public List <IsosResult> getIsosResults(string isosInputFile, Globals.MSFileType fileType) { var isoUtil = new IsosResultUtilities(); isoUtil.LoadResults(isosInputFile, fileType); return(isoUtil.Results); }
public List <IsosResult> getIsosResults(string isosInputFile, 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()); }
public PeakListTextExporter(Globals.MSFileType fileType, int triggerValue, string outputFileName) { FileName = outputFileName; TriggerToWriteValue = triggerValue; //will write out peaks if trigger value is reached m_delimiter = '\t'; m_FileType = fileType; // need to know filetype so that frame_num can be outputted for UIMF data bool fileExists; try { fileExists = File.Exists(outputFileName); } catch (Exception ex) { Logger.Instance.AddEntry("PeakExporter failed. Details: " + ex.Message, true); throw new Exception("Peak exporter failed. Check to see if output file is already open."); } if (fileExists) { try { File.Delete(outputFileName); } catch (Exception ex) { Logger.Instance.AddEntry("PeakExporter failed. Details: " + ex.Message, true); throw new Exception("Peak exporter failed. Check to see if output file is already open."); } } initializeAndWriteHeader(); }
public MSFileTypeSelectorForm(string filename) { InitializeComponent(); this.listBox1.DataSource = System.Enum.GetValues(typeof(Globals.MSFileType)); Globals.MSFileType guessedFileType = guessFileTypeFromFileName(filename); this.listBox1.SelectedItem = guessedFileType; }
public IsosImporter(string importFilename, Globals.MSFileType msFileType) { delimiter = ','; fileType = msFileType; filepath = importFilename; minVal = int.MinValue; maxVal = int.MaxValue; try { reader = new StreamReader(importFilename); } catch (Exception) { throw new IOException("There was a problem reading the _isos data file " + filepath); } }
public static ScanResultExporter CreateScansExporter(Globals.MSFileType fileType, Globals.ExporterType exporterType, string outputFileName) { ScanResultExporter scansExporter; switch (fileType) { case Globals.MSFileType.PNNL_UIMF: switch (exporterType) { case Globals.ExporterType.Text: scansExporter = new UIMFScanResult_TextFileExporter(outputFileName); break; case Globals.ExporterType.Sqlite: scansExporter = new UIMFScanResult_SqliteExporter(outputFileName); break; default: scansExporter = new UIMFScanResult_TextFileExporter(outputFileName); break; } break; default: switch (exporterType) { case Globals.ExporterType.Text: scansExporter = new BasicScanResult_TextFileExporter(outputFileName); break; case Globals.ExporterType.Sqlite: scansExporter = new BasicScanResult_SqliteExporter(outputFileName); break; default: scansExporter = new BasicScanResult_TextFileExporter(outputFileName); break; } break; } return(scansExporter); }
public static ExporterBase <ScanResult> CreateMSScanInfoExporterFactory(Globals.ExporterType exporterType, Globals.MSFileType msFileType, string outputFileName) { Check.Assert(!string.IsNullOrEmpty(outputFileName), "MSScanInfoExporterFactory cannot work. OutputFileName is empty - which is bad."); ExporterBase <ScanResult> msFeatureExporter; switch (exporterType) { case Globals.ExporterType.Text: switch (msFileType) { case Globals.MSFileType.PNNL_UIMF: msFeatureExporter = new MSScanInfoToTextFileExporterUIMF(outputFileName); break; default: msFeatureExporter = new MSScanInfoToTextFileExporterBasic(outputFileName); break; } break; case Globals.ExporterType.Sqlite: switch (msFileType) { case Globals.MSFileType.PNNL_UIMF: msFeatureExporter = new MSScanInfoToSQLiteExporterUIMF(outputFileName); break; default: msFeatureExporter = new MSScanInfoToSQLiteExporterBasic(outputFileName); break; } break; default: throw new NotImplementedException(); } return(msFeatureExporter); }
public static IPeakListExporter Create(Globals.ExporterType exporterType, Globals.MSFileType fileType, int triggerValue, string outputFileName) { IPeakListExporter exporter; switch (exporterType) { case Globals.ExporterType.Text: exporter = new PeakListTextExporter(fileType, triggerValue, outputFileName); break; case Globals.ExporterType.Sqlite: exporter = new PeakListSQLiteExporter(triggerValue, outputFileName); break; default: exporter = new PeakListTextExporter(fileType, triggerValue, outputFileName); break; } return(exporter); }
public void LoadResults(string isosTextFile, Globals.MSFileType fileType, int minVal, int maxVal) { var fileExists = false; try { fileExists = File.Exists(isosTextFile); } catch (Exception) { // Ignore exceptions } Check.Require(fileExists, "IsosResultUtilities cannot open input file"); var importer = new IsosImporter(isosTextFile, fileType, minVal, maxVal); var isosResults = importer.Import(); Results = isosResults; }
public void LoadResults(string isosTextFile, Globals.MSFileType fileType) { var fileExists = false; try { fileExists = System.IO.File.Exists(isosTextFile); } catch (Exception) { } Check.Require(fileExists, "IsosResultUtilities cannot open input file"); var isosResults = new List <IsosResult>(); var importer = new IsosImporter(isosTextFile, fileType); isosResults = importer.Import(); this.results = isosResults; }
