private void TextBox_TextChanged(object sender, TextChangedEventArgs e)
{
string txt = (sender as TextBox).Text;
MetaDrawLogic.FilterPsmsByString(txt);
}
public static void MetaDraw_XlSearchTaskWithChildScansTest()
{
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"MetaDraw_XlSearchTaskTest");
string proteinDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlTestData\BSA.fasta");
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlTestData\ms2mixed_bsa_xlink.mzML");
// run task
CommonParameters commonParameters = new CommonParameters(dissociationType: DissociationType.CID, ms2childScanDissociationType: DissociationType.ETD,
trimMsMsPeaks: false);
Directory.CreateDirectory(outputFolder);
var xlSearchTask = new XLSearchTask()
{
CommonParameters = commonParameters
};
xlSearchTask.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(proteinDatabase, false)
}, new List <string> {
spectraFile
}, "");
//TODO: test other files (XL_Interlinks.tsv, Deadends.tsv, Looplinks.tsv, SinglePeptides.tsv)
var csmFile = Path.Combine(outputFolder, @"XL_Intralinks.tsv");
// load results into metadraw
var metadrawLogic = new MetaDrawLogic();
metadrawLogic.SpectraFilePaths.Add(spectraFile);
metadrawLogic.PsmResultFilePaths.Add(csmFile);
var errors = metadrawLogic.LoadFiles(true, true);
Assert.That(!errors.Any());
Assert.That(metadrawLogic.FilteredListOfPsms.Any());
// test results filter
MetaDrawSettings.QValueFilter = 0.01;
MetaDrawSettings.ShowDecoys = false;
metadrawLogic.FilterPsms();
Assert.That(metadrawLogic.FilteredListOfPsms.All(p => p.DecoyContamTarget == "T"));
Assert.That(metadrawLogic.FilteredListOfPsms.All(p => p.QValue <= 0.01));
// test text search filter (filter by full sequence)
string filterString = @"SLGKVGTR";
metadrawLogic.FilterPsmsByString(filterString);
int c = 0;
foreach (var filteredPsm in metadrawLogic.PeptideSpectralMatchesView)
{
var psmObj = (PsmFromTsv)filteredPsm;
Assert.That(psmObj.FullSequence.Contains(filterString));
c++;
}
Assert.That(c > 0);
// test text search filter (filter by MS2 scan number)
filterString = @"2";
metadrawLogic.FilterPsmsByString(filterString);
c = 0;
foreach (var filteredPsm in metadrawLogic.PeptideSpectralMatchesView)
{
var psmObj = (PsmFromTsv)filteredPsm;
Assert.That(psmObj.Ms2ScanNumber.ToString().Contains(filterString));
c++;
}
Assert.That(c > 0);
// draw PSM
var plotView = new OxyPlot.Wpf.PlotView();
var canvas = new Canvas();
var parentChildView = new ParentChildScanPlotsView();
var csm = metadrawLogic.FilteredListOfPsms.First();
metadrawLogic.DisplaySpectrumMatch(plotView, canvas, csm, parentChildView, out errors);
Assert.That(errors == null || !errors.Any());
// test that plot was drawn
var peak = (LineSeries)plotView.Model.Series[0]; // the first m/z peak
var peakPoints = peak.Points;
Assert.That(Math.Round(peakPoints[0].X, 2) == 142.12); // m/z
Assert.That(Math.Round(peakPoints[1].X, 2) == 142.12);
Assert.That((int)peakPoints[0].Y == 0); // intensity
Assert.That((int)peakPoints[1].Y == 1114);
var plotAxes = plotView.Model.Axes;
Assert.That(plotAxes.Count == 2);
// test that base sequence annotation was drawn
