OpenMS  2.5.0
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_(const MSSpectrum::ConstIterator& it_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 
225  White2Original exp_centroided_mapping_;
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 
bool mz_tolerance_unit_in_ppm_
unit for m/z shift tolerance (ppm - true, Da - false)
Definition: MultiplexFiltering.h:260
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:104
double peptide_similarity_
peptide similarity
Definition: MultiplexFiltering.h:265
double rt_band_
RT range used for filtering.
Definition: MultiplexFiltering.h:250
base class for filtering centroided and profile data for peak patterns
Definition: MultiplexFiltering.h:73
double averagine_similarity_scaling_
averagine similarity scaling
Definition: MultiplexFiltering.h:275
MSExperiment exp_centroided_white_
"white" centroided experimental data
Definition: MultiplexFiltering.h:220
String averagine_type_
type of averagine to use
Definition: MultiplexFiltering.h:281
size_t isotopes_per_peptide_max_
maximum number of isotopic peaks per peptide
Definition: MultiplexFiltering.h:240
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
std::vector< MultiplexIsotopicPeakPattern > patterns_
list of peak patterns
Definition: MultiplexFiltering.h:230
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
size_t isotopes_per_peptide_min_
minimum number of isotopic peaks per peptide
Definition: MultiplexFiltering.h:235
double mz_tolerance_
m/z shift tolerance
Definition: MultiplexFiltering.h:255
MSExperiment exp_centroided_
centroided experimental data
Definition: MultiplexFiltering.h:208
double averagine_similarity_
averagine similarity
Definition: MultiplexFiltering.h:270
data structure storing a single peak that passed all filters
Definition: MultiplexFilteredPeak.h:70
std::vector< std::vector< int > > blacklist_
auxiliary structs for blacklisting
Definition: MultiplexFiltering.h:213
White2Original exp_centroided_mapping_
mapping of peak indices from a &#39;white&#39; experiment <exp_centroided_white_> to its original experiment ...
Definition: MultiplexFiltering.h:225
double intensity_cutoff_
intensity cutoff
Definition: MultiplexFiltering.h:245
std::vector< std::map< int, int > > White2Original
index mapping from a &#39;white&#39; experiment to its original experiment
Definition: MultiplexFiltering.h:88
data structure for pattern of isotopic peaks
Definition: MultiplexIsotopicPeakPattern.h:54
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
A more convenient string class.
Definition: String.h:58
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46