OpenMS  3.0.0
FeatureFinderAlgorithm.h
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31 // $Maintainer: Timo Sachsenberg $
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34 
35 #pragma once
36 
42 
43 namespace OpenMS
44 {
45 
46  // forward declaration
47  class FeatureFinder;
48  class FeatureMap;
49 
51  struct OPENMS_DLLAPI Summary
52  {
53  std::map<String, UInt> exception;
55  std::map<String, UInt> mz_model;
56  std::map<float, UInt> mz_stdev;
57  std::vector<UInt> charge;
58  double corr_mean, corr_max, corr_min; //boxplot for correlation
59 
61  Summary() :
62  no_exceptions(0),
63  corr_mean(0),
64  corr_max(0),
65  corr_min(1)
66  {}
67 
68  };
69 
75  public DefaultParamHandler
76  {
77 public:
79  typedef PeakMap MapType;
84 
87  DefaultParamHandler("FeatureFinderAlgorithm"),
88  map_(nullptr),
89  features_(nullptr),
90  ff_(nullptr)
91  {
92  }
93 
96  {
97  }
98 
100  static void registerChildren();
101 
103  virtual void run() = 0;
104 
110  virtual Param getDefaultParameters() const
111  {
112  return this->defaults_;
113  }
114 
116  void setData(const MapType& map, FeatureMap& features, FeatureFinder& ff)
117  {
118  map_ = &map;
119  features_ = &features;
120  ff_ = &ff;
121  }
122 
128  virtual void setSeeds(const FeatureMap& seeds)
129  {
130  if (!seeds.empty())
131  {
132  throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "The used feature detection algorithm does not support user-specified seed lists!");
133  }
134  }
135 
136 protected:
137 
139  const MapType* map_;
140 
143 
146 
147 private:
148 
151 
154 
155  };
156 }
157 
DefaultParamHandler.h
OpenMS::FeatureFinderAlgorithm::run
virtual void run()=0
Main method that implements the actual algorithm.
OpenMS::Summary::Summary
Summary()
Initial values.
Definition: FeatureFinderAlgorithm.h:61
OpenMS::FeatureFinderAlgorithm::FeatureFinderAlgorithm
FeatureFinderAlgorithm()
default constructor
Definition: FeatureFinderAlgorithm.h:86
double
OpenMS::Exception::IllegalArgument
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
OpenMS::FeatureFinderAlgorithm::operator=
FeatureFinderAlgorithm & operator=(const FeatureFinderAlgorithm &)
Not implemented.
OpenMS::Summary::mz_model
std::map< String, UInt > mz_model
count used mz models
Definition: FeatureFinderAlgorithm.h:55
OpenMS::FeatureFinderAlgorithm::ff_
FeatureFinder * ff_
Pointer to the calling FeatureFinder that is used to access the feature flags.
Definition: FeatureFinderAlgorithm.h:145
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Summary::no_exceptions
UInt no_exceptions
Definition: FeatureFinderAlgorithm.h:54
OpenMS::FeatureFinderAlgorithm::setData
void setData(const MapType &map, FeatureMap &features, FeatureFinder &ff)
Sets a reference to the calling FeatureFinder.
Definition: FeatureFinderAlgorithm.h:116
OpenMS::FeatureFinderAlgorithm::IntensityType
MapType::IntensityType IntensityType
Intensity type of peaks.
Definition: FeatureFinderAlgorithm.h:83
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::Summary::mz_stdev
std::map< float, UInt > mz_stdev
count used mz standard deviations
Definition: FeatureFinderAlgorithm.h:56
FeatureFinder.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
FeatureMap.h
OpenMS::FeatureFinder
The main feature finder class.
Definition: FeatureFinder.h:56
OpenMS::FeatureFinderAlgorithm::map_
const MapType * map_
Input data pointer.
Definition: FeatureFinderAlgorithm.h:139
OpenMS::FeatureFinderAlgorithm::MapType
PeakMap MapType
Input map type.
Definition: FeatureFinderAlgorithm.h:79
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::FeatureFinderAlgorithm::registerChildren
static void registerChildren()
register all derived classes here (see FeatureFinderAlgorithm_impl.h)
OpenMS::FeatureFinderAlgorithm
Abstract base class for FeatureFinder algorithms.
Definition: FeatureFinderAlgorithm.h:74
OpenMS::Summary::charge
std::vector< UInt > charge
count used charges
Definition: FeatureFinderAlgorithm.h:57
MSExperiment.h
OpenMS::Summary::exception
std::map< String, UInt > exception
count exceptions
Definition: FeatureFinderAlgorithm.h:53
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::FeatureFinderAlgorithm::CoordinateType
MapType::CoordinateType CoordinateType
Coordinate/Position type of peaks.
Definition: FeatureFinderAlgorithm.h:81
float
OpenMS::FeatureFinderAlgorithm::setSeeds
virtual void setSeeds(const FeatureMap &seeds)
Sets a reference to the calling FeatureFinder.
Definition: FeatureFinderAlgorithm.h:128
OpenMS::Summary
Summary of fitting results.
Definition: FeatureFinderAlgorithm.h:51
OpenMS::DefaultParamHandler::defaults_
Param defaults_
Container for default parameters. This member should be filled in the constructor of derived classes!
Definition: DefaultParamHandler.h:173
OpenMS::FeatureFinderAlgorithm::~FeatureFinderAlgorithm
~FeatureFinderAlgorithm() override
destructor
Definition: FeatureFinderAlgorithm.h:95
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::FeatureFinderAlgorithm::features_
FeatureMap * features_
Output data pointer.
Definition: FeatureFinderAlgorithm.h:142
StandardTypes.h
OpenMS::Summary::corr_min
double corr_min
Definition: FeatureFinderAlgorithm.h:58
OpenMS::FeatureFinderAlgorithm::getDefaultParameters
virtual Param getDefaultParameters() const
Returns the default parameters. Reimplement.
Definition: FeatureFinderAlgorithm.h:110