------------
 
#pragma once
 
#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();
 
    ~FeatureFinder() override;
 
    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