| OpenMS 2.5.0

FeatureFinder.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm, Clemens Groepl $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderDefs.h>
38 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h>
39 #include <OpenMS/CONCEPT/ProgressLogger.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41 #include <OpenMS/KERNEL/FeatureMap.h>
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 virtual ~FeatureFinder();
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::String
A more convenient string class.
Definition: String.h:58
FeatureFinderAlgorithm.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
FeatureFinderDefs.h
OpenMS::FeatureFinder::flags_
std::vector< std::vector< Flag > > flags_
Container for flags attached to input data.
Definition: FeatureFinder.h:106
OpenMS::FeatureFinder::getPeakFlag
const Flag & getPeakFlag(const IndexPair &index) const
Returns a non-mutable reference to a peak flag.
Definition: FeatureFinder.h:89
FeatureMap.h
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::FeatureFinderDefs
The purpose of this struct is to provide definitions of classes and typedefs which are used throughou...
Definition: FeatureFinderDefs.h:50
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::FeatureFinderDefs::IndexPair
IsotopeCluster::IndexPair IndexPair
Index to peak consisting of two UInts (scan index / peak index)
Definition: FeatureFinderDefs.h:53
OpenMS::FeatureFinder
The main feature finder class.
Definition: FeatureFinder.h:56
OpenMS::FeatureFinder::getPeakFlag
Flag & getPeakFlag(const IndexPair &index)
Returns mutable reference to a peak flag.
Definition: FeatureFinder.h:95