/// <summary> /// Constructor /// </summary> /// <param name="parameters"></param> public LcMsFeatureFinderLauncher(LcMsFeatureFinderInputParameter parameters = null) { Parameters = parameters ?? new LcMsFeatureFinderInputParameter(); try { _likelihoodScorer = new LcMsFeatureLikelihood(Parameters.LikelihoodScoreThreshold); } catch (FileNotFoundException fe) { ShowErrorMessage(fe.Message); return; } }
static int Main(string[] args) { try { var handle = Process.GetCurrentProcess().MainWindowHandle; SetConsoleMode(handle, EnableExtendedFlags); //args = new string[] {"-i", @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf", "-minMass", "3000", "-maxMass", "30000"}; if (args.Length == 0) { PrintUsageInfo(); return -1; } if (args.Length % 2 != 0) { PrintUsageInfo("The number of arguments must be even."); return -1; } // initialize parameters _paramDic = new Dictionary<string, string> { {LcMsFeatureFinderInputParameter.INPUT_FILE_PATH, null}, {LcMsFeatureFinderInputParameter.OUTPUT_FOLDER_PATH, null}, {LcMsFeatureFinderInputParameter.MINIMUM_CHARGE, "1"}, {LcMsFeatureFinderInputParameter.MAXIMUM_CHARGE, "60"}, {LcMsFeatureFinderInputParameter.MINIMUM_MASS, "2000.0"}, {LcMsFeatureFinderInputParameter.MAXIMUM_MASS, "50000.0"}, {LcMsFeatureFinderInputParameter.INCLUDE_ADDITIONAL_SCORES, "n"}, {LcMsFeatureFinderInputParameter.SAVE_CSV, "n"}, {LcMsFeatureFinderInputParameter.SAVE_PNG_FEATURE_MAP, "y"}, {LcMsFeatureFinderInputParameter.LIKELIHOOD_SCORE_THRESHOLD, "-10"}, {LcMsFeatureFinderInputParameter.MAXIMUM_THREADS, "0"}, {LcMsFeatureFinderInputParameter.EXISTING_MS1FT_FILE, ""} }; for (var i = 0; i < args.Length / 2; i++) { var key = args[2 * i]; var value = args[2 * i + 1]; if (!_paramDic.ContainsKey(key)) { PrintUsageInfo("Invalid parameter: " + key); return -1; } _paramDic[key] = value; } // Parse command line parameters var inputFilePath = _paramDic["-i"]; if (inputFilePath == null) { PrintUsageInfo("Missing required parameter -i!"); return -1; } if (!File.Exists(inputFilePath) && !Directory.Exists(inputFilePath)) { PrintUsageInfo("File not found: " + inputFilePath); return -1; } } catch (Exception ex) { Console.WriteLine("Exception while parsing the command line parameters: " + ex.Message); return -5; } #if (!DEBUG) try { #endif var param = new LcMsFeatureFinderInputParameter(_paramDic); Console.WriteLine("************ {0} {1} ************", Name, Version); param.Display(); var launcher = new LcMsFeatureFinderLauncher(param); int errorCode; if (string.IsNullOrWhiteSpace(param.ExistingFeaturesFilePath)) { errorCode = launcher.Run(); } else { errorCode = launcher.CreateFeatureMapImage(param.InputPath, param.ExistingFeaturesFilePath); } return errorCode; #if (!DEBUG) } catch (Exception ex) { // NOTE: The DMS Analysis Manager looks for this text; do not change it Console.WriteLine("Exception while processing: " + ex.Message); Console.WriteLine(ex.StackTrace); var errorCode = -Math.Abs(ex.Message.GetHashCode()); if (errorCode == 0) return -1; return errorCode; } #endif }
