protected override void DoTest()
{
// Skyline Targeted Method Refinement
var folderMethodRefine = UseRawFiles ? "MethodRefine" : "MethodRefineMzml"; // Not L10N
// Results Data, p. 2
var doc = SkylineWindow.Document;
RunUI(() => SkylineWindow.OpenFile(TestFilesDirs[1].GetTestPath(folderMethodRefine + @"\WormUnrefined.sky"))); // Not L10N
WaitForDocumentChangeLoaded(doc);
RunUI(() =>
{
// Adjust font sizes for better screen shots
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.SpectrumFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].Nodes[0];
SkylineWindow.AutoZoomBestPeak(); // TODO: Mention this in the tutorial
SkylineWindow.Size = new Size(1160, 660);
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode.Text, "YLGAYLLATLGGNASPSAQDVLK"); // Not L10N
});
PauseForScreenShot("Main window", 2);
// TODO: Update tutorial to view b-ions.
RunUI(() => SkylineWindow.GraphSpectrumSettings.ShowBIons = true);
// Unrefined Methods, p. 3
{
var exportDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportDlg.ExportStrategy = ExportStrategy.Buckets;
exportDlg.MethodType = ExportMethodType.Standard;
exportDlg.OptimizeType = ExportOptimize.NONE;
exportDlg.MaxTransitions = 59;
});
PauseForScreenShot("Export Transition List form", 3); // Not L10N
OkDialog(exportDlg, () => exportDlg.OkDialog(TestFilesDirs[1].GetTestPath(folderMethodRefine + @"\worm"))); // Not L10N
}
for (int i = 1; i < 10; i++)
{
Assert.IsTrue(File.Exists(TestFilesDirs[1].GetTestPath(folderMethodRefine + @"\worm_000" + i + TextUtil.EXT_CSV))); // Not L10N
}
for (int i = 10; i < 40; i++)
{
Assert.IsTrue(File.Exists(TestFilesDirs[1].GetTestPath(folderMethodRefine + @"\worm_00" + i + TextUtil.EXT_CSV))); // Not L10N
}
// Importing Multiple Injection Data, p. 4
Assert.IsTrue(SkylineWindow.Document.Settings.HasResults);
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, manageResultsDlg =>
{
manageResultsDlg.RemoveReplicates();
Assert.AreEqual(manageResultsDlg.Chromatograms.ToArray().Length, 0);
manageResultsDlg.OkDialog();
});
RunUI(() => SkylineWindow.SaveDocument());
Assert.IsFalse(SkylineWindow.Document.Settings.HasResults);
const string replicateName = "Unrefined"; // Not L10N
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg =>
{
importResultsDlg.RadioAddNewChecked = true;
var namedPathSets = DataSourceUtil.GetDataSourcesInSubdirs(TestFilesDirs[0].FullPath).ToArray();
importResultsDlg.NamedPathSets =
new[] { new KeyValuePair <string, MsDataFileUri[]>(replicateName, namedPathSets[0].Value.Take(15).ToArray()) };
importResultsDlg.OkDialog();
});
WaitForOpenForm <AllChromatogramsGraph>(); // To make the AllChromatogramsGraph form accessible to the SkylineTester forms tab
PauseForScreenShot <AllChromatogramsGraph>("Loading Chromatograms: Take screenshot at about 25% loaded...", 5);
WaitForCondition(15 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 15 minutes
Assert.IsTrue(SkylineWindow.Document.Settings.HasResults);
Assert.AreEqual(15, SkylineWindow.Document.Settings.MeasuredResults.CachedFilePaths.ToArray().Length);
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg =>
{
importResultsDlg.RadioAddExistingChecked = true;
var namedPathSets = DataSourceUtil.GetDataSourcesInSubdirs(TestFilesDirs[0].FullPath).ToArray();
importResultsDlg.NamedPathSets =
new[] { new KeyValuePair <string, MsDataFileUri[]>(replicateName, namedPathSets[0].Value.Skip(15).ToArray()) };
importResultsDlg.OkDialog();
});
WaitForCondition(20 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 15 minutes
Assert.AreEqual(39, SkylineWindow.Document.Settings.MeasuredResults.CachedFilePaths.ToArray().Length);
RunUI(SkylineWindow.AutoZoomNone);
RestoreViewOnScreen(7);
PauseForScreenShot("Chromatogram graph metafile", 7);
// Simple Manual Refinement, p. 6
int startingNodeCount = SkylineWindow.SequenceTree.Nodes[0].GetNodeCount(false);
Assert.AreEqual("YLGAYLLATLGGNASPSAQDVLK", SkylineWindow.SequenceTree.Nodes[0].Nodes[0].Text); // Not L10N
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].Nodes[0];
SkylineWindow.AutoZoomNone();
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.EditDelete();
SkylineWindow.ShowRTLinearRegressionGraph();
});
Assert.AreEqual(SkylineWindow.SequenceTree.Nodes[0].GetNodeCount(false), startingNodeCount - 1);
Assert.AreEqual("VLEAGGLDCDMENANSVVDALK", SkylineWindow.SequenceTree.Nodes[0].Nodes[0].Text); // Not L10N
PauseForScreenShot("Retention Times Regression plot metafile", 8);
RunDlg <RegressionRTThresholdDlg>(SkylineWindow.ShowRegressionRTThresholdDlg, rtThresholdDlg =>
{
rtThresholdDlg.Threshold = 0.95;
rtThresholdDlg.OkDialog();
});
WaitForConditionUI(() => SkylineWindow.RTGraphController.RegressionRefined != null);
WaitForGraphs();
PauseForScreenShot("Retention Times Regression plot metafile with 0.95 threshold", 9); // Not L10N
TestRTResidualsSwitch();
RunDlg <EditRTDlg>(SkylineWindow.CreateRegression, editRTDlg => editRTDlg.OkDialog());
RunUI(() => SkylineWindow.ShowGraphRetentionTime(false));
RunUI(SkylineWindow.AutoZoomNone);
PauseForScreenShot("Chromatogram graph metafile zoomed out", 10); // Not L10N
// Missing Data, p. 10
RunUI(() =>
{
SkylineWindow.RTGraphController.SelectPeptide(SkylineWindow.Document.GetPathTo(1, 163));
Assert.AreEqual("YLAEVASEDR", SkylineWindow.SequenceTree.SelectedNode.Text); // Not L10N
});
RestoreViewOnScreen(11);
// Restoring the view changes the selection
RunUI(SkylineWindow.CollapsePeptides);
FindNode("YLAEVASEDR");
RunUI(() => SkylineWindow.SequenceTree.TopNode = SkylineWindow.SequenceTree.Nodes[0].Nodes[153]);
PauseForScreenShot("Targets view clipped from the main window", 11);
RunUI(() =>
{
var nodePep = (PeptideDocNode)((SrmTreeNode)SkylineWindow.SequenceTree.SelectedNode).Model;
Assert.AreEqual(null,
nodePep.GetPeakCountRatio(
SkylineWindow.SequenceTree.GetDisplayResultsIndex(nodePep)));
SkylineWindow.SequenceTree.SelectedPath = SkylineWindow.Document.GetPathTo(1, 157);
Assert.AreEqual("VTVVDDQSVILK", SkylineWindow.SequenceTree.SelectedNode.Text);
});
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.ActivateReplicate("Unrefined");
SkylineWindow.AutoZoomNone();
});
PauseForScreenShot("Unrefined chromatogram graph page clipped from main window", 12); // Not L10N
// foreach (var peptideDocNode in SkylineWindow.Document.Peptides)
// {
// var nodeGroup = ((TransitionGroupDocNode)peptideDocNode.Children[0]);
// Console.WriteLine("{0} - {1}", peptideDocNode.Peptide.Sequence,
// nodeGroup.GetDisplayText(SkylineWindow.SequenceTree.GetDisplaySettings(peptideDocNode)));
// }
// Console.WriteLine("---------------------------------");
RunUI(() =>
{
var graphChrom = SkylineWindow.GetGraphChrom("Unrefined"); // Not L10N
Assert.AreEqual(2, graphChrom.Files.Count);
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0];
// Picking Measurable Peptides and Transitions, p. 12
SkylineWindow.ExpandPeptides();
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].Nodes[0];
});
RunUI(SkylineWindow.AutoZoomBestPeak);
RestoreViewOnScreen(13);
RunUI(() => SkylineWindow.ShowGraphSpectrum(false));
PauseForScreenShot("Targets view clipped from the main window and chromatogram graph metafile", 13);
