private O18QuanEnvelope GetCorrespondingEnvelope(IRawFile rawFile, double theoreticalMz, int charge, double mzTolerance, int scan) { PeakList <Peak> pkl = rawFile.GetPeakList(scan); if (pkl.ScanTimes.Count == 0) { pkl.ScanTimes.Add(new ScanTime(scan, rawFile.ScanToRetentionTime(scan))); } PeakList <Peak> O16 = pkl.FindEnvelopeDirectly(theoreticalMz, charge, mzTolerance, 4, () => new Peak()); PeakList <Peak> O181 = pkl.FindEnvelopeDirectly(theoreticalMz + chargeGapMap1[charge], charge, mzTolerance, 2, () => new Peak()); for (int i = 2; i < 4; i++) { if (O16[i].Intensity < O181[i - 2].Intensity) { O16[i].Mz = O181[i - 2].Mz; O16[i].Intensity = O181[i - 2].Intensity; } } PeakList <Peak> O182 = pkl.FindEnvelopeDirectly(theoreticalMz + chargeGapMap2[charge], charge, mzTolerance, 2, () => new Peak()); O16.AddRange(O182); return(new O18QuanEnvelope(O16)); }
private PeakList <Peak> ReadScan(int scan) { if (pklMap.ContainsKey(scan)) { return(pklMap[scan]); } PeakList <Peak> pkl = reader.GetPeakList(scan); pkl.ScanTimes.Clear(); pkl.ScanTimes.Add(new ScanTime(scan, reader.ScanToRetentionTime(scan))); pklMap[scan] = pkl; return(pkl); }
protected void DoGetOffsets(List <OffsetEntry> result, IRawFile reader, string msg) { var firstScan = reader.GetFirstSpectrumNumber(); var lastScan = reader.GetLastSpectrumNumber(); SetMessage(msg); SetRange(firstScan, lastScan); for (int scan = firstScan; scan <= lastScan; scan++) { if (reader.GetMsLevel(scan) == 1) { SetPosition(scan); if (IsLoopStopped) { return; } if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } var pkl = reader.GetPeakList(scan); var rt = reader.ScanToRetentionTime(scan); var offsetValues = GetOffsetsFromPeakList(pkl); if (offsetValues.Count > 0) { var weightedPPM = GetWeightedPPM(offsetValues); result.Add(new OffsetEntry(scan, rt, weightedPPM, offsetValues.Count)); } else { result.Add(new OffsetEntry(scan, rt, 0, 0)); } } } CalculateOffset(result, m => m.InitValue); }
private bool AddPeaks(IRawFile rawReader, int scan, SimplePeakChro chro, bool bIdentified) { var pkl = rawReader.GetPeakList(scan, chro.Mz - chro.MzTolerance, chro.Mz + chro.MzTolerance); if (pkl.Count == 0) { return(false); } var p = (from o in pkl where (o.Charge == chro.Charge) || (o.Charge == 0) orderby o.Intensity descending select o).FirstOrDefault(); if (null == p) { return(false); } var iit = rawReader.GetIonInjectionTime(scan); if (iit <= 0) { iit = 1.0; } chro.Peaks.Add(new ScanPeak() { Mz = p.Mz, Intensity = p.Intensity, Charge = p.Charge, Scan = scan, RetentionTime = rawReader.ScanToRetentionTime(scan), IonInjectionTime = iit, Identified = bIdentified }); return(true); }
private SilacPeakListPair GetLightHeavyPeakList(IRawFile rawFile, SilacCompoundInfo sci, int maxIndex, double mzTolerance, int scan, bool force = false) { PeakList <Peak> pkl = rawFile.GetPeakList(scan); if (pkl.Count == 0) { return(null); } var scantime = new ScanTime(scan, rawFile.ScanToRetentionTime(scan)); PeakList <Peak> light = pkl.FindEnvelopeDirectly(sci.Light.Profile, option.ProfileLength, mzTolerance, () => new Peak()); //如果电荷不对,则认为该scan无效。 if (!CheckPeakListCharge(light, maxIndex, sci.Light.Charge) && !force) { return(null); } PeakList <Peak> heavy = pkl.FindEnvelopeDirectly(sci.Heavy.Profile, option.ProfileLength, mzTolerance, () => new Peak()); //如果电荷不对,则认为该scan无效。 if (!CheckPeakListCharge(heavy, maxIndex, sci.Heavy.Charge) && !force) { return(null); } //如果轻或者重的总强度为0,则认为该scan无效。 if ((0 == light.Sum(m => m.Intensity) || 0 == heavy.Sum(m => m.Intensity)) && !force) { return(null); } light.ScanTimes.Add(scantime); heavy.ScanTimes.Add(scantime); return(new SilacPeakListPair(light, heavy)); }