public PeakListTextExporter(Globals.MSFileType fileType, string outputFileName) : this(fileType, 100000, outputFileName) // default allowed MSLevels = 1 { }
public static MSGenerator CreateMSGenerator(Globals.MSFileType fileType) { MSGenerator msGenerator; switch (fileType) { case Globals.MSFileType.Undefined: msGenerator = new GenericMSGenerator(); break; case Globals.MSFileType.Agilent_WIFF: msGenerator = new GenericMSGenerator(); break; case Globals.MSFileType.Agilent_D: msGenerator = new GenericMSGenerator(); break; case Globals.MSFileType.Ascii: msGenerator = new GenericMSGenerator(); break; case Globals.MSFileType.Bruker: msGenerator = new GenericMSGenerator(); break; case Globals.MSFileType.Bruker_Ascii: msGenerator = new GenericMSGenerator(); break; case Globals.MSFileType.Thermo_Raw: msGenerator = new GenericMSGenerator(); break; case Globals.MSFileType.ICR2LS_Rawdata: msGenerator = new GenericMSGenerator(); break; case Globals.MSFileType.Micromass_Rawdata: msGenerator = new GenericMSGenerator(); break; case Globals.MSFileType.MZXML_Rawdata: msGenerator = new GenericMSGenerator(); break; case Globals.MSFileType.PNNL_IMS: msGenerator = new GenericMSGenerator(); break; case Globals.MSFileType.PNNL_UIMF: msGenerator = new UIMF_MSGenerator(); break; case Globals.MSFileType.SUNEXTREL: msGenerator = new GenericMSGenerator(); break; default: msGenerator = new GenericMSGenerator(); break; } return(msGenerator); }
public Run CreateRun(Globals.MSFileType filetype, string f) { Run run; if (filetype == Globals.MSFileType.MZXML_Rawdata) { pwiz.ProteowizardWrapper.DependencyLoader.ValidateLoader(); } var fileName = getFullPath(f); switch (filetype) { case Globals.MSFileType.Undefined: run = null; break; case Globals.MSFileType.Agilent_WIFF: run = null; break; case Globals.MSFileType.Agilent_D: run = new AgilentDRun(fileName); break; case Globals.MSFileType.Ascii: run = new MSScanFromTextFileRun(fileName); break; case Globals.MSFileType.Bruker: run = new BrukerV3Run(fileName); break; #if !Disable_DeconToolsV2 case Globals.MSFileType.Bruker_V2: run = new BrukerV2Run(fileName); break; #endif case Globals.MSFileType.Bruker_Ascii: run = null; break; case Globals.MSFileType.Finnigan: run = new XCaliburRun2(fileName); break; case Globals.MSFileType.ICR2LS_Rawdata: run = null; break; case Globals.MSFileType.Micromass_Rawdata: run = null; break; case Globals.MSFileType.MZXML_Rawdata: run = new MzRun(fileName); break; #if !Disable_DeconToolsV2 case Globals.MSFileType.PNNL_IMS: run = new IMFRun(fileName); break; #endif case Globals.MSFileType.PNNL_UIMF: run = new UIMFRun(fileName); break; case Globals.MSFileType.SUNEXTREL: run = null; break; // Deprecated in February 2017 // case Globals.MSFileType.YAFMS: // run = new YAFMSRun(fileName); // break; default: run = null; break; } return(run); }
public IsosImporter(string importFilename, Globals.MSFileType msFileType, int minValue, int maxValue) : this(importFilename, msFileType) { minVal = minValue; maxVal = maxValue; }
private Run GetRunFromIsosFilename(string p, Globals.MSFileType msFileType) { var runFilename = p.Replace("_isos", ""); var replacementExtension = ""; switch (msFileType) { 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.Thermo_Raw: 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 = runFilename.Replace(".csv", replacementExtension); var factory = new RunFactory(); Run run; try { run = factory.CreateRun(runFilename); } catch (Exception) { run = null; } return(run); }
public static ExporterBase <IsosResult> CreateMSFeatureExporter(Globals.ExporterType exporterType, Globals.MSFileType msFileType, string outputFileName) { Check.Assert(!string.IsNullOrEmpty(outputFileName), "MSFeatureExporterFactory cannot work. OutputFileName is empty - which is bad."); ExporterBase <IsosResult> msFeatureExporter; switch (exporterType) { case Globals.ExporterType.Text: //IMS and UIMF filetypes have their own special export formats. All others will use a standard format. switch (msFileType) { case Globals.MSFileType.PNNL_IMS: msFeatureExporter = new MSFeatureToTextFileExporterIMF(outputFileName); break; case Globals.MSFileType.PNNL_UIMF: msFeatureExporter = new MSFeatureToTextFileExporterUIMF(outputFileName); break; default: msFeatureExporter = new MSFeatureToTextFileExporterBasic(outputFileName); break; } break; case Globals.ExporterType.Sqlite: switch (msFileType) { case Globals.MSFileType.PNNL_UIMF: msFeatureExporter = new MSFeatureToSQLiteExporterUIMF(outputFileName); break; default: msFeatureExporter = new MSFeatureToSQLiteExporterBasic(outputFileName); break; } break; default: throw new NotImplementedException(); //break; } return(msFeatureExporter); }
private void btnOK_Click(object sender, EventArgs e) { this.DialogResult = DialogResult.OK; this.selectedFiletype = (Globals.MSFileType)listBox1.SelectedItem; this.Close(); }
public void LoadResults(string uimfIsos1, Globals.MSFileType mSFileType, int frameNum) { Check.Require(mSFileType == Globals.MSFileType.PNNL_UIMF, "This option only works for UIMF files"); }