RunUI(() => SkylineWindow.ShowGraphSpectrum(true));
PauseForScreenShot("Library Match plot metafile", 14);
RunUI(() =>
{
SkylineWindow.ShowGraphSpectrum(false);
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Transitions, 0);
SkylineWindow.SelectedNode.Expand();
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
});
PauseForScreenShot("Targetes view clipped from the main window", 14); // Not L10N
RunUI(() =>
{
double dotpExpect = Math.Round(Statistics.AngleToNormalizedContrastAngle(0.78), 2); // 0.57
AssertEx.Contains(SkylineWindow.SequenceTree.SelectedNode.Nodes[0].Text,
dotpExpect.ToString(LocalizationHelper.CurrentCulture));
SkylineWindow.EditDelete();
dotpExpect = 0.34; // Math.Round(Statistics.AngleToNormalizedContrastAngle(0.633), 2); // 0.44
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].Nodes[0];
AssertEx.Contains(SkylineWindow.SequenceTree.SelectedNode.Nodes[0].Text,
dotpExpect.ToString(LocalizationHelper.CurrentCulture));
SkylineWindow.EditDelete();
PeptideTreeNode nodePep;
for (int i = 0; i < 2; i++)
{
nodePep = (PeptideTreeNode)SkylineWindow.SequenceTree.Nodes[0].Nodes[i];
nodePep.ExpandAll();
foreach (TransitionTreeNode nodeTran in nodePep.Nodes[0].Nodes)
{
TransitionDocNode nodeTranDoc = (TransitionDocNode)nodeTran.Model;
Assert.AreEqual((int)SequenceTree.StateImageId.peak,
TransitionTreeNode.GetPeakImageIndex(nodeTranDoc,
(PeptideDocNode)nodePep.Model,
SkylineWindow.SequenceTree));
var resultsIndex = SkylineWindow.SequenceTree.GetDisplayResultsIndex(nodePep);
var rank = nodeTranDoc.GetPeakRank(resultsIndex);
if (rank == null || rank > 3)
{
SkylineWindow.SequenceTree.SelectedNode = nodeTran;
}
SkylineWindow.SequenceTree.KeysOverride = Keys.Control;
}
}
nodePep = (PeptideTreeNode)SkylineWindow.SequenceTree.Nodes[0].Nodes[2];
nodePep.ExpandAll();
foreach (TransitionTreeNode nodeTran in nodePep.Nodes[0].Nodes)
{
TransitionDocNode nodeTranDoc = (TransitionDocNode)nodeTran.Model;
Assert.AreEqual((int)SequenceTree.StateImageId.peak,
TransitionTreeNode.GetPeakImageIndex(nodeTranDoc,
(PeptideDocNode)nodePep.Model,
SkylineWindow.SequenceTree));
var name = ((TransitionDocNode)nodeTran.Model).FragmentIonName;
if (!(name == "y11" || name == "y13" || name == "y14")) // Not L10N
{
SkylineWindow.SequenceTree.SelectedNode = nodeTran;
}
SkylineWindow.SequenceTree.KeysOverride = Keys.Control;
}
SkylineWindow.SequenceTree.KeysOverride = Keys.None;
SkylineWindow.EditDelete();
for (int i = 0; i < 3; i++)
{
Assert.IsTrue(SkylineWindow.SequenceTree.Nodes[0].Nodes[i].Nodes[0].Nodes.Count == 3);
}
SkylineWindow.AutoZoomNone();
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Transitions, 5);
SkylineWindow.Size = new Size(722, 449);
});
RunUI(SkylineWindow.AutoZoomBestPeak);
RestoreViewOnScreen(15);
PauseForScreenShot("Targetes view clipped from main window and chromatogram graph metafile", 15);
// Automated Refinement, p. 16
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, refineDlg =>
{
refineDlg.MaxTransitionPeakRank = 3;
refineDlg.PreferLargerIons = true;
refineDlg.RemoveMissingResults = true;
refineDlg.RTRegressionThreshold = 0.95;
refineDlg.DotProductThreshold = Statistics.AngleToNormalizedContrastAngle(0.95); // Convert from original cos(angle) dot-product
refineDlg.OkDialog();
});
WaitForCondition(() => SkylineWindow.Document.PeptideCount < 73);
// foreach (var peptideDocNode in SkylineWindow.Document.Peptides)
// {
// var nodeGroup = ((TransitionGroupDocNode) peptideDocNode.Children[0]);
// Console.WriteLine("{0} - {1}", peptideDocNode.Peptide.Sequence,
// nodeGroup.GetDisplayText(SkylineWindow.SequenceTree.GetDisplaySettings(peptideDocNode)));
// }
RunUI(() =>
{
Assert.AreEqual(72, SkylineWindow.Document.PeptideCount);
Assert.AreEqual(216, SkylineWindow.Document.PeptideTransitionCount);
SkylineWindow.CollapsePeptides();
SkylineWindow.Undo();
});
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, refineDlg =>
{
refineDlg.MaxTransitionPeakRank = 6;
refineDlg.RemoveMissingResults = true;
refineDlg.RTRegressionThreshold = 0.90;
refineDlg.DotProductThreshold = Statistics.AngleToNormalizedContrastAngle(0.90); // Convert from original cos(angle) dot-product
refineDlg.OkDialog();
});
WaitForCondition(() => SkylineWindow.Document.PeptideCount < 120);
RunUI(() =>
{
Assert.AreEqual(113, SkylineWindow.Document.PeptideCount);
// Scheduling for Efficient Acquisition, p. 17
SkylineWindow.Undo();
});
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, mResults =>
{
Assert.AreEqual(1, mResults.Chromatograms.Count());
mResults.SelectedChromatograms =
SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Where(
set => Equals("Unrefined", set.Name)); // Not L10N
mResults.RemoveReplicates();
Assert.AreEqual(0, mResults.Chromatograms.Count());
mResults.OkDialog();
});
var importResultsDlg0 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0];
importResultsDlg0.RadioCreateMultipleMultiChecked = true;
importResultsDlg0.NamedPathSets =
DataSourceUtil.GetDataSourcesInSubdirs(Path.Combine(TestFilesDirs[1].FullPath,
Path.GetFileName(TestFilesDirs[1].FullPath) ??
string.Empty)).ToArray();
});
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg0.OkDialog);
RunUI(importResultsNameDlg.NoDialog);
WaitForCondition(15 * 60 * 1000, () => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 15 minutes
var docCurrent = SkylineWindow.Document;
RunUI(SkylineWindow.RemoveMissingResults);
WaitForDocumentChange(docCurrent);
Assert.AreEqual(86, SkylineWindow.Document.PeptideCount);
Assert.AreEqual(255, SkylineWindow.Document.PeptideTransitionCount);
TestRTResidualsSwitch();
// Measuring Retention Times, p. 17
{
var exportDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() => exportDlg.MaxTransitions = 130);
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 18);
OkDialog(exportDlg, () => exportDlg.OkDialog(TestFilesDirs[1].FullPath + "\\unscheduled")); // Not L10N
}
///////////////////////
// Reviewing Retention Time Runs, p. 18
RunUI(() =>
{
SkylineWindow.ShowGraphSpectrum(false);
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.AutoZoomNone();
SkylineWindow.AutoZoomBestPeak();
});
FindNode("FWEVISDEHGIQPDGTFK");
RunUI(() => SkylineWindow.Size = new Size(1060, 550));
RestoreViewOnScreen(19);
PauseForScreenShot("Main window", 19); // Not L10N
RunUI(() => SkylineWindow.ShowRTSchedulingGraph());
WaitForCondition(() => SkylineWindow.GraphRetentionTime != null);
PauseForScreenShot("Retention Times - Scheduling graph metafile", 19);
RestoreViewOnScreen(20);
// Creating a Scheduled Transition List, p. 20
{
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Prediction;
peptideSettingsUI.TimeWindow = 4;
});
PauseForScreenShot <PeptideSettingsUI.PredictionTab>("Peptide Settings - Prediction tab", 21);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog); // Not L10N
}
var exportMethodDlg1 = ShowDialog <ExportMethodDlg>(() =>
SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg1.ExportStrategy = ExportStrategy.Single;
exportMethodDlg1.MethodType = ExportMethodType.Scheduled;
});
// TODO: Update tutorial to mention the scheduling options dialog.