public bool RunSearch(double corrThreshold = 0.7, CancellationToken? cancellationToken = null, IProgress<ProgressData> progress = null) { // Get the Normalized spec file/folder path SpecFilePath = MassSpecDataReaderFactory.NormalizeDatasetPath(SpecFilePath); var prog = new Progress<ProgressData>(); var progData = new ProgressData(progress); if (progress != null) { prog = new Progress<ProgressData>(p => { progData.Status = p.Status; progData.StatusInternal = p.StatusInternal; progData.Report(p.Percent); }); } var sw = new Stopwatch(); var swAll = new Stopwatch(); swAll.Start(); ErrorMessage = string.Empty; Console.Write(@"Reading raw file..."); progData.Status = "Reading spectra file"; progData.StepRange(10.0); sw.Start(); _run = PbfLcMsRun.GetLcMsRun(SpecFilePath, 0, 0, prog); _ms2ScanNums = _run.GetScanNumbers(2).ToArray(); _isolationWindowTargetMz = new double[_run.MaxLcScan + 1]; foreach (var ms2Scan in _ms2ScanNums) { var ms2Spec = _run.GetSpectrum(ms2Scan) as ProductSpectrum; if (ms2Spec == null) continue; _isolationWindowTargetMz[ms2Scan] = ms2Spec.IsolationWindow.IsolationWindowTargetMz; } sw.Stop(); Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); progData.StepRange(20.0); ISequenceFilter ms1Filter; if (this.ScanNumbers != null && this.ScanNumbers.Any()) { ms1Filter = new SelectedMsMsFilter(this.ScanNumbers); } else if (string.IsNullOrWhiteSpace(FeatureFilePath)) { // Checks whether SpecFileName.ms1ft exists var ms1FtFilePath = MassSpecDataReaderFactory.ChangeExtension(SpecFilePath, LcMsFeatureFinderLauncher.FileExtension); if (!File.Exists(ms1FtFilePath)) { Console.WriteLine(@"Running ProMex..."); sw.Start(); var param = new LcMsFeatureFinderInputParameter { InputPath = SpecFilePath, MinSearchMass = MinSequenceMass, MaxSearchMass = MaxSequenceMass, MinSearchCharge = MinPrecursorIonCharge, MaxSearchCharge = MaxPrecursorIonCharge, CsvOutput = false, ScoreReport = false, LikelihoodScoreThreshold = -10 }; var featureFinder = new LcMsFeatureFinderLauncher(param); featureFinder.Run(); } sw.Reset(); sw.Start(); Console.Write(@"Reading ProMex results..."); ms1Filter = new Ms1FtFilter(_run, PrecursorIonTolerance, ms1FtFilePath, -10); } else { sw.Reset(); sw.Start(); var extension = Path.GetExtension(FeatureFilePath); if (extension.ToLower().Equals(".csv")) { Console.Write(@"Reading ICR2LS/Decon2LS results..."); ms1Filter = new IsosFilter(_run, PrecursorIonTolerance, FeatureFilePath); } else if (extension.ToLower().Equals(".ms1ft")) { Console.Write(@"Reading ProMex results..."); ms1Filter = new Ms1FtFilter(_run, PrecursorIonTolerance, FeatureFilePath, -10); } else if (extension.ToLower().Equals(".msalign")) { Console.Write(@"Reading MS-Align+ results..."); ms1Filter = new MsDeconvFilter(_run, PrecursorIonTolerance, FeatureFilePath); } else ms1Filter = null; //new Ms1FeatureMatrix(_run); } sw.Stop(); Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); // pre-generate deconvoluted spectra for scoring _massBinComparer = new FilteredProteinMassBinning(AminoAcidSet, MaxSequenceMass+1000); _ms2ScorerFactory2 = new CompositeScorerFactory(_run, _massBinComparer, AminoAcidSet, MinProductIonCharge, MaxProductIonCharge, ProductIonTolerance); sw.Reset(); Console.WriteLine(@"Generating deconvoluted spectra for MS/MS spectra..."); sw.Start(); var pfeOptions = new ParallelOptions { MaxDegreeOfParallelism = MaxNumThreads, CancellationToken = cancellationToken ?? CancellationToken.None }; Parallel.ForEach(_ms2ScanNums, pfeOptions, ms2ScanNum => { _ms2ScorerFactory2.DeconvonluteProductSpectrum(ms2ScanNum); }); sw.Stop(); Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); progData.StepRange(10.0); progData.Status = "Reading Fasta File"; // Target database var targetDb = new FastaDatabase(DatabaseFilePath); targetDb.Read(); // Generate sequence tags for all MS/MS spectra if (TagBasedSearch) { progData.StepRange(25.0); progData.Status = "Generating Sequence