public MetaDraw()
{
UsefulProteomicsDatabases.Loaders.LoadElements();
InitializeComponent();
MetaDrawLogic = new MetaDrawLogic();
BindingOperations.EnableCollectionSynchronization(MetaDrawLogic.PsmResultFilePaths, MetaDrawLogic.ThreadLocker);
BindingOperations.EnableCollectionSynchronization(MetaDrawLogic.SpectraFilePaths, MetaDrawLogic.ThreadLocker);
BindingOperations.EnableCollectionSynchronization(MetaDrawLogic.FilteredListOfPsms, MetaDrawLogic.ThreadLocker);
BindingOperations.EnableCollectionSynchronization(MetaDrawLogic.PsmsGroupedByFile, MetaDrawLogic.ThreadLocker);
itemsControlSampleViewModel = new ParentChildScanPlotsView();
ParentChildScanViewPlots.DataContext = itemsControlSampleViewModel;
propertyView = new DataTable();
propertyView.Columns.Add("Name", typeof(string));
propertyView.Columns.Add("Value", typeof(string));
dataGridProperties.DataContext = propertyView.DefaultView;
dataGridScanNums.DataContext = MetaDrawLogic.PeptideSpectralMatchesView;
Title = "MetaDraw: version " + GlobalVariables.MetaMorpheusVersion;
base.Closing += this.OnClosing;
ParentChildScanView.Visibility = Visibility.Collapsed;
ParentScanView.Visibility = Visibility.Collapsed;
PsmStatPlotFiles = new ObservableCollection <string>();
selectSourceFileListBox.DataContext = PsmStatPlotFiles;
plotTypes = new ObservableCollection <string>();
SetUpPlots();
plotsListBox.ItemsSource = plotTypes;
}
public static void TestPsmFromTsvIonParsing()
{
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestPsmFromTsvIonParsing");
string proteinDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\P16858.fasta");
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\slicedMouse.raw");
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 PsmFromTsv matched ion properties
var lines = File.ReadAllLines(psmFile);
int ind = Array.IndexOf(lines[0].Split('\t'), "Matched Ion Mass-To-Charge Ratios");
var ionStrings = lines[1].Split('\t')[ind].Split(new char[] { ',', ';' })
.Select(p => p.Trim().Replace("[", string.Empty).Replace("]", string.Empty)).ToList();
var parsedIons = metadrawLogic.FilteredListOfPsms[0].MatchedIons;
for (int i = 0; i < ionStrings.Count; i++)
{
var ionString = ionStrings[i];
var parsedIon = parsedIons[i];
var split = ionString.Split(new char[] { '+', ':' });
string ion = split[0];
int charge = int.Parse(split[1]);
double mz = double.Parse(split[2]);
Assert.That(mz == parsedIon.Mz);
Assert.That(mz.ToMass(charge) == parsedIon.NeutralTheoreticalProduct.NeutralMass);
Assert.That(charge == parsedIon.Charge);
Assert.That(ion == parsedIon.NeutralTheoreticalProduct.ProductType.ToString() + parsedIon.NeutralTheoreticalProduct.FragmentNumber);
}
// delete output
Directory.Delete(outputFolder, true);
}
public static void TestMetaDrawLoadingWithWeirdFileNames()
{
// test loading when the file has a periods, commas, spaces in the name
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestMetaDrawLoadingWithWeirdFileNames");
string proteinDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\smalldb.fasta");
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SmallCalibratible_Yeast.mzML");
string pathWithPeriodInIt = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\S.m,al. lC,al.ib r.at,i ble_Ye.ast.mzML");
File.Copy(spectraFile, pathWithPeriodInIt, true);
spectraFile = pathWithPeriodInIt;
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.PsmResultFilePaths.Add(psmFile);
metadrawLogic.SpectraFilePaths.Add(pathWithPeriodInIt);
var errors = metadrawLogic.LoadFiles(true, true);
Assert.That(!errors.Any());
Assert.That(metadrawLogic.FilteredListOfPsms.First().FileNameWithoutExtension == "S.m,al. lC,al.ib r.at,i ble_Ye.ast");
var plotView = new OxyPlot.Wpf.PlotView();
var canvas = new Canvas();
var parentChildScanPlotsView = new ParentChildScanPlotsView();
// plot PSM
metadrawLogic.DisplaySpectrumMatch(plotView, canvas, metadrawLogic.FilteredListOfPsms.First(), parentChildScanPlotsView, out errors);
Assert.That(errors == null || !errors.Any());
// export to PDF
metadrawLogic.ExportToPdf(plotView, canvas, new List <PsmFromTsv> {
metadrawLogic.FilteredListOfPsms.First()
}, parentChildScanPlotsView, outputFolder, out errors);
Assert.That(!errors.Any());
// clean up resources
metadrawLogic.CleanUpResources();
// delete output
File.Delete(pathWithPeriodInIt);
Directory.Delete(outputFolder, true);
}
public static void MetaDrawLogicTestOglyco()
{
var metadrawLogic = new MetaDrawLogic();
string psmFile = @"TestData\oglyco.psmtsv";
metadrawLogic.PsmResultFilePaths.Add(psmFile);
var errors = metadrawLogic.LoadFiles(false, true);
Assert.That(!errors.Any());
}
public static void TestMetaDrawErrors()
{
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestMetaDrawErrors");
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 (skipping spectra file, to produce an error msg)
var metadrawLogic = new MetaDrawLogic();
metadrawLogic.PsmResultFilePaths.Add(psmFile);