PauseForScreenShot("Export Transition List form", 22); // Not L10N
RunDlg <SchedulingOptionsDlg>(() =>
exportMethodDlg1.OkDialog(TestFilesDirs[1].FullPath + "\\scheduled"), // Not L10N
schedulingOptionsDlg => schedulingOptionsDlg.OkDialog());
WaitForClosedForm(exportMethodDlg1);
// Reviewing Multi-Replicate Data, p. 22
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, manageResultsDlg =>
{
manageResultsDlg.RemoveAllReplicates();
manageResultsDlg.OkDialog();
});
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunDlg <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets = importResultsDlg1.GetDataSourcePathsFile(null),
openDataSourceDialog =>
{
openDataSourceDialog.SelectAllFileType(ExtThermoRaw);
openDataSourceDialog.Open();
});
RunDlg <ImportResultsNameDlg>(importResultsDlg1.OkDialog, importResultsNameDlg0 =>
{
importResultsNameDlg0.Prefix = "Scheduled_"; // Not L10N
importResultsNameDlg0.YesDialog();
});
WaitForCondition(15 * 60 * 1000, () => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 15 minutes
Assert.AreEqual(5, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden));
RunUI(() =>
{
SkylineWindow.RemoveMissingResults();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowGraphRetentionTime(false);
});
WaitForCondition(() => SkylineWindow.GraphRetentionTime.IsHidden);
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].Nodes[0];
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.CollapsePeptides();
SkylineWindow.ShowChromatogramLegends(false);
SkylineWindow.Size = new Size(1024, 768);
});
RestoreViewOnScreen(24);
WaitForGraphs();
PauseForScreenShot("Main window", 24); // Not L10N
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
protected override void DoTest()
{
string skyFile = TestFilesDirs[0].GetTestPath(@"DriftTimePrediction\BSA-Training.sky");
RunUI(() => SkylineWindow.OpenFile(skyFile));
var document = WaitForDocumentLoaded(240 * 1000); // 4 minutes
RunUI(() => SkylineWindow.Size = new Size(880, 560));
RestoreViewOnScreen(2);
PauseForScreenShot("Document open - full window", 2);
AssertEx.IsDocumentState(document, null, 1, 34, 38, 404);
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(() =>
SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.FullScan));
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Full-scan settings", 3);
RunUI(() =>
{
Assert.AreEqual(FullScanPrecursorIsotopes.Count, transitionSettingsUI.PrecursorIsotopesCurrent);
Assert.AreEqual(20 * 1000, transitionSettingsUI.PrecursorRes);
Assert.AreEqual(FullScanMassAnalyzerType.tof, transitionSettingsUI.PrecursorMassAnalyzer);
Assert.AreEqual(IsolationScheme.SpecialHandlingType.ALL_IONS, transitionSettingsUI.IsolationSchemeName);
Assert.AreEqual(20 * 1000, transitionSettingsUI.ProductRes);
Assert.AreEqual(FullScanMassAnalyzerType.tof, transitionSettingsUI.ProductMassAnalyzer);
});
OkDialog(transitionSettingsUI, transitionSettingsUI.CancelDialog);
}
{
var importResults = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() => importResults.ImportSimultaneousIndex = 2);
PauseForScreenShot <ImportResultsDlg>("Import results form", 4);
// Importing raw data from a sample which is a mixture of yeast and BSA
var openDataSourceDialog = ShowDialog <OpenDataSourceDialog>(importResults.OkDialog);
RunUI(() =>
{
openDataSourceDialog.CurrentDirectory = new MsDataFilePath(DataPath);
openDataSourceDialog.SelectAllFileType(".d");
});
PauseForScreenShot <OpenDataSourceDialog>("Import results files", 5);
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
}
string yeastReplicateName = Path.GetFileNameWithoutExtension(Yeast_BSA);
PauseForScreenShot <AllChromatogramsGraph>("Importing results form", 6);
WaitForDocumentChangeLoaded(document, 1000 * 60 * 60 * 10); // 10 minutes
// Arrange graphs tiled
RunUI(() =>
{
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ShowSplitChromatogramGraph(true);
});
FindNode("R.FKDLGEEHFK.G");
RunUI(() => SkylineWindow.Size = new Size(1075, 799));
RestoreViewOnScreen(7);
PauseForScreenShot("Zoomed split graph panes onely", 7);
RunUI(() => SkylineWindow.AutoZoomNone());
PauseForScreenShot("Unzoomed split graph panes onely", 8);
RunUI(() =>
{
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowChromatogramLegends(false);
SkylineWindow.ShowPeakAreaLegend(false);
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view);
SkylineWindow.SynchronizeZooming(true);
SkylineWindow.Size = new Size(1547, 855);
});
RestoreViewOnScreen(9);
PauseForScreenShot("Full window", 9);
FindNode("TCVADESHAGCEK");
var noteDlg = ShowDialog <EditNoteDlg>(SkylineWindow.EditNote);
RunUI(() => noteDlg.NoteText = "Lost in yeast samples");
PauseForScreenShot("Peptide note", 10);
OkDialog(noteDlg, noteDlg.OkDialog);
FindNode("NECFLSHKDDSPDLPK");
PauseForScreenShot("Yeast chromatograms and RT only - prtsc-paste-edit", 11);
PauseForScreenShot("Hover over BSA in water chromatogram - prtsc-paste-edit", 12);
RestoreViewOnScreen(13);
PauseForScreenShot("Full scan 2D MS1 graph", 13);
{
const double clickTime1 = 41.06;
ClickChromatogram(clickTime1, 1.62E+6, PaneKey.PRECURSORS);
var fullScanGraph = FindOpenForm <GraphFullScan>();
RunUI(() => fullScanGraph.SetSpectrum(false));
PauseForScreenShot("Full scan 3D MS1 graph", 13);
ValidateClickTime(fullScanGraph, clickTime1);
RunUI(() => fullScanGraph.SetZoom(false));
PauseForScreenShot("Full scan unzoomed 3D MS1 graph", 14);
const double clickTime2 = 41.02;
RunUI(() => fullScanGraph.SetZoom(true));
ClickChromatogram(clickTime2, 5.8E+4, PaneKey.PRODUCTS);
PauseForScreenShot("Full scan 3D MS/MS graph", 15);
ValidateClickTime(fullScanGraph, clickTime2);
RunUI(() => fullScanGraph.SetZoom(false));
PauseForScreenShot("Full scan unzoomed 3D MS/MS graph", 14);
const double clickTime3 = 41.48;
ClickChromatogram(yeastReplicateName, clickTime3, 3.14E+4, PaneKey.PRODUCTS);
PauseForScreenShot("Interference full scan unzoomed 3D MS/MS graph", 15);
ValidateClickTime(fullScanGraph, clickTime3);
RunUI(SkylineWindow.HideFullScanGraph);
}
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
dlg.SelectedChromatograms = SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Skip(1);
dlg.RemoveReplicates();
dlg.OkDialog();
});
RunUI(() => SkylineWindow.SaveDocument());
{
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Prediction);
var driftPredictor = ShowDialog <EditDriftTimePredictorDlg>(peptideSettingsUI.AddDriftTimePredictor);
const string predictorName = "BSA";
RunUI(() =>
{
driftPredictor.SetPredictorName(predictorName);
driftPredictor.SetResolvingPower(50);
driftPredictor.GetDriftTimesFromResults();
});
PauseForScreenShot("Edit predictor form", 18);
OkDialog(driftPredictor, () => driftPredictor.OkDialog());
PauseForScreenShot("Peptide Settings - Prediction", 19);
RunUI(() =>
{
Assert.IsTrue(peptideSettingsUI.IsUseMeasuredRT);
Assert.AreEqual(6, peptideSettingsUI.TimeWindow);
Assert.AreEqual(predictorName, peptideSettingsUI.SelectedDriftTimePredictor);
});
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
}
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettingsUI.SetRetentionTimeFilter(RetentionTimeFilterType.scheduling_windows, 3);
});
PauseForScreenShot("Transition Settings - Full-Scan", 20);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
}
using (new WaitDocumentChange(1, true, 1000 * 60 * 60 * 5))
{
var choosePredictionReplicates = ShowDialog <ChooseSchedulingReplicatesDlg>(SkylineWindow.ImportResults);
PauseForScreenShot("Choose Replicates form", 21);
RunUI(() => choosePredictionReplicates.SelectOrDeselectAll(true));
var importResults = ShowDialog <ImportResultsDlg>(choosePredictionReplicates.OkDialog);
RunDlg <OpenDataSourceDialog>(importResults.OkDialog, openDataSourceDialog =>
{
openDataSourceDialog.CurrentDirectory = new MsDataFilePath(DataPath);
openDataSourceDialog.SelectAllFileType(Yeast_BSA);
openDataSourceDialog.Open();
});
}
WaitForGraphs();
// CONSIDER: Test the peak annotations to ensure the filtering happened
PauseForScreenShot("Yeast chromatogram and RTs - prtsc-paste-edit", 22);
{
const double clickTime = 42.20;
ClickChromatogram(yeastReplicateName, clickTime, 2.904E+4, PaneKey.PRODUCTS);
var fullScanGraph = FindOpenForm <GraphFullScan>();
RunUI(() => fullScanGraph.SetZoom(true));
PauseForScreenShot("Full-scan graph zoomed", 23);
RunUI(() => Assert.IsTrue(fullScanGraph.TitleText.Contains(clickTime.ToString(CultureInfo.CurrentCulture))));
RunUI(SkylineWindow.HideFullScanGraph);
}
FindNode("FKDLGEEHFK");
PauseForScreenShot("Chromatograms (copy metafile) and legend - prtsc-paste-edit", 23);
PauseForScreenShot("Peak area percentages (copy metafile)", 24);