Assert.That(canvas.Children.Count > 0);
// test that the plots were drawn in the parent/child view
Assert.That(parentChildView.Plots.Count == 2);
// test parent scan
var parentPlot = parentChildView.Plots[0];
Assert.That(parentPlot.SpectrumLabel == "Scan: 2 Dissociation Type: CID MsOrder: 2 Selected Mz: 492.02 Retention Time: 23.9");
int numAnnotatedResidues = csm.BaseSeq.Length;
int numAnnotatedIons = csm.MatchedIons.Count(p => p.NeutralTheoreticalProduct.ProductType != ProductType.M);
int numAnnotatedMods = csm.FullSequence.Count(p => p == '[');
Assert.That(parentPlot.TheCanvas.Children.Count == numAnnotatedResidues + numAnnotatedIons + numAnnotatedMods);
peak = (LineSeries)parentPlot.Plot.Model.Series[0]; // the first m/z peak
peakPoints = peak.Points;
Assert.That(Math.Round(peakPoints[0].X, 2) == 142.12); // m/z
Assert.That(Math.Round(peakPoints[1].X, 2) == 142.12);
Assert.That((int)peakPoints[0].Y == 0); // intensity
Assert.That((int)peakPoints[1].Y == 1114);
// test child scan
var childPlot = parentChildView.Plots[1];
Assert.That(childPlot.SpectrumLabel == "Scan: 3 Dissociation Type: ETD MsOrder: 2 Selected Mz: 492.02 RetentionTime: 23.9");
Assert.That(childPlot.TheCanvas.Children.Count > 0);
numAnnotatedResidues = csm.BaseSeq.Length;
numAnnotatedIons = csm.ChildScanMatchedIons[3].Concat(csm.BetaPeptideChildScanMatchedIons[3])
.Count(p => p.NeutralTheoreticalProduct.ProductType != ProductType.M);
numAnnotatedMods = csm.FullSequence.Count(p => p == '[');
Assert.That(childPlot.TheCanvas.Children.Count == numAnnotatedResidues + numAnnotatedIons + numAnnotatedMods);
peak = (LineSeries)childPlot.Plot.Model.Series[0]; // the first m/z peak
peakPoints = peak.Points;
Assert.That(Math.Round(peakPoints[0].X, 2) == 122.92); // m/z
Assert.That(Math.Round(peakPoints[1].X, 2) == 122.92);
Assert.That((int)peakPoints[0].Y == 0); // intensity
Assert.That((int)peakPoints[1].Y == 857);
// write pdf
var psmsToExport = metadrawLogic.FilteredListOfPsms.Where(p => p.FullSequence == "SLGKVGTR(4)").ToList();
metadrawLogic.ExportToPdf(plotView, canvas, psmsToExport, parentChildView, outputFolder, out errors);
// test that pdf exists
Assert.That(File.Exists(Path.Combine(outputFolder, @"2_SLGKVGTR(4).pdf"))); // parent scan
Assert.That(File.Exists(Path.Combine(outputFolder, @"3_SLGKVGTR(4).pdf"))); // child scan
// clean up resources
metadrawLogic.CleanUpResources();
Assert.That(!metadrawLogic.FilteredListOfPsms.Any());
Assert.That(!metadrawLogic.PsmResultFilePaths.Any());
Assert.That(!metadrawLogic.SpectraFilePaths.Any());
// delete output
Directory.Delete(outputFolder, true);
}
public static void MetaDraw_GlycoSearchTaskWithChildScansTest()
{
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"MetaDraw_GlycoSearchTaskTest");
string proteinDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\leukosialin.fasta");
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\sliced_glyco_hcd_ethcd.raw");
// run task
CommonParameters commonParameters = new CommonParameters(dissociationType: DissociationType.HCD, ms2childScanDissociationType: DissociationType.EThcD);
Directory.CreateDirectory(outputFolder);