public override IEnumerable <string> Process(string fileName) { string resultFile = new FileInfo(targetDir + "\\" + FileUtils.ChangeExtension(new FileInfo(fileName).Name, ".txt")).FullName; reader.Open(fileName); try { using (StreamWriter sw = new StreamWriter(resultFile)) { sw.NewLine = "\n"; sw.WriteLine(); sw.WriteLine("FUNCTION 1"); int firstScan = reader.GetFirstSpectrumNumber(); int lastScan = reader.GetLastSpectrumNumber(); for (int i = firstScan; i <= lastScan; i++) { var pkl = reader.GetPeakList(i); sw.WriteLine(""); sw.WriteLine("Scan\t\t{0}", i); sw.WriteLine("Retention Time\t{0:0.000}", reader.ScanToRetentionTime(i)); sw.WriteLine(""); foreach (var peak in pkl) { sw.WriteLine("{0:0.0000}\t{1:0}", peak.Mz, peak.Intensity); } } } } finally { reader.Close(); } return(new string[] { resultFile }); }
private List <SrmScan> GetMRMScans(string directory) { var fileName = GetPeakFileName(directory); if (File.Exists(fileName)) { SetProgressMessage("Reading scan from " + fileName + " ..."); return(new SrmScanFileFormat().ReadFromFile(fileName)); } else { List <PeakList <Peak> > pkls = new List <PeakList <Peak> >(); SetProgressMessage("Reading scan from " + directory + " ..."); IRawFile reader = RawFileFactory.GetRawFileReader(directory); try { var firstCount = reader.GetFirstSpectrumNumber(); var lastCount = reader.GetLastSpectrumNumber(); Progress.SetRange(firstCount, lastCount); Progress.SetPosition(firstCount); for (int i = firstCount; i <= lastCount; i++) { if (reader.GetMsLevel(i) != 2) { continue; } if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } Progress.Increment(1); var pkl = reader.GetPeakList(i); var precursor = reader.GetPrecursorPeak(i); if (precursor != null) { pkl.PrecursorMZ = precursor.Mz; pkl.PrecursorCharge = precursor.Charge; } pkl.ScanTimes.Add(new ScanTime(i, reader.ScanToRetentionTime(i))); pkls.Add(pkl); } List <SrmScan> result = new List <SrmScan>(); pkls.ForEach(m => m.ForEach(n => result.Add(new SrmScan(m.PrecursorMZ, n.Mz, m.ScanTimes[0].RetentionTime, n.Intensity, true)))); new SrmScanFileFormat().WriteToFile(fileName, result); SetProgressMessage("finished."); return(result); } finally { reader.Close(); } } }
public override IEnumerable <string> Process(string targetDir) { foreach (var raw in rawFiles) { List <SimplePeakChro> waitingPeaks = new List <SimplePeakChro>(); foreach (var peak in targetPeaks) { string file = GetTargetFile(targetDir, raw, peak); if (force || !File.Exists(file)) { waitingPeaks.Add(peak); } else { var p = new SimplePeakChroXmlFormat().ReadFromFile(file); peak.MaxRetentionTime = p.MaxRetentionTime; peak.Peaks = p.Peaks; } } if (waitingPeaks.Count == 0) { continue; } rawReader.Open(raw); try { int firstScan = rawReader.GetFirstSpectrumNumber(); int lastScan = rawReader.GetLastSpectrumNumber(); var lastRt = rawReader.ScanToRetentionTime(lastScan); waitingPeaks.ForEach(m => { m.Peaks.Clear(); m.MaxRetentionTime = lastRt; }); Progress.SetMessage("Processing chromotograph extracting..."); Progress.SetRange(firstScan, lastScan); for (int scan = firstScan; scan <= lastScan; scan++) { if (rawReader.GetMsLevel(scan) != 1) { continue; } Progress.SetPosition(scan); if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } PeakList <Peak> pkl = rawReader.GetPeakList(scan); double rt = rawReader.ScanToRetentionTime(scan); foreach (var peak in waitingPeaks) { var env = pkl.FindPeak(peak.Mz, peak.MzTolerance); Peak findPeak = new Peak(peak.Mz, 0.0, 0); if (env.Count > 0) { if (env.Count == 1) { findPeak = env[0]; } else { var charge = env.FindCharge(peak.Charge); if (charge.Count > 0) { if (charge.Count == 1) { findPeak = charge[0]; } else { findPeak = charge.FindMaxIntensityPeak(); } } else { findPeak = env.FindMaxIntensityPeak(); } } } peak.Peaks.Add(new ScanPeak() { Mz = findPeak.Mz, Intensity = findPeak.Intensity, Scan = scan, RetentionTime = rt, Charge = findPeak.Charge, PPMDistance = PrecursorUtils.mz2ppm(peak.Mz, findPeak.Mz - peak.Mz) }); } } waitingPeaks.ForEach(m => m.TrimPeaks(minRetentionTime)); } finally { rawReader.Close(); } Progress.SetMessage("Saving ... "); foreach (var peak in waitingPeaks) { string file = GetTargetFile(targetDir, raw, peak); new SimplePeakChroXmlFormat().WriteToFile(file, peak); } Progress.SetMessage("Finished."); Progress.End(); } return(new string[] { targetDir }); }