var docFiltered = SkylineWindow.Document;
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, manageDlg =>
{
manageDlg.SelectedChromatograms = SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Take(1);
manageDlg.ReimportResults();
manageDlg.OkDialog();
});
WaitForDocumentChangeLoaded(docFiltered, 1000 * 60 * 60 * 5); // 5 minutes
// TODO: Check peak ranks before and after
}
protected override void DoTest()
{
// Clear all the settings lists that will be defined in this tutorial
ClearSettingsLists();
// Open the file
RunUI(() => SkylineWindow.OpenFile(GetTestPath(DIA_START_CHECKPOINT)));
WaitForDocumentLoaded();
// Specify DIA acquisition scheme and machine settings
var transitionSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettings.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettings.AcquisitionMethod = FullScanAcquisitionMethod.DIA;
transitionSettings.PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
transitionSettings.PrecursorMassAnalyzer = FullScanMassAnalyzerType.orbitrap;
transitionSettings.PrecursorRes = 35000;
transitionSettings.PrecursorResMz = 200;
transitionSettings.ProductMassAnalyzer = FullScanMassAnalyzerType.orbitrap;
transitionSettings.ProductRes = 17500;
transitionSettings.ProductResMz = 200;
});
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Transition Settings - Full-Scan", 4);
// Set up isolation scheme
var isolationSchemeDlg = ShowDialog <EditIsolationSchemeDlg>(transitionSettings.AddIsolationScheme);
PauseForScreenShot <EditIsolationSchemeDlg>("Edit Isolation Scheme form", 5);
RunUI(() =>
{
isolationSchemeDlg.UseResults = false;
});
var calculateIsolationDlg = ShowDialog <CalculateIsolationSchemeDlg>(isolationSchemeDlg.Calculate);
RunUI(() =>
{
calculateIsolationDlg.WindowWidth = 20;
calculateIsolationDlg.Start = 500;
calculateIsolationDlg.End = 900;
calculateIsolationDlg.OptimizeWindowPlacement = true;
});
PauseForScreenShot <CalculateIsolationSchemeDlg>("Calculate Isolation Scheme form", 6);
OkDialog(calculateIsolationDlg, calculateIsolationDlg.OkDialog);
PauseForScreenShot <EditIsolationSchemeDlg>("Edit Isolation Scheme Dialog Filled", 7);
var isolationSchemeGraphDlg = ShowDialog <DiaIsolationWindowsGraphForm>(isolationSchemeDlg.OpenGraph);
PauseForScreenShot <DiaIsolationWindowsGraphForm>("Graph of Isolation Scheme", 8);
OkDialog(isolationSchemeGraphDlg, isolationSchemeGraphDlg.CloseButton);
RunUI(() => isolationSchemeDlg.IsolationSchemeName = "500 to 900 by 20");
OkDialog(isolationSchemeDlg, isolationSchemeDlg.OkDialog);
OkDialog(transitionSettings, transitionSettings.OkDialog);
// Export isolation scheme
var exportIsolationDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.IsolationList));
PauseForScreenShot <ExportMethodDlg>("Export Isolation List form", 9);
OkDialog(exportIsolationDlg, () => exportIsolationDlg.OkDialog(GetTestPath("DIA_tutorial_isolation_list.csv")));
// Adjust modifications and filter
var newPeptideSettings = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => newPeptideSettings.AutoSelectMatchingPeptides = true);
OkDialog(newPeptideSettings, newPeptideSettings.OkDialog);
// Set up chromatogram retention time restriction
var newTransitionSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => newTransitionSettings.SetRetentionTimeFilter(RetentionTimeFilterType.ms2_ids, 5.0));
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Retention time filtering options", 16);
// Adjust library transition ranking
RunUI(() =>
{
newTransitionSettings.SelectedTab = TransitionSettingsUI.TABS.Library;
newTransitionSettings.UseLibraryPick = true;
newTransitionSettings.Filtered = true;
});
PauseForScreenShot <TransitionSettingsUI.LibraryTab>("Transition Settings - Library tab", 22);
OkDialog(newTransitionSettings, newTransitionSettings.OkDialog);
PauseForScreenShot <SequenceTreeForm>("Targets pane with precursors and best 5 transitions only", 23);
// Build spectral library using Import Peptide Search
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(DIA_TUTORIAL_CHECKPOINT)));
// "Build Spectral Library" page
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(() => SkylineWindow.ShowImportPeptideSearchDlg());
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(new[] { GetTestPath("interact-20130311_DDA_Pit01.pep.xml") }); // Not L10N
importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.dia;
});
PauseForScreenShot <BuildLibraryDlg>("Build Library form - input files", 10);
const string prefixKeep = "DIA_Pit0";
if (IsFullImportMode)
{
SrmDocument doc = SkylineWindow.Document;
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
doc = WaitForDocumentChange(doc);
// "Extract Chromatograms" page
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page);
importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles =
_importFiles.Select(f => new ImportPeptideSearch.FoundResultsFile(f, GetTestPath(f + ExtensionTestContext.ExtThermoRaw))).ToList();
});
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
RunUI(() =>
{
string prefix = importResultsNameDlg.Prefix;
Assert.IsTrue(prefix.EndsWith(prefixKeep));
importResultsNameDlg.Prefix = prefix.Substring(0, prefix.Length - prefixKeep.Length);
importResultsNameDlg.YesDialog();
});
WaitForClosedForm(importResultsNameDlg);
// "Add Modifications" page
RunUI(() =>
{
const string modCarbamidomethyl = "Carbamidomethyl (C)";
const string modOxidation = "Oxidation (M)";
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page);
// Define expected matched/unmatched modifications
var expectedMatched = new[] { modCarbamidomethyl, modOxidation };
// Verify matched/unmatched modifications
AssertEx.AreEqualDeep(expectedMatched, importPeptideSearchDlg.MatchModificationsControl.MatchedModifications.ToArray());
Assert.IsFalse(importPeptideSearchDlg.MatchModificationsControl.UnmatchedModifications.Any());
importPeptideSearchDlg.MatchModificationsControl.CheckedModifications = new[] { modCarbamidomethyl };
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
WaitForDocumentChange(doc);
// "Configure Transition Settings" page
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.transition_settings_page);
importPeptideSearchDlg.TransitionSettingsControl.PrecursorCharges = new[] { 1, 2, 3, 4 };
importPeptideSearchDlg.TransitionSettingsControl.IonCharges = new[] { 1, 2 };
importPeptideSearchDlg.TransitionSettingsControl.IonTypes = new[] { IonType.y, IonType.b, IonType.precursor };
importPeptideSearchDlg.TransitionSettingsControl.ExclusionUseDIAWindow = true;
importPeptideSearchDlg.TransitionSettingsControl.IonCount = 5;
importPeptideSearchDlg.TransitionSettingsControl.IonMatchTolerance = 0.05;
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
// "Configure Full-Scan Settings" page
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
// "Import FASTA" page
RunUI(() =>
{
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(GetTestPath("pituitary_database.fasta"));
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
WaitForClosedForm(importPeptideSearchDlg);
WaitForCondition(10 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 10 minutes
RunUI(() =>
{
SkylineWindow.SaveDocument(GetTestPath(DIA_IMPORTED_CHECKPOINT));
SkylineWindow.SaveDocument(GetTestPath(DIA_TUTORIAL_CHECKPOINT));
});
}
else
{
OkDialog(importPeptideSearchDlg, importPeptideSearchDlg.CancelDialog);
RunUI(() => SkylineWindow.OpenFile(GetTestPath(DIA_IMPORTED_CHECKPOINT)));
}
WaitForDocumentLoaded();
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
SkylineWindow.Size = new Size(750, 788);
});
// Generate decoys
// var decoysDlg = ShowDialog<GenerateDecoysDlg>(SkylineWindow.ShowGenerateDecoysDlg);
// PauseForScreenShot<GenerateDecoysDlg>("Add Decoy Peptides form", 24);
// RunUI(() =>
// {
// decoysDlg.NumDecoys = 26;
// Assert.AreEqual(decoysDlg.DecoysMethod, DecoyGeneration.SHUFFLE_SEQUENCE);
// });
// OkDialog(decoysDlg, decoysDlg.OkDialog);
// RunUI(() => SkylineWindow.SequenceTree.TopNode = SkylineWindow.SequenceTree.SelectedNode.PrevNode.Nodes[6]);
// PauseForScreenShot<SequenceTreeForm>("Targets pane with decoys added", 25);
RunUI(() =>
{
SkylineWindow.CollapsePeptides();
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 6);
var nodePepTree = SkylineWindow.SelectedNode as PeptideTreeNode;
Assert.IsNotNull(nodePepTree);
Assert.AreEqual("VLQAVLPPLPQVVCTYR", nodePepTree.DocNode.Peptide.Sequence);
SkylineWindow.ShowSplitChromatogramGraph(true);
SkylineWindow.AutoZoomBestPeak();
var graphChrom = SkylineWindow.GetGraphChrom(prefixKeep + "1");
var labelStrings = graphChrom.GetAnnotationLabelStrings().ToArray();