var glycoSearchTask = new GlycoSearchTask()
{
CommonParameters = commonParameters
};
glycoSearchTask.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(proteinDatabase, false)
}, new List <string> {
spectraFile
}, "");
var psmFile = Path.Combine(outputFolder, @"oglyco.psmtsv");
// load results into metadraw
var metadrawLogic = new MetaDrawLogic();
metadrawLogic.SpectraFilePaths.Add(spectraFile);
metadrawLogic.PsmResultFilePaths.Add(psmFile);
var errors = metadrawLogic.LoadFiles(true, true);
Assert.That(!errors.Any());
Assert.That(metadrawLogic.FilteredListOfPsms.Any());
// test results filter
MetaDrawSettings.QValueFilter = 0.01;
MetaDrawSettings.ShowDecoys = false;
metadrawLogic.FilterPsms();
Assert.That(metadrawLogic.FilteredListOfPsms.All(p => p.DecoyContamTarget == "T"));
Assert.That(metadrawLogic.FilteredListOfPsms.All(p => p.QValue <= 0.01));
// test text search filter (filter by full sequence)
string filterString = @"STTAVQ";
metadrawLogic.FilterPsmsByString(filterString);
int c = 0;
foreach (var filteredPsm in metadrawLogic.PeptideSpectralMatchesView)
{
var psmObj = (PsmFromTsv)filteredPsm;
Assert.That(psmObj.FullSequence.Contains(filterString));
c++;
}
Assert.Greater(c, 0);
// test text search filter (filter by MS2 scan number)
filterString = @"2";
metadrawLogic.FilterPsmsByString(filterString);
c = 0;
foreach (var filteredPsm in metadrawLogic.PeptideSpectralMatchesView)
{
var psmObj = (PsmFromTsv)filteredPsm;
Assert.That(psmObj.Ms2ScanNumber.ToString().Contains(filterString));
c++;
}
Assert.Greater(c, 0);
// draw PSM
var plotView = new OxyPlot.Wpf.PlotView();
var canvas = new Canvas();
var parentChildView = new ParentChildScanPlotsView();
var psm = metadrawLogic.FilteredListOfPsms.First();
metadrawLogic.DisplaySpectrumMatch(plotView, canvas, psm, parentChildView, out errors);
Assert.That(errors == null || !errors.Any());
// test that plot was drawn
var peak = (LineSeries)plotView.Model.Series[0]; // the first m/z peak
var peakPoints = peak.Points;
Assert.That(Math.Round(peakPoints[0].X, 2) == 101.07); // m/z
Assert.That(Math.Round(peakPoints[1].X, 2) == 101.07);
Assert.That((int)peakPoints[0].Y == 0); // intensity
Assert.That((int)peakPoints[1].Y == 3847);
var plotAxes = plotView.Model.Axes;
Assert.AreEqual(2, plotAxes.Count);
// test that base sequence annotation was drawn
Assert.Greater(canvas.Children.Count, 0);
// test that the plots were drawn in the parent/child view
Assert.AreEqual(2, parentChildView.Plots.Count);
// test parent scan
var parentPlot = parentChildView.Plots[0];
Assert.AreEqual("Scan: 27 Dissociation Type: HCD MsOrder: 2 Selected Mz: 924.12 Retention Time: 32.65", parentPlot.SpectrumLabel);
int numAnnotatedResidues = psm.BaseSeq.Length;
int numAnnotatedIons = psm.MatchedIons.Count(p => p.NeutralTheoreticalProduct.ProductType != ProductType.M &&
p.NeutralTheoreticalProduct.ProductType != ProductType.D);
int numAnnotatedMods = psm.FullSequence.Count(p => p == '[');
Assert.AreEqual(numAnnotatedResidues + numAnnotatedIons + numAnnotatedMods, parentPlot.TheCanvas.Children.Count);
peak = (LineSeries)parentPlot.Plot.Model.Series[0]; // the first m/z peak
peakPoints = peak.Points;
