public static double CalculateMassError(double experimental, double theoretical, MassToleranceUnits massErrorUnits) { if(massErrorUnits == MassToleranceUnits.Da) { return experimental - theoretical; } else if(massErrorUnits == MassToleranceUnits.ppm) { return (experimental - theoretical) / theoretical * 1e6; } else { return double.NaN; } }
static void Main(string[] args) { if (args.Length > 0) { Arguments arguments = new Arguments(args); List <string> data = new List <string>(arguments["d"].Split(',')); int min_assumed_precursor_charge_state = 2; if (arguments["minprecz"] != null) { min_assumed_precursor_charge_state = int.Parse(arguments["minprecz"]); } int max_assumed_precursor_charge_state = 4; if (arguments["maxprecz"] != null) { max_assumed_precursor_charge_state = int.Parse(arguments["maxprecz"]); } double abs_threshold = -1.0; if (arguments["at"] != null) { abs_threshold = double.Parse(arguments["at"], CultureInfo.InvariantCulture); } double rel_threshold_percent = -1.0; if (arguments["rt"] != null) { rel_threshold_percent = double.Parse(arguments["rt"], CultureInfo.InvariantCulture); } int max_peaks = 400; if (arguments["mp"] != null) { max_peaks = int.Parse(arguments["mp"]); } bool assign_charge_states = true; if (arguments["acs"] != null) { assign_charge_states = bool.Parse(arguments["acs"]); } bool deisotope = true; if (arguments["di"] != null) { deisotope = bool.Parse(arguments["di"]); } string database = arguments["db"]; Dictionary <string, Modification> known_variable_modifications = null; HashSet <Modification> variable_mods = new HashSet <Modification>(); if (Path.GetExtension(database).Equals(".xml", StringComparison.InvariantCultureIgnoreCase)) { bool no_uniprot_mods = false; if (arguments["noup"] != null) { no_uniprot_mods = bool.Parse(arguments["noup"]); } if (!no_uniprot_mods) { known_variable_modifications = ProteomeDatabaseReader.ReadUniProtXmlModifications(database); variable_mods.UnionWith(known_variable_modifications.Values); } } bool append_decoys = false; if (arguments["ad"] != null) { append_decoys = bool.Parse(arguments["ad"]); } else { append_decoys = Path.GetExtension(database).Equals(".xml", StringComparison.InvariantCultureIgnoreCase) || !ProteomeDatabaseReader.HasDecoyProteins(database); } ProteaseDictionary proteases = ProteaseDictionary.Instance; Protease protease = proteases["trypsin (no proline rule)"]; if (arguments["p"] != null) { protease = proteases[arguments["p"]]; } int max_missed_cleavages = 2; if (arguments["mmc"] != null) { max_missed_cleavages = int.Parse(arguments["mmc"]); } InitiatorMethionineBehavior initiator_methionine_behavior = InitiatorMethionineBehavior.Variable; if (arguments["imb"] != null) { initiator_methionine_behavior = (InitiatorMethionineBehavior)Enum.Parse(typeof(InitiatorMethionineBehavior), arguments["imb"], true); } ModificationDictionary mods = ModificationDictionary.Instance; List <Modification> fixed_mods = new List <Modification>(); if (arguments["fm"] != null) { foreach (string fixed_mod in arguments["fm"].Split(';')) { fixed_mods.Add(mods[fixed_mod]); } } if (arguments["vm"] != null) { foreach (string variable_mod in arguments["vm"].Split(';')) { Modification mod; if (!mods.TryGetValue(variable_mod, out mod)) { known_variable_modifications.TryGetValue(variable_mod, out mod); } variable_mods.Add(mod); } } int max_variable_mod_isoforms_per_peptide = 1024; if (arguments["mvmi"] != null) { max_variable_mod_isoforms_per_peptide = int.Parse(arguments["mvmi"]); } double precursor_mass_tolerance_value = 2.1; if (arguments["precmtv"] != null) { precursor_mass_tolerance_value = double.Parse(arguments["precmtv"], CultureInfo.InvariantCulture); } MassToleranceUnits precursor_mass_tolerance_units = MassToleranceUnits.Da; if (arguments["precmtu"] != null) { precursor_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["precmtu"], true); } MassTolerance precursor_mass_tolerance = new MassTolerance(precursor_mass_tolerance_value, precursor_mass_tolerance_units); MassType precursor_mass_type = MassType.Monoisotopic; if (arguments["precmt"] != null) { precursor_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["precmt"], true); } List <double> accepted_precursor_mass_errors = new List <double>(); if (arguments["apme"] != null && arguments["apme"].Length > 0) { foreach (string accepted_precursor_mass_error in arguments["apme"].Split(';')) { accepted_precursor_mass_errors.Add(double.Parse(accepted_precursor_mass_error, CultureInfo.InvariantCulture)); } } else { accepted_precursor_mass_errors.Add(0.0); } double product_mass_tolerance_value = 0.015; if (arguments["prodmtv"] != null) { product_mass_tolerance_value = double.Parse(arguments["prodmtv"], CultureInfo.InvariantCulture); } MassToleranceUnits product_mass_tolerance_units = MassToleranceUnits.Da; if (arguments["prodmtu"] != null) { product_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["prodmtu"], true); } MassTolerance product_mass_tolerance = new MassTolerance(product_mass_tolerance_value, product_mass_tolerance_units); MassType product_mass_type = MassType.Monoisotopic; if (arguments["prodmt"] != null) { product_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["prodmt"], true); } double max_fdr = 0.01; if (arguments["fdr"] != null) { max_fdr = double.Parse(arguments["fdr"], CultureInfo.InvariantCulture) / 100.0; } bool consider_mods_unique = false; if (arguments["cmu"] != null) { consider_mods_unique = bool.Parse(arguments["cmu"]); } int max_threads = Environment.ProcessorCount; if (arguments["mt"] != null) { max_threads = int.Parse(arguments["mt"]); } bool minimize_memory_usage = false; if (arguments["mmu"] != null) { minimize_memory_usage = bool.Parse(arguments["mmu"]); } string output_folder = Environment.CurrentDirectory; if (arguments["o"] != null) { output_folder = arguments["o"]; } DatabaseSearcher database_searcher = new DatabaseSearcher(data, min_assumed_precursor_charge_state, max_assumed_precursor_charge_state, abs_threshold, rel_threshold_percent, max_peaks, assign_charge_states, deisotope, database, append_decoys, protease, max_missed_cleavages, initiator_methionine_behavior, fixed_mods, variable_mods, max_variable_mod_isoforms_per_peptide, precursor_mass_tolerance, precursor_mass_type, accepted_precursor_mass_errors, product_mass_tolerance, product_mass_type, max_fdr, consider_mods_unique, max_threads, minimize_memory_usage, output_folder); database_searcher.Starting += HandleStarting; database_searcher.StartingFile += HandleStartingFile; database_searcher.UpdateStatus += HandleUpdateStatus; database_searcher.UpdateProgress += HandleUpdateProgress; database_searcher.ThrowException += HandleThrowException; database_searcher.FinishedFile += HandleFinishedFile; database_searcher.Finished += HandleFinished; database_searcher.Search(); } else { Console.WriteLine(Program.GetProductNameAndVersion() + " USAGE"); } }
public MassTolerance(double value, MassToleranceUnits units) { Value = value; Units = units; }
private void ScoreMatch(MassTolerance productMassTolerance) { double[] theoretical_product_masses = Peptide.CalculateProductMasses(PRODUCT_TYPES[Spectrum.FragmentationMethod]).ToArray(); TotalProducts = theoretical_product_masses.Length; // speed optimizations int num_theoretical_products = theoretical_product_masses.Length; double[] experimental_masses = Spectrum.Masses; double[] experimental_intensities = Spectrum.Intensities; int num_experimental_peaks = experimental_masses.Length; double product_mass_tolerance_value = productMassTolerance.Value; MassToleranceUnits product_mass_tolerance_units = productMassTolerance.Units; MatchingProducts = 0; int t = 0; int e = 0; while (t < num_theoretical_products && e < num_experimental_peaks) { double mass_difference = experimental_masses[e] - theoretical_product_masses[t]; if (product_mass_tolerance_units == MassToleranceUnits.ppm) { mass_difference = mass_difference / theoretical_product_masses[t] * 1e6; } if (Math.Abs(mass_difference) <= product_mass_tolerance_value) { MatchingProducts++; t++; } else if (mass_difference < 0) { e++; } else if (mass_difference > 0) { t++; } } MatchingProductsFraction = (double)MatchingProducts / TotalProducts; MatchingIntensity = 0.0; int e2 = 0; int t2 = 0; while (e2 < num_experimental_peaks && t2 < num_theoretical_products) { double mass_difference = experimental_masses[e2] - theoretical_product_masses[t2]; if (product_mass_tolerance_units == MassToleranceUnits.ppm) { mass_difference = mass_difference / theoretical_product_masses[t2] * 1e6; } if (Math.Abs(mass_difference) <= product_mass_tolerance_value) { MatchingIntensity += experimental_intensities[e2]; e2++; } else if (mass_difference < 0) { e2++; } else if (mass_difference > 0) { t2++; } } MatchingIntensityFraction = MatchingIntensity / Spectrum.TotalIntensity; MorpheusScore = MatchingProducts + MatchingIntensityFraction; }
private static bool isIsotopicPeak(double[,] labelData, int index, double massTolerance, MassToleranceUnits massToleranceUnits) { int charge = (int)labelData[(int)RawLabelDataColumn.Charge, index] == 0 ? 1 : (int)labelData[(int)RawLabelDataColumn.Charge, index]; double minimum_mz = labelData[(int)RawLabelDataColumn.MZ, index] - MAXIMUM_ISOTOPIC_SPACING / charge; double maximum_mz = labelData[(int)RawLabelDataColumn.MZ, index] - MINIMUM_ISOTOPIC_SPACING / charge; switch(massToleranceUnits) { case MassToleranceUnits.Da: minimum_mz -= massTolerance; maximum_mz += massTolerance; break; case MassToleranceUnits.mmu: minimum_mz -= massTolerance / 1000.0; maximum_mz += massTolerance / 1000.0; break; case MassToleranceUnits.ppm: minimum_mz -= massTolerance * minimum_mz / 1e6; maximum_mz += massTolerance * maximum_mz / 1e6; break; } int i = index; while(i > labelData.GetLowerBound(1) && labelData[(int)RawLabelDataColumn.MZ, i] >= minimum_mz) { i--; if(labelData[(int)RawLabelDataColumn.MZ, i] >= minimum_mz && labelData[(int)RawLabelDataColumn.MZ, i] <= maximum_mz) { if(labelData[(int)RawLabelDataColumn.Charge, i] == labelData[(int)RawLabelDataColumn.Charge, index]) { return true; } } } return false; }
public static double CalculateMassError(double experimental, double theoretical, MassToleranceUnits massErrorUnits) { if (massErrorUnits == MassToleranceUnits.Da) { return(experimental - theoretical); } else if (massErrorUnits == MassToleranceUnits.ppm) { return((experimental - theoretical) / theoretical * 1e6); } else { return(double.NaN); } }
public static double MzDifference(double mz1, double mz2, MassToleranceUnits tol) { return(Math.Abs(CalculateMassError(mz1, mz2, tol))); }//*/