Assert.IsTrue(labelStrings.Contains(string.Format("{0}\n+{1} ppm\n(idotp {2})", 75.4, 3, 0.59)),
string.Format("Missing expected label in {0}", string.Join("|", labelStrings)));
SkylineWindow.Width = 1250;
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RestoreViewOnScreen(27);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile", 26);
RunUI(() =>
{
SkylineWindow.SelectedNode.Expand();
var nodeTree = SkylineWindow.SelectedNode.Nodes[0].Nodes[0] as SrmTreeNode;
Assert.IsNotNull(nodeTree);
Assert.AreEqual((int)SequenceTree.StateImageId.no_peak, nodeTree.StateImageIndex);
});
PauseForScreenShot <SequenceTreeForm>("Targets view - ", 27);
RunUI(() =>
{
SkylineWindow.SetIntegrateAll(true);
var nodeTree = SkylineWindow.SelectedNode.Nodes[0].Nodes[0] as SrmTreeNode;
Assert.IsNotNull(nodeTree);
Assert.AreEqual((int)SequenceTree.StateImageId.peak, nodeTree.StateImageIndex);
var nodeGroupTree = SkylineWindow.SelectedNode.Nodes[0] as TransitionGroupTreeNode;
Assert.IsNotNull(nodeGroupTree);
Assert.AreEqual(0.99, nodeGroupTree.DocNode.GetIsotopeDotProduct(0) ?? 0, 0.005);
Assert.AreEqual(0.83, nodeGroupTree.DocNode.GetLibraryDotProduct(0) ?? 0, 0.005);
SkylineWindow.ShowOtherRunPeptideIDTimes(true);
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - with ID lines", 28);
RunUI(() =>
{
SkylineWindow.AutoZoomNone();
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 1);
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - zoomed out and small peak", 30);
RunUI(SkylineWindow.AutoZoomBestPeak);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - zoomed to peak", 31);
if (IsFullImportMode)
{
ClickChromatogram(74.9, 1.775E+7, PaneKey.PRECURSORS);
RestoreViewOnScreen(33);
PauseForScreenShot <GraphFullScan>("Full Scan graph with precursors - zoom manually", 32);
ClickChromatogram(74.8, 1.753E+6, PaneKey.PRODUCTS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing y7", 33);
ClickChromatogram(74.9, 9.64E+5, PaneKey.PRODUCTS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing b3 - zoom manually", 34);
ClickChromatogram(74.9, 1.25E+5, PaneKey.PRODUCTS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing y3 - zoom manually", 34);
}
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 2);
Assert.AreEqual("CNTDYSDCIHEAIK", ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode.Peptide.Sequence);
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - split between two precursors", 35);
RunUI(() =>
{
SkylineWindow.SelectedNode.Expand();
SkylineWindow.SelectedPath = ((SrmTreeNode)SkylineWindow.SelectedNode.Nodes[0]).Path;
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - double charged precursor", 36);
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 3);
Assert.AreEqual("ELVYETVR", ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode.Peptide.Sequence);
});
RunUI(() =>
{
SkylineWindow.SelectedNode.Expand();
var nodeGroupTree = SkylineWindow.SelectedNode.Nodes[0] as TransitionGroupTreeNode;
Assert.IsNotNull(nodeGroupTree);
Assert.AreEqual(0.99, nodeGroupTree.DocNode.GetIsotopeDotProduct(0) ?? 0, 0.005);
Assert.AreEqual(0.99, nodeGroupTree.DocNode.GetIsotopeDotProduct(0) ?? 0, 0.005);
});
RestoreViewOnScreen(38);
PauseForScreenShot <GraphSpectrum>("Library Match view - zoom manually", 37);
RestoreViewOnScreen(39);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile", 38);
if (IsFullImportMode)
{
RestoreViewOnScreen(40);
ClickChromatogram(41.9, 1.166E+8, PaneKey.PRECURSORS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing precursor interference - zoom manually", 39);
RunUI(() => SkylineWindow.GraphFullScan.ChangeScan(-12));
CheckFullScanSelection(41.7, 1.532E+8, PaneKey.PRECURSORS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing transition between interference and real peak - zoom manually", 39);
}
// Clear all the settings lists that were defined in this tutorial
ClearSettingsLists();
}
private void autoZoomNoneMenuItem_Click(object sender, EventArgs e)
{
SkylineWindow.AutoZoomNone();
}
protected override void DoTest()
{
// Check backward compatibility with 19.1.9.338 and 350 when combined IMS got written to MsDataFilePath
string legacyFile_19_1_9 = TestFilesDirs[1].GetTestPath(@"BSA-Training.sky");
RunUI(() => SkylineWindow.OpenFile(legacyFile_19_1_9));
VerifyCombinedIonMobility(WaitForDocumentLoaded());
RunUI(() =>
{
SkylineWindow.SaveDocument();
SkylineWindow.NewDocument();
SkylineWindow.OpenFile(legacyFile_19_1_9);
});
VerifyCombinedIonMobility(WaitForDocumentLoaded());
var oldDoc = SkylineWindow.Document;
string skyFile = TestFilesDirs[0].GetTestPath(@"IMSFiltering\BSA-Training.sky");
RunUI(() => SkylineWindow.OpenFile(skyFile));
var document = WaitForDocumentChangeLoaded(oldDoc, 240 * 1000); // 4 minutes
RunUI(() => SkylineWindow.Size = new Size(880, 560));
RestoreViewOnScreen(2);
PauseForScreenShot("Document open - full window", 2);
AssertEx.IsDocumentState(document, null, 1, 34, 38, 404);
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(() =>
SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.FullScan));
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Full-scan settings", 3);
RunUI(() =>
{
Assert.AreEqual(FullScanPrecursorIsotopes.Count, transitionSettingsUI.PrecursorIsotopesCurrent);
Assert.AreEqual(20 * 1000, transitionSettingsUI.PrecursorRes);
Assert.AreEqual(FullScanMassAnalyzerType.tof, transitionSettingsUI.PrecursorMassAnalyzer);
Assert.AreEqual(IsolationScheme.SpecialHandlingType.ALL_IONS, transitionSettingsUI.IsolationSchemeName);
Assert.AreEqual(20 * 1000, transitionSettingsUI.ProductRes);
Assert.AreEqual(FullScanMassAnalyzerType.tof, transitionSettingsUI.ProductMassAnalyzer);
});
OkDialog(transitionSettingsUI, transitionSettingsUI.CancelDialog);
}
{
var importResults = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() => importResults.ImportSimultaneousIndex = 2);
PauseForScreenShot <ImportResultsDlg>("Import results form", 4);
// Importing raw data from a sample which is a mixture of yeast and BSA
var openDataSourceDialog = ShowDialog <OpenDataSourceDialog>(importResults.OkDialog);
RunUI(() =>
{
openDataSourceDialog.CurrentDirectory = new MsDataFilePath(DataPath);
openDataSourceDialog.SelectAllFileType(".d");
});
PauseForScreenShot <OpenDataSourceDialog>("Import results files", 5);
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
}
string yeastReplicateName = Path.GetFileNameWithoutExtension(Yeast_BSA);
PauseForScreenShot <AllChromatogramsGraph>("Importing results form", 6);
WaitForDocumentChangeLoaded(document, 1000 * 60 * 60 * 10); // 10 minutes
// Arrange graphs tiled
RunUI(() =>
{
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ShowSplitChromatogramGraph(true);
});
FindNode("R.FKDLGEEHFK.G");
RunUI(() => SkylineWindow.Size = new Size(1075, 799));
RestoreViewOnScreen(7);
PauseForScreenShot("Zoomed split graph panes only", 7);
RunUI(() => SkylineWindow.AutoZoomNone());
PauseForScreenShot("Unzoomed split graph panes only", 8);
const int wideWidth = 1547;
RunUI(() =>
{
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowChromatogramLegends(false);
SkylineWindow.ShowPeakAreaLegend(false);
SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL);
SkylineWindow.SynchronizeZooming(true);
SkylineWindow.Size = new Size(wideWidth, 855);
});
RestoreViewOnScreen(9);
PauseForScreenShot("Full window", 9);
FindNode("TCVADESHAGCEK");
var noteDlg = ShowDialog <EditNoteDlg>(SkylineWindow.EditNote);
RunUI(() => noteDlg.NoteText = "Lost in yeast samples");
PauseForScreenShot("Peptide note", 10);
OkDialog(noteDlg, noteDlg.OkDialog);
FindNode("NECFLSHKDDSPDLPK");
RestoreViewOnScreen(11);
const int narrowWidth = 1350;
RunUI(() => SkylineWindow.Width = narrowWidth);
PauseForScreenShot("Yeast chromatograms and RT only - prtsc-paste-edit", 11);
PauseForScreenShot("Hover over BSA in water chromatogram - prtsc-paste-edit", 12);
RunUI(() => SkylineWindow.Width = wideWidth);
RestoreViewOnScreen(13);
{
const double clickTime1 = 41.06;
ClickChromatogram(clickTime1, 1.62E+6, PaneKey.PRECURSORS);
PauseForScreenShot("Full scan 2D MS1 graph", 13);
var fullScanGraph = FindOpenForm <GraphFullScan>();
RunUI(() => fullScanGraph.SetSpectrum(false));
PauseForScreenShot("Full scan 3D MS1 graph", 13);
ValidateClickTime(fullScanGraph, clickTime1);
RunUI(() => fullScanGraph.SetZoom(false));
PauseForScreenShot("Full scan unzoomed 3D MS1 graph", 14);
const double clickTime2 = 41.02;
RunUI(() => fullScanGraph.SetZoom(true));
ClickChromatogram(clickTime2, 5.8E+4, PaneKey.PRODUCTS);
PauseForScreenShot("Full scan 3D MS/MS graph", 15);
ValidateClickTime(fullScanGraph, clickTime2);
RunUI(() => fullScanGraph.SetZoom(false));
