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()
{
var folderAbsoluteQuant = UseRawFiles ? "AbsoluteQuant" : "AbsoluteQuantMzml";
// Generating a Transition List, p. 4
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI.PrecursorMassType = MassType.Monoisotopic;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.RegressionCEName = "Thermo TSQ Vantage";
transitionSettingsUI.RegressionDPName = Resources.SettingsList_ELEMENT_NONE_None;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 4);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.PrecursorCharges = "2";
transitionSettingsUI.ProductCharges = "1";
transitionSettingsUI.FragmentTypes = "y";
transitionSettingsUI.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_3;
transitionSettingsUI.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion_minus_1;
transitionSettingsUI.SpecialIons = new string[0];
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 4);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
// Configuring Peptide settings p. 4
PeptideSettingsUI peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Modifications);
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab", 5);
var modHeavyK = new StaticMod("Label:13C(6)15N(2) (C-term K)", "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15,
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUI, "Edit Isotope Modification over Transition Settings", 5);
RunUI(() => peptideSettingsUI.PickedHeavyMods = new[] { modHeavyK.Name });
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab with mod added", 5);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
// Inserting a peptide sequence p. 5
using (new CheckDocumentState(1, 1, 2, 10))
{
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pasteDlg.PastePeptides);
WaitForProteinMetadataBackgroundLoaderCompletedUI();
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 6);
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
RunUI(SkylineWindow.ExpandPrecursors);
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
WaitForCondition(() => File.Exists(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
PauseForScreenShot("Main window with Targets view", 6);
// Exporting a transition list p. 6
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO;
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.OptimizeType = ExportOptimize.NONE;
exportMethodDlg.MethodType = ExportMethodType.Standard;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List", 7);
OkDialog(exportMethodDlg, () =>
exportMethodDlg.OkDialog(TestFilesDir.GetTestPath("Quant_Abs_Thermo_TSQ_Vantage.csv")));
}
// Importing RAW files into Skyline p. 7
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
PauseForScreenShot <ImportResultsDlg>("Import Results - click OK to get shot of Import Results Files and then cancel", 8);
RunUI(() =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Skip(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg.NamedPathSets = namedPathSets.ToArray();
});
RunDlg <ImportResultsNameDlg>(importResultsDlg.OkDialog,
importResultsNameDlg => importResultsNameDlg.NoDialog());
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
Settings.Default.ArrangeGraphsOrder = GroupGraphsOrder.Document.ToString();
Settings.Default.ArrangeGraphsReversed = false;
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.AutoZoomBestPeak();
});
WaitForCondition(() => Equals(8, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden)),
"unexpected visible graphChromatogram count");
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot("Main window with imported data", 9);
// Analyzing SRM Data from FOXN1-GST Sample p. 9
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults,
importResultsDlg1 =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Take(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg1.NamedPathSets = namedPathSets.ToArray();
importResultsDlg1.OkDialog();
});
WaitForGraphs();
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
WaitForCondition(5 * 60 * 1000, // five minutes
() =>
SkylineWindow.Document.Settings.HasResults &&
SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RunUI(() =>
{
SkylineWindow.ToggleIntegrateAll();
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ShowPeakAreaReplicateComparison();
// Total normalization
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view);
});
RunUI(() => SkylineWindow.ActivateReplicate("FOXN1-GST"));
WaitForGraphs();
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 0));
WaitForGraphs();
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphPeakArea.ResultsIndex);
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphRetentionTime.ResultsIndex);
});
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.First().TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for light", 10);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 1));
WaitForGraphs();
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.ToArray()[1].TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for heavy", 10);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0));
WaitForGraphs();
// Heavy normalization
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_ratio_view));
WaitForGraphs();
RunUI(() =>
{
int transitionGroupCount = SkylineWindow.DocumentUI.Peptides.First().TransitionGroupCount;
CheckGstGraphs(transitionGroupCount, transitionGroupCount - 1);
});
PauseForScreenShot("Main window with totals graphs for light and heavy and FOXN1-GST", 11);
// Peptide Quantitification Settings p. 11
var peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
const string quantUnits = "fmol/ul";
RunUI(() =>
{
peptideSettingsUi.SelectedTab = PeptideSettingsUI.TABS.Quantification;
peptideSettingsUi.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUi.QuantNormalizationMethod = new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUi.QuantUnits = quantUnits;
});
PauseForScreenShot("Peptide Settings Quantification Tab", 12);
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
// Specify analyte concentrations of external standards
RunUI(() => SkylineWindow.ShowDocumentGrid(true));
var documentGridForm = FindOpenForm <DocumentGridForm>();
RunUI(() =>
{
documentGridForm.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates);
});
WaitForConditionUI(() => documentGridForm.IsComplete);
var concentrations = new[] { 40, 12.5, 5, 2.5, 1, .5, .25, .1 };
for (int iRow = 0; iRow < concentrations.Length; iRow++)
{
// ReSharper disable AccessToModifiedClosure
RunUI(() =>
{
var colSampleType = documentGridForm.FindColumn(PropertyPath.Root.Property("SampleType"));
documentGridForm.DataGridView.Rows[iRow].Cells[colSampleType.Index].Value = SampleType.STANDARD;
});
WaitForConditionUI(() => documentGridForm.IsComplete);
RunUI(() =>
{
var colAnalyteConcentration =
documentGridForm.FindColumn(PropertyPath.Root.Property("AnalyteConcentration"));
var cell = documentGridForm.DataGridView.Rows[iRow].Cells[colAnalyteConcentration.Index];
documentGridForm.DataGridView.CurrentCell = cell;
cell.Value = concentrations[iRow];
});
// ReSharper restore AccessToModifiedClosure
WaitForConditionUI(() => documentGridForm.IsComplete);
}
PauseForScreenShot("Document grid with concentrations filled in", 13);
// View the calibration curve p. 13
RunUI(() => SkylineWindow.ShowCalibrationForm());
var calibrationForm = FindOpenForm <CalibrationForm>();
PauseForScreenShot("View calibration curve", 14);
Assert.AreEqual(CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, quantUnits), calibrationForm.ZedGraphControl.GraphPane.XAxis.Title.Text);
Assert.AreEqual(string.Format(QuantificationStrings.CalibrationCurveFitter_PeakAreaRatioText__0___1__Peak_Area_Ratio, IsotopeLabelType.light.Title, IsotopeLabelType.heavy.Title),
calibrationForm.ZedGraphControl.GraphPane.YAxis.Title.Text);
}
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()
{
// 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()
{
// iRT Retention Time Prediction
string standardDocumentFile = GetTestPath("iRT-C18 Standard.sky"); // Not L10N
RunUI(() => SkylineWindow.OpenFile(standardDocumentFile));
WaitForDocumentLoaded(); // might have some updating to do for protein metadata
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("iRT-C18 Calibrate.sky"))); // Not L10N
// Load raw files for iRT calculator calibration p. 2
const string unschedHuman1Fileroot = "A_D110907_SiRT_HELA_11_nsMRM_150selected_1_30min-5-35"; // Not L10N
string unschedHuman1Name = unschedHuman1Fileroot.Substring(41);
const string unschedHuman2Fileroot = "A_D110907_SiRT_HELA_11_nsMRM_150selected_2_30min-5-35"; // Not L10N
string unschedHuman2Name = unschedHuman2Fileroot.Substring(41);
ImportNewResults(new[] { unschedHuman1Fileroot, unschedHuman2Fileroot }, 41, false, false);
var docCalibrate = WaitForProteinMetadataBackgroundLoaderCompletedUI();
const int pepCount = 11, tranCount = 33;
AssertEx.IsDocumentState(docCalibrate, null, 1, pepCount, pepCount, tranCount);
AssertResult.IsDocumentResultsState(docCalibrate, unschedHuman1Name, pepCount, pepCount, 0, tranCount, 0);
AssertResult.IsDocumentResultsState(docCalibrate, unschedHuman2Name, pepCount, pepCount, 0, tranCount, 0);
RunUI(() =>
{
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowRTPeptideGraph();
using (var enumLabels = SkylineWindow.RTGraphController.GraphSummary.Categories.GetEnumerator())
{
foreach (var nodePep in docCalibrate.Peptides)
{
Assert.IsTrue(enumLabels.MoveNext() && enumLabels.Current != null);
Assert.IsTrue(nodePep.Peptide.Sequence.StartsWith(enumLabels.Current.Substring(0, 3)));
}
}
});
// Page 3.
