OpenMS  3.0.0
ConsensusMapNormalizerAlgorithmMedian.h
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34 
35 #pragma once
36 
39 
40 namespace OpenMS
41 {
42 
48  {
51 
52 private:
55 
58 
59 public:
62 
65 
70  enum NormalizationMethod { NM_SCALE, NM_SHIFT };
71 
79  static void normalizeMaps(ConsensusMap & map, NormalizationMethod method, const String& acc_filter, const String& desc_filter);
80 
89  static Size computeMedians(const ConsensusMap & map, std::vector<double> & medians, const String& acc_filter, const String& desc_filter);
90 
100  static bool passesFilters_(ConsensusMap::ConstIterator cf_it, const ConsensusMap& map, const String& acc_filter, const String& desc_filter);
101  };
102 
103 } // namespace OpenMS
104 
ConsensusXMLFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
FileHandler.h
FileTypes.h
OpenMS::ConsensusMapNormalizerAlgorithmThreshold::computeCorrelation
static std::vector< double > computeCorrelation(const ConsensusMap &map, const double &ratio_threshold, const String &acc_filter, const String &desc_filter)
determines the ratio of all maps to the map with the most features
OpenMS::DataProcessing::NORMALIZATION
Normalization of intensity values.
Definition: DataProcessing.h:70
OpenMS::ConsensusMap::sortBySize
void sortBySize()
Sorts with respect to the size (number of elements)
OpenMS::String
A more convenient string class.
Definition: String.h:58
ConsensusMap.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
ConsensusMapNormalizerAlgorithmQuantile.h
OPENMS_LOG_WARN
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ConsensusMap::ConstIterator
std::vector< ConsensusFeature >::const_iterator ConstIterator
Non-mutable iterator.
Definition: ConsensusMap.h:168
ConsensusMapNormalizerAlgorithmThreshold.h
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::ConsensusMapNormalizerAlgorithmMedian::NM_SHIFT
Definition: ConsensusMapNormalizerAlgorithmMedian.h:70
OpenMS::ConsensusMapNormalizerAlgorithmThreshold::normalizeMaps
static void normalizeMaps(ConsensusMap &map, const std::vector< double > &ratios)
applies the given ratio to the maps of the consensusMap
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::ConsensusMapNormalizerAlgorithmQuantile::normalizeMaps
static void normalizeMaps(ConsensusMap &map)
normalizes the maps of the consensusMap
OpenMS::ConsensusMapNormalizerAlgorithmMedian::NormalizationMethod
NormalizationMethod
The NormalizationMethod enum Whether to scale to same median using division/multiplication or shift u...
Definition: ConsensusMapNormalizerAlgorithmMedian.h:70
OpenMS::ConsensusMapNormalizerAlgorithmMedian::NM_SCALE
Definition: ConsensusMapNormalizerAlgorithmMedian.h:70
OpenMS::ConsensusMapNormalizerAlgorithmMedian::normalizeMaps
static void normalizeMaps(ConsensusMap &map, NormalizationMethod method, const String &acc_filter, const String &desc_filter)
normalizes the maps of the consensusMap
OpenMS::Internal::ClassTest::infile
std::ifstream infile
Questionable file tested by TEST_FILE_EQUAL.
TOPPBase.h
OpenMS::ConsensusMapNormalizerAlgorithmMedian
Algorithms of ConsensusMapNormalizer.
Definition: ConsensusMapNormalizerAlgorithmMedian.h:47
OpenMS::ConsensusMapNormalizerAlgorithmThreshold
Algorithms of ConsensusMapNormalizer.
Definition: ConsensusMapNormalizerAlgorithmThreshold.h:46
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:58
ConsensusMapNormalizerAlgorithmMedian.h