OpenSearchModificationAnalysis Member List

This is the complete list of members for OpenSearchModificationAnalysis, including all inherited members.

analyzeDeltaMassPatterns(const PeptideIdentificationList &peptide_ids, bool use_smoothing=false, bool debug=false) const	OpenSearchModificationAnalysis
analyzeModifications(PeptideIdentificationList &peptide_ids, double precursor_mass_tolerance=5.0, bool precursor_mass_tolerance_unit_ppm=true, bool use_smoothing=false, const String &output_file="") const	OpenSearchModificationAnalysis
analyzeModificationsWithStatistics(PeptideIdentificationList &peptide_ids, double precursor_mass_tolerance=5.0, bool precursor_mass_tolerance_unit_ppm=true, bool use_smoothing=false, const String &output_file="") const	OpenSearchModificationAnalysis
analyzeResidueFrequency(const PeptideIdentificationList &peptide_ids, double delta_mass, double tolerance=0.01) const	OpenSearchModificationAnalysis
buildModificationMassLookup_() const	OpenSearchModificationAnalysis	private
countUniquePeptides_(const PeptideIdentificationList &peptide_ids, double delta_mass, double tolerance) const	OpenSearchModificationAnalysis	private
DELTA_MASS_ZERO_THRESHOLD_	OpenSearchModificationAnalysis	privatestatic
DeltaMassHistogram typedef	OpenSearchModificationAnalysis
DeltaMassToChargeCount typedef	OpenSearchModificationAnalysis
findPeaksInHistogram_(const DeltaMassHistogram &histogram, double count_threshold=0.0, double snr=2.0)	OpenSearchModificationAnalysis	privatestatic
gaussian_(double x, double sigma)	OpenSearchModificationAnalysis	privatestatic
generateDeltaMassStatistics(const DeltaMassHistogram &histogram, const DeltaMassToChargeCount &charge_histogram, const PeptideIdentificationList &peptide_ids, double precursor_mass_tolerance=5.0, bool precursor_mass_tolerance_unit_ppm=true) const	OpenSearchModificationAnalysis
generatePTMStatistics(const PeptideIdentificationList &peptide_ids, double precursor_mass_tolerance=5.0, bool precursor_mass_tolerance_unit_ppm=true) const	OpenSearchModificationAnalysis
getTargetResidues_(const String &mod_name) const	OpenSearchModificationAnalysis	private
mapDeltaMassesToModifications(const DeltaMassHistogram &delta_mass_histogram, const DeltaMassToChargeCount &charge_histogram, PeptideIdentificationList &peptide_ids, double precursor_mass_tolerance=5.0, bool precursor_mass_tolerance_unit_ppm=true, const String &output_file="") const	OpenSearchModificationAnalysis
MAX_MOD_MAPPING_TOL_	OpenSearchModificationAnalysis	privatestatic
OpenSearchModificationAnalysis()=default	OpenSearchModificationAnalysis
smoothDeltaMassHistogram_(const DeltaMassHistogram &histogram, double sigma=0.001)	OpenSearchModificationAnalysis	privatestatic
writeDeltaMassStatistics(const DeltaMassStatistics &stats, const String &output_file) const	OpenSearchModificationAnalysis
writeModificationSummary_(const std::vector< ModificationSummary > &modifications, const String &output_file) const	OpenSearchModificationAnalysis	private
writePTMStatistics(const PTMStatistics &stats, const String &output_file) const	OpenSearchModificationAnalysis
~OpenSearchModificationAnalysis()=default	OpenSearchModificationAnalysis