Assert.AreEqual(101.07, Math.Round(peakPoints[0].X, 2)); // m/z
Assert.AreEqual(101.07, (Math.Round(peakPoints[1].X, 2)));
Assert.AreEqual(0, (int)peakPoints[0].Y); // intensity
Assert.AreEqual(3847, (int)peakPoints[1].Y);
// test child scan
var childPlot = parentChildView.Plots[1];
Assert.AreEqual("Scan: 30 Dissociation Type: EThcD MsOrder: 2 Selected Mz: 924.12 RetentionTime: 32.66",
childPlot.SpectrumLabel);
Assert.Greater(childPlot.TheCanvas.Children.Count, 0);
numAnnotatedResidues = psm.BaseSeq.Length;
numAnnotatedIons = psm.ChildScanMatchedIons[30]
.Count(p => p.NeutralTheoreticalProduct.ProductType != ProductType.M &&
p.NeutralTheoreticalProduct.ProductType != ProductType.D);
numAnnotatedMods = psm.FullSequence.Count(p => p == '[');
Assert.AreEqual(numAnnotatedResidues + numAnnotatedIons + numAnnotatedMods, childPlot.TheCanvas.Children.Count);
peak = (LineSeries)childPlot.Plot.Model.Series[0]; // the first m/z peak
peakPoints = peak.Points;
Assert.AreEqual(126.06, Math.Round(peakPoints[0].X, 2)); // m/z
Assert.AreEqual(126.06, Math.Round(peakPoints[1].X, 2));
Assert.AreEqual(0, (int)peakPoints[0].Y); // intensity
Assert.AreEqual(8496, (int)peakPoints[1].Y);
// write pdf
var psmsToExport = metadrawLogic.FilteredListOfPsms.Where(p => p.FullSequence == "STTAVQTPTSGEPLVST[O-Glycosylation:H1N1 on X]SEPLSSK").ToList();
metadrawLogic.ExportToPdf(plotView, canvas, psmsToExport, parentChildView, outputFolder, out errors);
// test that pdf exists
Assert.That(File.Exists(Path.Combine(outputFolder, @"27_STTAVQTPTSGEPLVST[O-Glycosylat.pdf"))); // parent scan
Assert.That(File.Exists(Path.Combine(outputFolder, @"30_STTAVQTPTSGEPLVST[O-Glycosylat.pdf"))); // child scan
// clean up resources
metadrawLogic.CleanUpResources();
Assert.That(!metadrawLogic.FilteredListOfPsms.Any());
Assert.That(!metadrawLogic.PsmResultFilePaths.Any());
Assert.That(!metadrawLogic.SpectraFilePaths.Any());
// delete output
Directory.Delete(outputFolder, true);
}
public static void MetaDraw_SearchTaskTest()
{
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"MetaDraw_SearchTaskTest");
string proteinDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\smalldb.fasta");
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML");
Directory.CreateDirectory(outputFolder);
// run search task
var searchtask = new SearchTask();
searchtask.RunTask(outputFolder, new List <DbForTask> {
new DbForTask(proteinDatabase, false)
}, new List <string> {
spectraFile
}, "");
var psmFile = Path.Combine(outputFolder, @"AllPSMs.psmtsv");
// load results into metadraw
var metadrawLogic = new MetaDrawLogic();
metadrawLogic.SpectraFilePaths.Add(spectraFile);
metadrawLogic.PsmResultFilePaths.Add(psmFile);
var errors = metadrawLogic.LoadFiles(true, true);
Assert.That(!errors.Any());
Assert.That(metadrawLogic.FilteredListOfPsms.Any());
// test results filter
MetaDrawSettings.QValueFilter = 0.01;
MetaDrawSettings.ShowDecoys = false;
metadrawLogic.FilterPsms();
Assert.That(metadrawLogic.FilteredListOfPsms.All(p => p.DecoyContamTarget == "T"));
Assert.That(metadrawLogic.FilteredListOfPsms.All(p => p.QValue <= 0.01));
