private void writeSingleSpectrum(string sourceFile, string nativeID, string outFileName) { MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig(); writeConfig.format = MSDataFile.Format.Format_MGF; writeConfig.precision = MSDataFile.Precision.Precision_32; //var predicate = new SpectrumList_FilterPredicate_IndexSet(); //predicate.indexSet.Add(nativeID); var predicate = new SpectrumList_FilterPredicate_NativeIDSet(); predicate.nativeIDSet.Add(nativeID); try { //Workspace.SetText("\r\nWriting selected spectrum to " + outFileName); MainForm.SetText(this, "Start writing selected spectrum to " + outFileName + "\r\n"); using (MSDataFile msFile = new MSDataFile(sourceFile)) { msFile.run.spectrumList = new SpectrumList_Filter(msFile.run.spectrumList, new SpectrumList_FilterAcceptSpectrum(predicate.accept)); msFile.write(outFileName, writeConfig); } MainForm.SetText(this, "Finished writing selected spectrum to " + outFileName + "\r\n"); } catch (Exception exc) { //throw new Exception("Error in writiing new spectra file", exc); //Workspace.SetText("\r\nError in writing new spectra file\r\n"); tbPepNovoResult.AppendText("\r\nError in writing new spectra file\r\n"); throw new Exception(exc.Message); } }
public static List<string> IDList(string idpXML, string mzML) { List<string> list = new List<string>(); MSDataFile foo = new MSDataFile(mzML); SpectrumList sl = foo.run.spectrumList; IDPicker.Workspace workspace = new IDPicker.Workspace(); Package.loadWorkspace(ref workspace, idpXML); foreach (IDPicker.SourceGroupList.MapPair groupItr in workspace.groups) foreach (IDPicker.SourceInfo source in groupItr.Value.getSources(true)) foreach (IDPicker.SpectrumList.MapPair sItr in source.spectra) { IDPicker.ResultInstance ri = sItr.Value.results[1]; IDPicker.VariantInfo vi = ri.info.peptides.Min; bool boolCharge = sItr.Value.id.charge.Equals(3); if (boolCharge) { string rawPepSequence = vi.ToString(); string interpretation = vi.ToSimpleString(); // Look up the index with nativeID object idOrIndex = null; if (sItr.Value.nativeID != null && sItr.Value.nativeID.Length > 0) { idOrIndex = sItr.Value.nativeID; list.Add(idOrIndex.ToString()); } }//end if (boolcharge) }//end foreach return list; }
public IList <string> WriteSpectra(MSDataFile.WriteConfig config) { var outputPaths = new List <string>(); foreach (SpectrumSource ss in session.Query <SpectrumSource>()) { if (ss.Metadata == null) { continue; } string outputSuffix; switch (config.format) { case MSDataFile.Format.Format_mzML: outputSuffix = ".mzML"; break; case MSDataFile.Format.Format_mzXML: outputSuffix = ".mzXML"; break; case MSDataFile.Format.Format_MGF: outputSuffix = ".mgf"; break; case MSDataFile.Format.Format_MS2: outputSuffix = ".ms2"; break; default: config.format = MSDataFile.Format.Format_mzML; outputSuffix = ".mzML"; break; } MSDataFile.write(ss.Metadata, ss.Name + outputSuffix, config); outputPaths.Add(ss.Name + outputSuffix); } return(outputPaths); }
static void openButton_Click(object sender, EventArgs e) { string filepath = _fileTextBox.Text; if (!File.Exists(filepath)) { MessageBox.Show("That filepath does not exist.", "404 File not found", MessageBoxButtons.OK, MessageBoxIcon.Error); return; } try { var msd = new MSDataFile(filepath); var sl = msd.run.spectrumList; MessageBox.Show(String.Format("The file has {0} spectra.", sl.size()), "Spectra Count"); } catch (Exception ex) { string message = ex.ToString(); if (ex.InnerException != null) { message += "\n\nAdditional information: " + ex.InnerException.ToString(); } MessageBox.Show(message, "Error opening file", MessageBoxButtons.OK, MessageBoxIcon.Error, MessageBoxDefaultButton.Button1, 0, false); } }
protected void calculateSHA1() { lock (calculateSHA1Mutex) { jobInfo.log("SHA1 Checking", "SHA1 Checking"); MSDataFile.calculateSHA1Checksums(msd); } }
public void SetRawFile(MSDataFile dataFile) { MsnDataScan scan = dataFile[ScanNumber] as MsnDataScan; IsolationMZ = scan.IsolationRange.Mean; Spectrum = dataFile.GetSpectrum(ScanNumber); ScanWidth = scan.MzRange.Width; }
public void MyTestInitialize() { dataFile = new MSDataFile(Properties.Settings.Default.mzXMLTestFile1); spectrumCache = new SpectrumCache(); ticGenerator = new TicGenerator(dataFile.run, spectrumCache); timer = new Stopwatch(); }
public DataSource( string filepath ) { msDataFile = new MSDataFile(filepath); sourceFilepath = filepath; /*setInputFileWaitHandle = new EventWaitHandle( false, EventResetMode.ManualReset ); setInputFileDelegate = new ParameterizedThreadStart( startSetInputFile ); Thread setInputFileThread = new Thread( setInputFileDelegate ); setInputFileThread.Start( (object) filepath );*/ }
public void GenerateFromMSMS() { dataFile = new MSDataFile(Properties.Settings.Default.mzXMLTestFile2); spectrumCache = new SpectrumCache(); xicGenerator = new XicGenerator(dataFile.run, spectrumCache); IXYData xic = xicGenerator.Generate(592.3, 592.3, 0.01, TimeUnit.Seconds); Assert.AreEqual(239, xic.XValues.Count); Assert.AreEqual(7.6804, Math.Round(xic.GetXYPair(168).XValue, 10)); Assert.AreEqual(519, xic.GetXYPair(168).YValue); }
public void Convert(string omssaCSV, MSDataFile dataFile) { string filePath = Path.ChangeExtension(omssaCSV, ".pepxml"); using (PepXmlWriter writer = new PepXmlWriter(filePath)) { writer.WriteSampleProtease(Protease); writer.StartSearchSummary("OMSSA", true, true); writer.WriteProteinDatabase(FastaDatabaseFile); writer.WriteSearchProtease(Protease, MissedClevages); foreach (int modNumber in FixedMods) { OmssaModification mod; if (OmssaModification.TryGetModification(modNumber, out mod)) { writer.WriteModification(mod, mod.Sites, true); } } foreach (int modNumber in VariableMods) { OmssaModification mod; if (OmssaModification.TryGetModification(modNumber, out mod)) { writer.WriteModification(mod, mod.Sites, false); } } writer.SetCurrentStage(PepXmlWriter.Stage.Spectra, true); using (OmssaCsvPsmReader reader = new OmssaCsvPsmReader(omssaCSV, UserModFile)) { reader.AddMSDataFile(dataFile); reader.LoadProteins(FastaDatabaseFile); foreach (PeptideSpectralMatch psm in reader.ReadNextPsm()) { writer.StartSpectrum(psm.SpectrumNumber, psm.Spectrum.RetentionTime, psm.Spectrum.PrecursorMz, psm.Spectrum.PrecursorCharge); writer.WritePSM(psm); writer.EndSpectrum(); } } } }
private SourceInfo[] getSourceInfo(DirectoryInfo dirInfo, bool getDetails) { var sourceInfoList = new List <SourceInfo>(); sourceInfoList.Add(new SourceInfo()); sourceInfoList[0].type = getSourceType(dirInfo); sourceInfoList[0].name = dirInfo.Name; sourceInfoList[0].path = new MSDataRunPath(dirInfo.FullName, 0); sourceInfoList[0].dateModified = dirInfo.LastWriteTime; sourceInfoList[0].hasDetails = getDetails; if (!getDetails) { return(sourceInfoList.ToArray()); } if (sourceInfoList[0].type == "File Folder") { return(sourceInfoList.ToArray()); } else if (sourceInfoList[0].type != String.Empty) { try { MSDataFile msInfo = new MSDataFile(dirInfo.FullName); sourceInfoList[0].populateFromMSData(msInfo); } catch (ThreadAbortException) { return(null); } catch { sourceInfoList[0].spectra = 0; sourceInfoList[0].type = "Invalid " + sourceInfoList[0].type; } sourceInfoList[0].size = 0; sourceInfoList[0].dateModified = DateTime.MinValue; foreach (FileInfo fileInfo in dirInfo.GetFiles("*", SearchOption.AllDirectories)) { sourceInfoList[0].size += (UInt64)fileInfo.Length; if (fileInfo.LastWriteTime > sourceInfoList[0].dateModified) { sourceInfoList[0].dateModified = fileInfo.LastWriteTime; } } return(sourceInfoList.ToArray()); } return(null); }
public void Convert(string omssaCSV, MSDataFile dataFile) { string filePath = Path.ChangeExtension(omssaCSV, ".pepxml"); using (PepXmlWriter writer = new PepXmlWriter(filePath)) { writer.WriteSampleProtease(Protease); writer.StartSearchSummary("OMSSA", true, true); writer.WriteProteinDatabase(FastaDatabaseFile); writer.WriteSearchProtease(Protease, MissedClevages); foreach (int modNumber in FixedMods) { OmssaModification mod; if (OmssaModification.TryGetModification(modNumber, out mod)) { writer.WriteModification(mod, mod.Sites, true); } } foreach (int modNumber in VariableMods) { OmssaModification mod; if (OmssaModification.TryGetModification(modNumber, out mod)) { writer.WriteModification(mod, mod.Sites, false); } } writer.SetCurrentStage(PepXmlWriter.Stage.Spectra, true); using (OmssaCsvPsmReader reader = new OmssaCsvPsmReader(omssaCSV, UserModFile)) { reader.AddMSDataFile(dataFile); reader.LoadProteins(FastaDatabaseFile); foreach (PeptideSpectralMatch psm in reader.ReadNextPsm()) { writer.StartSpectrum(psm.SpectrumNumber, psm.Spectrum.RetentionTime, psm.Spectrum.PrecursorMz, psm.Spectrum.PrecursorCharge); writer.WritePSM(psm); writer.EndSpectrum(); } } } }
public ParseSpectraFile(string mzmlPath, HashSet <int> scanNumSet, string ext) { int currentScanNum = -1; try { MSDataFile msd = new MSDataFile(mzmlPath); SpectrumList spectrumList = msd.run.spectrumList; for (int i = 0; i < spectrumList.size(); ++i) { Spectrum spectrum = spectrumList.spectrum(i, true); if (int.Parse(spectrum.cvParams[0].value) == 2) { Match match = scanNumPattern.Match(spectrum.id); currentScanNum = int.Parse(match.Groups[1].Value); if (scanNumSet.Contains(currentScanNum)) { MZIntensityPairList mzIntensityPairs = new MZIntensityPairList(); spectrum.getMZIntensityPairs(ref mzIntensityPairs); Dictionary <float, int> originalPeakList = new Dictionary <float, int>(mzIntensityPairs.Count); foreach (MZIntensityPair mzIntensity in mzIntensityPairs) { originalPeakList[(float)mzIntensity.mz] = (int)mzIntensity.intensity; } spectraMap[currentScanNum] = originalPeakList; } } } } catch (Exception ex) { MessageBox.Show(ex.Message + ": " + currentScanNum, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error); Application.Exit(); } }