PauseForScreenShot <GraphSummary.RTGraphView>("RT graph metafile", 3); // Peptide RT graph
RunUI(() =>
{
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.SelectedPath = docCalibrate.GetPathTo((int)SrmDocument.Level.Molecules, 0);
});
// Ensure graphs look like p. 3 and 4
WaitForGraphs();
RestoreViewOnScreen(04);
PauseForScreenShot("Main window showing chromatograms and RT graph", 4); // Skyline window with docked RT replicate comparison graph
RunUI(() =>
{
Assert.AreEqual(3, SkylineWindow.RTGraphController.GraphSummary.CurveCount);
Assert.AreEqual(2, SkylineWindow.RTGraphController.GraphSummary.Categories.Count());
var chromGraphs = SkylineWindow.GraphChromatograms.ToArray();
Assert.AreEqual(2, chromGraphs.Length);
Assert.AreEqual(11.3, chromGraphs[0].GraphItems.First().BestPeakTime, 0.05);
Assert.AreEqual(11.2, chromGraphs[1].GraphItems.First().BestPeakTime, 0.05);
});
var listTimes = new List <double>();
for (int i = 0; i < docCalibrate.PeptideCount; i++)
{
int iPeptide = i;
RunUI(() =>
{
SkylineWindow.SelectedPath = docCalibrate.GetPathTo((int)SrmDocument.Level.Molecules, iPeptide);
});
WaitForGraphs();
RunUI(() =>
{
var chromGraphs = SkylineWindow.GraphChromatograms.ToArray();
double time1 = chromGraphs[0].GraphItems.First(g => g.BestPeakTime > 0).BestPeakTime;
double time2 = chromGraphs[1].GraphItems.First(g => g.BestPeakTime > 0).BestPeakTime;
listTimes.Add((time1 + time2) / 2);
Assert.AreEqual(time1, time2, 0.2);
});
}
// Calibrate a calculator p. 4-5
const string irtCalcName = "iRT-C18";
var peptideSettingsUI1 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editIrtCalc1 = ShowDialog <EditIrtCalcDlg>(peptideSettingsUI1.AddCalculator);
RunUI(() =>
{
editIrtCalc1.CalcName = irtCalcName;
editIrtCalc1.CreateDatabase(GetTestPath("iRT-C18.irtdb")); // Not L10N
});
{
var calibrateDlg = ShowDialog <CalibrateIrtDlg>(editIrtCalc1.Calibrate);
RunUI(() =>
{
calibrateDlg.UseResults();
Assert.AreEqual(11, calibrateDlg.StandardPeptideCount);
calibrateDlg.SetFixedPoints(1, 10);
for (int i = 0; i < calibrateDlg.StandardPeptideCount; i++)
{
Assert.AreEqual(listTimes[i], calibrateDlg.StandardPeptideList[i].RetentionTime, 0.2);
}
});
PauseForScreenShot <CalibrateIrtDlg>("Calibrate iRT Calculator form", 5); // Calibrate iRT Calculator form
RunUI(calibrateDlg.OkDialog);
}
Assert.IsTrue(WaitForConditionUI(() => editIrtCalc1.StandardPeptideCount == 11));
PauseForScreenShot <EditIrtCalcDlg>("Edit iRT Calculater form", 6); // Edit iRT Caclulator form
// Check iRT values and update to defined values p. 6-7
var irtDefinitionPath = GetTestPath("iRT definition.xlsx"); // Not L10N
string irtDefText = GetExcelFileText(irtDefinitionPath, "iRT-C18", 2, true); // Not L10N
RunUI(() =>
{
var standardPeptidesArray = editIrtCalc1.StandardPeptides.ToArray();
Assert.AreEqual(11, standardPeptidesArray.Length);
Assert.AreEqual(0, standardPeptidesArray[1].Irt, 0.00001);
Assert.AreEqual(100, standardPeptidesArray[10].Irt, 0.00001);
CheckIrtStandardPeptides(standardPeptidesArray, irtDefText, 6);
SetClipboardText(irtDefText);
editIrtCalc1.DoPasteStandard();
standardPeptidesArray = editIrtCalc1.StandardPeptides.ToArray();
Assert.AreEqual(11, standardPeptidesArray.Length);
Assert.AreEqual(0, standardPeptidesArray[1].Irt, 0.001);
Assert.AreEqual(100, standardPeptidesArray[10].Irt, 0.005);
CheckIrtStandardPeptides(standardPeptidesArray, irtDefText, 0.00001);
});
OkDialog(editIrtCalc1, editIrtCalc1.OkDialog);
OkDialog(peptideSettingsUI1, peptideSettingsUI1.OkDialog);
// Inspect RT regression graph p. 8
RunUI(SkylineWindow.ShowRTRegressionGraphScoreToRun);
WaitForRegression();
RestoreViewOnScreen(08);
PauseForScreenShot <GraphSummary.RTGraphView>("Retention Times Regression graph metafile", 8); // RT Regression graph
RunUI(() =>
{
VerifyRTRegression(0.15, 15.09, 0.9991);
SkylineWindow.ShowSingleReplicate();
SkylineWindow.SequenceTree.Focus(); // If the focus is left on the results tab, then the next line does nothing
SkylineWindow.SelectedResultsIndex = 0;
});
WaitForRegression();
RunUI(() =>
{
VerifyRTRegression(0.15, 15.15, 0.9991);
SkylineWindow.SelectedResultsIndex = 1;
});
WaitForRegression();
RunUI(() => VerifyRTRegression(0.15, 15.04, 0.9991));
RunUI(() => SkylineWindow.ShowAverageReplicates());
RunUI(() => SkylineWindow.SaveDocument());
// Create a document containing human and standard peptides, p. 9
RunUI(() => SkylineWindow.OpenFile(GetTestPath("iRT Human.sky")));
WaitForProteinMetadataBackgroundLoaderCompletedUI(); // let peptide metadata background loader do its work
RunUI(() =>
{
SkylineWindow.SelectedPath = new IdentityPath(SequenceTree.NODE_INSERT_ID);
SkylineWindow.ImportFiles(standardDocumentFile);
});
WaitForProteinMetadataBackgroundLoaderCompletedUI(); // let peptide metadata background loader do its work
RestoreViewOnScreen(09);
PauseForScreenShot("Targets tree clipped out of main winodw", 9); // Target tree
RunUI(() =>
{
Assert.AreEqual("iRT-C18 Standard Peptides", SkylineWindow.SelectedNode.Text); // Not L10N
Assert.AreEqual(1231, SkylineWindow.DocumentUI.PeptideTransitionCount);
SkylineWindow.SaveDocument(GetTestPath("iRT Human+Standard.sky")); // Not L10N
SkylineWindow.SaveDocument(GetTestPath("iRT Human+Standard Calibrate.sky")); // Not L10N
});
// Remove heavy precursors, p. 10
var docHumanAndStandard = SkylineWindow.Document;
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, refineDlg =>
{
refineDlg.RefineLabelType = IsotopeLabelType.heavy;
refineDlg.OkDialog();
});
var docLightOnly = WaitForDocumentChange(docHumanAndStandard);
Assert.AreEqual(632, docLightOnly.PeptideTransitionCount);
// Create auto-calculate regression RT predictor, p. 10
const string irtPredictorName = "iRT-C18"; // Not L10N
{
var docPre = SkylineWindow.Document;
var peptideSettingsUI2 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI2.ChooseRegression(irtPredictorName));
var regressionDlg = ShowDialog <EditRTDlg>(peptideSettingsUI2.EditRegression);
RunUI(() =>
{
Assert.AreEqual(irtPredictorName, regressionDlg.Regression.Name);
Assert.AreEqual(irtCalcName, regressionDlg.Regression.Calculator.Name);
regressionDlg.SetAutoCalcRegression(true);
regressionDlg.SetTimeWindow(5);
});
PauseForScreenShot("Edit Retention Time Predictor form", 10); // Edit retention time predictor form
OkDialog(regressionDlg, regressionDlg.OkDialog);
OkDialog(peptideSettingsUI1, peptideSettingsUI2.OkDialog);
// Make sure iRT calculator is loaded
WaitForDocumentChangeLoaded(docPre);
}
// Export unscheduled transition list, p. 11
{
const string calibrateBasename = "iRT Human+Standard Calibrate"; // Not L10N
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.ExportStrategy = ExportStrategy.Buckets;
exportMethodDlg.IgnoreProteins = true;
exportMethodDlg.MaxTransitions = 335;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 11);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath(calibrateBasename + TextUtil.EXT_CSV)));
WaitForClosedForm(exportMethodDlg);
Assert.AreEqual(332, File.ReadAllLines(GetTestPath(calibrateBasename + "_0001.csv")).Length); // Not L10N
Assert.AreEqual(333 + (TestSmallMolecules ? 2 : 0), File.ReadAllLines(GetTestPath(calibrateBasename + "_0002.csv")).Length); // Not L10N
}
// Import human peptide calibration results p. 12
ImportNewResults(new[] { unschedHuman1Fileroot, unschedHuman2Fileroot }, -1, true);
// Review iRT-C18 graph p. 12-13
RunUI(() => SkylineWindow.ChooseCalculator(irtCalcName));
RunUI(SkylineWindow.ShowRTRegressionGraphScoreToRun);
WaitForRegression();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 13);
RunUI(() =>
{
VerifyRTRegression(0.15, 15.09, 0.9991);
Assert.AreEqual(11, SkylineWindow.DocumentUI.PeptideCount -
SkylineWindow.RTGraphController.Outliers.Length);
});
// Find all unintegrated transitions, p. 13-14
{
var findDlg = ShowDialog <FindNodeDlg>(SkylineWindow.ShowFindNodeDlg);
RunUI(() =>
{
findDlg.FindOptions = new FindOptions().ChangeText(string.Empty)
.ChangeCustomFinders(Finders.ListAllFinders().Where(f => f is UnintegratedTransitionFinder));
});
PauseForScreenShot <FindNodeDlg>("Find form", 14);
RestoreViewOnScreen(15);
RunUI(() =>
{
findDlg.FindAll();
findDlg.Close();
});
WaitForClosedForm(findDlg);
}
PauseForScreenShot <FindResultsForm>("Find Results pane", 14);
var findAllForm = WaitForOpenForm <FindResultsForm>();
Assert.IsNotNull(findAllForm);
const int expectedItems = 6;
RunUI(() =>
{
Assert.AreEqual(expectedItems, findAllForm.ItemCount);
SkylineWindow.ShowAllTransitions();
SkylineWindow.AutoZoomBestPeak();
});
// Review peaks with missing transitions, p. 15
for (int i = 0; i < expectedItems; i++)
{
int iItem = i;
RunUI(() => findAllForm.ActivateItem(iItem));
WaitForGraphs();
RunUI(() => Assert.AreEqual((int)SequenceTree.StateImageId.no_peak,
SkylineWindow.SelectedNode.StateImageIndex));
