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);
}
