public void TestDisplaySpectra(string rawFile, string idFile)
{
// init
var idFileReader = IdFileReaderFactory.CreateReader(idFile);
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);
}
idList.Sort(new PrSm.PrSmScoreComparer());
var prsm = idList[0];
// init XicPlotViewModel
var dialogService = new TestableMainDialogService();
var spectrumViewModel = new SpectrumViewModel(dialogService, lcms);
// init test ions
var baseIonTypes = new List <BaseIonType> {
BaseIonType.B, BaseIonType.Y
};
var neutralLosses = new List <NeutralLoss> {
NeutralLoss.NoLoss
};
const int charge = 1;
const int minCharge = 1, maxCharge = 2;
var ionTypeFactory = new IonTypeFactory(maxCharge);
var ionTypes = IonUtils.GetIonTypes(ionTypeFactory, baseIonTypes, neutralLosses, minCharge, maxCharge);
var ions = IonUtils.GetFragmentIonLabels(prsm.Sequence, charge, ionTypes);
var ionVms = ions.Select(label => new LabeledIonViewModel(label.Composition, label.IonType, label.IsFragmentIon, lcms, label.PrecursorIon, label.IsChargeState, label.Index)).ToList();
}
public void 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);
// plot should contain 1 stem series (the spectrum stem series)
Assert.True(spectrumPlotViewModel.PlotModel.Series.Count == 1);
}
public void TestClearFilters()
{
// init test data
var idFileReader = IdFileReaderFactory.CreateReader(idFile);
var ids = idFileReader.Read();
var idList = ids.ToList();
foreach (var id in idList)
{
id.LcMs = null;
id.RawFileName = Path.GetFileNameWithoutExtension(rawFile);
}
var prsms = idList;
// init scan vm
var scanVm = new ScanViewModel(new TestableMainDialogService(), prsms);
scanVm.ClearFilters();
// add filters
////scanVm.AddFilter("Sequence", "EAQ");
var sequenceFilter = scanVm.Filters.FirstOrDefault(x => x.Name == "Sequence") as MultiValueFilterViewModel;
Assert.NotNull(sequenceFilter);
sequenceFilter.Values.Add("EAQ");
/////scanVm.AddFilter("Protein", "YLR");
var proteinFilter =
scanVm.Filters.FirstOrDefault(x => x.Name == "Protein Name") as MultiValueFilterViewModel;
Assert.NotNull(proteinFilter);
sequenceFilter.Values.Add("YLR");
// Sanity check: there should be fewer PrSms than before
Assert.True(scanVm.FilteredData.Length < prsms.Count);
// Clear filters
scanVm.ClearFilters();
// All prsms should now be showing
Assert.True(scanVm.FilteredData.Length == prsms.Count);
}
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 void TestMassExportPeakLists(string rawFile, string idFile)
{
// Read files
var lcms = PbfLcMsRun.GetLcMsRun(rawFile);
var idFileReader = IdFileReaderFactory.CreateReader(idFile);
var ids = idFileReader.Read();
foreach (var id in ids)
{
id.LcMs = lcms;
id.RawFileName = Path.GetFileNameWithoutExtension(rawFile);
}
var dirPath = @"C:\Users\wilk011\Documents\DataFiles\TestResults\ExporterTest";
Directory.CreateDirectory(dirPath);
var exporter = new SpectrumPeakExporter(dirPath);
exporter.Export(ids.ToList());
}
public void TestHideUnidentifedScans()
{
// init test data
var idFileReader = IdFileReaderFactory.CreateReader(idFile);
var ids = idFileReader.Read();
var idList = ids.ToList();
var lcms = PbfLcMsRun.GetLcMsRun(rawFile);
foreach (var id in idList)
{
id.LcMs = lcms;
id.RawFileName = Path.GetFileNameWithoutExtension(rawFile);
}
var scans = lcms.GetScanNumbers(2);
foreach (var scan in scans)
{
idList.Add(new PrSm {
Scan = scan, LcMs = lcms, RawFileName = Path.GetFileNameWithoutExtension(rawFile), Score = double.NaN
});
}
var prsms = idList;
// init scan vm
var scanVm = new ScanViewModel(new TestableMainDialogService(), prsms);
scanVm.ClearFilters();
Assert.AreEqual(prsms.Count, scanVm.FilteredData.Length);
////scanVm.HideUnidentifiedScans = true;
Assert.True(prsms.Count > scanVm.FilteredData.Length);
}
/// <summary>
/// Implementation for <see cref="StartMsPfSearchCommand" />.
/// Gets a command that starts an MSPathFinder with this data set.
