35 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXFILTERING_H 36 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_MULTIPLEXFILTERING_H 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);
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;
152 bool monoIsotopicPeakIntensityFilter(
MultiplexPeakPattern pattern,
int spectrum_index,
const std::vector<int>& mz_shifts_actual_indices)
const;
166 bool zerothPeakFilter(
MultiplexPeakPattern pattern,
const std::vector<double>& intensities_actual)
const;
183 bool peptideSimilarityFilter(
MultiplexPeakPattern pattern,
const std::vector<double>& intensities_actual,
int peaks_found_in_all_peptides_spline)
const;
198 bool averagineSimilarityFilter(
MultiplexPeakPattern pattern,
const std::vector<double>& intensities_actual,
int peaks_found_in_all_peptides_spline,
double mz)
const;
209 void blacklistPeaks(
MultiplexPeakPattern pattern,
int spectrum,
const std::vector<int>& mz_shifts_actual_indices,
int peaks_found_in_all_peptides_spline);
222 int getPeakIndex(std::vector<double> peak_position,
int start,
double mz,
double scaling)
const;
233 double getPatternSimilarity(std::vector<double> pattern1, std::vector<double> pattern2)
const;
243 double getAveragineSimilarity(std::vector<double> pattern,
double m)
const;
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