if (i == 2)
{
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile (1 of 2)", 15);
}
if (i == 3)
{
RunUI(() =>
{
var document = SkylineWindow.DocumentUI;
var nodeGroup = document.FindNode(SkylineWindow.SelectedPath.Parent) as TransitionGroupDocNode;
Assert.IsNotNull(nodeGroup);
var nodeTran = document.FindNode(SkylineWindow.SelectedPath) as TransitionDocNode;
Assert.IsNotNull(nodeTran);
var graph = SkylineWindow.GetGraphChrom(Resources.ImportResultsDlg_DefaultNewName_Default_Name);
// New peak picking picks correct peak
Assert.AreEqual(19.8, graph.BestPeakTime.Value, 0.05);
// TransitionGroupDocNode nodeGroupGraph;
// TransitionDocNode nodeTranGraph;
// var scaledRT = graph.FindAnnotatedPeakRetentionTime(19.8, out nodeGroupGraph, out nodeTranGraph);
// Assert.AreSame(nodeGroup, nodeGroupGraph);
// Assert.AreNotSame(nodeTran, nodeTranGraph);
// Assert.AreEqual(7, nodeTranGraph.Transition.Ordinal); // y7
// graph.FirePickedPeak(nodeGroupGraph, nodeTranGraph, scaledRT);
});
}
if (i == 4)
{
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile (2 of 2)", 15); // Chromatogram graph
}
}
// New peak picking picks correct peak
// RunUI(() => findAllForm.ActivateItem(3));
// PauseForScreenShot<GraphChromatogram>("Chromatogram graph metafile (3 of 3)", 15);
RunUI(SkylineWindow.ToggleIntegrateAll);
RunUI(findAllForm.Close);
WaitForClosedForm(findAllForm);
RestoreViewOnScreen(17);
// Calculate new iRT values for human peptides, p. 16
{
var editIrtCalc2 = ShowDialog <EditIrtCalcDlg>(SkylineWindow.ShowEditCalculatorDlg);
RunUI(() => Assert.AreEqual(0, editIrtCalc2.LibraryPeptideCount));
var addPeptidesDlg = ShowDialog <AddIrtPeptidesDlg>(editIrtCalc2.AddResults);
PauseForScreenShot <AddIrtPeptidesDlg>("Add Peptides form", 15);
RunUI(() =>
{
Assert.AreEqual(148, addPeptidesDlg.PeptidesCount);
Assert.AreEqual(2, addPeptidesDlg.RunsConvertedCount);
Assert.AreEqual(0, addPeptidesDlg.RunsFailedCount);
});
var recalibrateDlg = ShowDialog <MultiButtonMsgDlg>(addPeptidesDlg.OkDialog);
OkDialog(recalibrateDlg, recalibrateDlg.Btn1Click);
PauseForScreenShot <EditIrtCalcDlg>("Edit iRT Calculator form", 16);
RunUI(() => Assert.AreEqual(148, editIrtCalc2.LibraryPeptideCount));
RunUI(editIrtCalc2.OkDialog);
WaitForClosedForm(editIrtCalc2);
}
// Check the RT regression, p. 17
WaitForRegression();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 17);
RunUI(() =>
{
VerifyRTRegression(0.15, 15.09, 0.99985);
Assert.AreEqual(0, SkylineWindow.RTGraphController.Outliers.Length);
SkylineWindow.SaveDocument();
SkylineWindow.HideFindResults();
});
// Recalibrate method to 90-minute gradient, p. 18
RunUI(() => SkylineWindow.OpenFile(GetTestPath("iRT Human+Standard.sky"))); // Not L10N
RunDlg <FindNodeDlg>(SkylineWindow.ShowFindNodeDlg, findDlg =>
{
findDlg.FindOptions = new FindOptions().ChangeText("NSAQ"); // Not L10N
findDlg.FindNext();
findDlg.Close();
});
RunUI(SkylineWindow.EditDelete);
{
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Prediction;
peptideSettingsUI.ChooseRegression(irtPredictorName);
peptideSettingsUI.IsUseMeasuredRT = true;
peptideSettingsUI.TimeWindow = 5;
});
PauseForScreenShot <PeptideSettingsUI.PredictionTab>("Peptide Settings - Prediction tab", 18);
RunUI(peptideSettingsUI.OkDialog);
WaitForClosedForm(peptideSettingsUI);
}
// Import 90-minute standard mix run, p. 19
const string unsched90MinFileroot = "A_D110913_SiRT_HELA_11_nsMRM_150selected_90min-5-40_TRID2215_01"; // Not L10N
ImportNewResults(new[] { unsched90MinFileroot }, -1, false);
WaitForGraphs();
// Verify regression graph, p. 19
RunUI(SkylineWindow.ShowRTRegressionGraphScoreToRun);
WaitForRegression();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 19);
RunUI(() =>
{
VerifyRTRegression(0.40, 24.77, 0.9998);
Assert.AreEqual(147, SkylineWindow.RTGraphController.Outliers.Length);
});
// Check scheduling graph, p. 20
RunUI(SkylineWindow.ShowRTSchedulingGraph);
RunDlg <SchedulingGraphPropertyDlg>(() => SkylineWindow.ShowRTPropertyDlg(SkylineWindow.GraphRetentionTime), propertyDlg =>
{
propertyDlg.TimeWindows = new[] { 2.0, 5.0, 10.0 };
propertyDlg.OkDialog();
});
WaitForGraphs();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Scheduling graph metafile", 20);
// Export new 90-minute scheduled transition list, p. 22
const string scheduledBasename = "iRT Human+Standard"; // Not L10N
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.ExportStrategy = ExportStrategy.Buckets;
exportMethodDlg.MaxTransitions = 265;
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 21);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath(scheduledBasename + TextUtil.EXT_CSV)));
WaitForClosedForm(exportMethodDlg);
}
Assert.AreEqual(1223 + (TestSmallMolecules ? 4 : 0), File.ReadAllLines(GetTestPath(scheduledBasename + "_0001.csv")).Length); // Not L10N
Assert.IsFalse(File.Exists(GetTestPath("iRT Human+Standard_0002.csv"))); // Not L10N
// Import scheduled data, p. 23
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, manageResultsDlg =>
{
manageResultsDlg.RemoveAllReplicates();
manageResultsDlg.OkDialog();
});
RunUI(() => SkylineWindow.SaveDocument());
const string sched90MinFileroot = "A_D110913_SiRT_HELA_11_sMRM_150selected_90min-5-40_SIMPLE"; // Not L10N
ImportNewResults(new[] { sched90MinFileroot }, -1, false);
RunUI(SkylineWindow.ShowRTRegressionGraphScoreToRun);
WaitForRegression();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 23);
// Review regression and outliers, p. 24
RunUI(() =>
{
VerifyRTRegression(0.358, 25.920, 0.91606);
Assert.AreEqual(0, SkylineWindow.RTGraphController.Outliers.Length);
});
RunDlg <RegressionRTThresholdDlg>(SkylineWindow.ShowRegressionRTThresholdDlg, thresholdDlg =>
{
thresholdDlg.Threshold = 0.998;
thresholdDlg.OkDialog();
});
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 24);
// Verify 2 outliers highlighed and removed, p. 25
WaitForConditionUI(() => SkylineWindow.RTGraphController.Outliers.Length == 2);
RunUI(() =>
{
VerifyRTRegression(0.393, 24.85, 0.9989);
SkylineWindow.RemoveRTOutliers();
});
WaitForRegression();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 25);
// Check outlier removal, p. 25
RunUI(() =>
{
VerifyRTRegression(0.393, 24.85, 0.9989);
Assert.AreEqual(0, SkylineWindow.RTGraphController.Outliers.Length);
});
// Review a peak and its predicted retention time, p. 26
RunDlg <FindNodeDlg>(SkylineWindow.ShowFindNodeDlg, findDlg =>
{
findDlg.FindOptions = new FindOptions().ChangeText("DATNVG"); // Not L10N
findDlg.FindNext();
findDlg.Close();
});
WaitForGraphs();
RestoreViewOnScreen(27);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile", 26); // Chromatogram graph
RunUI(() =>
{
var graphChrom = SkylineWindow.GetGraphChrom(sched90MinFileroot);
Assert.IsTrue(graphChrom.BestPeakTime.HasValue);
Assert.AreEqual(47.3, graphChrom.BestPeakTime.Value, 0.05);
Assert.IsTrue(graphChrom.PredictedRT.HasValue);
Assert.AreEqual(47.6, graphChrom.PredictedRT.Value, 0.05);
});
// Import retention times from a spectral library, p. 27
RestoreViewOnScreen(17); // get regression graph back
{
var editIrtCalc = ShowDialog <EditIrtCalcDlg>(SkylineWindow.ShowEditCalculatorDlg);
var addLibrayDlg = ShowDialog <AddIrtSpectralLibrary>(editIrtCalc.AddLibrary);
RunUI(() =>
{
addLibrayDlg.Source = SpectralLibrarySource.file;
addLibrayDlg.FilePath = GetTestPath(Path.Combine("Yeast+Standard", // Not L10N
"Yeast_iRT_C18_0_00001.blib")); // Not L10N
});
PauseForScreenShot <AddIrtSpectralLibrary>("Add Spectral Library form", 27);
// Verify converted peptide iRT values and OK dialogs, p. 28
var addPeptidesDlg = ShowDialog <AddIrtPeptidesDlg>(addLibrayDlg.OkDialog);
RunUI(() =>
{
Assert.AreEqual(558, addPeptidesDlg.PeptidesCount);
Assert.AreEqual(1, addPeptidesDlg.RunsConvertedCount); // Libraries now convert through internal alignment to single RT scale
Assert.AreEqual(3, addPeptidesDlg.KeepPeptidesCount);
});
PauseForScreenShot <AddIrtPeptidesDlg>("Add Peptides form", 28);
var recalibrateDlg = ShowDialog <MultiButtonMsgDlg>(addPeptidesDlg.OkDialog);
OkDialog(recalibrateDlg, recalibrateDlg.Btn1Click);
Assert.IsTrue(WaitForConditionUI(() => editIrtCalc.LibraryPeptideCount == 706));
RunUI(editIrtCalc.OkDialog);
WaitForClosedForm(editIrtCalc);
}
// Inspect MS1 filtered Skyline file created from library DDA data, p. 29
RunUI(() => SkylineWindow.OpenFile(GetTestPath(Path.Combine("Yeast+Standard", // Not L10N
"Yeast+Standard (refined) - 2min.sky"))));
WaitForDocumentLoaded();
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0));
WaitForRegression();
// Verify numbers that show up in the screenshot
RunUI(() =>
{
// If the cache gets rebuilt, then because the chromatograms
// were minimized, the peak picking is not exactly the same
// using the minimized chromatograms.