PauseForScreenShot("Full scan unzoomed 3D MS/MS graph", 15);
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RestoreCoverViewOnScreen();
ClickChromatogram(clickTime2, 5.8E+4, PaneKey.PRODUCTS);
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
RenameReplicate(manageResultsDlg, 0, "BSA");
RenameReplicate(manageResultsDlg, 1, "Yeast_BSA");
OkDialog(manageResultsDlg, manageResultsDlg.OkDialog);
RunUI(SkylineWindow.FocusDocument);
TakeCoverShot();
return;
}
const double clickTime3 = 41.48;
ClickChromatogram(yeastReplicateName, clickTime3, 3.14E+4, PaneKey.PRODUCTS);
PauseForScreenShot("Interference full scan unzoomed 3D MS/MS graph", 16);
ValidateClickTime(fullScanGraph, clickTime3);
RunUI(SkylineWindow.HideFullScanGraph);
}
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
dlg.SelectedChromatograms = SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Skip(1);
dlg.RemoveReplicates();
dlg.OkDialog();
});
RunUI(() => SkylineWindow.SaveDocument());
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.IonMobility;
transitionSettingsUI.IonMobilityControl.WindowWidthType = IonMobilityWindowWidthCalculator
.IonMobilityWindowWidthType.resolving_power;
transitionSettingsUI.IonMobilityControl.IonMobilityFilterResolvingPower = 50;
});
PauseForScreenShot("Setting ion mobility filter width calculation values", 17);
var editIonMobilityLibraryDlg = ShowDialog <EditIonMobilityLibraryDlg>(transitionSettingsUI.IonMobilityControl.AddIonMobilityLibrary);
const string libraryName = "BSA";
var databasePath = TestFilesDirs[1].GetTestPath(libraryName + IonMobilityDb.EXT);
RunUI(() =>
{
editIonMobilityLibraryDlg.LibraryName = libraryName;
editIonMobilityLibraryDlg.CreateDatabaseFile(databasePath); // Simulate user click on Create button
editIonMobilityLibraryDlg.SetOffsetHighEnergySpectraCheckbox(true);
editIonMobilityLibraryDlg.GetIonMobilitiesFromResults();
});
PauseForScreenShot("Edit ion mobility library form", 18);
// Check that a new value was calculated for all precursors
RunUI(() => Assert.AreEqual(SkylineWindow.Document.MoleculeTransitionGroupCount, editIonMobilityLibraryDlg.LibraryMobilitiesFlatCount));
OkDialog(editIonMobilityLibraryDlg, () => editIonMobilityLibraryDlg.OkDialog());
PauseForScreenShot <TransitionSettingsUI.IonMobilityTab>("Transition Settings - Ion Mobility", 19);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettingsUI.SetRetentionTimeFilter(RetentionTimeFilterType.scheduling_windows, 3);
});
PauseForScreenShot("Transition Settings - Full-Scan", 20);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Prediction);
PauseForScreenShot("Peptide Settings - Prediction", 21);
RunUI(() =>
{
Assert.IsTrue(peptideSettingsUI.IsUseMeasuredRT);
Assert.AreEqual(6, peptideSettingsUI.TimeWindow);
});
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
}
using (new WaitDocumentChange(1, true, 1000 * 60 * 60 * 5))
{
var choosePredictionReplicates = ShowDialog <ChooseSchedulingReplicatesDlg>(SkylineWindow.ImportResults);
PauseForScreenShot("Choose Replicates form", 22);
RunUI(() => choosePredictionReplicates.SelectOrDeselectAll(true));
var importResults = ShowDialog <ImportResultsDlg>(choosePredictionReplicates.OkDialog);
RunDlg <OpenDataSourceDialog>(importResults.OkDialog, openDataSourceDialog =>
{
openDataSourceDialog.CurrentDirectory = new MsDataFilePath(DataPath);
openDataSourceDialog.SelectAllFileType(Yeast_BSA);
openDataSourceDialog.Open();
});
}
WaitForGraphs();
// Test to ensure the filtering happened
if (!IsPauseForScreenShots) // Don't bring up unexpected UI in a screenshot run
{
TestReports();
}
RestoreViewOnScreen(11);
RunUI(() => SkylineWindow.Width = narrowWidth);
PauseForScreenShot("Yeast chromatogram and RTs - prtsc-paste-edit", 23);
RunUI(() => SkylineWindow.Width = wideWidth);
RestoreViewOnScreen(13);
{
const double clickTime = 42.20;
ClickChromatogram(yeastReplicateName, clickTime, 2.904E+4, PaneKey.PRODUCTS);
var fullScanGraph = FindOpenForm <GraphFullScan>();
RunUI(() => fullScanGraph.SetZoom(true));
RunUI(() => fullScanGraph.Parent.Parent.Size = new Size(671, 332));
PauseForScreenShot("Full-scan graph zoomed", 24);
RunUI(() => Assert.IsTrue(fullScanGraph.TitleText.Contains(clickTime.ToString(CultureInfo.CurrentCulture))));
RunUI(SkylineWindow.HideFullScanGraph);
}
FindNode("FKDLGEEHFK");
RunUI(() =>
{
SkylineWindow.Size = new Size(1547, 689);
SkylineWindow.ShowProductTransitions();
SkylineWindow.ShowPeakAreaLegend(true);
});
RestoreViewOnScreen(25);
PauseForScreenShot("Chromatograms and Peak Areas - prtsc-paste-edit", 25);
var docFiltered = SkylineWindow.Document;
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, manageDlg =>
{
manageDlg.SelectedChromatograms = SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Take(1);
manageDlg.ReimportResults();
manageDlg.OkDialog();
});
WaitForDocumentChangeLoaded(docFiltered, 1000 * 60 * 60 * 5); // 5 minutes
// TODO: Check peak ranks before and after
AssertEx.IsFalse(IsRecordMode); // Make sure we turn this off before commit!
}
protected override void DoTest()
{
// IsPauseForScreenShots = true;
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("SplitGraphUnitTest.sky")));
CollectionAssert.AreEqual(new[] { "SplitGraph_rev1.clib" }, SkylineWindow.Document.Settings.PeptideSettings.Libraries.LibrarySpecs
.Select(spec => Path.GetFileName(spec.FilePath)).ToArray());
WaitForDocumentLoaded();
// Test that AutoZoomNone and AutoZoomBestPeak work
var graphChromatogram = Application.OpenForms.OfType <GraphChromatogram>().First();
var graphChromatogramGraphControl = AllControls(graphChromatogram).OfType <ZedGraphControl>().First();
RunUI(() =>
{
// Select the first transition group
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo(2, 0);
SkylineWindow.AutoZoomBestPeak();
// Make sure that we are zoomed in to approximately the best peak
Assert.AreEqual(graphChromatogramGraphControl.GraphPane.XAxis.Scale.Min, 13.0, 1.0);
Assert.AreEqual(graphChromatogramGraphControl.GraphPane.XAxis.Scale.Max, 14.0, 1.0);
// Remember the zoom state so that we can pretend to manually zoom later
var zoomStateAuto = new ZoomState(graphChromatogramGraphControl.GraphPane, ZoomState.StateType.Zoom);
SkylineWindow.AutoZoomNone();
Assert.AreEqual(graphChromatogramGraphControl.GraphPane.XAxis.Scale.Min, 0.0, 1.0);
Assert.AreEqual(graphChromatogramGraphControl.GraphPane.XAxis.Scale.Max, 35.0, 1.0);
// Pretend to manually zoom
zoomStateAuto.ApplyState(graphChromatogramGraphControl.GraphPane);
Assert.AreEqual(graphChromatogramGraphControl.GraphPane.XAxis.Scale.Min, 13.0, 1.0);
// Select some other transition group:
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo(2, 1);
SkylineWindow.ShowPeakAreaReplicateComparison();
});
WaitForGraphs();
// Ensure that we zoomed out when the selected transition group changed
Assert.AreEqual(graphChromatogramGraphControl.GraphPane.XAxis.Scale.Min, 0.0, 1.0);
var peakAreaSummary = Application.OpenForms.OfType <GraphSummary>().First();
var graphLibraryMatch = Application.OpenForms.OfType <GraphSpectrum>().First();
var libraryMatchGraphControl = AllControls(graphLibraryMatch).OfType <ZedGraphControl>().First();
RunUI(() =>
{
Assert.IsTrue(Settings.Default.ShowLibraryChromatograms);
AssertCurveListsSame(graphChromatogram.CurveList,
libraryMatchGraphControl.GraphPane.CurveList);
AssertCurveListsSame(graphChromatogram.CurveList,
peakAreaSummary.GraphControl.GraphPane.CurveList);
Assert.AreEqual(9, graphChromatogram.CurveList.Count);
Assert.AreEqual(1, graphChromatogramGraphControl.MasterPane.PaneList.Count);
Assert.AreEqual(1, peakAreaSummary.GraphControl.MasterPane.PaneList.Count);
SkylineWindow.ShowPrecursorTransitions();
Assert.AreEqual(3, graphChromatogram.CurveList.Count);
// TODO(nicksh): Enable this when libraries filter based on precursor/product
//AssertCurveListsSame(graphChromatogram.CurveList, libraryMatchGraphControl.GraphPane.CurveList);
AssertCurveListsSame(graphChromatogram.CurveList,
peakAreaSummary.GraphControl.GraphPane.CurveList);
SkylineWindow.ShowProductTransitions();
Assert.AreEqual(6, graphChromatogram.CurveList.Count);
// TODO(nicksh): Enable this when libraries filter based on precursor/product
AssertCurveListsSame(graphChromatogram.CurveList,
libraryMatchGraphControl.GraphPane.CurveList);
AssertCurveListsSame(graphChromatogram.CurveList,
peakAreaSummary.GraphControl.GraphPane.CurveList);
SkylineWindow.ShowAllTransitions();
SkylineWindow.ShowSplitChromatogramGraph(true);
});
WaitForGraphs();
Assert.AreEqual(2, graphChromatogramGraphControl.MasterPane.PaneList.Count);
Assert.AreEqual(2, peakAreaSummary.GraphControl.MasterPane.PaneList.Count);
