/// <summary> /// Get IonType from IonTypeFactory. /// </summary> /// <param name="baseIonType">Base ion type of ion type to get.</param> /// <param name="neutralLoss">Neutral loss of ion type to get.</param> /// <param name="charge">Charge of ion type to get</param> /// <returns>IonType with the given base ion type, neutral loss, and charge.</returns> public IonType GetIonType(BaseIonType baseIonType, NeutralLoss neutralLoss, int charge) { var chargeStr = charge.ToString(CultureInfo.InvariantCulture); if (charge == 1) { chargeStr = string.Empty; } var name = baseIonType.Symbol + chargeStr + neutralLoss.Name; return(IonTypeFactory.GetIonType(name)); }
/// <summary> /// Get an product ion type from an ion type factory. /// </summary> /// <param name="ionTypeFactory">IonTypeFactory for obtaining ion information (mass, charge, etc.)</param> /// <param name="baseIonType">The base ion type.</param> /// <param name="neutralLoss">The neutral loss of ion type.</param> /// <param name="charge">The charge of product ion type.</param> /// <returns>Ion type with given base ion type, neutral loss, and charge.</returns> public static IonType GetIonType( IonTypeFactory ionTypeFactory, BaseIonType baseIonType, NeutralLoss neutralLoss, int charge) { var chargeStr = string.Empty; if (charge > 1) { chargeStr = charge.ToString(CultureInfo.InvariantCulture); } var name = string.Format("{0}{1}{2}", baseIonType.Symbol, chargeStr, neutralLoss.Name); return(ionTypeFactory.GetIonType(name)); }
public void ReadConfigurationFile(string configurationFile) { var reader = new ConfigFileReader(configurationFile); // Read program variables var config = reader.GetNodes("vars").First(); PrecursorCharge = Convert.ToInt32(config.Contents["precursorcharge"]); PrecursorOffsetThreshold = Convert.ToDouble(config.Contents["precursoroffsetthreshold"]); WindowWidth = Convert.ToInt32(config.Contents["searchwidth"]); PrecursorOffsetWidth = Convert.ToInt32(config.Contents["precursoroffsetwidth"]); RetentionCount = Convert.ToInt32(config.Contents["retentioncount"]); RelativeIntensityThreshold = Convert.ToDouble(config.Contents["relativeintensitythreshold"]); SelectedIonThreshold = Convert.ToDouble(config.Contents["selectedionthreshold"]); MassBinSize = Convert.ToInt32(config.Contents["massbinsize"]); var actStr = config.Contents["activationmethod"].ToLower(); switch (actStr) { case "hcd": ActivationMethod = ActivationMethod.HCD; Tolerance = _defaultTolerancePpm; break; case "cid": ActivationMethod = ActivationMethod.CID; Tolerance = _defaultToleranceMz; break; case "etd": ActivationMethod = ActivationMethod.ETD; Tolerance = _defaultTolerancePpm; break; default: throw new FormatException("Invalid Activation Method."); } var acqStr = config.Contents["acquisitionmethod"].ToLower(); switch (acqStr) { case "dia": AcquisitionMethod = AcquisitionMethod.Dia; break; case "dda": AcquisitionMethod = AcquisitionMethod.Dda; break; default: throw new FormatException("Invalid Acquisition Method."); } MassErrorTolerance = _defaultToleranceMz; MaxRanks = Convert.ToInt32(config.Contents["maxranks"]); var smoothingRanksStr = config.Contents["smoothingranks"].Split(','); SmoothingRanks = new int[smoothingRanksStr.Length]; var smoothingWindowSizeStr = config.Contents["smoothingwindowsize"].Split(','); SmoothingWindowSize = new int[smoothingWindowSizeStr.Length]; if (SmoothingRanks.Length != SmoothingWindowSize.Length) { throw new ArgumentException("SmoothingRanks and SmoothingWindowSize unequal lengths."); } for (int i = 0; i < SmoothingRanks.Length; i++) { if (smoothingRanksStr[i] == "Max") { SmoothingRanks[i] = Int32.MaxValue; } else { SmoothingRanks[i] = Convert.ToInt32(smoothingRanksStr[i]); } SmoothingWindowSize[i] = Convert.ToInt32(smoothingWindowSizeStr[i]); } // Read ion data var ionInfo = reader.GetNodes("ion").First(); int totalCharges = Convert.ToInt32(ionInfo.Contents["totalcharges"]); var ionTypeStr = ionInfo.Contents["iontype"].Split(','); var ions = new BaseIonType[ionTypeStr.Length]; for (int i = 0; i < ionTypeStr.Length; i++) { switch (ionTypeStr[i].ToLower()) { case "a": ions[i] = BaseIonType.A; break; case "b": ions[i] = BaseIonType.B; break; case "c": ions[i] = BaseIonType.C; break; case "x": ions[i] = BaseIonType.X; break; case "y": ions[i] = BaseIonType.Y; break; case "z": ions[i] = BaseIonType.Z; break; } } var ionLossStr = ionInfo.Contents["losses"].Split(','); var ionLosses = new NeutralLoss[ionLossStr.Length]; for (int i = 0; i < ionLossStr.Length; i++) { switch (ionLossStr[i].ToLower()) { case "noloss": ionLosses[i] = NeutralLoss.NoLoss; break; case "nh3": ionLosses[i] = NeutralLoss.NH3; break; case "h2o": ionLosses[i] = NeutralLoss.H2O; break; } } _ionTypeFactory = new IonTypeFactory(ions, ionLosses, totalCharges); IonTypes = _ionTypeFactory.GetAllKnownIonTypes().ToArray(); var tempIonList = new List <IonType>(); if (ionInfo.Contents.ContainsKey("exclusions")) { var ionExclusions = ionInfo.Contents["exclusions"].Split(','); tempIonList.AddRange(IonTypes.Where(ionType => !ionExclusions.Contains(ionType.Name))); IonTypes = tempIonList.ToArray(); } // Read input and output file names var fileInfo = reader.GetNodes("fileinfo").First(); DataSets = fileInfo.Contents["name"].Split(','); var dataFormat = fileInfo.Contents["format"]; switch (dataFormat) { case "mgf": DataFormat = DataFileFormat.Mgf; break; case "icbottomup": DataFormat = DataFileFormat.IcBottomUp; break; case "dia": DataFormat = DataFileFormat.Dia; break; default: throw new FormatException("Invalid Acquisition Method."); } TsvPath = fileInfo.Contents["tsvpath"]; DataPath = fileInfo.Contents["datapath"]; var outPathtemp = fileInfo.Contents["outpath"]; OutputPath = outPathtemp; OutputFileName = OutputPath + fileInfo.Contents["outputfile"]; }
// Read Configuration file private void InitTest(ConfigFileReader reader) { // Read program variables var config = reader.GetNodes("vars").First(); _precursorCharge = Convert.ToInt32(config.Contents["precursorcharge"]); var actStr = config.Contents["activationmethod"].ToLower(); _combineCharges = (config.Contents.ContainsKey("combinecharges") && config.Contents["combinecharges"].ToLower() == "true"); _useDecoy = (config.Contents.ContainsKey("usedecoy") && config.Contents["usedecoy"].ToLower() == "true"); _relativeIntensityThreshold = Convert.ToDouble(config.Contents["relativeintensitythreshold"]); // Read ion data var ionInfo = reader.GetNodes("ion").First(); int totalCharges = Convert.ToInt32(ionInfo.Contents["totalcharges"]); var ionTypeStr = ionInfo.Contents["iontype"].Split(','); var ions = new BaseIonType[ionTypeStr.Length]; for (int i = 0; i < ionTypeStr.Length; i++) { switch (ionTypeStr[i].ToLower()) { case "a": ions[i] = BaseIonType.A; break; case "b": ions[i] = BaseIonType.B; break; case "c": ions[i] = BaseIonType.C; break; case "x": ions[i] = BaseIonType.X; break; case "y": ions[i] = BaseIonType.Y; break; case "z": ions[i] = BaseIonType.Z; break; } } var ionLossStr = ionInfo.Contents["losses"].Split(','); var ionLosses = new NeutralLoss[ionLossStr.Length]; for (int i = 0; i < ionLossStr.Length; i++) { switch (ionLossStr[i].ToLower()) { case "noloss": ionLosses[i] = NeutralLoss.NoLoss; break; case "nh3": ionLosses[i] = NeutralLoss.NH3; break; case "h2o": ionLosses[i] = NeutralLoss.H2O; break; } } _ionTypeFactory = new IonTypeFactory(ions, ionLosses, totalCharges); _ionTypes = _ionTypeFactory.GetAllKnownIonTypes().ToList(); var tempIonList = new List <IonType>(); if (ionInfo.Contents.ContainsKey("exclusions")) { var ionExclusions = ionInfo.Contents["exclusions"].Split(','); tempIonList.AddRange(_ionTypes.Where(ionType => !ionExclusions.Contains(ionType.Name))); _ionTypes = tempIonList; } // Read input and output file names var fileInfo = reader.GetNodes("fileinfo").First(); _names = fileInfo.Contents["name"].Split(','); _preTsv = fileInfo.Contents["tsvpath"]; _preRaw = fileInfo.Contents["rawpath"]; var outPathtemp = fileInfo.Contents["outpath"]; _outPre = outPathtemp; var outFiletemp = fileInfo.Contents["outfile"]; _outFileName = _outPre + outFiletemp; }