VerifyRTRegression(0.3, 19.37, 0.9998);
var graphChrom = SkylineWindow.GetGraphChrom("Velos_2011_1110_RJ_16"); // Not L10N
Assert.AreEqual(37.6, graphChrom.RetentionMsMs[0], 0.05);
Assert.IsTrue(graphChrom.BestPeakTime.HasValue);
Assert.AreEqual(37.6, graphChrom.BestPeakTime.Value, 0.05);
graphChrom = SkylineWindow.GetGraphChrom("Velos_2011_1110_RJ_14"); // Not L10N
Assert.AreEqual(37.3, graphChrom.RetentionMsMs[0], 0.05);
Assert.AreEqual(37.6, graphChrom.RetentionMsMs[1], 0.05);
Assert.IsTrue(graphChrom.BestPeakTime.HasValue);
Assert.AreEqual(37.4, graphChrom.BestPeakTime.Value, 0.05);
});
PauseForScreenShot("Main window", 29);
// Add results and verify add dialog counts, p. 29-30
{
var editIrtCalc = ShowDialog <EditIrtCalcDlg>(SkylineWindow.ShowEditCalculatorDlg);
var addPeptidesDlg = ShowDialog <AddIrtPeptidesDlg>(editIrtCalc.AddResults);
RunUI(() =>
{
Assert.AreEqual(0, addPeptidesDlg.PeptidesCount);
Assert.AreEqual(2, addPeptidesDlg.RunsConvertedCount);
Assert.AreEqual(558, addPeptidesDlg.OverwritePeptidesCount);
Assert.AreEqual(3, addPeptidesDlg.ExistingPeptidesCount);
});
PauseForScreenShot <AddIrtPeptidesDlg>("Add Peptides form", 30);
var recalibrateDlg = ShowDialog <MultiButtonMsgDlg>(addPeptidesDlg.OkDialog);
OkDialog(recalibrateDlg, recalibrateDlg.Btn1Click);
RunUI(editIrtCalc.OkDialog);
WaitForClosedForm(editIrtCalc);
}
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
protected override void DoTest()
{
TestSmallMolecules = false; // The presence of the extra test node without any results is incompatible with what's being tested here.
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
d => d.ChangeSettings(SrmSettingsList.GetDefault())));
SrmDocument doc = SkylineWindow.Document;
const string documentBaseName = "Ms1FilterTutorial";
string documentFile = GetTestPath(documentBaseName + SrmDocument.EXT);
RunUI(() => SkylineWindow.SaveDocument(documentFile));
// show the empty Transition Setting dialog
var transitionSettingsDlg = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => transitionSettingsDlg.SelectedTab = TransitionSettingsUI.TABS.FullScan);
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Transition Settings - Full-Scan tab nothing set", 2);
OkDialog(transitionSettingsDlg, transitionSettingsDlg.OkDialog);
// Launch the wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
// We're on the "Build Spectral Library" page of the wizard.
// Add the test xml file to the search files list and try to
// build the document library.
string[] searchFiles =
{
GetTestPath("100803_0001_MCF7_TiB_L.group.xml"), // Not L10N
GetTestPath("100803_0005b_MCF7_TiTip3.group.xml") // Not L10N
};
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library empty page", 3);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library populated page", 4);
var ambiguousDlg = ShowDialog <MessageDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
OkDialog(ambiguousDlg, ambiguousDlg.OkDialog);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(documentFile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// We're on the "Extract Chromatograms" page of the wizard.
// All the test results files are in the same directory as the
// document file, so all the files should be found, and we should
// just be able to move to the next page.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page);
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsPage>("Import Peptide Search - Extract Chromatograms page", 5);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
PauseForScreenShot <ImportResultsNameDlg>("Import Results - Common prefix form", 6);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
// Wait for the "Add Modifications" page of the wizard.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page);
List <string> modsToCheck = new List <string> {
"Phospho (ST)", "Phospho (Y)", "Oxidation (M)"
}; // Not L10N
RunUI(() =>
{
importPeptideSearchDlg.MatchModificationsControl.CheckedModifications = modsToCheck;
});
PauseForScreenShot <ImportPeptideSearchDlg.MatchModsPage>("Import Peptide Search - Add Modifications page", 7);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// We're on the "Configure MS1 Full-Scan Settings" page of the wizard.
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
importPeptideSearchDlg.FullScanSettingsControl.PrecursorCharges = new[] { 2, 3, 4 };
importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof;
importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes = 10 * 1000;
Assert.AreEqual(importPeptideSearchDlg.FullScanSettingsControl.PrecursorIsotopesCurrent, FullScanPrecursorIsotopes.Count);
Assert.AreEqual(FullScanMassAnalyzerType.tof, importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer);
Assert.AreEqual(10 * 1000, importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes);
Assert.AreEqual(3, importPeptideSearchDlg.FullScanSettingsControl.Peaks);
Assert.AreEqual(RetentionTimeFilterType.ms2_ids, importPeptideSearchDlg.FullScanSettingsControl.RetentionTimeFilterType);
Assert.AreEqual(5, importPeptideSearchDlg.FullScanSettingsControl.TimeAroundMs2Ids);
});
PauseForScreenShot <ImportPeptideSearchDlg.Ms1FullScanPage>("Import Peptide Search - Configure MS1 Full-Scan Settings page", 8);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// Last page of wizard - Import Fasta.
string fastaPath = GetTestPath("12_proteins.062011.fasta");
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page);
Assert.AreEqual("Trypsin [KR | P]", importPeptideSearchDlg.ImportFastaControl.Enzyme.GetKey());
importPeptideSearchDlg.ImportFastaControl.MaxMissedCleavages = 2;
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(fastaPath);
Assert.IsFalse(importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled);
});
PauseForScreenShot <ImportPeptideSearchDlg.FastaPage>("Import Peptide Search - Import FASTA page", 10);
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(() => importPeptideSearchDlg.ClickNextButton());
WaitForCondition(() => peptidesPerProteinDlg.DocumentFinalCalculated);
RunUI(() =>
{
int proteinCount, peptideCount, precursorCount, transitionCount;
peptidesPerProteinDlg.NewTargetsAll(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
peptidesPerProteinDlg.NewTargetsFinal(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
});
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 11);
WaitForDocumentChangeLoaded(doc, 8 * 60 * 1000); // 10 minutes
var libraryExplorer = ShowDialog <ViewLibraryDlg>(() => SkylineWindow.OpenLibraryExplorer(documentBaseName));
var matchedPepModsDlg = WaitForOpenForm <AddModificationsDlg>();
PauseForScreenShot <MultiButtonMsgDlg>("Add mods alert", 12);
RunUI(() =>
{
Assert.AreEqual(13, matchedPepModsDlg.NumMatched);
Assert.AreEqual(0, matchedPepModsDlg.NumUnmatched);
matchedPepModsDlg.CancelDialog();
});
RunUI(() =>
{
libraryExplorer.GraphSettings.ShowBIons = true;
libraryExplorer.GraphSettings.ShowYIons = true;
libraryExplorer.GraphSettings.ShowCharge1 = true;
libraryExplorer.GraphSettings.ShowCharge2 = true;
libraryExplorer.GraphSettings.ShowPrecursorIon = true;
});
PauseForScreenShot <ViewLibraryDlg>("Spectral Library Explorer", 13);
RunUI(() =>
{
const string sourceFirst = "100803_0005b_MCF7_TiTip3.wiff";
const double timeFirst = 35.2128;
Assert.AreEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreEqual(timeFirst, libraryExplorer.RetentionTime, 0.0001);
libraryExplorer.SelectedIndex++;
Assert.AreNotEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreNotEqual(timeFirst, libraryExplorer.RetentionTime, 0.0001);
});
OkDialog(libraryExplorer, libraryExplorer.CancelDialog);
const int TIB_L = 0; // index for Tib_L
const int TIP3 = 1; // index for Tip3
AssertEx.IsDocumentState(SkylineWindow.Document, null, 11, 51, 52, 156);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIB_L]), 51, 52, 0, 156, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIP3]), 51, 52, 0, 156, 0);
string Tib_LFilename = searchFiles[TIB_L].Replace(".group.xml", PreferedExtAbWiff);
string Tip3Filename = searchFiles[TIP3].Replace(".group.xml", PreferedExtAbWiff);
// Select the first transition group.