private void SetupMSMSData() { dataFile = new MSDataFile(Properties.Settings.Default.mzXMLTestFile2); spectrumCache = new SpectrumCache(); timePointToRtConverter = new RtToTimePointConverter(dataFile.run, spectrumCache); }
public void MyTestInitialize() { dataFile = new MSDataFile(Properties.Settings.Default.mzXMLTestFile1); spectrumCache = new SpectrumCache(); timePointToRtConverter = new RtToTimePointConverter(dataFile.run, spectrumCache); }
public void UpdatePsmInformation(MSDataFile dataFile, bool is2dFDR = true, bool useMedian = true, double evalueThreshold = 1e-3) { List <double> errors = new List <double>(); MaximumPrecursorMassError = 0; int count = 0; int msms = 0; int ms = 0; int localMSMS = -1; List <int> msmsBetweenMS = new List <int>(); List <double> injectionTimes = new List <double>(); for (int sn = dataFile.FirstSpectrumNumber; sn <= dataFile.LastSpectrumNumber; sn++) { int order = dataFile.GetMsnOrder(sn); if (order == 1) { ms++; if (localMSMS >= 0) { msmsBetweenMS.Add(localMSMS); } localMSMS = 0; } else { localMSMS++; msms++; injectionTimes.Add(dataFile.GetInjectionTime(sn)); } } MaxMSMSScansBetweenMS = msmsBetweenMS.Max(); AverageMSMSSCansBetweenMS = msmsBetweenMS.Average(); TotalMSMSscans = msms; TotalMSscans = ms; AverageMSMSInjectionTime = injectionTimes.Average(); MaxMSMSInjectionTime = injectionTimes.Max(); foreach (KeyValuePair <int, SortedMaxSizedContainer <PSM> > kvp in _data) { int scanNumber = kvp.Key; SortedMaxSizedContainer <PSM> psms = kvp.Value; double isolationMZ = dataFile.GetPrecusorMz(scanNumber); Polarity polarity = dataFile.GetPolarity(scanNumber); foreach (PSM psm in psms) { psm.Charge *= (int)polarity; // For negative mode ions psm.IsolationMz = isolationMZ; double isolationMass = Mass.MassFromMz(isolationMZ, psm.Charge); double theoreticalMass = psm.MonoisotopicMass; int nominalMassOffset; double adjustedIsolationMass; Tolerance tolerancePPM = Tolerance.CalculatePrecursorMassError(theoreticalMass, isolationMass, out nominalMassOffset, out adjustedIsolationMass); psm.AdjustedIsolationMass = adjustedIsolationMass; psm.IsotopeSelected = nominalMassOffset; if (!HasPPMInfo) { psm.PrecursorMassError = tolerancePPM.Value; } double positive = Math.Abs(psm.PrecursorMassError); if (positive > MaximumPrecursorMassError) { MaximumPrecursorMassError = positive; } if (psm.FdrScoreMetric <= evalueThreshold) { errors.Add(psm.PrecursorMassError); } count++; } } SystematicPrecursorMassError = useMedian ? GetMedianValue(errors) : errors.Average(); // Adjust all psms to foreach (PSM psm in PeptideSpectralMatches) { psm.CorrectedPrecursorMassError = psm.PrecursorMassError - SystematicPrecursorMassError; } }
public void GetMSMSSpectrum() { dataFile = new MSDataFile(Properties.Settings.Default.mzXMLTestFile2); spectrumCache = new SpectrumCache(); averagedSpectrumExtractor = new AveragedSpectrumExtractor(dataFile.run, spectrumCache); Domain.ISpectrum msmsSpectrum = averagedSpectrumExtractor.GetMSMSSpectrum(7.8, 1, 592.3, 0.5); Assert.AreEqual(42279, msmsSpectrum.Count); Assert.AreEqual(37, Math.Round(msmsSpectrum.GetXYPair(63).YValue, 5)); }
public static void quantify(Workspace ws, string rootInputDirectory, QuantitationInfo.Method method) { if (method == QuantitationInfo.Method.None) return; ws.groups.assembleParentGroups(); foreach (SourceInfo source in ws.groups["/"].getSources(true)) { source.filepath = Util.FindSourceInSearchPath(source.name, rootInputDirectory); using (MSDataFile msd = new MSDataFile(source.filepath)) using (pwiz.CLI.msdata.SpectrumList sl = msd.run.spectrumList) { foreach (SpectrumInfo si in source.spectra.Values) { int index = sl.find(si.nativeID); if (index == sl.size()) throw new KeyNotFoundException("spectrum \"" + si.nativeID + "\" not found in " + source.filepath); si.quantitation = new QuantitationInfo() { method = method, ITRAQ_113_intensity = 0, ITRAQ_114_intensity = 0, ITRAQ_115_intensity = 0, ITRAQ_116_intensity = 0, ITRAQ_117_intensity = 0, ITRAQ_118_intensity = 0, ITRAQ_119_intensity = 0, ITRAQ_121_intensity = 0 }; const double tolerance = 0.5; // TODO: make user configurable? pwiz.CLI.msdata.Spectrum s = sl.spectrum(index, true); BinaryData mzData = s.getMZArray().data; BinaryData intensityData = s.getIntensityArray().data; if (method == QuantitationInfo.Method.ITRAQ4Plex) for (int i = 0; i < mzData.Count; ++i) { if (mzData[i] < 113) continue; else if (inTolerance(mzData[i], 114, tolerance)) si.quantitation.ITRAQ_114_intensity += intensityData[i]; else if (inTolerance(mzData[i], 115, tolerance)) si.quantitation.ITRAQ_115_intensity += intensityData[i]; else if (inTolerance(mzData[i], 116, tolerance)) si.quantitation.ITRAQ_116_intensity += intensityData[i]; else if (inTolerance(mzData[i], 117, tolerance)) si.quantitation.ITRAQ_117_intensity += intensityData[i]; else if (mzData[i] > 117) break; } else if(method == QuantitationInfo.Method.ITRAQ8Plex) for (int i = 0; i < mzData.Count; ++i) { if (mzData[i] < 112) continue; else if (inTolerance(mzData[i], 113, tolerance)) si.quantitation.ITRAQ_113_intensity += intensityData[i]; else if (inTolerance(mzData[i], 114, tolerance)) si.quantitation.ITRAQ_114_intensity += intensityData[i]; else if (inTolerance(mzData[i], 115, tolerance)) si.quantitation.ITRAQ_115_intensity += intensityData[i]; else if (inTolerance(mzData[i], 116, tolerance)) si.quantitation.ITRAQ_116_intensity += intensityData[i]; else if (inTolerance(mzData[i], 117, tolerance)) si.quantitation.ITRAQ_117_intensity += intensityData[i]; else if (inTolerance(mzData[i], 118, tolerance)) si.quantitation.ITRAQ_118_intensity += intensityData[i]; else if (inTolerance(mzData[i], 119, tolerance)) si.quantitation.ITRAQ_119_intensity += intensityData[i]; else if (inTolerance(mzData[i], 121, tolerance)) si.quantitation.ITRAQ_121_intensity += intensityData[i]; else if (mzData[i] > 121) break; } } } } }
public MsnDataScan(int spectrumNumber, int msnOrder, MSDataFile <TSpectrum> parentFile = null) : base(spectrumNumber, msnOrder, parentFile) { }
//get pepSequence,source,scanID, write into a csv file. //have tons of information: theretical ion intensity, pep info, chargeLabel... public static void idpReader(string idpXMLFile, string mzMLFile, double TicCutoffPercentage, int z, int model) { //get the path and filename of output csv file: string fileName = Path.GetFileNameWithoutExtension(idpXMLFile); string filePath = Path.GetDirectoryName(idpXMLFile); string csvFile = Path.Combine(filePath, fileName) + "_" + z.ToString() + ".csv"; IDPicker.Workspace workspace = new IDPicker.Workspace(); Package.loadWorkspace(ref workspace, idpXMLFile); using (StreamWriter file = new StreamWriter(csvFile)) { //TODO idOrIndex + "," + pepSequence + "," + pepBond + "," + AA + "," + bIons + "," + yIons; file.WriteLine("nativeID,pepSequence,bond,b1,b2,y1,y2"); MSDataFile foo = new MSDataFile(mzMLFile); SpectrumList sl = foo.run.spectrumList; foreach (IDPicker.SourceGroupList.MapPair groupItr in workspace.groups) foreach (IDPicker.SourceInfo source in groupItr.Value.getSources(true)) foreach (IDPicker.SpectrumList.MapPair sItr in source.spectra) { IDPicker.ResultInstance ri = sItr.Value.results[1]; IDPicker.VariantInfo vi = ri.info.peptides.Min; string ss = vi.ToString() + "," + sItr.Value.id.source.name + "," + sItr.Value.nativeID; bool boolCharge = sItr.Value.id.charge.Equals(z); if (boolCharge) { string rawPepSequence = vi.ToString(); string pepSequence = vi.peptide.sequence; int len = pepSequence.Length; // Look up the index with nativeID object idOrIndex = null; if( sItr.Value.nativeID != null && sItr.Value.nativeID.Length > 0 ) idOrIndex = sItr.Value.nativeID; int spectrumIndex = sl.find(idOrIndex as string); // Trust the local index, if the nativeID lookup fails if( spectrumIndex >= sl.size() ) spectrumIndex = sItr.Value.id.index; // Bail of the loca index is larger than the spectrum list size if( spectrumIndex >= sl.size() ) throw new Exception( "Can't find spectrum associated with the index." ); //get base peak and TIC and converted to string Spectrum spec1 = sl.spectrum(spectrumIndex, true); MZIntensityPairList peaks = new MZIntensityPairList(); spec1.getMZIntensityPairs(ref peaks); Set<Peak> peakList = new Set<Peak>(); //get base peak and TIC double basePeakValue = 0; double TICValue = 0; CVParamList list = spec1.cvParams; foreach (CVParam CVP in list) { if (CVP.name == "base peak intensity") { basePeakValue = CVP.value; } if (CVP.name == "total ion current") { TICValue = CVP.value; } } string basePeak = basePeakValue.ToString(); string TIC = TICValue.ToString(); //very important. Surendra put them here //to change those with modifications {} into a format //that fragment method will accept. string interpretation = vi.ToSimpleString(); Peptide peptide = new Peptide(interpretation, ModificationParsing.ModificationParsing_Auto, ModificationDelimiter.ModificationDelimiter_Brackets); Fragmentation fragmentation = peptide.fragmentation(true, true); //prepare the qualified peaklist double intenThreshhold = 0; int totalIntenClass = 0; double[] intenArray = new double[peaks.Count]; //used during the foreach loop int indexPeaks = 0; //get all the peaks no matter how small they are //then calculate the threshhold TIC //test here foreach (MZIntensityPair mzIntensity in peaks) { //Peak p = new Peak(mzIntensity.mz, mzIntensity.intensity); //peakList.Add(p); intenArray[indexPeaks] = mzIntensity.intensity; indexPeaks++; } Array.Sort(intenArray); Array.Reverse(intenArray, 