public void importerTest1() { string importedResultFile = Path.Combine(FileRefs.OutputFolderPath, "UnlabelledTargetedResultsExporterOutput1.txt"); UnlabelledTargetedResultFromTextImporter importer = new UnlabelledTargetedResultFromTextImporter(importedResultFile); TargetedResultRepository repo = importer.Import(); Assert.IsNotNull(repo); Assert.IsTrue(repo.Results.Count > 0); TargetedResult testResult1 = repo.Results[0]; Assert.AreEqual("QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18", testResult1.DatasetName); Assert.AreEqual(24698, testResult1.MassTagID); Assert.AreEqual(3, testResult1.ChargeState); Assert.AreEqual(5880, testResult1.ScanLC); Assert.AreEqual(5876, testResult1.ScanLCStart); Assert.AreEqual(5888, testResult1.ScanLCEnd); Assert.AreEqual(0.3160, (decimal)testResult1.NET); Assert.AreEqual(1, testResult1.NumChromPeaksWithinTol); Assert.AreEqual(2311.07759, (decimal)testResult1.MonoMass); Assert.AreEqual(771.36647, (decimal)testResult1.MonoMZ); Assert.AreEqual(8247913, (decimal)testResult1.Intensity); Assert.AreEqual(0.0119, (decimal)testResult1.FitScore); Assert.AreEqual(0, (decimal)testResult1.IScore); }
private clsUMC convertDeconToolsTargetedFeatureToUMC(TargetedResult feature) { clsUMC umc = new clsUMC(); umc.AbundanceMax = feature.Intensity; umc.AbundanceSum = (long)feature.Intensity; umc.AverageDeconFitScore = feature.FitScore; umc.AverageInterferenceScore = feature.IScore; umc.ChargeMax = feature.ChargeState; umc.ChargeRepresentative = (short)feature.ChargeState; umc.ClusterId = 0; umc.CombinedScore = 0; umc.ConformationFitScore = 0; umc.ConformationId = 0; umc.DatasetId = 0; umc.DriftTime = 0; umc.DriftTimeUncorrected = 0; umc.Id = (int)feature.MassTagID; umc.Mass = feature.MonoMass; umc.MZForCharge = feature.MonoMZ; umc.Net = feature.NET; umc.Scan = feature.ScanLC; umc.ScanEnd = feature.ScanLCEnd; umc.ScanStart = feature.ScanLCStart; umc.SpectralCount = 0; return(umc); }
public override TargetedResultRepository Import() { TargetedResultRepository repos = new TargetedResultRepository(); StreamReader reader; try { reader = new StreamReader(this._filename); } catch (Exception) { throw new System.IO.IOException("There was a problem importing from the file."); } using (StreamReader sr = reader) { if (sr.Peek() == -1) { sr.Close(); throw new InvalidDataException("There is no data in the file we are trying to read."); } string headerLine = sr.ReadLine(); CreateHeaderLookupTable(headerLine); bool areHeadersValid = ValidateHeaders(); if (!areHeadersValid) { throw new InvalidDataException("There is a problem with the column headers."); } string line; int lineCounter = 1; //used for tracking which line is being processed. //read and process each line of the file while (sr.Peek() > -1) { line = sr.ReadLine(); List <string> processedData = ProcessLine(line); //ensure that processed line is the same size as the header line if (processedData.Count != m_columnHeaders.Count) { throw new InvalidDataException("Data in row #" + lineCounter.ToString() + "is invalid - \nThe number of columns does not match that of the header line"); } TargetedResult result = ConvertTextToDataObject(processedData); repos.Results.Add(result); lineCounter++; } sr.Close(); } return(repos); }