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedPath =
SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
SkylineWindow.GraphSpectrumSettings.ShowAIons = true;
SkylineWindow.GraphSpectrumSettings.ShowBIons = true;
SkylineWindow.GraphSpectrumSettings.ShowYIons = true;
SkylineWindow.GraphSpectrumSettings.ShowPrecursorIon = true;
SkylineWindow.ExpandPrecursors();
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RunDlg <SpectrumChartPropertyDlg>(SkylineWindow.ShowSpectrumProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunUI(() =>
{
// Make window screenshot size
if (IsPauseForScreenShots && SkylineWindow.WindowState != FormWindowState.Maximized)
{
SkylineWindow.Width = 1160;
SkylineWindow.Height = 792;
}
});
RestoreViewOnScreen(13);
PauseForScreenShot("Main window with imported data", 14);
// RunUIWithDocumentWait(() =>
// {
// SkylineWindow.ToggleIntegrateAll(); // TODO: No longer necessary. Change in tutorial
// });
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.none);
Settings.Default.ShowDotProductPeakArea = true;
Settings.Default.ShowLibraryPeakArea = true;
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas view (show context menu)", 16);
RestoreViewOnScreen(15);
RunUI(() =>
{
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowChromatogramLegends(false);
});
PauseForScreenShot("Main window layout", 17);
int atest = 0;
CheckAnnotations(TIB_L, 0, atest++);
int pepIndex = 3;
RunUI(() => SkylineWindow.CollapsePeptides());
RunUI(() => SkylineWindow.ShowAlignedPeptideIDTimes(true));
ChangePeakBounds(TIB_L, pepIndex, 38.79, 39.385);
PauseForScreenShot("Chromatogram graphs clipped from main window", 19);
CheckAnnotations(TIB_L, pepIndex, atest++);
var alignmentForm = ShowDialog <AlignmentForm>(() => SkylineWindow.ShowRetentionTimeAlignmentForm());
RunUI(() =>
{
alignmentForm.Width = 711;
alignmentForm.Height = 561;
alignmentForm.ComboAlignAgainst.SelectedIndex = 0; // to match what's in the tutorial doc
});
PauseForScreenShot <AlignmentForm>("Retention time alignment form", 20);
OkDialog(alignmentForm, alignmentForm.Close);
PauseForScreenShot("Status bar clipped from main window - 4/51 pep 4/52 prec 10/156 tran", 21);
pepIndex = JumpToPeptide("SSKASLGSLEGEAEAEASSPK");
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
Assert.IsTrue(8 == pepIndex);
PauseForScreenShot("Chromatogram graph metafiles for 9th peptide", 21);
CheckAnnotations(TIB_L, pepIndex, atest++);
ZoomSingle(TIP3, 32.6, 41.4); // simulate the wheel scroll described in tutorial
PauseForScreenShot("Chromatogram graph metafile showing all peaks for 1_MCF_TiB_L", 22);
CheckAnnotations(TIB_L, pepIndex, atest++);
// current TIB_L peak should have idotp .87 and ppm -6.9
Assert.AreEqual(0.87, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-10.8, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
ChangePeakBounds(TIB_L, pepIndex, 36.5, 38.0);
// now current TIB_L peak should have idotp .9 and ppm -6.5
Assert.AreEqual(0.9, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-9.4, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
CheckAnnotations(TIB_L, pepIndex, atest++);
var undoIndex = SkylineWindow.Document.RevisionIndex; // preserve for simulating ctrl-z
PickPeakBoth(pepIndex, 40.471035, 40.8134); // select peak for both chromatograms at these respective retention times
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 23);
int[] m1Thru4 = { 1, 2, 3, 4, 5 };
PickTransitions(pepIndex, m1Thru4, "Transition pick list filtered", 24, "Transition pick list unfiltered", 24); // turn on chromatograms
PickPeakBoth(pepIndex, 36.992836, 37.3896027); // select peak for both chromatograms at these respective retention times
ZoomSingle(TIP3, 32.4, 39.6); // set the view for screenshot
PauseForScreenShot("Chromatogram graph metafile comparing 33 and 37 minute peaks", 25);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("ASLGSLEGEAEAEASSPKGK"); // Not L10N
Assert.IsTrue(10 == pepIndex);
PauseForScreenShot("Chhromatogram graph meta files for peptide ASLGSLEGEAEAEASSPKGK", 26);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
PickTransitions(pepIndex, m1Thru4); // turn on M+3 and M+4
ChangePeakBounds(TIP3, pepIndex, 37.35, 38.08);
ZoomSingle(TIP3, 36.65, 39.11); // simulate the wheel scroll described in tutorial
PauseForScreenShot("upper - Chromatogram graph metafile for peptide ASLGSLEGEAEAEASSPKGK with adjusted integration", 27);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("AEGEWEDQEALDYFSDKESGK"); // Not L10N
PauseForScreenShot("lower - Chromatogram graph metafiles for peptide AEGEWEDQEALDYFSDKESGK", 27);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
int[] m1Thru5 = { 1, 2, 3, 4, 5, 6 };
PickTransitions(pepIndex, m1Thru5); // turn on M+3 M+4 and M+5
PauseForScreenShot("Chromatogram graph metafiles with M+3, M+4 and M+5 added", 28);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
JumpToPeptide("ALVEFESNPEETREPGSPPSVQR"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide ALVEFESNPEETREPGSPPSVQR", 29);
pepIndex = JumpToPeptide("YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR"); // Not L10N
PauseForScreenShot("upper - Peak Areas graph metafile for peptide YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR", 30);
int[] m1Thru7 = { 1, 2, 3, 4, 5, 6, 7, 8 };
PickTransitions(pepIndex, m1Thru7); // enable [M+3] [M+4] [M+5] [M+6] [M+7]
PauseForScreenShot("lower - Peak Areas graph metafile with M+3 through M+7 added", 30);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
// page 32 zooming setup
RunUI(() =>
{
SkylineWindow.SynchronizeZooming(true);
SkylineWindow.LockYChrom(false);
SkylineWindow.AlignToFile = SkylineWindow.GraphChromatograms.ToArray()[TIP3].GetChromFileInfoId(); // align to Tip3
});
ZoomBoth(36.5, 39.5, 1600); // simulate the wheel scroll described in tutorial
RunUI(() => SkylineWindow.ShowChromatogramLegends(false));
PauseForScreenShot("Chromatogram graphs clipped from main window with synchronized zooming", 32);
RestoreViewOnScreen(33); // float the Library Match window TODO this causes a crash at next call to ChangePeakBounds, in pwiz.Skyline.Controls.Graphs.GraphChromatogram.ChromGroupInfos.get() Line 492 , why?
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tip3Filename), 37.6076f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 5b_MCF7_TiTip3 (37.61 Min)", 33);
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tib_LFilename), 37.0335f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 1_MCF_TiB_L (37.03 min)", 33);
RestoreViewOnScreen(34); // back to normal view
pepIndex = JumpToPeptide("GVVDSEDLPLNISR"); // Not L10N
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
PauseForScreenShot("upper - Chromatogram graph metafiles for peptide GVVDSEDLPLNISR", 34);
ZoomBoth(35.05, 36.9, 480);
PauseForScreenShot("lower - Chromatogram graph metafile - effect of zoom ", 34);
ChangePeakBounds(TIP3, pepIndex, 35.7, 36.5); // adjust integration per tutorial
CheckAnnotations(TIP3, pepIndex, atest++); // check the new idotp values
/* pepIndex = */ JumpToPeptide("DQVANSAFVER"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide DQVANSAFVER", 35);
// int[] m1 = {2};
// PickTransitions(pepIndex, m1); // enable [M+1] only
// // Measured times in TIB_L are different from displayed times, because of alignment
// ChangePeakBounds(TIB_L, pepIndex, 23.99, 25.29);
// ChangePeakBounds(TIP3, pepIndex, 23.81, 25.21);
// // First transition selected for screenshot
// RunUI(() =>
// {
// var pathPep = SkylineWindow.SelectedPath;
// var nodePep = ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode;
// var nodeGroup = nodePep.TransitionGroups.First();
// var nodeTran = nodeGroup.Transitions.First();
// SkylineWindow.SelectedPath = new IdentityPath(
// new IdentityPath(pathPep, nodeGroup.TransitionGroup), nodeTran.Transition);
// });
// PauseForScreenShot("page 36 - M+1 only, with adjusted integration");
// CheckAnnotations(TIB_L, pepIndex, atest++);
// CheckAnnotations(TIP3, pepIndex, EXPECTED_ANNOTATIONS[atest]);
var docAfter = WaitForProteinMetadataBackgroundLoaderCompletedUI();
// Minimizing a chromatogram cache file.