0, peaks.Count); //if currTIC>=cutoff, then break double currTIC = 0; double cutOffTIC = TicCutoffPercentage * TICValue; foreach (double inten in intenArray) { currTIC = currTIC + inten; if (currTIC < cutOffTIC) { intenThreshhold = inten; totalIntenClass++; } else break; } //then based on that, generate a new peaklist that contains only ABC peaks //then calculate the intensity classes foreach (MZIntensityPair mzIntensity in peaks) { if (mzIntensity.intensity >= intenThreshhold) { //note 0 here. This is to tell people that the orbiorbi fragment charge is unknown. //the peaklist will be updated later. Peak p = new Peak(mzIntensity.mz, mzIntensity.intensity,0); peakList.Add(p); } } Console.WriteLine("nativeID: =============" + idOrIndex); //update peaklist for charge states. peakList = Package.chargeAssignment(peakList); //int ones = 0; //int twos = 0; //foreach (var peak in peakList) //{ // //Console.WriteLine(peak.fragmentCharge); // if (peak.fragmentCharge == 1) ones++; // else if (peak.fragmentCharge == 2) twos++; //} //Console.WriteLine("charge 1: " + ones); //Console.WriteLine("charge 2: " + twos); //rowDic contains row information of each peptide bond Dictionary<int, string> rowDic = new Dictionary<int, string>(); //intensityDic contains intensity information of fragment ions for each peptide bond Dictionary<int, List<double>> intensityDic = new Dictionary<int, List<double>>(); //commonList contains the common intensities List<double> duplicateList = new List<double>(); //call the method List<double> completeIntensityList = new List<double>(); for (int k = 1; k < len; k++) { List<double> intensityList = new List<double>(); string bion = pepSequence.Substring(0, k); string yion = pepSequence.Substring(k, len - k); int NR = Package.parseAAResidues(bion, 'R'); int NK = Package.parseAAResidues(bion, 'K'); int NH = Package.parseAAResidues(bion, 'H'); int NL = k; int CR = Package.parseAAResidues(yion, 'R'); int CK = Package.parseAAResidues(yion, 'K'); int CH = Package.parseAAResidues(yion, 'H'); int CL = len - k; int pepBond = k; int NBasicAA = NR + NK + NH; int CBasicAA = CR + CK + CH; string AA = NR + "," + NK + "," + NH + "," + NL + "," + CR + "," + CK + "," + CH + "," + CL; double[] bCharge = new double[z + 1]; double[] yCharge = new double[z + 1]; //double[] bIntensity = new double[z + 1]; //double[] yIntensity = new double[z + 1]; //add variable for "real" charges if (model == 0) //naive model { int[] bFragmentCharge = new int[z + 1]; int[] yFragmentCharge = new int[z + 1]; //return the b ion charge 1 Intensity, if matched for (int i = 1; i < z; i++) { bCharge[i] = fragmentation.b(k, i); yCharge[i] = fragmentation.y(len - k, i); //change for ORBI-ORBI purposes. Peak bmatched = Package.findClose(peakList, bCharge[i], bCharge[i] * 30 * Math.Pow(10, -6)); Peak ymatched = Package.findClose(peakList, yCharge[i], yCharge[i] * 30 * Math.Pow(10, -6)); if (bmatched != null) { //bIntensity[i] = bmatched.rankOrIntensity; int fragmentCharge = bmatched.fragmentCharge; if (fragmentCharge == i) bFragmentCharge[i] = 3; else bFragmentCharge[i] = 2; //intensityList.Add(bmatched.rankOrIntensity); //completeIntensityList.Add(bmatched.rankOrIntensity); } else bFragmentCharge[i] = 1; //else bIntensity[i] = 0; if (ymatched != null) { //yIntensity[i] = ymatched.rankOrIntensity; //yFragmentCharge[i] = ymatched.fragmentCharge; int fragmentCharge = ymatched.fragmentCharge; if (fragmentCharge == i) yFragmentCharge[i] = 3; else yFragmentCharge[i] = 2; //intensityList.Add(ymatched.rankOrIntensity); //completeIntensityList.Add(ymatched.rankOrIntensity); } else yFragmentCharge[i] = 1; //else yIntensity[i] = 0; } string finalString = idOrIndex + "," + pepSequence + "," + pepBond + "," + bFragmentCharge[1] + "," + bFragmentCharge[2] + "," + yFragmentCharge[1] + "," + yFragmentCharge[2]; file.WriteLine(finalString); } else if (model == 1) //my binary logistic regression basophile model { int b1=0, b2=0, y1=0, y2 = 0; double y1_logit = 0.1098112 * NR + 0.2085831 * NK + 0.1512109 * NH + 0.0460839 * NL - 0.3872417 * CR - 0.3684911 * CK - 0.1634741 * CH - 0.1693931 * CL + 1.2632997; double y2_logit =-0.6345364 * NR - 0.3365917 * NK - 0.4577882 * NH - 0.1492703 * NL + 0.7738133 * CR + 0.6036758 * CK + 0.5942542 * CH + 0.0701467 * CL + 0.0806280; double b1_logit = 0.0801432 * NR - 0.1088081 * NK - 0.1338220 * NH - 0.1413059 * NL - 0.3157957 * CR - 0.2708274 * CK - 0.3703136 * CH + 0.0157418 * CL + 1.2124699; double b2_logit = 0.8606449 * NR + 0.2763119 * NK + 0.4969152 * NH + 0.0685712 * NL - 1.3346995 * CR - 1.0977316 * CK - 1.0973677 * CH - 0.2028884 * CL + 1.9355980; if (b1_logit > -0.5) { double mz_b1 = fragmentation.b(k, 1); Peak matched = Package.findClose(peakList, mz_b1, mz_b1 * 30 * Math.Pow(10, -6)); if (matched != null) { if (matched.fragmentCharge == 1) b1 = 3; else b1 = 2; } else b1 = 1; } else b1 = 0; if (b2_logit > 0) { double mz_b2 = fragmentation.b(k, 2); Peak matched = Package.findClose(peakList, mz_b2, mz_b2 * 30 * Math.Pow(10, -6)); if (matched != null) { if (matched.fragmentCharge == 2) b2 = 3; else b2 = 2; } else b2 = 1; } else b2 = 0; if (y1_logit > -0.5) { double mz_y1 = fragmentation.y(len - k, 1); Peak matched = Package.findClose(peakList, mz_y1, mz_y1 * 30 * Math.Pow(10, -6)); if (matched != null) { if (matched.fragmentCharge == 1) y1 = 3; else y1 = 2; } else y1 = 1; } else y1 = 0; if (y2_logit > -0.5) { double mz_y2 = fragmentation.y(len - k, 2); Peak matched = Package.findClose(peakList, mz_y2, mz_y2 * 30 * Math.Pow(10, -6)); if (matched != null) { if (matched.fragmentCharge == 2) y2 = 3; else y2 = 2; } else y2 = 1; } else y2 = 0; string finalString = idOrIndex + "," + pepSequence + "," + pepBond + "," + b1 + "," + b2 + "," + y1 + "," + y2; file.WriteLine(finalString); } else if (model == 2) //Surendra's ordinal model { int b1 = 0, b2 = 0, y1 = 0, y2 = 0; double logit = NR * 0.9862 + NH * 0.8772 + NK * 0.7064 + NL * 0.4133 - CR * 1.1688 - CH * 0.3948 - CK * 0.6710 - CL * 0.4859; //charge Label = "1", generate b+,y++ if (logit < -2.2502) { double mz_b1 = fragmentation.b(k, 1); Peak b1matched = Package.findClose(peakList, mz_b1, mz_b1 * 30 * Math.Pow(10, -6)); if (b1matched != null) { if (b1matched.fragmentCharge == 1) b1 = 3; //matched, charge agree else b1 = 2; //matched, charge does not agree } else b1 = 1; //unmatched, but predicted. double mz_y2 = fragmentation.y(len - k, 2); Peak y2matched = Package.findClose(peakList, mz_y2, mz_y2 * 30 * Math.Pow(10, -6)); if (y2matched != null) { if (y2matched.fragmentCharge == 2) y2 = 3; //matched, charge agree else y2 = 2; //matched, charge does not agree } else y2 = 1; //unmatched, but predicted. } //ambiLabel = "2", generate b+, y+, b++, y++ else if (logit < 0.7872) { double mz_b1 = fragmentation.b(k, 1); Peak b1matched = Package.findClose(peakList, mz_b1, mz_b1 * 30 * Math.Pow(10, -6)); if (b1matched != null) { if (b1matched.fragmentCharge == 1) b1 = 3; //matched, charge agree else b1 = 2; //matched, charge does not agree } else b1 = 1; //unmatched, but predicted. double mz_y1 = fragmentation.y(len - k, 1); Peak y1matched = Package.findClose(peakList, mz_y1, mz_y1 * 30 * Math.Pow(10, -6)); if (y1matched != null) { if (y1matched.fragmentCharge == 1) y1 = 3; //matched, charge agree else y1 = 2; //matched, charge does not agree } else y1 = 1; //unmatched, but predicted. double mz_b2 = fragmentation.b(k, 2); Peak b2matched = Package.findClose(peakList, mz_b2, mz_b2 * 30 * Math.Pow(10, -6)); if (b2matched != null) { if (b2matched.fragmentCharge == 2) b2 = 3; //matched, charge agree else b2 = 2; //matched, charge does not agree } else b2 = 1; //unmatched, but predicted. double mz_y2 = fragmentation.y(len - k, 2); Peak y2matched = Package.findClose(peakList, mz_y2, mz_y2 * 30 * Math.Pow(10, -6)); if (y2matched != null) { if (y2matched.fragmentCharge == 2) y2 = 3; //matched, charge agree else y2 = 2; //matched, charge does not agree } else y2 = 1; //unmatched, but predicted. } //ambiLabel = "3", generate b++,y+ else { double mz_b2 = fragmentation.b(k, 2); Peak b2matched = Package.findClose(peakList, mz_b2, mz_b2 * 30 * Math.Pow(10, -6)); if (b2matched != null) { if (b2matched.fragmentCharge == 2) b2 = 3; //matched, charge agree else b2 = 2; //matched, charge does not agree } else b2 = 1; //unmatched, but predicted. double mz_y1 = fragmentation.y(len - k, 1); Peak y1matched = Package.findClose(peakList, mz_y1, mz_y1 * 30 * Math.Pow(10, -6)); if (y1matched != null) { if (y1matched.fragmentCharge == 1) y1 = 3; //matched, charge agree else y1 = 2; //matched, charge does not agree } else y1 = 1; //unmatched, but predicted. } string finalString = idOrIndex + "," + pepSequence + "," + pepBond + "," + b1 + "," + b2 + "," + y1 + "," + y2; file.WriteLine(finalString); } //intensityDic.Add(pepBond, intensityList); //rowDic.Add(pepBond, finalString); }//end for each peptide bond }//end if z==3 }//end foreach peptide }//end using }
public MSDataScan(int spectrumNumber, int msnOrder = 1, MSDataFile parentFile = null) { SpectrumNumber = spectrumNumber; MsnOrder = msnOrder; ParentFile = parentFile; }