// this should produce an error because an expected spectra file is not present
var errors = metadrawLogic.LoadFiles(loadSpectra: true, loadPsms: true);
Assert.That(errors.Any());
Assert.That(!metadrawLogic.FilteredListOfPsms.Any());
// this should not produce an error because we said not to load spectra
errors = metadrawLogic.LoadFiles(loadSpectra: false, loadPsms: true);
Assert.That(!errors.Any());
var psmsFromTsv = PsmTsvReader.ReadTsv(psmFile, out var warnings);
var plotView = new OxyPlot.Wpf.PlotView();
var canvas = new Canvas();
var parentChildScanPlotsView = new ParentChildScanPlotsView();
// plotting PSM should produce an error because spectra are not loaded
metadrawLogic.DisplaySpectrumMatch(plotView, canvas, psmsFromTsv.First(), parentChildScanPlotsView, out errors);
Assert.That(errors.Any());
// export to PDF should produce an error because spectra are not loaded
metadrawLogic.ExportToPdf(plotView, canvas, new List <PsmFromTsv> {
psmsFromTsv.First()
}, parentChildScanPlotsView, outputFolder, out errors);
Assert.That(errors.Any());
// clean up resources
metadrawLogic.CleanUpResources();
// delete output
Directory.Delete(outputFolder, true);
}
public static void IonsWithNoTerminusTest() //if internal fragments are selected using TerminusType == None, then "M" and "D" ions get lumped in and cause a crash
{
// load results into metadraw
var metadrawLogic = new MetaDrawLogic();
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlTestData\ms2mixed_bsa_xlink.mzML");
string psmFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"XlTestData\XL_Intralinks_MIons.tsv");
metadrawLogic.SpectraFilePaths.Add(spectraFile);
metadrawLogic.PsmResultFilePaths.Add(psmFile);
var errors = metadrawLogic.LoadFiles(true, true);
Assert.That(!errors.Any());
// draw sequence coverage for PSM
var sequenceText = new Canvas();
var map = new Canvas();
var psm = metadrawLogic.FilteredListOfPsms.First();
metadrawLogic.DrawSequenceCoverageMap(psm, sequenceText, map);
//test no errors
Assert.That(errors == null || !errors.Any());
}
public static void SequenceCoverageMapTest()
{
// load results into metadraw
var metadrawLogic = new MetaDrawLogic();
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\InternalTest.mgf");
string psmFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SequenceCoverageTestPSM.psmtsv");
metadrawLogic.SpectraFilePaths.Add(spectraFile);
metadrawLogic.PsmResultFilePaths.Add(psmFile);
var errors = metadrawLogic.LoadFiles(true, true);
Assert.That(!errors.Any());
// draw sequence coverage for PSM
var sequenceText = new Canvas();
var map = new Canvas();
var psm = metadrawLogic.FilteredListOfPsms.First();
metadrawLogic.DrawSequenceCoverageMap(psm, sequenceText, map);
//test no errors
Assert.That(errors == null || !errors.Any());
}
public static void TestMetaDrawWithSpectralLibrary()
{
string outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestMetaDrawWithSpectraLibrary");
string proteinDatabase = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\P16858.fasta");
string library1 = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\P16858_target.msp");
string library2 = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\P16858_decoy.msp");
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch\slicedMouse.raw");
Directory.CreateDirectory(outputFolder);
// run search task
var searchtask = new SearchTask();
searchtask.RunTask(outputFolder,
new List <DbForTask>
{
new DbForTask(proteinDatabase, false),
new DbForTask(library1, false),
new DbForTask(library2, 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);
metadrawLogic.SpectralLibraryPaths.Add(library1);
metadrawLogic.SpectralLibraryPaths.Add(library2);
var errors = metadrawLogic.LoadFiles(true, true);
Assert.That(!errors.Any());
// 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;
// test that library peaks were drawn in the mirror plot (these peaks have negative intensities)
var mirrorPlotPeaks = plotSeries.Where(p => ((LineSeries)p).Points[1].Y < 0).ToList();
Assert.That(mirrorPlotPeaks.Count == 52);
var plotAxes = plotView.Model.Axes;
Assert.That(plotAxes.Count == 2);
// write pdf
var psmsToExport = metadrawLogic.FilteredListOfPsms.Where(p => p.FullSequence == "VIHDNFGIVEGLMTTVHAITATQK").Take(1).ToList();
metadrawLogic.ExportToPdf(plotView, canvas, psmsToExport, parentChildView, outputFolder, out errors);
// test that pdf exists
Assert.That(File.Exists(Path.Combine(outputFolder, @"6_VIHDNFGIVEGLMTTVHAITATQK.pdf")));
// clean up resources
metadrawLogic.CleanUpResources();
Assert.That(!metadrawLogic.FilteredListOfPsms.Any());
Assert.That(!metadrawLogic.PsmResultFilePaths.Any());
Assert.That(!metadrawLogic.SpectraFilePaths.Any());
Assert.That(!metadrawLogic.SpectralLibraryPaths.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_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_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);
}