RunUI(SkylineWindow.CollapsePeptides);
for (int i = 0; i < 5; i++) // just do the first 5
{
int iPeptide = i;
var path = docAfter.GetPathTo((int)SrmDocument.Level.Molecules, iPeptide);
RunUI(() =>
{
SkylineWindow.SelectedPath = path;
});
WaitForGraphs();
}
// Eliminate extraneous chromatogram data.
doc = WaitForProteinMetadataBackgroundLoaderCompletedUI();
var minimizedFile = GetTestPath("Ms1FilteringTutorial-2min.sky"); // Not L10N
var cacheFile = Path.ChangeExtension(minimizedFile, ChromatogramCache.EXT);
{
// TODO: Figure out why the minimize fails to unlock the .skyd file, if not minimized to current file
RunUI(() => SkylineWindow.SaveDocument(minimizedFile));
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
var minimizeResultsDlg = ShowDialog <MinimizeResultsDlg>(manageResultsDlg.MinimizeResults);
RunUI(() =>
{
minimizeResultsDlg.LimitNoiseTime = true;
minimizeResultsDlg.NoiseTimeRange = 2; // Not L10N
});
PauseForScreenShot <MinimizeResultsDlg>("Minimize Results form (percentages vary slightly)", 36); // old p. 23
OkDialog(minimizeResultsDlg, () => minimizeResultsDlg.MinimizeToFile(minimizedFile));
WaitForCondition(() => File.Exists(cacheFile));
WaitForClosedForm(manageResultsDlg);
}
WaitForDocumentChange(doc);
// Inclusion list method export for MS1 filtering
doc = SkylineWindow.Document;
RunDlg <PeptideSettingsUI>(() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction), dlg =>
{
dlg.IsUseMeasuredRT = true;
dlg.TimeWindow = 10;
dlg.OkDialog();
});
WaitForDocumentChangeLoaded(doc);
// Now deviating from the tutorial script for a moment to make sure we can choose a Scheduled export method.
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, dlg =>
{
dlg.MinPeptides = 1; // Not L10N
const double minPeakFoundRatio = 0.1;
dlg.MinPeakFoundRatio = minPeakFoundRatio;
dlg.OkDialog();
});
// Ready to export, although we will just cancel out of the dialog.
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.ABI_TOF; // Not L10N
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
exportMethodDlg.CancelButton.PerformClick();
});
WaitForClosedForm(exportMethodDlg);
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
protected override void DoTest()
{
RunUI(() => SkylineWindow.SetUIMode(SrmDocument.DOCUMENT_TYPE.small_molecules));
// Inserting a Transition List, p. 5
{
var doc = SkylineWindow.Document;
SetCsvFileClipboardText(GetTestPath("Energy_TransitionList.csv"));
RunUI(() =>
{
SkylineWindow.Paste();
AdjustSequenceTreePanelWidth();
});
PauseForScreenShot <SkylineWindow>("Main window after paste from csv", 5);
var docTargets = WaitForDocumentChange(doc);
AssertEx.IsDocumentState(docTargets, null, 3, 18, 36, 36);
Assert.IsFalse(docTargets.MoleculeTransitions.Any(t => t.Transition.IsPrecursor()));
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI.RegressionCEName = "Waters Xevo"; // Collision Energy
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 6);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.SmallMoleculePrecursorAdducts = Adduct.M_MINUS.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentAdducts = Adduct.M_MINUS.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentTypes = TransitionFilter.SMALL_MOLECULE_FRAGMENT_CHAR;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings -Filter tab", 7);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(docTargets);
}
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("EnergyMet.sky")));
// Export method - 2 minutes
{
var exportMethodDlg2 = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg2.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportMethodDlg2.MethodType = ExportMethodType.Standard;
exportMethodDlg2.RunLength = 2;
exportMethodDlg2.SetTemplateFile("VerifyETemplate.exp");
});
PauseForScreenShot <ExportMethodDlg>("Exporting 2 minute method", 9);
OkDialog(exportMethodDlg2, exportMethodDlg2.CancelDialog);
}
// Export transition list
{
var exportTransitionList = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportTransitionList.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportTransitionList.MethodType = ExportMethodType.Standard;
exportTransitionList.RunLength = 2;
});
PauseForScreenShot <ExportMethodDlg>("Exporting transition list", 10);
OkDialog(exportTransitionList, exportTransitionList.CancelDialog);
}
using (new WaitDocumentChange(1, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("Unscheduled"));
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
PauseForScreenShot <OpenDataSourceDialog>("Import Results Files form", 11);
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
PauseForScreenShot <ImportResultsNameDlg>("Import Results common name form", 12);
OkDialog(importResultsNameDlg, importResultsNameDlg.OkDialog);
OkDialog(importResultsDlg1, importResultsDlg1.OkDialog);
}
SelectNode(SrmDocument.Level.Molecules, 0);
SelectNode(SrmDocument.Level.MoleculeGroups, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-target graph", 13);
// Renaming replicates
{
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
string[] repNames = new[] { "2 min", "5 min" };
RunUI(() => manageResultsDlg.Left = SkylineWindow.Right + 50);
for (var i = 0; i < 2; i++)
{
doc = SkylineWindow.Document;
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
var chrom = chromatograms[i];
RunUI(() =>
{
manageResultsDlg.SelectedChromatograms = new[] { chrom };
});
var renameDlg = ShowDialog <RenameResultDlg>(manageResultsDlg.RenameResult);
RunUI(() => renameDlg.ReplicateName = repNames[i]);
if (i == 0)
{
PauseForScreenShot <SkylineWindow>("Manage Results and Rename Replicate (PrtScn and select in Paint)", 14);
}
OkDialog(renameDlg, renameDlg.OkDialog);
}
OkDialog(manageResultsDlg, manageResultsDlg.OkDialog);
}
PauseForScreenShot <SkylineWindow>("Skyline window (renamed)", 15);
var docResults = SkylineWindow.Document;
var msg = "";
foreach (var chromatogramSet in docResults.Settings.MeasuredResults.Chromatograms)
{
try
{
AssertResult.IsDocumentResultsState(docResults, chromatogramSet.Name, 18, 18, 18, 18, 18);
}
catch (Exception x)
{
msg += TextUtil.LineSeparate(x.Message);
}
}
if (!string.IsNullOrEmpty(msg))
{
Assert.IsTrue(string.IsNullOrEmpty(msg), msg);
}
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ArrangeGraphsTiled();
});
RestoreViewOnScreen(16);
SelectNode(SrmDocument.Level.MoleculeGroups, 0);
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.Size = new Size(1054, 587);
AdjustSequenceTreePanelWidth(true);
});
PauseForScreenShot <SkylineWindow>("Skyline window multi-replicate layout", 16);
// Set zoom to show better peak separation in 5 minute run
for (var i = 0; i < 2; i++)
{
WaitForGraphs();
RunUI(() => SkylineWindow.GraphChromatograms.ToArray()[i].ZoomTo(.8, 1.8, 1.39e+8));
WaitForGraphs();
}
PauseForScreenShot <SkylineWindow>("Skyline window showing relative peak separation", 17);
// Set time window
{
var peptideSettingsDlg = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
// ReSharper disable once RedundantCast
peptideSettingsDlg.SelectedTab = (PeptideSettingsUI.TABS) 0; //regular enum does not work because of the hidden tabs in the Small Molecule mode.
peptideSettingsDlg.TimeWindow = 1;
});
PauseForScreenShot <PeptideSettingsUI>("Setting scheduled transition list time window", 18);
OkDialog(peptideSettingsDlg, peptideSettingsDlg.OkDialog);
}
// Export transition list
{
var exportTransitionList = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportTransitionList.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportTransitionList.MethodType = ExportMethodType.Scheduled;
exportTransitionList.OptimizeType = ExportOptimize.NONE;
});
PauseForScreenShot <ExportMethodDlg>("Exporting scheduled transition list", 19);
var schedulingOptionsDlg = ShowDialog <SchedulingOptionsDlg>(() => exportTransitionList.OkDialog(GetTestPath("EnergyMet_5minutes_scheduled.csv")));
RunUI(() =>
{
schedulingOptionsDlg.Algorithm = ExportSchedulingAlgorithm.Single;
schedulingOptionsDlg.ReplicateNum = 1; // 5 min
});
PauseForScreenShot <SchedulingOptionsDlg>("Exporting scheduled transition list - choose replicate", 19);
OkDialog(schedulingOptionsDlg, schedulingOptionsDlg.OkDialog);
WaitForClosedForm(exportTransitionList);
}
using (new WaitDocumentChange(1, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("Scheduled"));
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
RunUI(() => importResultsNameDlg.IsRemove = false);
PauseForScreenShot <ImportResultsNameDlg>("Import Results common name form, not changing names", 20);
OkDialog(importResultsNameDlg, importResultsNameDlg.OkDialog);
}
// Remove 2 minute gradient
// Renaming replicates
string[] newNames = { "1:1_1", "1:1_2", "2:1_2", "1:2_2" };
{
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
SelectReplicate(manageResultsDlg, 0);
PauseForScreenShot <SkylineWindow>("Manage Results removing 2 min", 21);
RunUI(manageResultsDlg.RemoveReplicates);
for (var i = 0; i < newNames.Length; i++)
{
SelectReplicate(manageResultsDlg, i + 1);
RunDlg <RenameResultDlg>(manageResultsDlg.RenameResult, renameDlg =>
{
renameDlg.ReplicateName = newNames[i];
renameDlg.OkDialog();
});
}
PauseForScreenShot <SkylineWindow>("Manage Results replicate renamed", 22);
OkDialog(manageResultsDlg, manageResultsDlg.OkDialog);
}
SelectNode(SrmDocument.Level.Molecules, 0);
RunUI(() =>
{
var molNode = SkylineWindow.SelectedNode;
molNode.Expand();
Assert.AreEqual(2, molNode.Nodes.Count);
molNode.Nodes[0].Expand();
molNode.Nodes[1].Expand();
SkylineWindow.ArrangeGraphsTabbed();
});
PauseForScreenShot <SkylineWindow>("Skyline window with calibration data", 23);
// Linearity
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates));
double[] concentrations = { 1, 1, 2, 0.5 };
var namedConcentrations = newNames.Select((n, i) => new Tuple <string, double?>(n, concentrations[i]));
SetDocumentGridSampleTypesAndConcentrations(namedConcentrations.ToDictionary(t => t.Item1,
t => new Tuple <SampleType, double?>(SampleType.STANDARD, t.Item2)));
RunUI(() =>
{
var gridFloatingWindow = documentGrid.Parent.Parent;
gridFloatingWindow.Size = new Size(370, 230);
gridFloatingWindow.Top = SkylineWindow.Top;