///<summary> ///original code for grabbing the required ions ///get pepSequence,source,scanID, write into a csv file. ///have tons of information: theretical ion intensity, pep info, chargeLabel... ///</summary> public static List<string> idpReader_original(string idpXMLFile, string mzMLFile, double TicCutoffPercentage, int z, List<string> pepList, List<string> output) { //get the path and filename of output csv file: string fileName = Path.GetFileNameWithoutExtension(idpXMLFile); string filePath = Path.GetDirectoryName(idpXMLFile); IDPicker.Workspace workspace = new IDPicker.Workspace(); Package.loadWorkspace(ref workspace, idpXMLFile); MSDataFile foo = new MSDataFile(mzMLFile); SpectrumList sl = foo.run.spectrumList; foreach (IDPicker.SourceGroupList.MapPair groupItr in workspace.groups) foreach (IDPicker.SourceInfo source in groupItr.Value.getSources(true)) foreach (IDPicker.SpectrumList.MapPair sItr in source.spectra) { IDPicker.ResultInstance ri = sItr.Value.results[1]; IDPicker.VariantInfo vi = ri.info.peptides.Min; string ss = vi.ToString() + "," + sItr.Value.id.source.name + "," + sItr.Value.nativeID; bool boolCharge = sItr.Value.id.charge.Equals(z); if (boolCharge) { string rawPepSequence = vi.ToString(); string pepSequence = vi.peptide.sequence; int len = pepSequence.Length; //make sure that the peptide is what we want if (pepList.Contains(pepSequence)) { // Look up the index with nativeID object idOrIndex = null; if (sItr.Value.nativeID != null && sItr.Value.nativeID.Length > 0) idOrIndex = sItr.Value.nativeID; int spectrumIndex = sl.find(idOrIndex as string); // Trust the local index, if the nativeID lookup fails if (spectrumIndex >= sl.size()) spectrumIndex = sItr.Value.id.index; // Bail of the loca index is larger than the spectrum list size if (spectrumIndex >= sl.size()) throw new Exception("Can't find spectrum associated with the index."); //Console.WriteLine(idOrIndex.ToString()); //get base peak and TIC and converted to string Spectrum spec1 = sl.spectrum(spectrumIndex, true); MZIntensityPairList peaks = new MZIntensityPairList(); spec1.getMZIntensityPairs(ref peaks); Set<Peak> peakList = new Set<Peak>(); //get base peak and TIC double basePeakValue = 0; double TICValue = 0; CVParamList list = spec1.cvParams; foreach (CVParam CVP in list) { if (CVP.name == "base peak intensity") { basePeakValue = CVP.value; } if (CVP.name == "total ion current") { TICValue = CVP.value; } } string basePeak = basePeakValue.ToString(); string TIC = TICValue.ToString(); //very important. Surendra put them here //to change those with modifications {} into a format //that fragment method will accept. string interpretation = vi.ToSimpleString(); Peptide peptide = new Peptide(interpretation, ModificationParsing.ModificationParsing_Auto, ModificationDelimiter.ModificationDelimiter_Brackets); Fragmentation fragmentation = peptide.fragmentation(true, true); //prepare the qualified peaklist double intenThreshhold = 0; int totalIntenClass = 0; double[] intenArray = new double[peaks.Count]; //used during the foreach loop int indexPeaks = 0; //get all the peaks no matter how small they are //then calculate the threshhold TIC //test here foreach (MZIntensityPair mzIntensity in peaks) { //Peak p = new Peak(mzIntensity.mz, mzIntensity.intensity); //peakList.Add(p); intenArray[indexPeaks] = mzIntensity.intensity; indexPeaks++; } Array.Sort(intenArray); Array.Reverse(intenArray, 0, peaks.Count); //if currTIC>=cutoff, then break double currTIC = 0; double cutOffTIC = TicCutoffPercentage * TICValue; foreach (double inten in intenArray) { currTIC = currTIC + inten; if (currTIC < cutOffTIC) { intenThreshhold = inten; totalIntenClass++; } else break; } //then based on that, generate a new peaklist that contains only ABC peaks //then calculate the intensity classes foreach (MZIntensityPair mzIntensity in peaks) { if (mzIntensity.intensity >= intenThreshhold) { Peak p = new Peak(mzIntensity.mz, mzIntensity.intensity); peakList.Add(p); } } //rowDic contains row information of each peptide bond Dictionary<int, string> rowDic = new Dictionary<int, string>(); //intensityDic contains intensity information of fragment ions for each peptide bond Dictionary<int, List<double>> intensityDic = new Dictionary<int, List<double>>(); //commonList contains the common intensities List<double> duplicateList = new List<double>(); //call the method List<double> completeIntensityList = new List<double>(); for (int k = 1; k < len; k++) { List<double> intensityList = new List<double>(); string bion = pepSequence.Substring(0, k); string yion = pepSequence.Substring(k, len - k); int NR = Package.parseAAResidues(bion, 'R'); int NK = Package.parseAAResidues(bion, 'K'); int NH = Package.parseAAResidues(bion, 'H'); int NL = k; int CR = Package.parseAAResidues(yion, 'R'); int CK = Package.parseAAResidues(yion, 'K'); int CH = Package.parseAAResidues(yion, 'H'); int CL = len - k; int R = NR - CR; int K = NK - CK; int H = NH - CH; int L = NL - CL; int pepBond = k; int NBasicAA = NR + NK + NH; int CBasicAA = CR + CK + CH; string AA = NBasicAA + "," + CBasicAA + "," + NR + "," + NK + "," + NH + "," + NL + "," + CR + "," + CK + "," + CH + "," + CL + "," + R + "," + K + "," + H + "," + L; double[] bCharge = new double[z + 1]; double[] yCharge = new double[z + 1]; double[] bIntensity = new double[z + 1]; double[] yIntensity = new double[z + 1]; string bIonIntensity = ""; string yIonIntensity = ""; //to judge if the sum of intensities are 0 //so to exclude the case with all "0s" double sumIntensity = 0; //return the b ion charge 1 Intensity, if matched for (int i = 1; i <= z; i++) { bCharge[i] = fragmentation.b(k, i); yCharge[i] = fragmentation.y(len - k, i); //change for Q-star purposes. Peak bmatched = Package.findClose(peakList, bCharge[i], 70 * bCharge[i] * Math.Pow(10, -6)); Peak ymatched = Package.findClose(peakList, yCharge[i], 70 * yCharge[i] * Math.Pow(10, -6)); if (bmatched != null) { bIntensity[i] = bmatched.rankOrIntensity; intensityList.Add(bmatched.rankOrIntensity); completeIntensityList.Add(bmatched.rankOrIntensity); } else bIntensity[i] = 0; if (ymatched != null) { yIntensity[i] = ymatched.rankOrIntensity; intensityList.Add(ymatched.rankOrIntensity); completeIntensityList.Add(ymatched.rankOrIntensity); } else yIntensity[i] = 0; sumIntensity = sumIntensity + bIntensity[i] + yIntensity[i]; //record b/y ion intensity information into a string bIonIntensity = bIonIntensity + "," + bIntensity[i]; yIonIntensity = yIonIntensity + "," + yIntensity[i]; } intensityDic.Add(pepBond, intensityList); //to determine charge label, need to split by precursor charge //first need to make a metric to determine if all intensities are "0" if (z == 3) { if (sumIntensity != 0) { //////////////////////////////////////////////// //set the ambiguity label as follows: //-3: (0/+3) y3 only //-2: (0/+3, +1/+2) y3, b1y2 //-1: (+1/+2): b1y2 //0: (+1/+2, +2/+1): b1y2, b2y1 //1: (+2/+1): b2y1 //2: (+2/+1, +3/0): b2y1, b3 //3: (+3/0): b3 only //////////////////////////////////////////////// double b1 = bIntensity[1]; double b2 = bIntensity[2]; double y1 = yIntensity[1]; double y2 = yIntensity[2]; double b3 = bIntensity[3]; double y3 = yIntensity[3]; double b1y2 = b1 + y2; double b2y1 = b2 + y1; string ambiguityLabel = ""; //first part: set the intensity group: y3, b1y2, b2y1, b3 //if one group was found, set the label //if two were found, but adjacent to each other, then ambiguity label is set if (y3 != 0 && (b1y2 + b2y1 + b3) == 0) ambiguityLabel = "-3"; else if (y3 != 0 && b1y2 != 0 && (b2y1 + b3) == 0) ambiguityLabel = "-2"; else if (b1y2 != 0 && (y3 + b2y1 + b3) == 0) ambiguityLabel = "-1"; else if (b1y2 != 0 && b2y1 != 0 && (y3 + b3) == 0) ambiguityLabel = "0"; else if (b2y1 != 0 && (y3 + b1y2 + b3) == 0) ambiguityLabel = "1"; else if (b2y1 != 0 && b3 != 0 && (y3 + b1y2) == 0) ambiguityLabel = "2"; else if (b3 != 0 && (y3 + b1y2 + b2y1) == 0) ambiguityLabel = "3"; else ambiguityLabel = "error"; string finalString = idOrIndex + "," + pepSequence + "," + basePeak + "," + TIC + bIonIntensity + yIonIntensity + "," + len + "," + pepBond + "," + AA + "," + ambiguityLabel; rowDic.Add(pepBond, finalString); } } }//end for each peptide bond //now we have: rowDic, intensityDic for each pep bond //and we have: and completeIntensityList for each peptide //the purpose of this is to remove such rows with duplicate matches duplicateList = Package.findCommon(completeIntensityList); foreach (int bond in rowDic.Keys) { bool unique = true; foreach (double inten in duplicateList) { if (intensityDic[bond].Contains(inten)) { unique = false; Console.WriteLine("kick"); break; } } if (unique) { output.Add(rowDic[bond]); } } }//end of if peplist contains pepsequence }//end if z==3 }//end foreach peptide return output; }
