OpenMS  3.0.0
MultiplexFiltering.h
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31 // $Maintainer: Lars Nilse $
32 // $Authors: Lars Nilse $
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34 
35 #pragma once
36 
45 
46 #include <vector>
47 #include <algorithm>
48 #include <iostream>
49 
50 #include <boost/serialization/strong_typedef.hpp>
51 
52 namespace OpenMS
53 {
73  class OPENMS_DLLAPI MultiplexFiltering :
74  public ProgressLogger
75  {
76 public:
88  typedef std::vector<std::map<int, int> > White2Original;
89 
105  MultiplexFiltering(const MSExperiment& exp_centroided, const std::vector<MultiplexIsotopicPeakPattern>& patterns, int isotopes_per_peptide_min,
106  int isotopes_per_peptide_max, double intensity_cutoff, double rt_band, double mz_tolerance, bool mz_tolerance_unit,
107  double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling, String averagine_type="peptide");
111  MSExperiment& getCentroidedExperiment();
112 
116  MSExperiment getBlacklist();
117 
118 protected:
126  void updateWhiteMSExperiment_();
127 
138  int checkForSignificantPeak_(double mz, double mz_tolerance, MSExperiment::ConstIterator& it_rt, double intensity_first_peak) const;
139 
155  bool filterPeakPositions_(double mz, const MSExperiment::ConstIterator& it_rt_begin, const MSExperiment::ConstIterator& it_rt_band_begin, const MSExperiment::ConstIterator& it_rt_band_end, const MultiplexIsotopicPeakPattern& pattern, MultiplexFilteredPeak& peak) const;
156 
164  void blacklistPeak_(const MultiplexFilteredPeak& peak);
165 
176  void blacklistPeak_(const MultiplexFilteredPeak& peak, unsigned pattern_idx);
177 
189  bool filterAveragineModel_(const MultiplexIsotopicPeakPattern& pattern, const MultiplexFilteredPeak& peak) const;
190 
203  bool filterPeptideCorrelation_(const MultiplexIsotopicPeakPattern& pattern, const MultiplexFilteredPeak& peak) const;
204 
209 
213  std::vector<std::vector<int> > blacklist_;
214 
221 
226 
230  std::vector<MultiplexIsotopicPeakPattern> patterns_;
231 
236 
241 
246 
250  double rt_band_;
251 
256 
261 
266 
271 
276 
282 
283  };
284 
285 }
286 
OpenMS::MultiplexFiltering::isotopes_per_peptide_min_
size_t isotopes_per_peptide_min_
minimum number of isotopic peaks per peptide
Definition: MultiplexFiltering.h:235
CubicSpline2d.h
OpenMS::MultiplexFiltering::mz_tolerance_unit_in_ppm_
bool mz_tolerance_unit_in_ppm_
unit for m/z shift tolerance (ppm - true, Da - false)
Definition: MultiplexFiltering.h:260
OpenMS::MultiplexFiltering::averagine_type_
String averagine_type_
type of averagine to use
Definition: MultiplexFiltering.h:281
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::MultiplexIsotopicPeakPattern
data structure for pattern of isotopic peaks
Definition: MultiplexIsotopicPeakPattern.h:54
OpenMS::MultiplexFiltering::exp_centroided_
MSExperiment exp_centroided_
centroided experimental data
Definition: MultiplexFiltering.h:208
OpenMS::MultiplexFiltering::exp_centroided_white_
MSExperiment exp_centroided_white_
"white" centroided experimental data
Definition: MultiplexFiltering.h:220
OpenMS::MultiplexFiltering::rt_band_
double rt_band_
RT range used for filtering.
Definition: MultiplexFiltering.h:250
MultiplexFilteredPeak.h
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::MultiplexFiltering::peptide_similarity_
double peptide_similarity_
peptide similarity
Definition: MultiplexFiltering.h:265
OpenMS::MultiplexFiltering::averagine_similarity_
double averagine_similarity_
averagine similarity
Definition: MultiplexFiltering.h:270
BaseFeature.h
MultiplexIsotopicPeakPattern.h
OpenMS::MultiplexFiltering::averagine_similarity_scaling_
double averagine_similarity_scaling_
averagine similarity scaling
Definition: MultiplexFiltering.h:275
OpenMS::MultiplexFiltering::intensity_cutoff_
double intensity_cutoff_
intensity cutoff
Definition: MultiplexFiltering.h:245
OpenMS::MultiplexFilteredPeak
data structure storing a single peak that passed all filters
Definition: MultiplexFilteredPeak.h:70
MSExperiment.h
OpenMS::MultiplexFiltering::isotopes_per_peptide_max_
size_t isotopes_per_peptide_max_
maximum number of isotopic peaks per peptide
Definition: MultiplexFiltering.h:240
OpenMS::MultiplexFiltering::patterns_
std::vector< MultiplexIsotopicPeakPattern > patterns_
list of peak patterns
Definition: MultiplexFiltering.h:230
OpenMS::MultiplexFiltering::blacklist_
std::vector< std::vector< int > > blacklist_
auxiliary structs for blacklisting
Definition: MultiplexFiltering.h:213
OpenMS::MSExperiment::ConstIterator
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:106
PeakPickerHiRes.h
OpenMS::MultiplexFiltering::White2Original
std::vector< std::map< int, int > > White2Original
index mapping from a 'white' experiment to its original experiment
Definition: MultiplexFiltering.h:88
StandardTypes.h
OpenMS::MultiplexFiltering
base class for filtering centroided and profile data for peak patterns
Definition: MultiplexFiltering.h:73
OpenMS::MultiplexFiltering::exp_centroided_mapping_
White2Original exp_centroided_mapping_
mapping of peak indices from a 'white' experiment exp_centroided_white_ to its original experiment ex...
Definition: MultiplexFiltering.h:225
OpenMS::MultiplexFiltering::mz_tolerance_
double mz_tolerance_
m/z shift tolerance
Definition: MultiplexFiltering.h:255