gridFloatingWindow.Left = SkylineWindow.Right + 20;
});
PauseForScreenShot <DocumentGridForm>("Document Grid - sample types and concentrations ", 23);
RunUI(() => SkylineWindow.ShowDocumentGrid(false));
using (new WaitDocumentChange(1, true))
{
// Quant settings
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
// ReSharper disable once RedundantCast
peptideSettingsUI.SelectedTab = (PeptideSettingsUI.TABS) 3;
peptideSettingsUI.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUI.QuantNormalizationMethod =
new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUI.QuantUnits = "ratio to heavy";
});
PauseForScreenShot <PeptideSettingsUI.QuantificationTab>("Peptide Settings - Quantitation", 24);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
}
var calibrationForm = ShowDialog <CalibrationForm>(() => SkylineWindow.ShowCalibrationForm());
RunUI(() =>
{
var calibrationFloatingWindow = calibrationForm.Parent.Parent;
calibrationFloatingWindow.Width = 565;
calibrationFloatingWindow.Top = SkylineWindow.Top;
calibrationFloatingWindow.Left = SkylineWindow.Right + 20;
});
PauseForScreenShot <CalibrationForm>("Calibration Curve ", 25);
OkDialog(calibrationForm, calibrationForm.Close); // Hide the calibration window
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction);
var editCurrentCE = ShowDialog <EditCEDlg>(transitionSettingsUI.EditCECurrent);
RunUI(() =>
{
editCurrentCE.StepSize = 2;
editCurrentCE.StepCount = 5;
});
PauseForScreenShot <EditCEDlg>("Edit Collision Energy Equation form", 26);
RunUI(() =>
{
editCurrentCE.OkDialog();
transitionSettingsUI.UseOptimized = true;
transitionSettingsUI.OptimizeType = OptimizedMethodType.Transition.GetLocalizedString();
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 27);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
}
// Export transition lists
{
var exportTransitionList = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportTransitionList.ExportStrategy = ExportStrategy.Buckets;
exportTransitionList.IgnoreProteins = true;
exportTransitionList.MaxTransitions = 100;
exportTransitionList.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportTransitionList.MethodType = ExportMethodType.Scheduled;
exportTransitionList.OptimizeType = ExportOptimize.CE;
});
PauseForScreenShot <ExportMethodDlg>("Exporting scheduled transition list", 28);
var scheduleDlg = ShowDialog <SchedulingOptionsDlg>(() => exportTransitionList.OkDialog(GetTestPath("EnergyMet_5minutes_ceopt.csv")));
PauseForScreenShot <SchedulingOptionsDlg>("Scheduling", 29);
OkDialog(scheduleDlg, scheduleDlg.OkDialog);
}
// Import CE optimization runs
using (new WaitDocumentChange(1, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
importResultsDlg1.RadioCreateMultipleChecked = true;
importResultsDlg1.OptimizationName = ExportOptimize.CE;
importResultsDlg1.ReplicateName = "CE Optimization";
});
PauseForScreenShot <ImportResultsDlg>("Setting new replicate name to CE Optimization", 30);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.OkDialog());
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("CE Optimization"));
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
PauseForScreenShot <OpenDataSourceDialog>("Import Results Files form", 31);
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
}
PauseForScreenShot <SkylineWindow>("Skyline shows new replicate \"CE Optimization\"", 32);
RunUI(() =>
{
SkylineWindow.Size = new Size(1600, 960);
SkylineWindow.ShowGraphRetentionTime(false, GraphTypeSummary.replicate);
SkylineWindow.AutoZoomBestPeak();
AdjustSequenceTreePanelWidth();
SkylineWindow.ShowSingleTransition();
SkylineWindow.ShowSplitChromatogramGraph(true);
});
PauseForScreenShot <SkylineWindow>("Split graph", 33);
RunUI(() =>
{
SkylineWindow.ShowPeakAreaLegend(false);
});
PauseForScreenShot <SkylineWindow>("No legend", 34);
// Show Pentose-P
SelectNode(SrmDocument.Level.Molecules, 6);
PauseForScreenShot <SkylineWindow>("Pentose-P", 35);
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.ShowChromatogramLegends(false);
});
RestoreCoverViewOnScreen();
TakeCoverShot();
return;
}
// Export final transition list
{
var exportTransitionList = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportTransitionList.ExportStrategy = ExportStrategy.Single;
exportTransitionList.IgnoreProteins = true;
exportTransitionList.MaxTransitions = 100;
exportTransitionList.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportTransitionList.MethodType = ExportMethodType.Scheduled;
});
PauseForScreenShot <ExportMethodDlg>("Exporting final optimized transition list", 36);
var scheduleDlg = ShowDialog <SchedulingOptionsDlg>(() => exportTransitionList.OkDialog(GetTestPath("EnergyMet_5minutes_optimal.csv")));
PauseForScreenShot <SchedulingOptionsDlg>("Final Scheduling", 37);
OkDialog(scheduleDlg, scheduleDlg.OkDialog);
}
}
}
private void arrangeTiledMenuItem_Click(object sender, EventArgs e)
{
SkylineWindow.ArrangeGraphsTiled();
}
protected override void DoTest()
{
// DDA with IDs and alignment
string filePathDda = TestFilesDir.GetTestPath(@"DDA\Bereman_5proteins_spikein_decoys.sky.zip");
RunUI(() => SkylineWindow.OpenSharedFile(filePathDda));
var doc = WaitForDocumentLoaded();
int expectedDecoys = RefinementSettings.SuggestDecoyCount(doc);
RunDlg <GenerateDecoysDlg>(() => SkylineWindow.ShowGenerateDecoysDlg(), decoysDlg =>
{
decoysDlg.DecoysMethod = DecoyGeneration.SHUFFLE_SEQUENCE;
decoysDlg.OkDialog();
});
doc = WaitForDocumentChange(doc);
Assert.AreEqual(expectedDecoys, doc.Peptides.Count(p => p.IsDecoy));
ImportResultsFiles(DDA_FILES.Select(s => GetDataFile("DDA", s)).Select(MsDataFileUri.Parse));
RunUI(() =>
{
SkylineWindow.SaveDocument();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowAlignedPeptideIDTimes(true);
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.SelectedNode.FirstNode;
});
// Random nature of decoys makes it hard to make this very deterministic
// But eventually we should see some peptides without IDs of their own
// All peptides should have aligned IDs, if they don't have a single ID,
// since it might be the only ID
int countWithIds = 0, countTotal = 0;
while (countWithIds < 20 || countTotal - 4 < countWithIds)
{
WaitForGraphs();
RunUI(() =>
{
foreach (var graphChromatogram in SkylineWindow.GraphChromatograms)
{
countTotal++;
int countIds = graphChromatogram.RetentionMsMs != null
? graphChromatogram.RetentionMsMs.Length
: 0;
if (countIds != 1)
{
Assert.IsNotNull(graphChromatogram.AlignedRetentionMsMs);
Assert.AreNotEqual(0, graphChromatogram.AlignedRetentionMsMs.Length);
}
if (countIds > 0)
{
ValidateTimeRange(graphChromatogram, graphChromatogram.RetentionMsMs, 6, 90);
countWithIds++;
}
else
{
ValidateTimeRange(graphChromatogram, graphChromatogram.AlignedRetentionMsMs, 6, 90);
}
}
var nextNode = SkylineWindow.SequenceTree.SelectedNode.NextNode;
if (nextNode != null)
{
SkylineWindow.SequenceTree.SelectedNode = nextNode;
}
});
}
// DIA with DDA IDs
string filePathDia = TestFilesDir.GetTestPath(@"DIA\Hoofnagle_QE_DIA_targeted_decoys.sky.zip");
RunUI(() => SkylineWindow.OpenSharedFile(filePathDia));
doc = WaitForDocumentLoaded();
expectedDecoys = RefinementSettings.SuggestDecoyCount(doc);
RunDlg <GenerateDecoysDlg>(() => SkylineWindow.ShowGenerateDecoysDlg(), decoysDlg =>
{
decoysDlg.DecoysMethod = DecoyGeneration.REVERSE_SEQUENCE;
decoysDlg.OkDialog();
});
doc = WaitForDocumentChange(doc);
Assert.AreEqual(expectedDecoys, doc.Peptides.Count(p => p.IsDecoy));
ImportResultsFiles(DIA_FILES.Select(s => GetDataFile("DIA", s)).Select(MsDataFileUri.Parse));
RunUI(() =>
{
SkylineWindow.SaveDocument();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowOtherRunPeptideIDTimes(true);
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.SelectedNode.FirstNode;
});
for (int i = 0; i < 6; i++)
{
WaitForGraphs();
RunUI(() =>
{
foreach (var graphChromatogram in SkylineWindow.GraphChromatograms)
{
Assert.IsNull(graphChromatogram.RetentionMsMs);
Assert.IsNull(graphChromatogram.AlignedRetentionMsMs);
Assert.IsNotNull(graphChromatogram.UnalignedRetentionMsMs);
Assert.AreNotEqual(0, graphChromatogram.UnalignedRetentionMsMs.Length);
ValidateTimeRange(graphChromatogram, graphChromatogram.UnalignedRetentionMsMs, 8, 120);
}
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.SelectedNode.NextNode;
});
}
// DIA with IRT values
string filePathDiaIrt = TestFilesDir.GetTestPath(@"DIA-iRT\AQUA4_Human_picked_napedro2_full_rescore_iRT_decoys.sky.zip");
RunUI(() => SkylineWindow.OpenSharedFile(filePathDiaIrt));
doc = WaitForDocumentLoaded();
expectedDecoys = RefinementSettings.SuggestDecoyCount(doc);
RunDlg <GenerateDecoysDlg>(() => SkylineWindow.ShowGenerateDecoysDlg(), decoysDlg =>
{
decoysDlg.DecoysMethod = DecoyGeneration.SHUFFLE_SEQUENCE;
decoysDlg.OkDialog();
});
doc = WaitForDocumentChange(doc);
Assert.AreEqual(expectedDecoys, doc.Peptides.Count(p => p.IsDecoy));
ImportResultsFile(GetDataFile("DIA-iRT", IRT_FILES[0]));
RunUI(() =>
{
SkylineWindow.SaveDocument();
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.SelectedNode.FirstNode;
});
for (int i = 0; i < 6; i++)
{
WaitForGraphs();
RunUI(() =>
{
foreach (var graphChromatogram in SkylineWindow.GraphChromatograms)
{
Assert.IsNull(graphChromatogram.RetentionMsMs);
Assert.IsNull(graphChromatogram.AlignedRetentionMsMs);
Assert.IsNull(graphChromatogram.UnalignedRetentionMsMs);
Assert.IsTrue(graphChromatogram.PredictedRT.HasValue);
ValidateTimeRange(graphChromatogram, new [] { graphChromatogram.PredictedRT.Value }, 8, 135);
}
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.SelectedNode.NextNode;
});
}
}
protected override void DoTest()
{
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
d => d.ChangeSettings(SrmSettingsList.GetDefault())));
SrmDocument doc = SkylineWindow.Document;
const string documentBaseName = "Ms1FilterTutorial";
string documentFile = GetTestPath(documentBaseName + SrmDocument.EXT);
RunUI(() => SkylineWindow.SaveDocument(documentFile));
// Launch the wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
// We're on the "Build Spectral Library" page of the wizard.
