public List <IsosResult> getIsosResults(string isosInputFile, DeconTools.Backend.Globals.MSFileType filetype) { var isoutil = new IsosResultUtilities(); isoutil.LoadResults(isosInputFile, filetype); return(isoutil.Results); }
public List <IsosResult> getIsosResults(string isosInputFile, DeconTools.Backend.Globals.MSFileType filetype, int minScan, int maxScan) { var isoutil = new IsosResultUtilities(); isoutil.LoadResults(isosInputFile, filetype); return(isoutil.Results.Where(p => p.ScanSet.PrimaryScanNumber >= minScan && p.ScanSet.PrimaryScanNumber <= maxScan).ToList()); }
private List <IsosResult> readInIsos(string canonIsosFilename, DeconTools.Backend.Globals.MSFileType filetype) { List <IsosResult> results = new List <IsosResult>(); IsosImporter importer = new IsosImporter(canonIsosFilename, filetype); importer.Import(results); return(results); }
public IsosImporter(string importFilename, DeconTools.Backend.Globals.MSFileType filetype) { this.importFilename = importFilename; this.delimiter = ','; this.fileType = filetype; this.minVal = int.MinValue; this.maxVal = int.MaxValue; try { this.reader = new StreamReader(importFilename); } catch (Exception) { throw new System.IO.IOException("There was a problem reading the _isos data file\n"); } }
public IsosImporter(string importFilename, DeconTools.Backend.Globals.MSFileType filetype, int minValue, int maxValue) : this(importFilename, filetype) { this.minVal = minValue; this.maxVal = maxValue; }
private Run getRunFromIsosFilename(string p, DeconTools.Backend.Globals.MSFileType filetype) { var runFilename = p.Replace("_isos", ""); var replacementExtension = ""; switch (filetype) { case Globals.MSFileType.Undefined: break; case Globals.MSFileType.Agilent_WIFF: replacementExtension = ".WIFF"; break; case Globals.MSFileType.Agilent_D: replacementExtension = ".D"; break; case Globals.MSFileType.Ascii: break; case Globals.MSFileType.Bruker: break; case Globals.MSFileType.Bruker_Ascii: break; case Globals.MSFileType.Finnigan: replacementExtension = ".RAW"; break; case Globals.MSFileType.ICR2LS_Rawdata: break; case Globals.MSFileType.Micromass_Rawdata: break; case Globals.MSFileType.MZXML_Rawdata: break; case Globals.MSFileType.PNNL_IMS: replacementExtension = ".IMF"; break; case Globals.MSFileType.PNNL_UIMF: replacementExtension = ".UIMF"; break; case Globals.MSFileType.SUNEXTREL: break; default: replacementExtension = ".undefined"; break; } runFilename.Replace(".csv", replacementExtension); var factory = new RunFactory(); Run run; try { run = factory.CreateRun(runFilename); } catch (Exception) { run = null; } return(run); }
private Globals.MSFileType guessFileTypeFromFileName(string filename) { RunFactory runFactory = new RunFactory(); Run run = runFactory.CreateRun(filename); if (run != null) { DeconTools.Backend.Globals.MSFileType filetype = run.MSFileType; run.Dispose(); return(filetype); } try { if (Directory.Exists(filename)) { if (filename.EndsWith(".d", StringComparison.OrdinalIgnoreCase)) { return(Globals.MSFileType.Agilent_D); } } if (!File.Exists(filename)) { return(Globals.MSFileType.Undefined); } string extension = Path.GetExtension(filename); if (extension == null) { return(Globals.MSFileType.Undefined); } switch (extension.ToLower()) { case ".d": return(Globals.MSFileType.Agilent_D); case ".raw": return(Globals.MSFileType.Finnigan); case ".imf": return(Globals.MSFileType.PNNL_IMS); case ".uimf": return(Globals.MSFileType.PNNL_UIMF); case ".mzxml": return(Globals.MSFileType.MZXML_Rawdata); // Deprecated in February 2017 // case ".yafms": // return Globals.MSFileType.YAFMS; default: var fileName = Path.GetFileName(filename); if (fileName != null && fileName.ToLower() == "acqus") { return(Globals.MSFileType.Bruker); } break; } return(Globals.MSFileType.Undefined); } catch (Exception) { return(Globals.MSFileType.Undefined); } }