void processFile(string filename, Config config, ReaderList readers, Map <string, int> usedOutputFilenames) { // read in data file using (var msdList = new MSDataList()) { string msg = String.Format("Opening file \"{0}\" for read...", filename); var stripCredentialsMatch = Regex.Match(filename, "https?://([^:]+:[^@]+@).*", RegexOptions.CultureInvariant | RegexOptions.IgnoreCase); if (stripCredentialsMatch.Success) { msg = msg.Replace(stripCredentialsMatch.Groups[1].Value, ""); } LogUpdate?.Invoke(msg, _info); StatusUpdate?.Invoke(msg, ProgressBarStyle.Marquee, _info); readers.read(filename, msdList, config.ReaderConfig); foreach (var msd in msdList) { try { var outputFilename = config.outputFilename(filename, msd); string deduplicatedFilename = outputFilename; StatusUpdate?.Invoke("Waiting...", ProgressBarStyle.Marquee, _info); // only one thread lock (_calculateSHA1Mutex) { // if output name is same as input name, add a suffix if (filename == outputFilename) { ++usedOutputFilenames[outputFilename]; } if (usedOutputFilenames.Contains(deduplicatedFilename)) { deduplicatedFilename = deduplicatedFilename.Replace(Path.GetExtension(outputFilename), String.Format(" ({0}).{1}", usedOutputFilenames[outputFilename] + 1, Path.GetExtension(outputFilename))); } ++usedOutputFilenames[outputFilename]; LogUpdate?.Invoke("Calculating SHA1 checksum...", _info); StatusUpdate?.Invoke("Calculating SHA1 checksum...", ProgressBarStyle.Marquee, _info); MSDataFile.calculateSHA1Checksums(msd); } var ilr = new IterationListenerRegistry(); ilr.addListenerWithTimer(this, 1); LogUpdate?.Invoke("Processing...", _info); StatusUpdate?.Invoke("Processing...", ProgressBarStyle.Marquee, _info); SpectrumListFactory.wrap(msd, config.Filters, ilr); config.WriteConfig.useWorkerThreads = msd.run.spectrumList.benefitsFromWorkerThreads(); if ((msd.run.spectrumList == null) || msd.run.spectrumList.empty()) { if ((msd.run.chromatogramList != null) && !msd.run.chromatogramList.empty()) { msg = "Note: input contains only chromatogram data."; switch (config.WriteConfig.format) { case MSDataFile.Format.Format_MZ5: case MSDataFile.Format.Format_mzML: break; default: msg += " The selected output format can only represent spectra. Consider using mzML instead."; break; } } else { msg = "Note: input contains no spectra or chromatogram data."; } LogUpdate?.Invoke(msg, _info); StatusUpdate?.Invoke(msg, ProgressBarStyle.Continuous, _info); } if (StatusUpdate != null && msd.run.spectrumList != null) { StatusUpdate(String.Format("Processing ({0} of {1})", DataGridViewProgressCell.MessageSpecialValue.CurrentValue, DataGridViewProgressCell.MessageSpecialValue.Maximum), ProgressBarStyle.Continuous, _info); } // write out the new data file msg = String.Format("Writing \"{0}\"...", deduplicatedFilename); LogUpdate?.Invoke(msg, _info); StatusUpdate?.Invoke(msg, ProgressBarStyle.Continuous, _info); MSDataFile.write(msd, deduplicatedFilename, config.WriteConfig, ilr); ilr.removeListener(this); } finally { msd.Dispose(); } } } }
public MsnDataScan(int spectrumNumber, int msnOrder, MSDataFile parentFile = null) : base(spectrumNumber, msnOrder, parentFile) { }
public void SetRawFile(MSDataFile dataFile) { MsnDataScan scan = dataFile[ScanNumber] as MsnDataScan; IsolationMZ = scan.IsolationRange.Mean; Spectrum = dataFile.GetReadOnlyMZSpectrum(ScanNumber, true); ScanWidth = scan.MzRange.Width; }
public static void RawFileToCsv <T>(MSDataFile <T> msDataFile, string outputFilePath) where T : ISpectrum { // See the BasicCsvWriting example for more details Console.WriteLine("Writing file to: " + outputFilePath); // The main field delimiter, for CSV it is a comma const char delimiter = ','; using (StreamWriter writer = new StreamWriter(outputFilePath)) { // Now that the stream is open, we can a line of text to it to serve as the header row. // CSV formats are just text files with fields separated by commas. writer.WriteLine("Spectrum Number,MS Level,Precursor m/z,# of Peaks in Spectrum,m/z Range"); // The using statement on the msDataFile will ensure that things are properly disposed of after // you are done using the file, or if an exception has occurred. using (msDataFile) { // MsDataFiles require opening their data connection manually. msDataFile.Open(); // Simply loop over every data scan in the file foreach (MSDataScan <T> scan in msDataFile) { StringBuilder sb = new StringBuilder(); sb.Append(scan.SpectrumNumber); sb.Append(delimiter); sb.Append(scan.MsnOrder); sb.Append(delimiter); // We need to check if this is an MS1 or MS2 scan. Both scans are of type MSDataScan, // but for MS2 scans, there is additional information (precursor m/z for example). So we need // to cast it to MsnDataScan to access those properties. // Try casting using the 'as' keyword. It will either return the cast object or null, so we need to // check for null before trying to access a property of it. MsnDataScan <T> msnScan = scan as MsnDataScan <T>; if (msnScan != null) { // It is a MS2 scan sb.Append(msnScan.GetPrecursorMz()); } else { // It is a MS1 scan, so no precursor information. So lets put Not an Number in this column. // you could skip this if you want to have blank cells. sb.Append(double.NaN); } sb.Append(delimiter); // We can just use the original scan object now sb.Append(scan.MassSpectrum.Count); sb.Append(delimiter); sb.Append(scan.MzRange); writer.WriteLine(sb.ToString()); } } } }
public void UpdatePsmInformation(MSDataFile dataFile, bool is2dFDR = true, bool useMedian = true, double evalueThreshold = 1e-3) { List<double> errors = new List<double>(); MaximumPrecursorMassError = 0; int count = 0; int msms = 0; int ms = 0; int localMSMS = -1; List<int> msmsBetweenMS = new List<int>(); List<double> injectionTimes = new List<double>(); for(int sn = dataFile.FirstSpectrumNumber; sn < dataFile.LastSpectrumNumber; sn++) { int order = dataFile.GetMsnOrder(sn); if (order == 1) { ms++; if(localMSMS >= 0) msmsBetweenMS.Add(localMSMS); localMSMS = 0; } else { localMSMS++; msms++; injectionTimes.Add(dataFile.GetInjectionTime(sn)); } } MaxMSMSScansBetweenMS = msmsBetweenMS.Max(); AverageMSMSSCansBetweenMS = msmsBetweenMS.Average(); TotalMSMSscans = msms; TotalMSscans = ms; AverageMSMSInjectionTime = injectionTimes.Average(); MaxMSMSInjectionTime = injectionTimes.Max(); foreach (KeyValuePair<int, SortedMaxSizedContainer<PSM>> kvp in _data) { int scanNumber = kvp.Key; SortedMaxSizedContainer<PSM> psms = kvp.Value; double isolationMZ = dataFile.GetPrecusorMz(scanNumber); foreach (PSM psm in psms) { psm.IsolationMz = isolationMZ; double isolationMass = Mass.MassFromMz(isolationMZ, psm.Charge); double theoreticalMass = psm.MonoisotopicMass; int nominalMassOffset; double adjustedIsolationMass; Tolerance tolerancePPM = Tolerance.CalculatePrecursorMassError(theoreticalMass, isolationMass, out nominalMassOffset, out adjustedIsolationMass); psm.AdjustedIsolationMass = adjustedIsolationMass; psm.IsotopeSelected = nominalMassOffset; if(!HasPPMInfo) psm.PrecursorMassError = tolerancePPM.Value; double positive = Math.Abs(psm.PrecursorMassError); if (positive > MaximumPrecursorMassError) { MaximumPrecursorMassError = positive; } if (psm.FdrScoreMetric <= evalueThreshold) { errors.Add(psm.PrecursorMassError); } count++; } } SystematicPrecursorMassError = useMedian ? GetMedianValue(errors) : errors.Average(); // Adjust all psms to foreach (PSM psm in PeptideSpectralMatches) { psm.CorrectedPrecursorMassError = psm.PrecursorMassError - SystematicPrecursorMassError; } }
public bool SetInputFile( string filepath ) { MSDataFile tempInterface; try { OnStatusReport( "Loading metadata from source file..." ); OnProgressReport( 0 ); tempInterface = new MSDataFile(filepath); pwiz.CLI.msdata.ChromatogramList cl = tempInterface.run.chromatogramList; pwiz.CLI.msdata.SpectrumList sl = tempInterface.run.spectrumList; int ticIndex = cl.findNative("TIC"); if( ticIndex < cl.size() ) { pwiz.CLI.msdata.Chromatogram tic = cl.chromatogram(ticIndex, true); chromatograms.Add( new Chromatogram( this, tic ) ); } CVParam spectrumType = tempInterface.fileDescription.fileContent.cvParamChild( CVID.MS_spectrum_type ); if( spectrumType.cvid == CVID.CVID_Unknown && !sl.empty() ) spectrumType = sl.spectrum(0).cvParamChild( CVID.MS_spectrum_type ); if( spectrumType.cvid == CVID.MS_SRM_spectrum ) { if( cl.empty() ) throw new Exception( "Error loading metadata: SRM file contains no chromatograms" ); // load the rest of the chromatograms for( int i = 0; i < cl.size(); ++i ) { if( i == ticIndex ) continue; pwiz.CLI.msdata.Chromatogram c = cl.chromatogram( i ); OnStatusReport( String.Format( "Loading chromatograms from source file ({0} of {1})...", ( i + 1 ), cl.size() ) ); OnProgressReport( ( i + 1 ) * 100 / cl.size() ); chromatograms.Add( new Chromatogram( this, c ) ); } } else if( spectrumType.cvid == CVID.MS_MS1_spectrum || spectrumType.cvid == CVID.MS_MSn_spectrum ) { // get all scans by sequential access for( int i = 0; i < sl.size(); ++i ) { pwiz.CLI.msdata.Spectrum s = sl.spectrum( i ); if( ( ( i + 1 ) % 100 ) == 0 || ( i + 1 ) == sl.size() ) { OnStatusReport( String.Format( "Loading spectra from source file ({0} of {1})...", ( i + 1 ), sl.size() ) ); OnProgressReport( ( i + 1 ) * 100 / sl.size() ); } spectra.Add( new MassSpectrum( this, s ) ); } } else throw new Exception( "Error loading metadata: unable to open files with spectrum type \"" + spectrumType.name + "\"" ); OnStatusReport( "Finished loading source metadata." ); OnProgressReport( 100 ); } catch( Exception ex ) { string message = "SeeMS encountered an error reading metadata from \"" + filepath + "\" (" + ex.Message + ")"; if( ex.InnerException != null ) message += "\n\nAdditional information: " + ex.InnerException.Message; MessageBox.Show( message, "Error reading source metadata", MessageBoxButtons.OK, MessageBoxIcon.Error, MessageBoxDefaultButton.Button1, 0, false ); OnStatusReport( "Failed to read source metadata." ); return false; } return true; }
