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IsobaricNormalizer.h
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34 
35 #ifndef OPENMS_ANALYSIS_QUANTITATION_ISOBARICNORMALIZER_H
36 #define OPENMS_ANALYSIS_QUANTITATION_ISOBARICNORMALIZER_H
37 
40 
42 
43 namespace OpenMS
44 {
48  class OPENMS_DLLAPI IsobaricNormalizer
49  {
50 public:
52  IsobaricNormalizer(const IsobaricQuantitationMethod* const quant_method);
53 
56 
58  IsobaricNormalizer& operator=(const IsobaricNormalizer& rhs);
59 
65  void normalize(ConsensusMap& consensus_map);
66 
67 private:
70 
73 
81  ConsensusFeature::HandleSetType::iterator findReferenceChannel_(ConsensusFeature& cf, const ConsensusMap& consensus_map) const;
82 
88  void buildVectorIndex_(const ConsensusMap& consensus_map);
89 
96  void collectRatios_(const ConsensusFeature& cf,
97  const Peak2D::IntensityType& ref_intensity);
98 
104  void computeNormalizationFactors_(std::vector<Peak2D::IntensityType>& normalization_factors);
105 
108 
111 
113  std::vector<std::vector<Peak2D::IntensityType> > peptide_ratios_;
114 
116  std::vector<std::vector<Peak2D::IntensityType> > peptide_intensities_;
117 
118  };
119 } // namespace
120 
121 #endif // OPENMS_ANALYSIS_QUANTITATION_ISOBARICNORMALIZER_H
Real IntensityType
Intensity type.
Definition: Peak2D.h:63
A container for consensus elements.
Definition: ConsensusMap.h:60
OPENSWATHALGO_DLLAPI void normalize(const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)
Normalize intensities in vector by normalization_factor.
Int reference_channel_name_
The name of the reference channel as given in the IsobaricChannelInformation.
Definition: IsobaricNormalizer.h:72
const IsobaricQuantitationMethod * quant_meth_
The selected quantitation method that will be used for the normalization.
Definition: IsobaricNormalizer.h:69
Size ref_map_id_
The index of the reference channel in the peptide ratio/intensity vectors.
Definition: IsobaricNormalizer.h:110
std::vector< std::vector< Peak2D::IntensityType > > peptide_ratios_
Collection containing the collected peptide ratios for the individual channels.
Definition: IsobaricNormalizer.h:113
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
std::vector< std::vector< Peak2D::IntensityType > > peptide_intensities_
Collection containing the collected peptide intensities for the individual channels.
Definition: IsobaricNormalizer.h:116
Map< Size, Size > map_to_vec_index_
The mapping between map indices and the corresponding indices in the peptide ratio/intensity vectors...
Definition: IsobaricNormalizer.h:107
Abstract base class describing an isobaric quantitation method in terms of the used channels and an i...
Definition: IsobaricQuantitationMethod.h:51
Performs median normalization on the extracted ratios of isobaric labeling experiment.
Definition: IsobaricNormalizer.h:48
int Int
Signed integer type.
Definition: Types.h:100
A 2-dimensional consensus feature.
Definition: ConsensusFeature.h:59

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:15 using doxygen 1.8.5