AssertCurveListsSame(graphChromatogram.GetCurveList(graphChromatogramGraphControl.MasterPane.PaneList[0]),
peakAreaSummary.GraphControl.MasterPane.PaneList[0].CurveList);
AssertCurveListsSame(graphChromatogram.GetCurveList(graphChromatogramGraphControl.MasterPane.PaneList[1]),
peakAreaSummary.GraphControl.MasterPane.PaneList[1].CurveList);
}
protected override void DoTest()
{
const double peakWidthZoomFactor = 2.0;
RunUI(() =>
{
SkylineWindow.OpenFile(TestFilesDir.GetTestPath("NoQuantitativeTransitionsTest.sky"));
SkylineWindow.AutoZoomBestPeak();
});
WaitForDocumentLoaded();
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.TimeRange = peakWidthZoomFactor;
dlg.IsPeakWidthRelative = true;
dlg.OkDialog();
});
// Do a rescore so that we can be sure that the way things are in the document and exactly
// how the current version of Skyline calculates them
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
RunDlg <RescoreResultsDlg>(manageResultsDlg.Rescore, dlg => dlg.Rescore(false));
WaitForDocumentLoaded();
var document = SkylineWindow.Document;
// Make sure that the TransitionGroupChromInfo's have their values set based on the quantitative peaks, unless there
// are no quantitative peaks
foreach (var transitionGroupDocNode in document.MoleculeTransitionGroups)
{
for (int iReplicate = 0; iReplicate < transitionGroupDocNode.Results.Count; iReplicate++)
{
var transitionGroupChromInfo = transitionGroupDocNode.Results[iReplicate][0];
var quanChromInfos = new List <TransitionChromInfo>();
var nonQuanChromInfos = new List <TransitionChromInfo>();
foreach (var t in transitionGroupDocNode.Transitions)
{
var chromInfo = t.Results[iReplicate][0];
if (chromInfo.IsEmpty)
{
continue;
}
if (t.IsQuantitative(document.Settings))
{
quanChromInfos.Add(chromInfo);
}
else
{
nonQuanChromInfos.Add(chromInfo);
}
}
if (quanChromInfos.Any())
{
AssertEx.AreEqual(transitionGroupChromInfo.StartRetentionTime, quanChromInfos.Min(c => c.StartRetentionTime));
AssertEx.AreEqual(transitionGroupChromInfo.EndRetentionTime, quanChromInfos.Max(c => c.EndRetentionTime));
AssertEx.AreEqual(transitionGroupChromInfo.Height, quanChromInfos.Max(c => c.Height));
}
else
{
AssertEx.AreEqual(transitionGroupChromInfo.StartRetentionTime, nonQuanChromInfos.Min(c => c.StartRetentionTime));
AssertEx.AreEqual(transitionGroupChromInfo.EndRetentionTime, nonQuanChromInfos.Max(c => c.EndRetentionTime));
AssertEx.IsNull(transitionGroupChromInfo.Height);
}
}
}
// Verify that the chromatogram graph correctly zooms to the best quantitative peak, or,
// if there are no quantitative peaks, falls back to the best non-quantitative peak,
// or is zoomed out entirely
foreach (var displayTypeChrom in new[]
{ DisplayTypeChrom.all, DisplayTypeChrom.single, DisplayTypeChrom.total })
{
RunUI(() => SkylineWindow.SetDisplayTypeChrom(displayTypeChrom));
for (int iReplicate = 0; iReplicate < document.Settings.MeasuredResults.Chromatograms.Count; iReplicate++)
{
var chromatogramSet = document.Settings.MeasuredResults.Chromatograms[iReplicate];
var graphChrom = SkylineWindow.GetGraphChrom(chromatogramSet.Name);
RunUI(() =>
{
graphChrom.Activate();
graphChrom.Focus();
});
foreach (var protein in SkylineWindow.Document.MoleculeGroups)
{
foreach (var peptide in protein.Molecules)
{
foreach (var precursor in peptide.TransitionGroups)
{
foreach (var transition in precursor.Transitions)
{
RunUI(() =>
{
SkylineWindow.SelectedPath = new IdentityPath(protein.Id, peptide.Id,
precursor.Id, transition.Id);
SkylineWindow.AutoZoomNone();
SkylineWindow.AutoZoomBestPeak();
});
var transitionChromInfos = new List <TransitionChromInfo>();
if (displayTypeChrom == DisplayTypeChrom.single)
{
var transitionChromInfo = transition.Results[iReplicate][0];
if (!transitionChromInfo.IsEmpty)
{
transitionChromInfos.Add(transitionChromInfo);
}
}
else
{
transitionChromInfos.AddRange(precursor.Transitions.Where(t => t.ExplicitQuantitative)
.Select(t => t.Results[iReplicate][0]).Where(t => !t.IsEmpty));
if (!transitionChromInfos.Any())
{
if (displayTypeChrom != DisplayTypeChrom.total ||
precursor.Transitions.All(t => !t.ExplicitQuantitative))
{
transitionChromInfos.AddRange(precursor.Transitions
.Select(t => t.Results[iReplicate][0]).Where(t => !t.IsEmpty));
}
}
}
var zoomState = graphChrom.ZoomState;
if (transitionChromInfos.Any())
{
var peakStartTime = transitionChromInfos.Min(t => t.StartRetentionTime);
var peakEndTime = transitionChromInfos.Max(t => t.EndRetentionTime);
var midPeak = (peakStartTime + peakEndTime) / 2;
var halfPeakWidth = (peakEndTime - peakStartTime) / 2;
double expectedZoomStart = midPeak - halfPeakWidth * peakWidthZoomFactor;
double expectedZoomEnd = midPeak + halfPeakWidth * peakWidthZoomFactor;
const double tolerance = .001;
AssertEx.AreEqual(expectedZoomStart, zoomState.XAxis.Min, tolerance);
AssertEx.AreEqual(expectedZoomEnd, zoomState.XAxis.Max, tolerance);
}
else
{
var expectedStart = graphChrom.ChromGroupInfos[0].TimeIntensitiesGroup.MinTime;
var expectedEnd = graphChrom.ChromGroupInfos[0].TimeIntensitiesGroup.MaxTime;
AssertEx.IsTrue(zoomState.XAxis.Min <= expectedStart);
AssertEx.IsTrue(zoomState.XAxis.Max >= expectedEnd);
}
}
}
}
}
}
}
}
private void TofTest()
{
// Working wih High-Resolution Mass Spectra.
// Import a new Document. High-Resolution Mass Spectra, working with TOF p22.
string newDocumentFile = GetTestPath(@"TOF\BSA_Agilent.sky");
WaitForCondition(() => File.Exists(newDocumentFile));
RunUI(() => SkylineWindow.OpenFile(newDocumentFile));
bool asSmallMolecules = AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none;
if (asSmallMolecules)
{
ConvertDocumentToSmallMolecules(AsSmallMoleculesTestMode);
}
var docCalibrate1 = WaitForDocumentLoaded();
const int pepCount1 = 5, preCount1 = 5, tranCount1 = 30;
AssertEx.IsDocumentState(docCalibrate1, null, 1, pepCount1, preCount1, tranCount1);
// Try to import a file to show it fails.
ImportResultsDlg importResultsDlg3 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() => importResultsDlg3.NamedPathSets = importResultsDlg3.GetDataSourcePathsFileReplicates(
new[] { MsDataFileUri.Parse(GetTestPath(@"TOF\6-BSA-500fmol" + ExtAgilentRaw)) }));
var importProgress = ShowDialog <AllChromatogramsGraph>(importResultsDlg3.OkDialog);
WaitForDocumentChangeLoaded(docCalibrate1);
WaitForConditionUI(() => importProgress.Finished);
string expectedErrorFormat = Resources.NoFullScanFilteringException_NoFullScanFilteringException_To_extract_chromatograms_from__0__full_scan_settings_must_be_enabled_;
WaitForConditionUI(() => !string.IsNullOrEmpty(importProgress.Error), "Missing expected error text: " + expectedErrorFormat);
RunUI(() => AssertEx.AreComparableStrings(expectedErrorFormat, importProgress.Error, 1));
RunUI(() =>
{
importProgress.ClickClose();
SkylineWindow.Undo();
});
var document = SkylineWindow.Document;
// Fill out Transition Settings Menu
int tranCount2 = (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) ? (tranCount1 + preCount1 * 3) : (tranCount1 + preCount1); // No iostopes for mass-only document
using (new CheckDocumentState(1, pepCount1, preCount1, tranCount2))
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettingsUI.PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
transitionSettingsUI.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof;
transitionSettingsUI.Peaks = 3;
transitionSettingsUI.AcquisitionMethod = FullScanAcquisitionMethod.Targeted;
transitionSettingsUI.ProductMassAnalyzer = FullScanMassAnalyzerType.tof;
});
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Transition Settings - Full-Scan tab for TOF", 28);
RunUI(() =>
{
transitionSettingsUI.RetentionTimeFilterType = RetentionTimeFilterType.none;
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.FragmentTypes += ", p";
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 29);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
}
var docHighRes = WaitForDocumentChange(document);
var tranSettingsHighRes = docHighRes.Settings.TransitionSettings;
Assert.AreEqual(FullScanPrecursorIsotopes.Count, tranSettingsHighRes.FullScan.PrecursorIsotopes);
Assert.AreEqual(FullScanMassAnalyzerType.tof, tranSettingsHighRes.FullScan.PrecursorMassAnalyzer);
Assert.AreEqual(FullScanAcquisitionMethod.Targeted, tranSettingsHighRes.FullScan.AcquisitionMethod);
Assert.IsTrue(ArrayUtil.EqualsDeep(new[] { IonType.y, IonType.b, IonType.precursor },
tranSettingsHighRes.Filter.IonTypes));
RunUI(() => SkylineWindow.ExpandPrecursors());
// Assert each peptide contains 3 precursors transitions (unless this is a masses-only small molecule doc).