/// <summary> /// write out a subset of high quality spectra based on ScanRanker metrics file /// using ProteoWizard library /// </summary> public void Write() { foreach (FileInfo file in inFileList) { string fileBaseName = Path.GetFileNameWithoutExtension(file.FullName); string metricsFileName = fileBaseName + metricsFileSuffix + ".txt"; string outFileName = fileBaseName + outFileSuffix + "." + outFormat; Workspace.SetText("\r\nStart writing high quality spectra for file: " + file.Name + " ...\r\n\r\n"); if (File.Exists(outFileName)) { File.Delete(outFileName); } if (!File.Exists(metricsFileName)) { Workspace.SetText("\r\nError: Cannot find quality metrics file: " + metricsFileName + " in output directory!"); Workspace.ChangeButtonTo("Close"); return; } //List<int> allIndices = new List<int>(); //List<int> highQualIndices = new List<int>(); List<string> allIndices = new List<string>(); List<string> highQualIndices = new List<string>(); // read metrics file, split and get high quality spectra indecies from the second column try { Workspace.SetText("\r\nExtracting scan index from metrics file: " + metricsFileName); using (TextReader tr = File.OpenText(metricsFileName)) { tr.ReadLine(); // read the header line but do nothing, first three lines are header tr.ReadLine(); // read the header line but do nothing tr.ReadLine(); // read the header line but do nothing string line = string.Empty; while ((line = tr.ReadLine()) != null) { string[] items = line.Split('\t'); //int index = Convert.ToInt32(items[1]); //index string index = Convert.ToString(items[1]); //nativeID if (!allIndices.Exists(element => element == index)) // remove duplicate index { allIndices.Add(index); } } } } catch (Exception exc) { //throw new Exception("Error in reading metrics file for spectra removal\r\n",exc); Workspace.SetText("\r\nError in reading metrics file for spectra removal\r\n"); Workspace.ChangeButtonTo("Close"); throw new Exception(exc.Message); } // get indices for high quality spectra Workspace.SetText("\r\nGenerating indices of high quality spectra"); int numOutputSpectra = Convert.ToInt32(allIndices.Count * cutoff); highQualIndices = allIndices.GetRange(0, numOutputSpectra); //highQualIndices.Sort(); //var predicate = new SpectrumList_FilterPredicate_IndexSet(); //foreach (int i in highQualIndices) //{ // predicate.indexSet.Add(i); //} var predicate = new SpectrumList_FilterPredicate_NativeIDSet(); foreach (string i in highQualIndices) { predicate.nativeIDSet.Add(i); } //var sorterPredicate = new SpectrumList_SorterPredicate_IndexSet(); //foreach (int i in highQualIndices) //{ // sorterPredicate.indexSet.Add(i); //} //MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig(MSDataFile.Format.Format_mzXML); MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig(); if (outFormat.Equals("mzXML") || outFormat.Equals("mzxml")) { writeConfig.format = MSDataFile.Format.Format_mzXML; } else if (outFormat.Equals("mzML") || outFormat.Equals("mzml")) { writeConfig.format = MSDataFile.Format.Format_mzML; } else if (outFormat.Equals("MGF") || outFormat.Equals("mgf")) { writeConfig.format = MSDataFile.Format.Format_MGF; } else if (outFormat.Equals("MS2") || outFormat.Equals("ms2")) { writeConfig.format = MSDataFile.Format.Format_MS2; } else { MessageBox.Show("Plese select output format"); } writeConfig.precision = MSDataFile.Precision.Precision_32; try { Workspace.SetText("\r\nWriting high quality spectra to file: " + outFileName); using (var msFile = new MSDataFile(file.FullName)) { var indexSet = new string[highQualIndices.Count]; var sl = msFile.run.spectrumList; for (int i=0; i < highQualIndices.Count; ++i) { string id = highQualIndices[i]; int index = sl.find(id); if (index == sl.size()) throw new Exception("nativeID \"" + id + "\" not found in file"); indexSet[i] = index.ToString(); } var indexSetString = String.Join(" ", indexSet); var predicate2 = new SpectrumList_FilterPredicate_IndexSet(indexSetString); var filter = new SpectrumList_Filter(msFile.run.spectrumList, predicate2); msFile.run.spectrumList = filter; //msFile.run.spectrumList = new SpectrumList_Sorter(msFile.run.spectrumList, new SpectrumList_Sorter_LessThan( sorterPredicate.lessThan )); //msFile.run.spectrumList = new SpectrumList_Sorter(msFile.run.spectrumList, new SpectrumList_Sorter_LessThan(lessThan)); //Workspace.SetText("\r\nFinished msFile.run.spectrumList"); msFile.write(outFileName, writeConfig); } } catch (Exception exc) { //throw new Exception("Error in writiing new spectra file", exc); Workspace.SetText("\r\nError in writing new spectra file\r\n"); Workspace.ChangeButtonTo("Close"); throw new Exception(exc.Message); } Workspace.SetText("\r\nFinished writing high quality spectra for file: " + file.Name + " \r\n\r\n"); }// end of foreach file Workspace.SetText("\r\nFinished writing high quality spectra!"); Workspace.ChangeButtonTo("Close"); } // end of write()
static void openButton_Click(object sender, EventArgs e) { string filepath = _fileTextBox.Text; if (!File.Exists(filepath)) { MessageBox.Show("That filepath does not exist.", "404 File not found", MessageBoxButtons.OK, MessageBoxIcon.Error); return; } try { var msd = new MSDataFile(filepath); var sl = msd.run.spectrumList; MessageBox.Show(String.Format("The file has {0} spectra.", sl.size()), "Spectra Count"); } catch (Exception ex) { string message = ex.ToString(); if (ex.InnerException != null) message += "\n\nAdditional information: " + ex.InnerException.ToString(); MessageBox.Show(message, "Error opening file", MessageBoxButtons.OK, MessageBoxIcon.Error, MessageBoxDefaultButton.Button1, 0, false); } }
public void AddMSDataFile(MSDataFile<ISpectrum> dataFile) { _dataFiles.Add(dataFile.Name, dataFile); }
public void AddMSDataFile(MSDataFile dataFile) { _dataFiles.Add(dataFile.Name, dataFile); }
void processFile(string filename, Config config, ReaderList readers) { // read in data file using (var msdList = new MSDataList()) { string msg = String.Format("Opening file \"{0}\" for read...", filename); if (LogUpdate != null) { LogUpdate(msg, _info); } if (StatusUpdate != null) { StatusUpdate(msg, ProgressBarStyle.Marquee, _info); } readers.read(filename, msdList); foreach (var msd in msdList) { var outputFilename = config.outputFilename(filename, msd); if (filename == outputFilename) { throw new ArgumentException("Output filepath is the same as input filepath"); } if (StatusUpdate != null) { StatusUpdate("Waiting...", ProgressBarStyle.Marquee, _info); } // only one thread lock (calculateSHA1Mutex) { if (LogUpdate != null) { LogUpdate("Calculating SHA1 checksum...", _info); } if (StatusUpdate != null) { StatusUpdate("Calculating SHA1 checksum...", ProgressBarStyle.Marquee, _info); } MSDataFile.calculateSHA1Checksums(msd); } if (LogUpdate != null) { LogUpdate("Processing...", _info); } if (StatusUpdate != null) { StatusUpdate("Processing...", ProgressBarStyle.Marquee, _info); } SpectrumListFactory.wrap(msd, config.Filters); if ((msd.run.spectrumList == null) || msd.run.spectrumList.empty()) { if ((msd.run.chromatogramList != null) && !msd.run.chromatogramList.empty()) { msg = "Note: input contains only chromatogram data."; switch (config.WriteConfig.format) { case MSDataFile.Format.Format_MZ5: case MSDataFile.Format.Format_mzML: break; default: msg += " The selected output format can only represent spectra. Consider using mzML instead."; break; } } else { msg = "Note: input contains no spectra or chromatogram data."; } if (LogUpdate != null) { LogUpdate(msg, _info); } if (StatusUpdate != null) { StatusUpdate(msg, ProgressBarStyle.Continuous, _info); } } if (StatusUpdate != null && msd.run.spectrumList != null) { StatusUpdate(String.Format("Processing ({0} of {1})", DataGridViewProgressCell.MessageSpecialValue.CurrentValue, DataGridViewProgressCell.MessageSpecialValue.Maximum), ProgressBarStyle.Continuous, _info); } // write out the new data file var ilr = new IterationListenerRegistry(); ilr.addListener(this, 100); msg = String.Format("Writing \"{0}\"...", outputFilename); if (LogUpdate != null) { LogUpdate(msg, _info); } if (StatusUpdate != null) { StatusUpdate(msg, ProgressBarStyle.Continuous, _info); } MSDataFile.write(msd, outputFilename, config.WriteConfig, ilr); ilr.removeListener(this); } } }
private void TestPWiz(string strFilePath) { const bool RUN_BENCHMARKS = false; try { var objPWiz2 = new MSDataFile(strFilePath); Console.WriteLine("Spectrum count: " + objPWiz2.run.spectrumList.size()); Console.WriteLine(); if (objPWiz2.run.spectrumList.size() > 0) { var intSpectrumIndex = 0; do { var oSpectrum = objPWiz2.run.spectrumList.spectrum(intSpectrumIndex, getBinaryData: true); pwiz.CLI.data.CVParam param; if (oSpectrum.scanList.scans.Count > 0) { if (clsProteowizardDataParser.TryGetCVParam(oSpectrum.scanList.scans[0].cvParams, pwiz.CLI.cv.CVID.MS_scan_start_time, out param)) { var intScanNum = intSpectrumIndex + 1; var dblStartTimeMinutes = param.timeInSeconds() / 60.0; Console.WriteLine("ScanIndex " + intSpectrumIndex + ", Scan " + intScanNum + ", Elution Time " + dblStartTimeMinutes + " minutes"); } } // Use the following to determine info on this spectrum if (clsProteowizardDataParser.TryGetCVParam(oSpectrum.cvParams, pwiz.CLI.cv.CVID.MS_ms_level, out param)) { int.TryParse(param.value, out _); } // Use the following to get the MZs and Intensities var oMZs = oSpectrum.getMZArray(); oSpectrum.getIntensityArray(); if (oMZs.data.Count > 0) { Console.WriteLine(" Data count: " + oMZs.data.Count); // ReSharper disable once ConditionIsAlwaysTrueOrFalse if (RUN_BENCHMARKS) { double dblTIC1 = 0; double dblTIC2 = 0; var dtStartTime = default(DateTime); var dtEndTime = default(DateTime); double dtRunTimeSeconds1 = 0; double dtRunTimeSeconds2 = 0; const int LOOP_ITERATIONS = 2000; // Note from Matt Chambers (matt.chambers42 at gmail) // Repeatedly accessing items directly via oMZs.data() can be very slow // With 700 points and 2000 iterations, it takes anywhere from 0.6 to 1.1 seconds to run from dtStartTime to dtEndTime dtStartTime = DateTime.Now; for (var j = 1; j <= LOOP_ITERATIONS; j++) { for (var intIndex = 0; intIndex <= oMZs.data.Count - 1; intIndex++) { dblTIC1 += oMZs.data[intIndex]; } } dtEndTime = DateTime.Now; dtRunTimeSeconds1 = dtEndTime.Subtract(dtStartTime).TotalSeconds; // The preferred method is to copy the data from .data to a locally-stored mzArray