public override IEnumerable <string> Process(string rawFilename) { string ms1Filename = GetResultFilename(rawFilename); string ms1IndexFilename = ms1Filename + ".index"; rawFile.Open(rawFilename); try { int firstScan = rawFile.GetFirstSpectrumNumber(); int lastScan = rawFile.GetLastSpectrumNumber(); int firstFullScan = 0; for (firstFullScan = firstScan; firstFullScan < lastScan; firstFullScan++) { if (rawFile.GetMsLevel(firstFullScan) == 1) { break; } } if (firstFullScan >= lastScan) { return(new List <string>()); } Progress.SetRange(firstScan, lastScan); using (var sw = new StreamWriter(ms1Filename)) { //write header sw.Write("H\tCreationDate\t{0:m/dd/yyyy HH:mm:ss}\n", DateTime.Now); sw.Write("H\tExtractor\t{0}\n", GetProgramName()); sw.Write("H\tExtractorVersion\t{0}\n", GetProgramVersion()); sw.Write("H\tComments\t{0} written by Quanhu Sheng, 2008-2009\n", GetProgramName()); sw.Write("H\tExtractorOptions\tMS1\n"); sw.Write("H\tAcquisitionMethod\tData-Dependent\n"); sw.Write("H\tDataType\tCentriod\n"); sw.Write("H\tScanType\tMS1\n"); sw.Write("H\tFirstScan\t{0}\n", firstScan); sw.Write("H\tLastScan\t{0}\n", lastScan); using (var swIndex = new StreamWriter(ms1IndexFilename)) { for (int scan = firstScan; scan <= lastScan; scan++) { if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } Progress.SetPosition(scan); if (rawFile.GetMsLevel(scan) == 1) { sw.Flush(); swIndex.Write("{0}\t{1}\n", scan, sw.BaseStream.Position); sw.Write("S\t{0}\t{0}\n", scan); sw.Write("I\tRetTime\t{0:0.####}\n", rawFile.ScanToRetentionTime(scan)); PeakList <Peak> pkl = rawFile.GetPeakList(scan); foreach (Peak p in pkl) { sw.Write("{0:0.0000} {1:0.0} {2}\n", p.Mz, p.Intensity, p.Charge); } } } } } } finally { rawFile.Close(); } Progress.End(); return(new[] { ms1Filename }); }
public void TestRTFromScanNum() { Assert.AreEqual(0.037, reader.ScanToRetentionTime(1)); }
public override IEnumerable <string> Process(string targetDir) { foreach (var raw in rawFiles) { List <RetentionTimePeak> waitingPeaks = new List <RetentionTimePeak>(); foreach (var peak in targetPeaks) { string file = GetTargetFile(targetDir, raw, peak); if (force || !File.Exists(file)) { waitingPeaks.Add(peak); } } if (waitingPeaks.Count == 0) { continue; } rawReader.Open(raw); try { int firstScan = rawReader.GetFirstSpectrumNumber(); int lastScan = rawReader.GetLastSpectrumNumber(); waitingPeaks.ForEach(m => m.Chromotographs.Clear()); for (int scan = firstScan; scan <= lastScan; scan++) { if (rawReader.GetMsLevel(scan) != 1) { continue; } if (Progress.IsCancellationPending()) { throw new UserTerminatedException(); } PeakList <Peak> pkl = rawReader.GetPeakList(scan); double rt = rawReader.ScanToRetentionTime(scan); var st = new ScanTime(scan, rt); foreach (var peak in waitingPeaks) { var env = pkl.FindEnvelopeDirectly(peak.PeakEnvelope, peak.MzTolerance, () => new Peak()); env.ScanTimes.Add(st); peak.Chromotographs.Add(env); } } waitingPeaks.ForEach(m => m.TrimPeaks()); } finally { rawReader.Close(); } foreach (var peak in waitingPeaks) { string file = GetTargetFile(targetDir, raw, peak); new RetentionTimePeakXmlFormat().WriteToFile(file, peak); } } return(new string[] { targetDir }); }