Tags"; sw.Reset(); Console.WriteLine(@"Generating sequence tags for MS/MS spectra..."); sw.Start(); var seqTagGen = GetSequenceTagGenerator(); _tagMs2ScanNum = seqTagGen.GetMs2ScanNumsContainingTags().ToArray(); sw.Stop(); Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); _tagSearchEngine = new ScanBasedTagSearchEngine(_run, seqTagGen, new LcMsPeakMatrix(_run, ms1Filter), targetDb, ProductIonTolerance, AminoAcidSet, _ms2ScorerFactory2, ScanBasedTagSearchEngine.DefaultMinMatchedTagLength, MaxSequenceMass, MinProductIonCharge, MaxProductIonCharge); } var specFileName = MassSpecDataReaderFactory.RemoveExtension(Path.GetFileName(SpecFilePath)); var targetOutputFilePath = Path.Combine(OutputDir, specFileName + TargetFileNameEnding); var decoyOutputFilePath = Path.Combine(OutputDir, specFileName + DecoyFileNameEnding); var tdaOutputFilePath = Path.Combine(OutputDir, specFileName + TdaFileNameEnding); progData.StepRange(60.0); progData.Status = "Running Target search"; if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Target)) { sw.Reset(); Console.Write(@"Reading the target database..."); sw.Start(); targetDb.Read(); sw.Stop(); Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); var targetMatches = new SortedSet<DatabaseSequenceSpectrumMatch>[_run.MaxLcScan + 1]; progData.MaxPercentage = 42.5; if (TagBasedSearch) { sw.Reset(); Console.WriteLine(@"Tag-based searching the target database"); sw.Start(); RunTagBasedSearch(targetMatches, targetDb, null, prog); Console.WriteLine(@"Target database tag-based search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); } progData.MaxPercentage = 60.0; sw.Reset(); Console.WriteLine(@"Searching the target database"); sw.Start(); RunSearch(targetMatches, targetDb, ms1Filter, null, prog); Console.WriteLine(@"Target database search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); // calculate spectral e-value usign generating function sw.Reset(); Console.WriteLine(@"Calculating spectral E-values for target-spectrum matches"); sw.Start(); var bestTargetMatches = RunGeneratingFunction(targetMatches); WriteResultsToFile(bestTargetMatches, targetOutputFilePath, targetDb); sw.Stop(); Console.WriteLine(@"Target-spectrum match E-value calculation elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); } progData.StepRange(95.0); // total to 95% progData.Status = "Running Decoy search"; if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Decoy)) { // Decoy database sw.Reset(); sw.Start(); var decoyDb = targetDb.Decoy(null, true); Console.Write(@"Reading the decoy database..."); decoyDb.Read(); Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); progData.MaxPercentage = 77.5; var decoyMatches = new SortedSet<DatabaseSequenceSpectrumMatch>[_run.MaxLcScan + 1]; if (TagBasedSearch) { sw.Reset(); Console.WriteLine(@"Tag-based searching the decoy database"); sw.Start(); RunTagBasedSearch(decoyMatches, decoyDb, null, prog); Console.WriteLine(@"Decoy database tag-based search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); } progData.MaxPercentage = 95.0; sw.Reset(); Console.WriteLine(@"Searching the decoy database"); sw.Start(); RunSearch(decoyMatches, decoyDb, ms1Filter, null, prog); Console.WriteLine(@"Decoy database search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); // calculate spectral e-value usign generating function sw.Reset(); Console.WriteLine(@"Calculating spectral E-values for decoy-spectrum matches"); sw.Start(); var bestDecoyMatches = RunGeneratingFunction(decoyMatches); WriteResultsToFile(bestDecoyMatches, decoyOutputFilePath, decoyDb); sw.Stop(); Console.WriteLine(@"Decoy-spectrum match E-value calculation elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); } progData.StepRange(100.0); progData.Status = "Writing combined results file"; if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Both)) { // Add "Qvalue" and "PepQValue" var fdrCalculator = new FdrCalculator(targetOutputFilePath, decoyOutputFilePath); if (fdrCalculator.HasError()) { ErrorMessage = fdrCalculator.ErrorMessage; Console.WriteLine(@"Error computing FDR: " + fdrCalculator.ErrorMessage); return false; } fdrCalculator.WriteTo(tdaOutputFilePath); } progData.Report(100.0); Console.WriteLine(@"Done."); swAll.Stop(); Console.WriteLine(@"Total elapsed time for search: {0:f1} sec ({1:f2} min)", swAll.Elapsed.TotalSeconds, swAll.Elapsed.TotalMinutes); return true; }
public bool RunSearch(double corrThreshold = 0.7, CancellationToken?cancellationToken = null, IProgress <ProgressData> progress = null) { // Get the Normalized spec file/folder path SpecFilePath = MassSpecDataReaderFactory.NormalizeDatasetPath(SpecFilePath); var prog = new Progress <ProgressData>(); var progData = new ProgressData(progress); if (progress != null) { prog = new Progress <ProgressData>(p => { progData.Status = p.Status; progData.StatusInternal = p.StatusInternal; progData.Report(p.Percent); }); } var sw = new Stopwatch(); var swAll = new Stopwatch(); swAll.Start(); ErrorMessage = string.Empty; Console.Write(@"Reading raw file..."); progData.Status = "Reading spectra file"; progData.StepRange(10.0); sw.Start(); _run = PbfLcMsRun.GetLcMsRun(SpecFilePath, 0, 0, prog); _ms2ScanNums = _run.GetScanNumbers(2).ToArray(); _isolationWindowTargetMz = new double[_run.MaxLcScan + 1]; foreach (var ms2Scan in _ms2ScanNums) { var ms2Spec = _run.GetSpectrum(ms2Scan) as ProductSpectrum; if (ms2Spec == null) { continue; } _isolationWindowTargetMz[ms2Scan] = ms2Spec.IsolationWindow.IsolationWindowTargetMz; } sw.Stop(); Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); progData.StepRange(20.0); ISequenceFilter ms1Filter; if (this.ScanNumbers != null && this.ScanNumbers.Any()) { ms1Filter = new SelectedMsMsFilter(this.ScanNumbers); } else if (string.IsNullOrWhiteSpace(FeatureFilePath)) { // Checks whether SpecFileName.ms1ft exists var ms1FtFilePath = MassSpecDataReaderFactory.ChangeExtension(SpecFilePath, LcMsFeatureFinderLauncher.FileExtension); if (!File.Exists(ms1FtFilePath)) { Console.WriteLine(@"Running ProMex..."); sw.Start(); var param = new LcMsFeatureFinderInputParameter { InputPath = SpecFilePath, MinSearchMass = MinSequenceMass, MaxSearchMass = MaxSequenceMass, MinSearchCharge = MinPrecursorIonCharge, MaxSearchCharge = MaxPrecursorIonCharge, CsvOutput = false, ScoreReport = false, LikelihoodScoreThreshold = -10 }; var featureFinder = new LcMsFeatureFinderLauncher(param); featureFinder.Run(); } sw.Reset(); sw.Start(); Console.Write(@"Reading ProMex results..."); ms1Filter = new Ms1FtFilter(_run, PrecursorIonTolerance, ms1FtFilePath, -10); } else { sw.Reset(); sw.Start(); var extension = Path.GetExtension(FeatureFilePath); if (extension.ToLower().Equals(".csv")) { Console.Write(@"Reading ICR2LS/Decon2LS results..."); ms1Filter = new IsosFilter(_run, PrecursorIonTolerance, FeatureFilePath); } else if (extension.ToLower().Equals(".ms1ft")) { Console.Write(@"Reading ProMex results..."); ms1Filter = new Ms1FtFilter(_run, PrecursorIonTolerance, FeatureFilePath, -10); } else