public IList <PeakData> ImportFile(TextReader peakViewReader)
{
var peakDatas = new List <PeakData>();
var msFileNames = new List <string>();
var fileReader = new DsvFileReader(peakViewReader, TextUtil.SEPARATOR_TSV);
Assert.AreEqual(fileReader.GetFieldIndex(PROTEIN), 0);
Assert.AreEqual(fileReader.GetFieldIndex(PEPTIDE), 1);
Assert.AreEqual(fileReader.GetFieldIndex(LABEL), 2);
Assert.AreEqual(fileReader.GetFieldIndex(PRECURSOR), 3);
Assert.AreEqual(fileReader.GetFieldIndex(CHARGE), 4);
Assert.AreEqual(fileReader.GetFieldIndex(RT), 5);
Assert.AreEqual(fileReader.GetFieldIndex(DECOY), 6);
for (int i = 7; i < fileReader.NumberOfFields; ++i)
{
msFileNames.Add(fileReader.FieldNames[i]);
}
while (fileReader.ReadLine() != null)
{
string modifiedSequence = fileReader.GetFieldByName(PEPTIDE);
string decoyString = fileReader.GetFieldByName(DECOY);
bool decoy;
Assert.IsTrue(bool.TryParse(decoyString, out decoy));
foreach (var msFileName in msFileNames)
{
string dataFieldString = fileReader.GetFieldByName(msFileName);
double dataField;
Assert.IsTrue(double.TryParse(dataFieldString, out dataField));
var peakData = new PeakData(dataField, modifiedSequence, msFileName, decoy);
peakDatas.Add(peakData);
}
}
return(peakDatas);
}
Dictionary <DataProcessedRowKey, double?> ReadDataProcessedRows(TextReader reader)
{
DsvFileReader csvReader = new DsvFileReader(reader, TextUtil.SEPARATOR_CSV);
var rows = new Dictionary <DataProcessedRowKey, double?>();
while (null != csvReader.ReadLine())
{
DataProcessedRowKey dataProcessedRow = new DataProcessedRowKey
{
Protein = csvReader.GetFieldByName("PROTEIN"),
Peptide = csvReader.GetFieldByName("PEPTIDE"),
Transition = csvReader.GetFieldByName("TRANSITION"),
Run = int.Parse(csvReader.GetFieldByName("RUN"), CultureInfo.InvariantCulture),
};
String strAbundance = csvReader.GetFieldByName("ABUNDANCE");
double?abundance = "NA" == strAbundance
? default(double?)
: double.Parse(strAbundance, CultureInfo.InvariantCulture);
rows.Add(dataProcessedRow, abundance);
}
return(rows);
}
protected override void DoTest()
{
Assert.AreEqual(_language, CultureInfo.CurrentUICulture);
RunUI(() => SkylineWindow.Paste(TextUtil.LineSeparate("ELVIS", "LIVES")));
var exportLiveReportDlg = ShowDialog <ExportLiveReportDlg>(SkylineWindow.ShowExportReportDialog);
RunUI(() => exportLiveReportDlg.ReportName = Resources.Resources_ReportSpecList_GetDefaults_Peptide_Quantification);
Directory.CreateDirectory(TestContext.TestDir);
string outputFile = Path.Combine(TestContext.TestDir, "file.csv");
OkDialog(exportLiveReportDlg, () => exportLiveReportDlg.OkDialog(outputFile, TextUtil.CsvSeparator));
using (var textReader = new StreamReader(outputFile))
{
var csvReader = new DsvFileReader(textReader, TextUtil.CsvSeparator);
CollectionAssert.Contains(csvReader.FieldNames, ColumnCaptions.CalibrationCurve);
Assert.IsNotNull(csvReader.ReadLine());
string actualCalibrationCurve = csvReader.GetFieldByName(ColumnCaptions.CalibrationCurve);
string expectedCalibrationCurve = string.Format(
QuantificationStrings.CalibrationCurve_ToString_Slope___0_,
1.0.ToString(Formats.CalibrationCurve));
Assert.AreEqual(expectedCalibrationCurve, actualCalibrationCurve);
}
}
public static IDictionary <string, LinearFitResult> ReadExpectedResults(Type type, string resourceName)
{
var result = new Dictionary <string, LinearFitResult>();
using (var reader = GetTextReaderForManifestResource(type, resourceName))
{
var csvReader = new DsvFileReader(reader, ',');
while (null != csvReader.ReadLine())
{
string protein = csvReader.GetFieldByName("Protein");
var linearFitResult = new LinearFitResult(Convert.ToDouble(csvReader.GetFieldByName("log2FC"), CultureInfo.InvariantCulture))
.SetStandardError(Convert.ToDouble(csvReader.GetFieldByName("SE"), CultureInfo.InvariantCulture))
.SetTValue(Convert.ToDouble(csvReader.GetFieldByName("Tvalue"), CultureInfo.InvariantCulture))
.SetDegreesOfFreedom(Convert.ToInt32(csvReader.GetFieldByName("DF"), CultureInfo.InvariantCulture))
.SetPValue(Convert.ToDouble(csvReader.GetFieldByName("pvalue"), CultureInfo.InvariantCulture));
result.Add(protein, linearFitResult);
}
}
return(result);
}