public async Task TestShowFilteredSpectrum(string rawFile)
{
var lcms = PbfLcMsRun.GetLcMsRun(rawFile);
var scans = lcms.GetScanNumbers(2);
var specPlotVm = new SpectrumPlotViewModel(new TestableMainDialogService(), new FragmentationSequenceViewModel(), 1.05, false);
foreach (var scan in scans)
{
var spectrum = lcms.GetSpectrum(scan);
var filteredSpectrum = spectrum.GetFilteredSpectrumBySlope(); // filtered spectrum to test against
specPlotVm.Spectrum = spectrum;
await MsPathFinderTest.SleepMillisecondsAsync(1000);
// check unfiltered spectrum
specPlotVm.ShowFilteredSpectrum = false;
await MsPathFinderTest.SleepMillisecondsAsync(1000);
var spectrumSeries = specPlotVm.PlotModel.Series[0] as StemSeries;
Assert.False(spectrumSeries == null);
Assert.True(spectrumSeries.Points.Count == spectrum.Peaks.Length); // should be the same length
for (var i = 0; i < spectrumSeries.Points.Count; i++)
{
// compare each peak in spectrum plot to actual spectrum
Assert.True(spectrumSeries.Points[i].X.Equals(spectrum.Peaks[i].Mz));
Assert.True(spectrumSeries.Points[i].Y.Equals(spectrum.Peaks[i].Intensity));
}
await MsPathFinderTest.SleepMillisecondsAsync(1000);
// check filtered spectrum
specPlotVm.ShowFilteredSpectrum = true;
await MsPathFinderTest.SleepMillisecondsAsync(1000);
var filteredSeries = (StemSeries)specPlotVm.PlotModel.Series[0];
Assert.True(filteredSeries.Points.Count == filteredSpectrum.Peaks.Length); // should be the same length
for (var i = 0; i < filteredSeries.Points.Count; i++)
{
// compare each peak in spectrum plot to actual filtered spectrum
Assert.True(filteredSeries.Points[i].X.Equals(filteredSpectrum.Peaks[i].Mz));
Assert.True(filteredSeries.Points[i].Y.Equals(filteredSpectrum.Peaks[i].Intensity));
}
}
}
public void TestMassExportPeakLists(string rawFile, string idFile)
{
// Read files
var lcms = PbfLcMsRun.GetLcMsRun(rawFile);
var idFileReader = IdFileReaderFactory.CreateReader(idFile);
var ids = idFileReader.Read().ToList();
foreach (var id in ids)
{
id.LcMs = lcms;
id.RawFileName = Path.GetFileNameWithoutExtension(rawFile);
}
var outputDir = MsPathFinderTest.CreateTestResultDirectory("ExporterTest");
var exporter = new SpectrumPeakExporter(outputDir.FullName);
exporter.Export(ids.ToList());
}
public async Task TestDisplaySpectrum(string rawFile, string tsvFile)
{
// init
var idFileReader = IdFileReaderFactory.CreateReader(tsvFile);
var ids = idFileReader.Read();
var lcms = PbfLcMsRun.GetLcMsRun(rawFile);
var idList = ids.ToList();
foreach (var id in idList)
{
id.LcMs = lcms;
id.RawFileName = Path.GetFileNameWithoutExtension(rawFile);
}
// init SpectrumPlotViewModel
var dialogService = new TestableMainDialogService();
var spectrumPlotViewModel = new SpectrumPlotViewModel(dialogService, new FragmentationSequenceViewModel(), 1.05, false);
// init test data
idList.Sort(new PrSm.PrSmScoreComparer());
var prsm = idList[0];
// init test ions
var ions = new ReactiveList <LabeledIonViewModel>();
spectrumPlotViewModel.Spectrum = prsm.Ms2Spectrum;
////spectrumPlotViewModel.Ions = ions;
// plot should not be null
Assert.NotNull(spectrumPlotViewModel.PlotModel);
// Give the PlotModel time to update
await MsPathFinderTest.SleepMillisecondsAsync(1000);
// plot should contain 1 stem series (the spectrum stem series)
Assert.True(spectrumPlotViewModel.PlotModel.Series.Count == 1);
}