if (extension.ToLower().Equals(".msalign")) { Console.Write(@"Reading MS-Align+ results..."); ms1Filter = new MsDeconvFilter(_run, PrecursorIonTolerance, FeatureFilePath); } else { ms1Filter = null; //new Ms1FeatureMatrix(_run); } } sw.Stop(); Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); // pre-generate deconvoluted spectra for scoring _massBinComparer = new FilteredProteinMassBinning(AminoAcidSet, MaxSequenceMass + 1000); _ms2ScorerFactory2 = new CompositeScorerFactory(_run, _massBinComparer, AminoAcidSet, MinProductIonCharge, MaxProductIonCharge, ProductIonTolerance); sw.Reset(); Console.WriteLine(@"Generating deconvoluted spectra for MS/MS spectra..."); sw.Start(); var pfeOptions = new ParallelOptions { MaxDegreeOfParallelism = MaxNumThreads, CancellationToken = cancellationToken ?? CancellationToken.None }; Parallel.ForEach(_ms2ScanNums, pfeOptions, ms2ScanNum => { _ms2ScorerFactory2.DeconvonluteProductSpectrum(ms2ScanNum); }); sw.Stop(); Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); progData.StepRange(10.0); progData.Status = "Reading Fasta File"; // Target database var targetDb = new FastaDatabase(DatabaseFilePath); targetDb.Read(); // Generate sequence tags for all MS/MS spectra if (TagBasedSearch) { progData.StepRange(25.0); progData.Status = "Generating Sequence Tags"; sw.Reset(); Console.WriteLine(@"Generating sequence tags for MS/MS spectra..."); sw.Start(); var seqTagGen = GetSequenceTagGenerator(); _tagMs2ScanNum = seqTagGen.GetMs2ScanNumsContainingTags().ToArray(); sw.Stop(); Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); _tagSearchEngine = new ScanBasedTagSearchEngine(_run, seqTagGen, new LcMsPeakMatrix(_run, ms1Filter), targetDb, ProductIonTolerance, AminoAcidSet, _ms2ScorerFactory2, ScanBasedTagSearchEngine.DefaultMinMatchedTagLength, MaxSequenceMass, MinProductIonCharge, MaxProductIonCharge); } var specFileName = MassSpecDataReaderFactory.RemoveExtension(Path.GetFileName(SpecFilePath)); var targetOutputFilePath = Path.Combine(OutputDir, specFileName + TargetFileNameEnding); var decoyOutputFilePath = Path.Combine(OutputDir, specFileName + DecoyFileNameEnding); var tdaOutputFilePath = Path.Combine(OutputDir, specFileName + TdaFileNameEnding); progData.StepRange(60.0); progData.Status = "Running Target search"; if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Target)) { sw.Reset(); Console.Write(@"Reading the target database..."); sw.Start(); targetDb.Read(); sw.Stop(); Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); var targetMatches = new SortedSet <DatabaseSequenceSpectrumMatch> [_run.MaxLcScan + 1]; progData.MaxPercentage = 42.5; if (TagBasedSearch) { sw.Reset(); Console.WriteLine(@"Tag-based searching the target database"); sw.Start(); RunTagBasedSearch(targetMatches, targetDb, null, prog); Console.WriteLine(@"Target database tag-based search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); } progData.MaxPercentage = 60.0; sw.Reset(); Console.WriteLine(@"Searching the target database"); sw.Start(); RunSearch(targetMatches, targetDb, ms1Filter, null, prog); Console.WriteLine(@"Target database search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); // calculate spectral e-value usign generating function sw.Reset(); Console.WriteLine(@"Calculating spectral E-values for target-spectrum matches"); sw.Start(); var bestTargetMatches = RunGeneratingFunction(targetMatches); WriteResultsToFile(bestTargetMatches, targetOutputFilePath, targetDb); sw.Stop(); Console.WriteLine(@"Target-spectrum