/// </summary>
private void StartMsPfSearchImplementation()
{
var searchSettings = new SearchSettingsViewModel(this.dialogService, this.MsPfParameters)
{
SpectrumFilePath = this.rawFilePath,
SelectedSearchMode = InternalCleavageType.SingleInternalCleavage,
FastaDbFilePath = this.FastaDbFilePath,
OutputFilePath = string.Format("{0}\\{1}", Directory.GetCurrentDirectory(), this.Title),
SelectedSequence = this.SelectedPrSm.Sequence.Aggregate(string.Empty, (current, aa) => current + aa.Residue)
};
// Set feature file path.
if (this.FeatureMapViewModel != null)
{
searchSettings.FeatureFilePath = this.FeatureMapViewModel.FeatureFilePath;
}
// Select the correct protein
if (searchSettings.FastaEntries.Count > 0)
{
foreach (var entry in searchSettings.FastaEntries)
{
entry.Selected = entry.ProteinName == this.SelectedPrSm.ProteinName;
}
}
// Set scan number of selected spectrum
var scanNum = 0;
if (this.SpectrumViewModel.Ms2SpectrumViewModel.Spectrum != null)
{
scanNum = this.SpectrumViewModel.Ms2SpectrumViewModel.Spectrum.ScanNum;
searchSettings.MinScanNumber = scanNum;
searchSettings.MaxScanNumber = scanNum;
}
// TODO: change this so it doesn't use an event and isn't void async
searchSettings.ReadyToClose += async(o, e) =>
{
if (searchSettings.Status)
{
var idFileReader = IdFileReaderFactory.CreateReader(searchSettings.GetIdFilePath());
var prsms = await idFileReader.ReadAsync();
var prsmList = prsms.ToList();
foreach (var prsm in prsmList)
{
prsm.LcMs = this.LcMs;
}
prsmList.Sort(new PrSm.PrSmScoreComparer());
this.ScanViewModel.Data.AddRange(prsmList);
var scanPrsms = prsmList.Where(prsm => prsm.Scan == scanNum).ToList();
if (scanNum > 0 && scanPrsms.Count > 0)
{
this.SelectedPrSm = scanPrsms[0];
}
else if (prsmList.Count > 0)
{
this.SelectedPrSm = prsmList[0];
}
}
};
this.dialogService.SearchSettingsWindow(searchSettings);
}
public void TestIsotopePeakAlignment(string rawFilePath, string idFilePath)
{
var idFileReader = IdFileReaderFactory.CreateReader(idFilePath);
var lcms = PbfLcMsRun.GetLcMsRun(rawFilePath);
var ids = idFileReader.Read();
var idList = ids.ToList();
var rawFileName = Path.GetFileNameWithoutExtension(rawFilePath);
foreach (var id in idList)
{
id.LcMs = lcms;
id.RawFileName = rawFileName;
}
var prsms = idList.Where(prsm => prsm.Sequence.Count > 0);
const double relIntThres = 0.1;
var tolerance = new Tolerance(10, ToleranceUnit.Ppm);
var toleranceValue = tolerance.GetValue();
const int maxCharge = 15;
var ionTypeFactory = new IonTypeFactory(maxCharge);
var ionTypes = ionTypeFactory.GetAllKnownIonTypes().ToArray();
var psmsValidated = 0;
var ionsValidated = 0;
var validationErrors = new List <string>();
foreach (var prsm in prsms)
{
foreach (var ionType in ionTypes)
{
var composition = prsm.Sequence.Aggregate(Composition.Zero, (current, aa) => current + aa.Composition);
var ion = ionType.GetIon(composition);
var observedPeaks = prsm.Ms2Spectrum.GetAllIsotopePeaks(ion, tolerance, relIntThres);
if (observedPeaks == null)
{
continue;
}
var errors = IonUtils.GetIsotopePpmError(observedPeaks, ion, relIntThres);
foreach (var error in errors)
{
if (error == null)
{
continue;
}
if (error > toleranceValue)
{
validationErrors.Add(string.Format("In scan {0}, PSM {1} has error {2:F1} for ion at {3} m/z",
prsm.Scan, prsm.SequenceText, error, ion.GetIsotopeMz(0)));
}
ionsValidated++;
}
}
psmsValidated++;
}
Console.WriteLine("Validated {0:N0} ions for {1:N0} PSMs", ionsValidated, psmsValidated);
if (validationErrors.Count <= 0)
{
return;
}
var validationMsg = string.Format("{0} ions had errors greater than {1} ppm", validationErrors.Count, tolerance);
Console.WriteLine(validationMsg);
foreach (var item in validationErrors.Take(10))
{
Console.WriteLine(item);
}
Assert.Fail(validationMsg);
}