var // With 700 points and 2000 iterations, it takes 0.016 seconds to run from dtStartTime to dtEndTime dtStartTime = DateTime.Now; for (var j = 1; j <= LOOP_ITERATIONS; j++) { var oMzArray = oMZs.data; for (var intIndex = 0; intIndex <= oMzArray.Count - 1; intIndex++) { dblTIC2 += oMzArray[intIndex]; } } dtEndTime = DateTime.Now; dtRunTimeSeconds2 = dtEndTime.Subtract(dtStartTime).TotalSeconds; Console.WriteLine(" " + oMZs.data.Count + " points with " + LOOP_ITERATIONS + " iterations gives Runtime1=" + dtRunTimeSeconds1.ToString("0.0##") + " sec. vs. Runtime2=" + dtRunTimeSeconds2.ToString("0.0##") + " sec."); if (Math.Abs(dblTIC1 - dblTIC2) > float.Epsilon) { Console.WriteLine(" TIC values don't agree; this is unexpected"); } } } if (intSpectrumIndex < 25) { intSpectrumIndex += 1; } else { intSpectrumIndex += 50; } } while (intSpectrumIndex < objPWiz2.run.spectrumList.size()); } if (objPWiz2.run.chromatogramList.size() > 0) { var intChromIndex = 0; do { var oTimeIntensityPairList = new TimeIntensityPairList(); // Note that even for a small .Wiff file (1.5 MB), obtaining the Chromatogram list will take some time (20 to 60 seconds) // The chromatogram at index 0 should be the TIC // The chromatogram at index >=1 will be each SRM var oChromatogram = objPWiz2.run.chromatogramList.chromatogram(intChromIndex, getBinaryData: true); // Determine the chromatogram type if (clsProteowizardDataParser.TryGetCVParam(oChromatogram.cvParams, pwiz.CLI.cv.CVID.MS_TIC_chromatogram, out var param)) { // Obtain the data oChromatogram.getTimeIntensityPairs(ref oTimeIntensityPairList); } if (clsProteowizardDataParser.TryGetCVParam(oChromatogram.cvParams, pwiz.CLI.cv.CVID.MS_selected_reaction_monitoring_chromatogram, out param)) { // Obtain the SRM scan oChromatogram.getTimeIntensityPairs(ref oTimeIntensityPairList); } intChromIndex += 1; } while (intChromIndex < 50 && intChromIndex < objPWiz2.run.chromatogramList.size()); } } catch (Exception ex) { OnErrorEvent("Error using ProteoWizard reader: " + ex.Message, ex); } }
private void writeUnidentifiedSpectra(string spectraFilename, string outFileSuffix, List <string> unidentifiedSpectra, float cutoff, string outFormat) { int numOutputSpectra = Convert.ToInt32(unidentifiedSpectra.Count * cutoff); //List<int> highQualIndices; List <string> highQualIndices; highQualIndices = unidentifiedSpectra.GetRange(0, numOutputSpectra); //var predicate = new SpectrumList_FilterPredicate_IndexSet(); //foreach (int i in highQualIndices) //{ // predicate.indexSet.Add(i); //} var predicate = new SpectrumList_FilterPredicate_NativeIDSet(); foreach (string i in highQualIndices) { predicate.nativeIDSet.Add(i); } //MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig(MSDataFile.Format.Format_mzXML); MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig(); if (outFormat.Equals("mzXML") || outFormat.Equals("mzxml")) { writeConfig.format = MSDataFile.Format.Format_mzXML; } else if (outFormat.Equals("mzML") || outFormat.Equals("mzml")) { writeConfig.format = MSDataFile.Format.Format_mzML; } else if (outFormat.Equals("MGF") || outFormat.Equals("mgf")) { writeConfig.format = MSDataFile.Format.Format_MGF; } else if (outFormat.Equals("MS2") || outFormat.Equals("ms2")) { writeConfig.format = MSDataFile.Format.Format_MS2; } else { MessageBox.Show("Plese select output format"); } writeConfig.precision = MSDataFile.Precision.Precision_32; try { string outFileName = Path.GetFileNameWithoutExtension(spectraFilename) + outFileSuffix + "-Top" + (recoveryCutoff * 100).ToString() + "PercUnidentSpec." + recoveryOutFormat; Workspace.SetText("\r\nWriting unidentified high quality spectra to file: " + outFileName); using (MSDataFile msFile = new MSDataFile(spectraFilename)) { msFile.run.spectrumList = new SpectrumList_Filter(msFile.run.spectrumList, new SpectrumList_FilterAcceptSpectrum(predicate.accept)); msFile.write(outFileName, writeConfig); } } catch (Exception exc) { //throw new Exception("Error in writiing new spectra file", exc); Workspace.SetText("\r\nError in writing new spectra file\r\n"); Workspace.ChangeButtonTo("Close"); throw new Exception(exc.Message); } }
public static void RawFileToCsv(MSDataFile msDataFile, string outputFilePath) { // See the BasicCsvWriting example for more details Console.WriteLine("Writing file to: " + outputFilePath); // The main field delimiter, for CSV it is a comma const char delimiter = ','; using (StreamWriter writer = new StreamWriter(outputFilePath)) { // Now that the stream is open, we can a line of text to it to serve as the header row. // CSV formats are just text files with fields separated by commas. writer.WriteLine("Spectrum Number,MS Level,Precursor m/z,# of Peaks in Spectrum,m/z Range"); // The using statement on the msDataFile will ensure that things are properly disposed of after // you are done using the file, or if an exception has occurred. using (msDataFile) { // MsDataFiles require opening their data connection manually. msDataFile.Open(); // Simply loop over every data scan in the file foreach (MSDataScan scan in msDataFile) { StringBuilder sb = new StringBuilder(); sb.Append(scan.SpectrumNumber); sb.Append(delimiter); sb.Append(scan.MsnOrder); sb.Append(delimiter); // We need to check if this is an MS1 or MS2 scan. Both scans are of type MSDataScan, // but for MS2 scans, there is additional information (precursor m/z for example). So we need // to cast it to MsnDataScan to access those properties. // Try casting using the 'as' keyword. It will either return the cast object or null, so we need to // check for null before trying to access a property of it. MsnDataScan msnScan = scan as MsnDataScan; if (msnScan != null) { // It is a MS2 scan sb.Append(msnScan.PrecursorMz); } else { // It is a MS1 scan, so no precursor information. So lets put Not an Number in this column. // you could skip this if you want to have blank cells. sb.Append(double.NaN); } sb.Append(delimiter); // We can just use the original scan object now sb.Append(scan.MassSpectrum.Count); sb.Append(delimiter); sb.Append(scan.MzRange); writer.WriteLine(sb.ToString()); } } } }
void processFile(string filename, Config config, ReaderList readers) { if (LogUpdate != null) { LogUpdate("Opening file...", _info); } if (StatusUpdate != null) { StatusUpdate("Opening file...", ProgressBarStyle.Marquee, _info); } // read in data file using (var msdList = new MSDataList()) { readers.read(filename, msdList); foreach (var msd in msdList) { var outputFilename = config.outputFilename(filename, msd); if (filename == outputFilename) { throw new ArgumentException("Output filepath is the same as input filepath"); } if (LogUpdate != null) { LogUpdate("Calculating SHA1 checksum...", _info); } if (StatusUpdate != null) { StatusUpdate("Calculating SHA1 checksum...", ProgressBarStyle.Marquee, _info); } // only one thread lock (calculateSHA1Mutex) MSDataFile.calculateSHA1Checksums(msd); if (LogUpdate != null) { LogUpdate("Processing...", _info); } if (StatusUpdate != null) { StatusUpdate("Processing...", ProgressBarStyle.Marquee, _info); } SpectrumListFactory.wrap(msd, config.Filters); if (StatusUpdate != null && msd.run.spectrumList != null) { StatusUpdate(String.Format("Processing ({0} of {1})", DataGridViewProgressCell.MessageSpecialValue.CurrentValue, DataGridViewProgressCell.MessageSpecialValue.Maximum), ProgressBarStyle.Continuous, _info); } // write out the new data file IterationListenerRegistry ilr = null; ilr = new IterationListenerRegistry(); ilr.addListener(this, 100); MSDataFile.write(msd, outputFilename, config.WriteConfig, ilr); } } }
public void MyTestCleanup() { dataFile.Dispose(); dataFile = null; }
/// <summary> /// write out a subset of high quality spectra based on ScanRanker metrics file /// using ProteoWizard library /// </summary> public void Write() { foreach (FileInfo file in inFileList) { string fileBaseName = Path.GetFileNameWithoutExtension(file.FullName); string metricsFileName = fileBaseName + metricsFileSuffix + ".txt"; string outFileName = fileBaseName + outFileSuffix + "." + outFormat; Workspace.SetText("\r\nStart writing high quality spectra for file: " + file.Name + " ...