protected List <PeakList <Peak> > ReadTandemMassFromRaw(FileInfo rawFilename, List <int> ignoreScans) { string experimental = FileUtils.ChangeExtension(rawFilename.Name, ""); var result = new List <PeakList <Peak> >(); bool bReadAgain = false; rawReader.Open(rawFilename.FullName); try { int firstSpectrumNumber = rawReader.GetFirstSpectrumNumber(); int lastSpectrumNumber = rawReader.GetLastSpectrumNumber(); Progress.SetRange(firstSpectrumNumber, lastSpectrumNumber); Progress.Begin(); try { for (int scan = firstSpectrumNumber; scan <= lastSpectrumNumber; scan++) { if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } if (ignoreScans.Contains(scan)) { continue; } Progress.SetPosition(scan); int msLevel = rawReader.GetMsLevel(scan); if (msLevel > 1) { PeakList <Peak> pkl; try { pkl = rawReader.GetPeakList(scan); } catch (RawReadException ex) { ignoreScans.Add(ex.Scan); File.WriteAllLines(GetIgnoreScanFile(rawFilename), (from i in ignoreScans let s = i.ToString() select s).ToArray()); bReadAgain = true; break; } pkl.Precursor = rawReader.GetPrecursorPeakWithMasterScan(scan); pkl.MsLevel = msLevel; pkl.Experimental = experimental; pkl.ScanTimes.Add(new ScanTime(scan, rawReader.ScanToRetentionTime(scan))); pkl.ScanMode = rawReader.GetScanMode(scan); if (pkl.PrecursorCharge == 0) { pkl.PrecursorCharge = PrecursorUtils.GuessPrecursorCharge(pkl, pkl.PrecursorMZ); } PeakList <Peak> pklProcessed = this.pklProcessor.Process(pkl); if (null != pklProcessed && pklProcessed.Count > 0) { result.Add(pklProcessed); } } } } finally { Progress.End(); } } finally { rawReader.Close(); } if (bReadAgain) { return(ReadTandemMassFromRaw(rawFilename, ignoreScans)); } else { return(result); } }
private int DoWritePeakList(IRawFile2 rawReader, int scan, string fileName, List <string> returnFiles, string experimental, int lastSpectrumNumber, List <int> ignoreScans, ref bool bReadAgain) { var result = scan + 1; if (ignoreScans.Contains(scan)) { return(result); } SetPosition(scan); int msLevel = rawReader.GetMsLevel(scan); if (!DoAcceptMsLevel(msLevel)) { return(result); } //Console.WriteLine("Reading scan {0}", scan); PeakList <Peak> pkl; try { pkl = rawReader.GetPeakList(scan); } catch (RawReadException ex) { ignoreScans.Add(ex.Scan); File.WriteAllLines(GetIgnoreScanFile(fileName), (from i in ignoreScans let s = i.ToString() select s).ToArray()); bReadAgain = true; return(result); } pkl.MsLevel = msLevel; pkl.Experimental = experimental; pkl.ScanTimes.Add(new ScanTime(scan, rawReader.ScanToRetentionTime(scan))); pkl.ScanMode = rawReader.GetScanMode(scan); PeakList <Peak> pklProcessed; if (msLevel > 1) { pkl.Precursor = new PrecursorPeak(rawReader.GetPrecursorPeak(scan)); if (pkl.PrecursorCharge == 0) { pkl.PrecursorCharge = PrecursorUtils.GuessPrecursorCharge(pkl, pkl.PrecursorMZ); } if (options.ExtractRawMS3 && pkl.MsLevel == 3) { pklProcessed = pkl; } else { pklProcessed = this.PeakListProcessor.Process(pkl); } } else { pklProcessed = pkl; } if (null != pklProcessed && pklProcessed.Count > 0) { DoWritePeakList(rawReader, pklProcessed, fileName, returnFiles); if (!options.MzXmlNestedScan) { var intent = GetScanIntent(pkl.MsLevel); sw.WriteLine(intent + "</scan>"); } while (result < lastSpectrumNumber && rawReader.GetMsLevel(result) > msLevel) { result = DoWritePeakList(rawReader, result, fileName, returnFiles, experimental, lastSpectrumNumber, ignoreScans, ref bReadAgain); if (bReadAgain) { return(result); } } if (options.MzXmlNestedScan) { var intent = GetScanIntent(pkl.MsLevel); sw.WriteLine(intent + "</scan>"); } } return(result); }
