OpenMS  2.4.0
MultiplexFiltering.h
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31 // $Maintainer: Lars Nilse $
32 // $Authors: Lars Nilse $
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34 
35 #pragma once
36 
46 
47 #include <vector>
48 #include <algorithm>
49 #include <iostream>
50 
51 #include <boost/serialization/strong_typedef.hpp>
52 
53 namespace OpenMS
54 {
74  class OPENMS_DLLAPI MultiplexFiltering :
75  public ProgressLogger
76  {
77 public:
89  typedef std::vector<std::map<int, int> > White2Original;
90 
106  MultiplexFiltering(const MSExperiment& exp_picked, const std::vector<MultiplexIsotopicPeakPattern>& patterns, int isotopes_per_peptide_min,
107  int isotopes_per_peptide_max, double intensity_cutoff, double rt_band, double mz_tolerance, bool mz_tolerance_unit,
108  double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling, String averagine_type="peptide");
109 
110 protected:
118  void updateWhiteMSExperiment_();
119 
130  bool checkForSignificantPeak_(double mz, double mz_tolerance, MSExperiment::ConstIterator& it_rt, double intensity_first_peak) const;
131 
147  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;
148 
156  void blacklistPeak_(const MultiplexFilteredPeak& peak);
157 
168  void blacklistPeak_(const MultiplexFilteredPeak& peak, unsigned pattern_idx);
169 
181  bool filterAveragineModel_(const MultiplexIsotopicPeakPattern& pattern, const MultiplexFilteredPeak& peak) const;
182 
195  bool filterPeptideCorrelation_(const MultiplexIsotopicPeakPattern& pattern, const MultiplexFilteredPeak& peak) const;
196 
201 
205  std::vector<std::vector<int> > blacklist_;
206 
213 
218 
222  std::vector<MultiplexIsotopicPeakPattern> patterns_;
223 
228 
233 
238 
242  double rt_band_;
243 
248 
253 
258 
263 
268 
273 
274  };
275 
276 }
277 
OpenMS::MultiplexFiltering::isotopes_per_peptide_min_
size_t isotopes_per_peptide_min_
minimum number of isotopic peaks per peptide
Definition: MultiplexFiltering.h:227
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:252
OpenMS::MultiplexFiltering::averagine_type_
String averagine_type_
type of averagine to use
Definition: MultiplexFiltering.h:272
OpenMS::String
A more convenient string class.
Definition: String.h:57
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::MultiplexIsotopicPeakPattern
data structure for pattern of isotopic peaks
Definition: MultiplexIsotopicPeakPattern.h:54
OpenMS::MultiplexFiltering::rt_band_
double rt_band_
RT range used for filtering.
Definition: MultiplexFiltering.h:242
OpenMS::MultiplexFiltering::exp_picked_mapping_
White2Original exp_picked_mapping_
mapping of peak indices from a 'white' experiment <exp_picked_white_> to its original experiment <exp...
Definition: MultiplexFiltering.h:217
MultiplexFilteredPeak.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
ProgressLogger.h
OpenMS::MultiplexFiltering::peptide_similarity_
double peptide_similarity_
peptide similarity
Definition: MultiplexFiltering.h:257
OpenMS::MultiplexFiltering::averagine_similarity_
double averagine_similarity_
averagine similarity
Definition: MultiplexFiltering.h:262
BaseFeature.h
MultiplexIsotopicPeakPattern.h
OpenMS::MultiplexFiltering::averagine_similarity_scaling_
double averagine_similarity_scaling_
averagine similarity scaling
Definition: MultiplexFiltering.h:267
OpenMS::MultiplexFiltering::exp_picked_
MSExperiment exp_picked_
centroided experimental data
Definition: MultiplexFiltering.h:200
OpenMS::MultiplexFiltering::intensity_cutoff_
double intensity_cutoff_
intensity cutoff
Definition: MultiplexFiltering.h:237
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:232
SplineSpectrum.h
OpenMS::MultiplexFiltering::patterns_
std::vector< MultiplexIsotopicPeakPattern > patterns_
list of peak patterns
Definition: MultiplexFiltering.h:222
OpenMS::MultiplexFiltering::blacklist_
std::vector< std::vector< int > > blacklist_
auxiliary structs for blacklisting
Definition: MultiplexFiltering.h:205
OpenMS::MSExperiment::ConstIterator
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
PeakPickerHiRes.h
OpenMS::MSSpectrum::ConstIterator
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:103
OpenMS::MultiplexFiltering::White2Original
std::vector< std::map< int, int > > White2Original
index mapping from a 'white' experiment to its original experiment
Definition: MultiplexFiltering.h:89
StandardTypes.h
OpenMS::MultiplexFiltering
base class for filtering centroided and profile data for peak patterns
Definition: MultiplexFiltering.h:74
OpenMS::MultiplexFiltering::exp_picked_white_
MSExperiment exp_picked_white_
"white" centroided experimental data
Definition: MultiplexFiltering.h:212
OpenMS::MultiplexFiltering::mz_tolerance_
double mz_tolerance_
m/z shift tolerance
Definition: MultiplexFiltering.h:247