\r\n\r\n"); if (File.Exists(outFileName)) { File.Delete(outFileName); } if (!File.Exists(metricsFileName)) { Workspace.SetText("\r\nError: Cannot find quality metrics file: " + metricsFileName + " in output directory!"); Workspace.ChangeButtonTo("Close"); return; } //List<int> allIndices = new List<int>(); //List<int> highQualIndices = new List<int>(); List <string> allIndices = new List <string>(); List <string> highQualIndices = new List <string>(); // read metrics file, split and get high quality spectra indecies from the second column try { Workspace.SetText("\r\nExtracting scan index from metrics file: " + metricsFileName); using (TextReader tr = File.OpenText(metricsFileName)) { tr.ReadLine(); // read the header line but do nothing, first three lines are header tr.ReadLine(); // read the header line but do nothing tr.ReadLine(); // read the header line but do nothing string line = string.Empty; while ((line = tr.ReadLine()) != null) { string[] items = line.Split('\t'); //int index = Convert.ToInt32(items[1]); //index string index = Convert.ToString(items[1]); //nativeID if (!allIndices.Exists(element => element == index)) // remove duplicate index { allIndices.Add(index); } } } } catch (Exception exc) { //throw new Exception("Error in reading metrics file for spectra removal\r\n",exc); Workspace.SetText("\r\nError in reading metrics file for spectra removal\r\n"); Workspace.ChangeButtonTo("Close"); throw new Exception(exc.Message); } // get indices for high quality spectra Workspace.SetText("\r\nGenerating indices of high quality spectra"); int numOutputSpectra = Convert.ToInt32(allIndices.Count * cutoff); highQualIndices = allIndices.GetRange(0, numOutputSpectra); //highQualIndices.Sort(); //var predicate = new SpectrumList_FilterPredicate_IndexSet(); //foreach (int i in highQualIndices) //{ // predicate.indexSet.Add(i); //} var predicate = new SpectrumList_FilterPredicate_NativeIDSet(); foreach (string i in highQualIndices) { predicate.nativeIDSet.Add(i); } //var sorterPredicate = new SpectrumList_SorterPredicate_IndexSet(); //foreach (int i in highQualIndices) //{ // sorterPredicate.indexSet.Add(i); //} //MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig(MSDataFile.Format.Format_mzXML); MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig(); if (outFormat.Equals("mzXML") || outFormat.Equals("mzxml")) { writeConfig.format = MSDataFile.Format.Format_mzXML; } else if (outFormat.Equals("mzML") || outFormat.Equals("mzml")) { writeConfig.format = MSDataFile.Format.Format_mzML; } else if (outFormat.Equals("MGF") || outFormat.Equals("mgf")) { writeConfig.format = MSDataFile.Format.Format_MGF; } else if (outFormat.Equals("MS2") || outFormat.Equals("ms2")) { writeConfig.format = MSDataFile.Format.Format_MS2; } else { MessageBox.Show("Plese select output format"); } writeConfig.precision = MSDataFile.Precision.Precision_32; try { Workspace.SetText("\r\nWriting high quality spectra to file: " + outFileName); using (var msFile = new MSDataFile(file.FullName)) { var indexSet = new string[highQualIndices.Count]; var sl = msFile.run.spectrumList; for (int i = 0; i < highQualIndices.Count; ++i) { string id = highQualIndices[i]; int index = sl.find(id); if (index == sl.size()) { throw new Exception("nativeID \"" + id + "\" not found in file"); } indexSet[i] = index.ToString(); } var indexSetString = String.Join(" ", indexSet); var predicate2 = new SpectrumList_FilterPredicate_IndexSet(indexSetString); var filter = new SpectrumList_Filter(msFile.run.spectrumList, predicate2); msFile.run.spectrumList = filter; //msFile.run.spectrumList = new SpectrumList_Sorter(msFile.run.spectrumList, new SpectrumList_Sorter_LessThan( sorterPredicate.lessThan )); //msFile.run.spectrumList = new SpectrumList_Sorter(msFile.run.spectrumList, new SpectrumList_Sorter_LessThan(lessThan)); //Workspace.SetText("\r\nFinished msFile.run.spectrumList"); msFile.write(outFileName, writeConfig); } } catch (Exception exc) { //throw new Exception("Error in writiing new spectra file", exc); Workspace.SetText("\r\nError in writing new spectra file\r\n"); Workspace.ChangeButtonTo("Close"); throw new Exception(exc.Message); } Workspace.SetText("\r\nFinished writing high quality spectra for file: " + file.Name + " \r\n\r\n"); }// end of foreach file Workspace.SetText("\r\nFinished writing high quality spectra!"); Workspace.ChangeButtonTo("Close"); } // end of write()
private SourceInfo[] getSourceInfo( DirectoryInfo dirInfo, bool getDetails ) { var sourceInfoList = new List<SourceInfo>(); sourceInfoList.Add( new SourceInfo() ); sourceInfoList[0].type = getSourceType( dirInfo ); sourceInfoList[0].name = dirInfo.Name; sourceInfoList[0].dateModified = dirInfo.LastWriteTime; sourceInfoList[0].hasDetails = getDetails; if( !getDetails ) return sourceInfoList.ToArray(); if( sourceInfoList[0].type == "File Folder" ) { return sourceInfoList.ToArray(); } else if( sourceInfoList[0].type != String.Empty ) { try { MSDataFile msInfo = new MSDataFile( dirInfo.FullName ); sourceInfoList[0].populateFromMSData( msInfo ); } catch( ThreadAbortException ) { return null; } catch { sourceInfoList[0].spectra = 0; sourceInfoList[0].type = "Invalid " + sourceInfoList[0].type; } sourceInfoList[0].size = 0; sourceInfoList[0].dateModified = DateTime.MinValue; foreach( FileInfo fileInfo in dirInfo.GetFiles( "*", SearchOption.AllDirectories ) ) { sourceInfoList[0].size += (UInt64) fileInfo.Length; if( fileInfo.LastWriteTime > sourceInfoList[0].dateModified ) sourceInfoList[0].dateModified = fileInfo.LastWriteTime; } return sourceInfoList.ToArray(); } return null; }
private void listView_ItemSelectionChanged( object sender, ListViewItemSelectionChangedEventArgs e ) { if( listView.SelectedItems.Count > 1 ) { List<string> dataSourceList = new List<string>(); foreach( ListViewItem item in listView.SelectedItems ) { if( item.SubItems[1].Text != "File Folder" ) dataSourceList.Add( String.Format( "\"{0}\"", item.SubItems[0].Text ) ); } sourcePathTextBox.Text = String.Join( " ", dataSourceList.ToArray() ); ticGraphControl.GraphPane.GraphObjList.Clear(); ticGraphControl.GraphPane.CurveList.Clear(); ticGraphControl.Visible = false; } else if( listView.SelectedItems.Count > 0 ) { sourcePathTextBox.Text = listView.SelectedItems[0].SubItems[0].Text; ticGraphControl.GraphPane.GraphObjList.Clear(); ticGraphControl.GraphPane.CurveList.Clear(); string sourcePath = Path.Combine( CurrentDirectory, sourcePathTextBox.Text ); string sourceType = getSourceType( sourcePath ); if( !String.IsNullOrEmpty( sourceType ) && sourceType != "File Folder" ) { using (MSDataFile msData = new MSDataFile( sourcePath )) using (ChromatogramList cl = msData.run.chromatogramList) { if( cl != null && !cl.empty() && cl.find( "TIC" ) != cl.size() ) { ticGraphControl.Visible = true; pwiz.CLI.msdata.Chromatogram tic = cl.chromatogram( cl.find( "TIC" ), true ); Map<double, double> sortedFullPointList = new Map<double, double>(); IList<double> timeList = tic.binaryDataArrays[0].data; IList<double> intensityList = tic.binaryDataArrays[1].data; int arrayLength = timeList.Count; for( int i = 0; i < arrayLength; ++i ) sortedFullPointList[timeList[i]] = intensityList[i]; ZedGraph.PointPairList points = new ZedGraph.PointPairList( new List<double>( sortedFullPointList.Keys ).ToArray(), new List<double>( sortedFullPointList.Values ).ToArray() ); ZedGraph.LineItem item = ticGraphControl.GraphPane.AddCurve( "TIC", points, Color.Black, ZedGraph.SymbolType.None ); item.Line.IsAntiAlias = true; ticGraphControl.AxisChange(); ticGraphControl.Refresh(); } else ticGraphControl.Visible = false; } } else ticGraphControl.Visible = false; } else sourcePathTextBox.Text = ""; }
private void listView_ItemSelectionChanged(object sender, ListViewItemSelectionChangedEventArgs e) { if (listView.SelectedItems.Count > 1) { List <string> dataSourceList = new List <string>(); foreach (ListViewItem item in listView.SelectedItems) { if (item.SubItems[1].Text != "File Folder") { dataSourceList.Add(String.Format("\"{0}\"", item.SubItems[0].Text)); } } sourcePathTextBox.Text = String.Join(" ", dataSourceList.ToArray()); ticGraphControl.GraphPane.GraphObjList.Clear(); ticGraphControl.GraphPane.CurveList.Clear(); ticGraphControl.Visible = false; } else if (listView.SelectedItems.Count > 0) { sourcePathTextBox.Text = listView.SelectedItems[0].SubItems[0].Text; ticGraphControl.GraphPane.GraphObjList.Clear(); ticGraphControl.GraphPane.CurveList.Clear(); string sourcePath = Path.Combine(CurrentDirectory, sourcePathTextBox.Text); string sourceType = getSourceType(sourcePath); if (!String.IsNullOrEmpty(sourceType) && sourceType != "File Folder") { using (MSDataFile msData = new MSDataFile(sourcePath)) using (ChromatogramList cl = msData.run.chromatogramList) { if (cl != null && !cl.empty() && cl.find("TIC") != cl.size()) { ticGraphControl.Visible = true; pwiz.CLI.msdata.Chromatogram tic = cl.chromatogram(cl.find("TIC"), true); Map <double, double> sortedFullPointList = new Map <double, double>(); IList <double> timeList = tic.binaryDataArrays[0].data; IList <double> intensityList = tic.binaryDataArrays[1].data; int arrayLength = timeList.Count; for (int i = 0; i < arrayLength; ++i) { sortedFullPointList[timeList[i]] = intensityList[i]; } ZedGraph.PointPairList points = new ZedGraph.PointPairList( new List <double>(sortedFullPointList.Keys).ToArray(), new List <double>(sortedFullPointList.Values).ToArray()); ZedGraph.LineItem item = ticGraphControl.GraphPane.AddCurve("TIC", points, Color.Black, ZedGraph.SymbolType.None); item.Line.IsAntiAlias = true; ticGraphControl.AxisChange(); ticGraphControl.Refresh(); } else { ticGraphControl.Visible = false; } } } else { ticGraphControl.Visible = false; } } else { sourcePathTextBox.Text = ""; } }
private void writeSingleSpectrum(string sourceFile, string nativeID, string outFileName) { MSDataFile.WriteConfig writeConfig = new MSDataFile.WriteConfig(); writeConfig.format = MSDataFile.Format.Format_MGF; writeConfig.precision = MSDataFile.Precision.Precision_32; //var predicate = new SpectrumList_FilterPredicate_IndexSet(); //predicate.indexSet.Add(nativeID); var predicate = new SpectrumList_FilterPredicate_NativeIDSet(); predicate.nativeIDSet.Add(nativeID); try { //Workspace.SetText("\r\nWriting selected spectrum to " + outFileName); MainForm.SetText(this, "Start writing selected spectrum to " + outFileName + "\r\n"); using (MSDataFile msFile = new MSDataFile(sourceFile)) { msFile.run.spectrumList = new SpectrumList_Filter(msFile.run.spectrumList, new SpectrumList_FilterAcceptSpectrum(predicate.accept)); msFile.write(outFileName, writeConfig); } MainForm.SetText(this, "Finished writing selected spectrum to " + outFileName + "\r\n"); } catch (Exception exc) { //throw new Exception("Error in writiing new spectra file", exc); //Workspace.SetText("\r\nError in writing new spectra file\r\n"); tbPepNovoResult.AppendText("\r\nError in writing new spectra file\r\n"); throw new Exception(exc.Message); } }