foreach (var nodeGroup in SkylineWindow.Document.MoleculeTransitionGroups)
{
for (int i = 0; i < nodeGroup.Children.Count; i++)
{
var nodeTran = (TransitionDocNode)nodeGroup.Children[i];
if (i < ((AsSmallMoleculesTestMode == RefinementSettings.ConvertToSmallMoleculesMode.masses_only) ? 1 : 3))
{
Assert.AreEqual(IonType.precursor, nodeTran.Transition.IonType);
}
else
{
Assert.AreNotEqual(IonType.precursor, nodeTran.Transition.IonType);
}
}
}
RestoreViewOnScreen(30);
PauseForScreenShot("Targets View tree clipped from main window", 30);
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg2 =>
{
string[] filePaths =
{
GetTestPath(@"TOF\6-BSA-500fmol" + ExtAgilentRaw)
};
importResultsDlg2.NamedPathSets = importResultsDlg2.GetDataSourcePathsFileReplicates(filePaths.Select(MsDataFileUri.Parse));
importResultsDlg2.OkDialog();
});
WaitForDocumentChangeLoaded(docHighRes);
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(asSmallMolecules ? "LVNELTEFAK" : "K.LVNELTEFAK.T [65, 74]");
}
else
{
FindNode(document.MoleculeTransitionGroups.First().CustomIon.DisplayName);
}
RunUI(() =>
{
SkylineWindow.CollapsePrecursors();
SkylineWindow.AutoZoomNone();
SkylineWindow.ShowGraphPeakArea(false);
SkylineWindow.ShowProductTransitions();
});
RestoreViewOnScreen(31);
RunUI(() => SkylineWindow.Width = 1013);
PauseForScreenShot("Main window full gradient import of high concentration and Targets tree clipped", 31);
{
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Prediction;
Assert.IsTrue(peptideSettingsUI.IsUseMeasuredRT);
Assert.AreEqual(2.0, peptideSettingsUI.TimeWindow);
});
PauseForScreenShot <PeptideSettingsUI.PredictionTab>("Peptide Settings - Prediction tab", 32);
OkDialog(peptideSettingsUI, peptideSettingsUI.CancelDialog);
}
using (new CheckDocumentState(1, pepCount1, preCount1, tranCount2))
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettingsUI.SetRetentionTimeFilter(RetentionTimeFilterType.scheduling_windows, 1);
});
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Transition Settings - Full-Scan tab wtih scheduled extraction", 33);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
}
var chooseSchedulingReplicateDlg = ShowDialog <ChooseSchedulingReplicatesDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
// Make sure UI is up to date to avoid race condition
chooseSchedulingReplicateDlg.UpdateUi();
chooseSchedulingReplicateDlg.SelectOrDeselectAll(true);
});
RunDlg <ImportResultsDlg>(chooseSchedulingReplicateDlg.OkDialog, importResultsDlg2 =>
{
string[] filePaths =
{
GetTestPath(@"TOF\1-BSA-50amol" + ExtAgilentRaw),
GetTestPath(@"TOF\2-BSA-100amol" + ExtAgilentRaw),
GetTestPath(@"TOF\3-BSA-1fmol" + ExtAgilentRaw),
GetTestPath(@"TOF\4-BSA-10fmol" + ExtAgilentRaw),
GetTestPath(@"TOF\5-BSA-100fmol" + ExtAgilentRaw),
};
importResultsDlg2.NamedPathSets = importResultsDlg2.GetDataSourcePathsFileReplicates(filePaths.Select(MsDataFileUri.Parse));
importResultsDlg2.OkDialog();
});
//Give the Raw files some time to be processed.
WaitForCondition(15 * 60 * 1000, () => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 15 minutes
WaitForClosedAllChromatogramsGraph();
RunUI(() => SkylineWindow.ShowGraphSpectrum(false));
WaitForGraphs();
TryWaitForConditionUI(() => SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden) == 6);
RunUI(() =>
{
Assert.IsFalse(SkylineWindow.IsGraphSpectrumVisible);
var listGraphs = SkylineWindow.GraphChromatograms.Where(graphChrom => !graphChrom.IsHidden).ToList();
if (listGraphs.Count != 6)
{
string hiddenGraphs = string.Empty;
var listHidden = SkylineWindow.GraphChromatograms.Where(graphChrom => graphChrom.IsHidden).ToList();
if (listHidden.Count != 0)
{
hiddenGraphs = TextUtil.LineSeparate(string.Empty, "Hidden:", TextUtil.LineSeparate(listHidden.Select(g => g.TabText)));
}
Assert.Fail(TextUtil.LineSeparate(string.Format("Expecting 6 visible graphs but found {0}", listGraphs.Count),
TextUtil.LineSeparate(listGraphs.Select(g => g.TabText)), hiddenGraphs));
}
var chromGraphs = SkylineWindow.GraphChromatograms.ToArray();
Assert.AreEqual(6, chromGraphs.Length);
});
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
for (int i = 0; i < 5; i++)
{
dlg.MoveDown();
}
dlg.OkDialog();
});
RunDlg <ArrangeGraphsGroupedDlg>(SkylineWindow.ArrangeGraphsGrouped, dlg =>
{
dlg.Groups = 6;
dlg.GroupOrder = GroupGraphsOrder.Document;
dlg.OkDialog();
});
WaitForGraphs();
RunUI(() => SkylineWindow.Height = 768);
PauseForScreenShot("Chromatogram graphs clipped from main window", 34);
RunUI(() =>
{
var graphChrom6 = SkylineWindow.GetGraphChrom("6-BSA-500fmol");
var graphChrom5 = SkylineWindow.GetGraphChrom("5-BSA-100fmol");
var graphChrom4 = SkylineWindow.GetGraphChrom("4-BSA-10fmol");
var graphChrom3 = SkylineWindow.GetGraphChrom("3-BSA-1fmol");
var graphChrom2 = SkylineWindow.GetGraphChrom("2-BSA-100amol");
var graphChrom1 = SkylineWindow.GetGraphChrom("1-BSA-50amol");
Assert.AreEqual(13.3, graphChrom6.BestPeakTime ?? 0, 0.05);
Assert.AreEqual(13.5, graphChrom5.BestPeakTime ?? 0, 0.05);
Assert.AreEqual(13.6, graphChrom4.BestPeakTime ?? 0, 0.05);
Assert.AreEqual(13.6, graphChrom3.BestPeakTime ?? 0, 0.05);
Assert.AreEqual(13.6, graphChrom2.BestPeakTime ?? 0, 0.05);
Assert.AreEqual(13.6, graphChrom1.BestPeakTime ?? 0, 0.05);
});
RunUI(SkylineWindow.AutoZoomBestPeak);
WaitForGraphs();
PauseForScreenShot("Chromatogram graphs clipped from main window zoomed", 35);
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowPeptideLogScale(true);
});
// p. 28
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Replicate Comparison graph metafile", 36);
WaitForDotProducts();
RunUI(() =>
{
Assert.AreEqual((AsSmallMoleculesTestMode == RefinementSettings.ConvertToSmallMoleculesMode.none) ? 7 : 6, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(6, SkylineWindow.GraphPeakArea.CurveCount);
});
VerifyDotProducts(0.87, 0.67, 0.91, 0.90, 0.90, 0.90);
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
SkylineWindow.ShowSplitChromatogramGraph(false);
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.ActivateReplicate("6-BSA-500fmol");
SkylineWindow.Size = new Size(745, 545);
SkylineWindow.ShowGraphPeakArea(false);
});
PauseForScreenShot("Chromatogram graph metafile for 500 fmol", 37);
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowPrecursorTransitions();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ActivateReplicate("4-BSA-10fmol");
});
WaitForDotProducts();
RunUI(() =>
{
Assert.AreEqual(7, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual((AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) ? 3 : 1, SkylineWindow.GraphPeakArea.CurveCount);
});
VerifyDotProducts(0.99, 0.52, 0.98, 1.00, 1.00, 1.00);
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(false);
SkylineWindow.Size = new Size(1013, 768);
});
PauseForScreenShot("Main window", 38);
RunUI(SkylineWindow.ShowPeakAreaReplicateComparison);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Replicate Comparison graph metafile", 39);
RunUI(() => SkylineWindow.SaveDocument());
WaitForConditionUI(() => !SkylineWindow.Dirty);
}