match E-value calculation elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); } progData.StepRange(95.0); // total to 95% progData.Status = "Running Decoy search"; if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Decoy)) { // Decoy database sw.Reset(); sw.Start(); var decoyDb = targetDb.Decoy(null, true); Console.Write(@"Reading the decoy database..."); decoyDb.Read(); Console.WriteLine(@"Elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); progData.MaxPercentage = 77.5; var decoyMatches = new SortedSet <DatabaseSequenceSpectrumMatch> [_run.MaxLcScan + 1]; if (TagBasedSearch) { sw.Reset(); Console.WriteLine(@"Tag-based searching the decoy database"); sw.Start(); RunTagBasedSearch(decoyMatches, decoyDb, null, prog); Console.WriteLine(@"Decoy database tag-based search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); } progData.MaxPercentage = 95.0; sw.Reset(); Console.WriteLine(@"Searching the decoy database"); sw.Start(); RunSearch(decoyMatches, decoyDb, ms1Filter, null, prog); Console.WriteLine(@"Decoy database search elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); // calculate spectral e-value usign generating function sw.Reset(); Console.WriteLine(@"Calculating spectral E-values for decoy-spectrum matches"); sw.Start(); var bestDecoyMatches = RunGeneratingFunction(decoyMatches); WriteResultsToFile(bestDecoyMatches, decoyOutputFilePath, decoyDb); sw.Stop(); Console.WriteLine(@"Decoy-spectrum match E-value calculation elapsed Time: {0:f1} sec", sw.Elapsed.TotalSeconds); } progData.StepRange(100.0); progData.Status = "Writing combined results file"; if (RunTargetDecoyAnalysis.HasFlag(DatabaseSearchMode.Both)) { // Add "Qvalue" and "PepQValue" var fdrCalculator = new FdrCalculator(targetOutputFilePath, decoyOutputFilePath); if (fdrCalculator.HasError()) { ErrorMessage = fdrCalculator.ErrorMessage; Console.WriteLine(@"Error computing FDR: " + fdrCalculator.ErrorMessage); return(false); } fdrCalculator.WriteTo(tdaOutputFilePath); } progData.Report(100.0); Console.WriteLine(@"Done."); swAll.Stop(); Console.WriteLine(@"Total elapsed time for search: {0:f1} sec ({1:f2} min)", swAll.Elapsed.TotalSeconds, swAll.Elapsed.TotalMinutes); return(true); }
public void TestGeneratingMs1FeatureFile() { var methodName = MethodBase.GetCurrentMethod().Name; TestUtils.ShowStarting(methodName); const string specFilePath = @"\\proto-11\MSXML_Cache\PBF_Gen_1_193\2015_2\QC_ShewIntact_1_19Jun15_Bane_14-09-01RZ.pbf"; if (!File.Exists(specFilePath)) { Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, specFilePath); } const string outFolderPath = @"\\proto-2\UnitTest_Files\InformedProteomics_TestFiles\Output"; if (!Directory.Exists(outFolderPath)) { Assert.Ignore(@"Skipping test {0} since folder not found: {1}", methodName, outFolderPath); } //const string specFilePath = @"D:\MassSpecFiles\test\QC_Shew_Intact_4_01Jan15_Bane_C2-14-08-02RZ.raw"; const int minScanCharge = 2; const int maxScanCharge = 60; const double minScanMass = 3000; const double maxScanMass = 5000; const int maxThreads = 10; var param = new LcMsFeatureFinderInputParameter() { InputPath = specFilePath, OutputPath = outFolderPath, MinSearchMass = minScanMass, MaxSearchMass = maxScanMass, MinSearchCharge = minScanCharge, MaxSearchCharge = maxScanCharge, CsvOutput = true, ScoreReport = false, MaxThreads = maxThreads }; var featureFinder = new LcMsFeatureFinderLauncher(param); featureFinder.Run(); }