protected override void DoInitialize(IRawFile2 rawFile, string rawFileName) { var resultFile = GetResultFile(rawFile, rawFileName); var scans = GetOutputScans(rawFile); this.scanIndeies = new List <Pair <int, long> >(); var utf8WithoutBom = new System.Text.UTF8Encoding(false); this.sw = new StreamWriter(resultFile, false, utf8WithoutBom); this.sw.NewLine = "\n"; /* * xml header and namespace info */ sw.WriteLine(@"<?xml version=""1.0"" encoding=""ISO-8859-1""?>"); sw.WriteLine(@"<mzXML xmlns=""http://sashimi.sourceforge.net/schema_revision/mzXML_3.1"""); sw.WriteLine(@" xmlns:xsi=""http://www.w3.org/2001/XMLSchema-instance"""); sw.WriteLine(@" xsi:schemaLocation=""http://sashimi.sourceforge.net/schema_revision/mzXML_3.1 http://sashimi.sourceforge.net/schema_revision/mzXML_3.1/mzXML_idx_3.1.xsd"" >"); int firstScan = rawFile.GetFirstSpectrumNumber(); int lastScan = rawFile.GetLastSpectrumNumber(); double startTime = rawFile.ScanToRetentionTime(firstScan) * 60; double endTime = rawFile.ScanToRetentionTime(lastScan) * 60; /* * begin msRun */ sw.WriteLine(MyConvert.Format(@" <msRun scanCount=""{0}"" startTime=""PT{1:G6}S"" endTime=""PT{2:G6}S"" >", scans.Count, startTime, endTime)); string sha1; try { sha1 = HashUtils.GetSHA1Hash(rawFileName).ToLower(); } catch (Exception ex) { throw new Exception("Exception when calculating sha1 value of file " + rawFileName, ex); } /* * parent (raw input) file */ //sw.WriteLine(@" <parentFile fileName=""file://DATA-PC/L/5168TP_mouse_phos_TMT/raw/6.raw"" fileType=""RAWData"" fileSha1=""f6db29dd3e26dec7eb16422138f0b2b06f02ba06"" />"); sw.WriteLine(@" <parentFile fileName=""file://{0}"" fileType=""RAWData"" fileSha1=""{1}""/>", rawFileName.Replace("\\", "/"), sha1); if (rawFile is RawFileImpl) { var impl = rawFile as RawFileImpl; /* * mass spec instrument section */ // get the instrument model string instModel = impl.GetInstModel(); // get acquisition software version string instSoftVersion = impl.GetInstSoftwareVersion(); sw.WriteLine(@" <msInstrument>"); sw.WriteLine(@" <msManufacturer category=""msManufacturer"" value=""Thermo Finnigan"" />"); sw.WriteLine(@" <msModel category=""msModel"" value=""{0}"" />", instModel); sw.WriteLine(@" <msIonisation category=""msIonisation"" value=""NSI"" />"); sw.WriteLine(@" <msMassAnalyzer category=""msMassAnalyzer"" value=""unknown"" />"); sw.WriteLine(@" <msDetector category=""msDetector"" value=""unknown"" />"); sw.WriteLine(@" <software type=""acquisition"" name=""Xcalibur"" version=""{0}"" />", instSoftVersion); sw.WriteLine(@" </msInstrument>"); } /* * data processing info */ sw.WriteLine(@" <dataProcessing>"); sw.WriteLine(@" <software type=""conversion"" name=""{0}"" version=""{1}"" />", this.DataProcessingSoftware, this.DataProcessingSoftwareVersion); foreach (string dataProcessingOperationName in this.dataProcessingOperations.Keys) { sw.WriteLine(MyConvert.Format(@" <processingOperation name=""{0}"" value=""{1}""/>", dataProcessingOperationName, this.dataProcessingOperations[dataProcessingOperationName])); } sw.WriteLine(" </dataProcessing>"); }
public double ScanToRetentionTime(int scan) { return(rawFile.ScanToRetentionTime(scan)); }