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MultiplexFiltering.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Lars Nilse $
32 // $Authors: Lars Nilse $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/BaseFeature.h>
38 #include <OpenMS/KERNEL/StandardTypes.h>
39 #include <OpenMS/KERNEL/MSExperiment.h>
40 #include <OpenMS/CONCEPT/ProgressLogger.h>
41 #include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
42 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexIsotopicPeakPattern.h>
43 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteredPeak.h>
44 #include <OpenMS/MATH/MISC/CubicSpline2d.h>
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
208 MSExperiment exp_centroided_;
209
213 std::vector<std::vector<int> > blacklist_;
214
220 MSExperiment exp_centroided_white_;
221
225 White2Original exp_centroided_mapping_;
226
230 std::vector<MultiplexIsotopicPeakPattern> patterns_;
231
235 size_t isotopes_per_peptide_min_;
236
240 size_t isotopes_per_peptide_max_;
241
245 double intensity_cutoff_;
246
250 double rt_band_;
251
255 double mz_tolerance_;
256
260 bool mz_tolerance_unit_in_ppm_;
261
265 double peptide_similarity_;
266
270 double averagine_similarity_;
271
275 double averagine_similarity_scaling_;
276
281 String averagine_type_;
282
283 };
284
285 }
286
OpenMS::MultiplexFiltering::exp_centroided_white_
MSExperiment exp_centroided_white_
"white" centroided experimental data
Definition: MultiplexFiltering.h:220
OpenMS::MultiplexFiltering::averagine_similarity_
double averagine_similarity_
averagine similarity
Definition: MultiplexFiltering.h:270
OpenMS::String
A more convenient string class.
Definition: String.h:58
MultiplexFilteredPeak.h
OpenMS::MSExperiment::ConstIterator
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
OpenMS::MultiplexFiltering
base class for filtering centroided and profile data for peak patterns
Definition: MultiplexFiltering.h:73
CubicSpline2d.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::MultiplexFilteredPeak
data structure storing a single peak that passed all filters
Definition: MultiplexFilteredPeak.h:70
StandardTypes.h
OpenMS::MultiplexFiltering::blacklist_
std::vector< std::vector< int > > blacklist_
auxiliary structs for blacklisting
Definition: MultiplexFiltering.h:213
OpenMS::MultiplexFiltering::peptide_similarity_
double peptide_similarity_
peptide similarity
Definition: MultiplexFiltering.h:265
PeakPickerHiRes.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::intensity_cutoff_
double intensity_cutoff_
intensity cutoff
Definition: MultiplexFiltering.h:245
OpenMS::MultiplexFiltering::rt_band_
double rt_band_
RT range used for filtering.
Definition: MultiplexFiltering.h:250
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::MultiplexFiltering::averagine_type_
String averagine_type_
type of averagine to use
Definition: MultiplexFiltering.h:281
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::patterns_
std::vector< MultiplexIsotopicPeakPattern > patterns_
list of peak patterns
Definition: MultiplexFiltering.h:230
OpenMS::MultiplexFiltering::exp_centroided_
MSExperiment exp_centroided_
centroided experimental data
Definition: MultiplexFiltering.h:208
OpenMS::MSSpectrum::ConstIterator
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:104
OpenMS::MultiplexFiltering::averagine_similarity_scaling_
double averagine_similarity_scaling_
averagine similarity scaling
Definition: MultiplexFiltering.h:275
OpenMS::MultiplexFiltering::mz_tolerance_
double mz_tolerance_
m/z shift tolerance
Definition: MultiplexFiltering.h:255
BaseFeature.h
MultiplexIsotopicPeakPattern.h
OpenMS::MultiplexFiltering::exp_centroided_mapping_
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
OpenMS::MultiplexFiltering::White2Original
std::vector< std::map< int, int > > White2Original
index mapping from a &#39;white&#39; experiment to its original experiment
Definition: MultiplexFiltering.h:88
OpenMS::MultiplexIsotopicPeakPattern
data structure for pattern of isotopic peaks
Definition: MultiplexIsotopicPeakPattern.h:54
OpenMS::MultiplexFiltering::isotopes_per_peptide_min_
size_t isotopes_per_peptide_min_
minimum number of isotopic peaks per peptide
Definition: MultiplexFiltering.h:235