MetaDrawSettings.QValueFilter = 1.0;
MetaDrawSettings.ShowDecoys = true;
metadrawLogic.FilterPsms();
Assert.That(metadrawLogic.FilteredListOfPsms.Any(p => p.DecoyContamTarget == "D"));
Assert.That(metadrawLogic.FilteredListOfPsms.Any(p => p.QValue > 0.01));
// test text search filter (filter by full sequence)
string filterString = @"QIVHDSGR";
metadrawLogic.FilterPsmsByString(filterString);
int c = 0;
foreach (var filteredPsm in metadrawLogic.PeptideSpectralMatchesView)
{
var psmObj = (PsmFromTsv)filteredPsm;
Assert.That(psmObj.FullSequence.Contains(filterString));
c++;
}
Assert.That(c > 0);
// test text search filter (filter by MS2 scan number)
filterString = @"120";
metadrawLogic.FilterPsmsByString(filterString);
c = 0;
foreach (var filteredPsm in metadrawLogic.PeptideSpectralMatchesView)
{
var psmObj = (PsmFromTsv)filteredPsm;
Assert.That(psmObj.Ms2ScanNumber.ToString().Contains(filterString));
c++;
}
Assert.That(c > 0);
// draw PSM
var plotView = new OxyPlot.Wpf.PlotView();
var canvas = new Canvas();
var parentChildView = new ParentChildScanPlotsView();
var psm = metadrawLogic.FilteredListOfPsms.First();
metadrawLogic.DisplaySpectrumMatch(plotView, canvas, psm, parentChildView, out errors);
Assert.That(errors == null || !errors.Any());
// test that plot was drawn
var plotSeries = plotView.Model.Series;
var series = plotSeries[0]; // the first m/z peak
var peakPoints = ((LineSeries)series).Points;
Assert.That(Math.Round(peakPoints[0].X, 2) == 101.07); // m/z
Assert.That(Math.Round(peakPoints[1].X, 2) == 101.07);
Assert.That((int)peakPoints[0].Y == 0); // intensity
Assert.That((int)peakPoints[1].Y == 35045);
var plotAxes = plotView.Model.Axes;
Assert.That(plotAxes.Count == 2);
// test that base sequence annotation was drawn
int numAnnotatedResidues = psm.BaseSeq.Length;
int numAnnotatedIons = psm.MatchedIons.Count;
int numAnnotatedMods = psm.FullSequence.Count(p => p == '[');
Assert.That(canvas.Children.Count == numAnnotatedResidues + numAnnotatedIons + numAnnotatedMods);
// write pdf
var psmsToExport = metadrawLogic.FilteredListOfPsms.Where(p => p.FullSequence == "QIVHDSGR").Take(3).ToList();
metadrawLogic.ExportToPdf(plotView, canvas, psmsToExport, parentChildView, outputFolder, out errors);
// test that pdf exists
Assert.That(File.Exists(Path.Combine(outputFolder, @"116_QIVHDSGR.pdf")));
Assert.That(File.Exists(Path.Combine(outputFolder, @"120_QIVHDSGR.pdf")));
Assert.That(File.Exists(Path.Combine(outputFolder, @"127_QIVHDSGR.pdf")));
// test displaying a PSM with a mod
var modPsm = metadrawLogic.FilteredListOfPsms.First(p => p.FullSequence.Contains("["));
metadrawLogic.DisplaySpectrumMatch(plotView, canvas, modPsm, parentChildView, out errors);
Assert.That(errors == null || !errors.Any());
Assert.That(canvas.Children.Count == modPsm.BaseSeq.Length + modPsm.MatchedIons.Count + modPsm.FullSequence.Count(p => p == '['));
// clean up resources
metadrawLogic.CleanUpResources();
Assert.That(!metadrawLogic.FilteredListOfPsms.Any());
Assert.That(!metadrawLogic.PsmResultFilePaths.Any());
Assert.That(!metadrawLogic.SpectraFilePaths.Any());
// delete output
Directory.Delete(outputFolder, true);
}
