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MultiplexFiltering.h
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34 
35 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXFILTERING_H
36 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXFILTERING_H
37 
46 
47 #include <vector>
48 #include <algorithm>
49 #include <iostream>
50 
51 namespace OpenMS
52 {
72  class OPENMS_DLLAPI MultiplexFiltering :
73  public ProgressLogger
74  {
75 public:
86  {
89  };
90 
98  {
99  bool black;
103  };
104 
120  MultiplexFiltering(const MSExperiment<Peak1D>& exp_picked, const std::vector<MultiplexPeakPattern> patterns, int peaks_per_peptide_min, int peaks_per_peptide_max, bool missing_peaks, double intensity_cutoff, double mz_tolerance, bool mz_tolerance_unit, double peptide_similarity, double averagine_similarity, double averagine_similarity_scaling);
121 
122 protected:
138  int positionsAndBlacklistFilter(MultiplexPeakPattern pattern, int spectrum, std::vector<double> peak_position, int peak, std::vector<double>& mz_shifts_actual, std::vector<int>& mz_shifts_actual_indices) const;
139 
152  bool monoIsotopicPeakIntensityFilter(MultiplexPeakPattern pattern, int spectrum_index, const std::vector<int>& mz_shifts_actual_indices) const;
153 
166  bool zerothPeakFilter(MultiplexPeakPattern pattern, const std::vector<double>& intensities_actual) const;
167 
183  bool peptideSimilarityFilter(MultiplexPeakPattern pattern, const std::vector<double>& intensities_actual, int peaks_found_in_all_peptides_spline) const;
184 
198  bool averagineSimilarityFilter(MultiplexPeakPattern pattern, const std::vector<double>& intensities_actual, int peaks_found_in_all_peptides_spline, double mz) const;
199 
209  void blacklistPeaks(MultiplexPeakPattern pattern, int spectrum, const std::vector<int>& mz_shifts_actual_indices, int peaks_found_in_all_peptides_spline);
210 
222  int getPeakIndex(std::vector<double> peak_position, int start, double mz, double scaling) const;
223 
233  double getPatternSimilarity(std::vector<double> pattern1, std::vector<double> pattern2) const;
234 
243  double getAveragineSimilarity(std::vector<double> pattern, double m) const;
244 
249 
253  std::vector<std::vector<PeakReference> > registry_;
254  std::vector<std::vector<BlackListEntry> > blacklist_;
255 
259  std::vector<MultiplexPeakPattern> patterns_;
260 
265 
270 
275 
280 
285 
290 
295 
300 
305 
306  };
307 
308 }
309 
310 #endif /* MULTIPLEXFILTERING_H_ */
bool mz_tolerance_unit_
unit for m/z shift tolerance (ppm - true, Da - false)
Definition: MultiplexFiltering.h:289
bool black
Definition: MultiplexFiltering.h:99
std::vector< std::vector< BlackListEntry > > blacklist_
Definition: MultiplexFiltering.h:254
std::vector< std::vector< PeakReference > > registry_
auxiliary structs for navigation and blacklisting
Definition: MultiplexFiltering.h:253
int peaks_per_peptide_max_
maximum number of isotopic peaks per peptide
Definition: MultiplexFiltering.h:269
bool missing_peaks_
flag for missing peaks
Definition: MultiplexFiltering.h:274
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
double intensity_cutoff_
intensity cutoff
Definition: MultiplexFiltering.h:279
double peptide_similarity_
peptide similarity
Definition: MultiplexFiltering.h:294
double averagine_similarity_
averagine similarity
Definition: MultiplexFiltering.h:299
MSExperiment< Peak1D > exp_picked_
centroided experimental data
Definition: MultiplexFiltering.h:248
int black_exception_charge
Definition: MultiplexFiltering.h:101
structure for peak blacklisting
Definition: MultiplexFiltering.h:97
int black_exception_mz_position
Definition: MultiplexFiltering.h:102
int peaks_per_peptide_min_
minimum number of isotopic peaks per peptide
Definition: MultiplexFiltering.h:264
double mz_tolerance_
m/z shift tolerance
Definition: MultiplexFiltering.h:284
int black_exception_mass_shift_index
Definition: MultiplexFiltering.h:100
std::vector< MultiplexPeakPattern > patterns_
list of peak patterns
Definition: MultiplexFiltering.h:259
int index_in_next_spectrum
Definition: MultiplexFiltering.h:88
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
structure for peak position in neighbouring spectra
Definition: MultiplexFiltering.h:85
double averagine_similarity_scaling_
averagine similarity scaling
Definition: MultiplexFiltering.h:304
data structure for pattern of isotopic peaks
Definition: MultiplexPeakPattern.h:54
int index_in_previous_spectrum
Definition: MultiplexFiltering.h:87
base class for filtering centroided and profile data for peak patterns
Definition: MultiplexFiltering.h:72

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:26 using doxygen 1.8.9.1