OpenMS  3.0.0
FeatureFinder.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm, Clemens Groepl $
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34 
35 #pragma once
36 
42 
43 namespace OpenMS
44 {
45 
56  class OPENMS_DLLAPI FeatureFinder :
57  public ProgressLogger,
58  public FeatureFinderDefs
59  {
60 
61 public:
63  FeatureFinder();
64 
66  ~FeatureFinder() override;
67 
86  void run(const String& algorithm_name, PeakMap& input_map, FeatureMap& features, const Param& param, const FeatureMap& seeds);
87 
89  const Flag& getPeakFlag(const IndexPair& index) const
90  {
91  return flags_[index.first][index.second];
92  }
93 
95  Flag& getPeakFlag(const IndexPair& index)
96  {
97  return flags_[index.first][index.second];
98  }
99 
101  Param getParameters(const String& algorithm_name) const;
102 
103 protected:
104 
106  std::vector<std::vector<Flag> > flags_;
107 
108  }; // class FeatureFinder
109 
110 } // namespace OpenMS
111 
OpenMS::FeatureFinderDefs
The purpose of this struct is to provide definitions of classes and typedefs which are used throughou...
Definition: FeatureFinderDefs.h:50
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::FeatureFinder::getPeakFlag
Flag & getPeakFlag(const IndexPair &index)
Returns mutable reference to a peak flag.
Definition: FeatureFinder.h:95
FeatureMap.h
OpenMS::FeatureFinder::flags_
std::vector< std::vector< Flag > > flags_
Container for flags attached to input data.
Definition: FeatureFinder.h:106
OpenMS::FeatureFinder
The main feature finder class.
Definition: FeatureFinder.h:56
OpenMS::FeatureFinderDefs::IndexPair
IsotopeCluster::IndexPair IndexPair
Index to peak consisting of two UInts (scan index / peak index)
Definition: FeatureFinderDefs.h:53
FeatureFinderDefs.h
MSExperiment.h
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::FeatureFinder::getPeakFlag
const Flag & getPeakFlag(const IndexPair &index) const
Returns a non-mutable reference to a peak flag.
Definition: FeatureFinder.h:89
FeatureFinderAlgorithm.h