| averagine_similarity_ | MultiplexFiltering | protected |
| averagine_similarity_scaling_ | MultiplexFiltering | protected |
| averagine_type_ | MultiplexFiltering | protected |
| averagineSimilarityFilter_(const MultiplexIsotopicPeakPattern &pattern, const std::vector< double > &intensities_actual, int peaks_found_in_all_peptides_spline, double mz) const | MultiplexFiltering | protected |
| blacklist_ | MultiplexFiltering | protected |
| blacklistPeaks_(const MultiplexIsotopicPeakPattern &pattern, int spectrum, const std::vector< int > &mz_shifts_actual_indices, int peaks_found_in_all_peptides_spline) | MultiplexFiltering | protected |
| boundaries_ | MultiplexFilteringProfile | private |
| CMD enum value | ProgressLogger | |
| current_logger_ | ProgressLogger | mutableprotected |
| endProgress() const | ProgressLogger | |
| exp_picked_ | MultiplexFiltering | protected |
| exp_profile_ | MultiplexFilteringProfile | private |
| filter() | MultiplexFilteringProfile | |
| findNearest_(int spectrum_index, double mz, double scaling) const | MultiplexFilteringProfile | private |
| getAveragineSimilarity_(const std::vector< double > &pattern, double m) const | MultiplexFiltering | protected |
| getLogType() const | ProgressLogger | |
| getPatternSimilarity_(const std::vector< double > &pattern1, const std::vector< double > &pattern2) const | MultiplexFiltering | protected |
| getPeakIndex_(const std::vector< double > &peak_position, int start, double mz, double scaling) const | MultiplexFiltering | protected |
| GUI enum value | ProgressLogger | |
| intensity_cutoff_ | MultiplexFiltering | protected |
| last_invoke_ | ProgressLogger | mutableprotected |
| LogType enum name | ProgressLogger | |
| logTypeToFactoryName_(LogType type) | ProgressLogger | protectedstatic |
| missing_peaks_ | MultiplexFiltering | protected |
| monoIsotopicPeakIntensityFilter_(const MultiplexIsotopicPeakPattern &pattern, int spectrum_index, const std::vector< int > &mz_shifts_actual_indices) const | MultiplexFiltering | protected |
| MultiplexFiltering(const PeakMap &exp_picked, const std::vector< MultiplexIsotopicPeakPattern > 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, String averagine_type="peptide") | MultiplexFiltering | |
| MultiplexFilteringProfile(const PeakMap &exp_profile, const PeakMap &exp_picked, const std::vector< std::vector< PeakPickerHiRes::PeakBoundary > > &boundaries, const std::vector< MultiplexIsotopicPeakPattern > 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, String averagine_type="peptide") | MultiplexFilteringProfile | |
| mz_tolerance_ | MultiplexFiltering | protected |
| mz_tolerance_unit_ | MultiplexFiltering | protected |
| NONE enum value | ProgressLogger | |
| nonLocalIntensityFilter_(const MultiplexIsotopicPeakPattern &pattern, const std::vector< double > &mz_shifts_actual, const std::vector< int > &mz_shifts_actual_indices, SplineSpectrum::Navigator nav, std::vector< double > &intensities_actual, int peaks_found_in_all_peptides, double mz) const | MultiplexFilteringProfile | private |
| operator=(const ProgressLogger &other) | ProgressLogger | |
| patterns_ | MultiplexFiltering | protected |
| peaks_per_peptide_max_ | MultiplexFiltering | protected |
| peaks_per_peptide_min_ | MultiplexFiltering | protected |
| peptide_similarity_ | MultiplexFiltering | protected |
| peptideSimilarityFilter_(const MultiplexIsotopicPeakPattern &pattern, const std::vector< double > &intensities_actual, int peaks_found_in_all_peptides_spline) const | MultiplexFiltering | protected |
| positionsAndBlacklistFilter_(const MultiplexIsotopicPeakPattern &pattern, int spectrum, const std::vector< double > &peak_position, int peak, std::vector< double > &mz_shifts_actual, std::vector< int > &mz_shifts_actual_indices) const | MultiplexFiltering | protected |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| recursion_depth_ | ProgressLogger | protectedstatic |
| registry_ | MultiplexFiltering | protected |
| setLogType(LogType type) const | ProgressLogger | |
| setProgress(SignedSize value) const | ProgressLogger | |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| type_ | ProgressLogger | mutableprotected |
| zerothPeakFilter_(const MultiplexIsotopicPeakPattern &pattern, const std::vector< double > &intensities_actual) const | MultiplexFiltering | protected |
| ~ProgressLogger() | ProgressLogger | |