// Add the test xml file to the search files list and try to
// build the document library.
string[] searchFiles =
{
GetTestPath("100803_0001_MCF7_TiB_L.group.xml"), // Not L10N
GetTestPath("100803_0005b_MCF7_TiTip3.group.xml") // Not L10N
};
foreach (var searchFile in searchFiles)
{
Assert.IsTrue(File.Exists(searchFile), string.Format("File {0} does not exist.", searchFile));
}
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library empty page", 3);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
// Sanity check here, because of failure getting both files for results import below
var searchNames = importPeptideSearchDlg.BuildPepSearchLibControl.SearchFilenames;
Assert.AreEqual(searchFiles.Length, searchNames.Length,
PathsMessage("Unexpected search files found.", searchNames));
var builder = importPeptideSearchDlg.BuildPepSearchLibControl.ImportPeptideSearch.GetLibBuilder(
SkylineWindow.DocumentUI, SkylineWindow.DocumentFilePath, false);
Assert.IsTrue(ArrayUtil.EqualsDeep(searchFiles, builder.InputFiles),
PathsMessage("Unexpected BlibBuild input files.", builder.InputFiles));
importPeptideSearchDlg.BuildPepSearchLibControl.DebugMode = true;
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library populated page", 4);
WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
var ambiguousDlg = ShowDialog <MessageDlg>(() => importPeptideSearchDlg.ClickNextButton());
RunUI(() => AssertEx.Contains(ambiguousDlg.Message,
Resources.BiblioSpecLiteBuilder_AmbiguousMatches_The_library_built_successfully__Spectra_matching_the_following_peptides_had_multiple_ambiguous_peptide_matches_and_were_excluded_));
OkDialog(ambiguousDlg, ambiguousDlg.OkDialog);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(documentFile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// Verify input paths sent to BlibBuild
string buildArgs = importPeptideSearchDlg.BuildPepSearchLibControl.LastBuildCommandArgs;
string buildOutput = importPeptideSearchDlg.BuildPepSearchLibControl.LastBuildOutput;
var argLines = buildArgs.Split(new[] { Environment.NewLine }, StringSplitOptions.None);
var dirCommon = PathEx.GetCommonRoot(searchFiles);
var searchLines = searchFiles.Select(f => PathEx.RemovePrefix(f, dirCommon)).ToArray();
Assert.IsTrue(ArrayUtil.EqualsDeep(searchLines, argLines.Skip(1).ToArray()), buildArgs);
// Verify resulting .blib file contains the expected files
var docLib = librarySettings.Libraries[0];
int expectedFileCount = searchFiles.Length;
int expectedRedundantSpectra = 813; // 446 with TiTip only
int expectedSpectra = 552; // 428 with TiTip3 only
if (expectedFileCount != docLib.FileCount)
{
var searchFileNames = searchFiles.Select(Path.GetFileName).ToArray();
using (var blibDbRedundant = BlibDb.OpenBlibDb(redundantDocLibPath))
{
VerifyLib(searchFileNames, expectedRedundantSpectra, blibDbRedundant.GetIdFilePaths(), blibDbRedundant.GetSpectraCount(),
"redundant library", buildArgs, buildOutput);
}
using (var blibDb = BlibDb.OpenBlibDb(docLibPath))
{
VerifyLib(searchFileNames, expectedSpectra, blibDb.GetIdFilePaths(), blibDb.GetSpectraCount(),
"SQLite library", buildArgs, buildOutput);
}
VerifyLib(searchFileNames, expectedSpectra, docLib.LibraryDetails.DataFiles.Select(d => d.IdFilePath).ToArray(), docLib.SpectrumCount,
"in memory", buildArgs, buildOutput);
}
// We're on the "Extract Chromatograms" page of the wizard.
// All the test results files are in the same directory as the
// document file, so all the files should be found, and we should
// just be able to move to the next page.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page &&
importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Count > 0 &&
importPeptideSearchDlg.IsNextButtonEnabled);
// Wait for extra for both source files in the list
TryWaitForConditionUI(10 * 1000, () => importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Count == searchFiles.Length);
RunUI(() =>
{
// Check for missing files
var missingFiles = importPeptideSearchDlg.ImportResultsControl.MissingResultsFiles.ToArray();
Assert.AreEqual(0, missingFiles.Length,
PathsMessage("Unexpected missing file found.", missingFiles));
// Check for expected results files
var resultsNames = importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Select(f => f.Name).ToArray();
Assert.AreEqual(searchFiles.Length, importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Count,
PathsMessage("Unexpected results files found.", resultsNames));
// Check for expected common prefix
var commonPrefix = ImportResultsDlg.GetCommonPrefix(resultsNames);
Assert.IsFalse(string.IsNullOrEmpty(commonPrefix),
PathsMessage("File names do not have a common prefix.", resultsNames));
Assert.AreEqual("100803_000", commonPrefix);
});
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsPage>("Import Peptide Search - Extract Chromatograms page", 6);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
PauseForScreenShot <ImportResultsNameDlg>("Import Results - Common prefix form", 7);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
// Wait for the "Add Modifications" page of the wizard.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page);
List <string> modsToCheck = new List <string> {
"Phospho (ST)", "Phospho (Y)", "Oxidation (M)"
}; // Not L10N
RunUI(() =>
{
importPeptideSearchDlg.MatchModificationsControl.CheckedModifications = modsToCheck;
});
PauseForScreenShot <ImportPeptideSearchDlg.MatchModsPage>("Import Peptide Search - Add Modifications page", 8);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// We're on the "Configure MS1 Full-Scan Settings" page of the wizard.
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
importPeptideSearchDlg.FullScanSettingsControl.PrecursorCharges = new[] { 2, 3, 4 };
importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof;
importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes = 10 * 1000;
Assert.AreEqual(importPeptideSearchDlg.FullScanSettingsControl.PrecursorIsotopesCurrent, FullScanPrecursorIsotopes.Count);
Assert.AreEqual(FullScanMassAnalyzerType.tof, importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer);
Assert.AreEqual(10 * 1000, importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes);
Assert.AreEqual(3, importPeptideSearchDlg.FullScanSettingsControl.Peaks);
Assert.AreEqual(RetentionTimeFilterType.ms2_ids, importPeptideSearchDlg.FullScanSettingsControl.RetentionTimeFilterType);
Assert.AreEqual(5, importPeptideSearchDlg.FullScanSettingsControl.TimeAroundMs2Ids);
});
PauseForScreenShot <ImportPeptideSearchDlg.Ms1FullScanPage>("Import Peptide Search - Configure MS1 Full-Scan Settings page", 9);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// Last page of wizard - Import Fasta.
string fastaPath = GetTestPath("12_proteins.062011.fasta");
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page);
Assert.AreEqual("Trypsin [KR | P]", importPeptideSearchDlg.ImportFastaControl.Enzyme.GetKey());
importPeptideSearchDlg.ImportFastaControl.MaxMissedCleavages = 2;
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(fastaPath);
Assert.IsFalse(importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled);
});
PauseForScreenShot <ImportPeptideSearchDlg.FastaPage>("Import Peptide Search - Import FASTA page", 12);
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(() => importPeptideSearchDlg.ClickNextButton());
WaitForCondition(() => peptidesPerProteinDlg.DocumentFinalCalculated);
RunUI(() =>
{
int proteinCount, peptideCount, precursorCount, transitionCount;
peptidesPerProteinDlg.NewTargetsAll(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
peptidesPerProteinDlg.NewTargetsFinal(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
});
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
var allChromGraph = WaitForOpenForm <AllChromatogramsGraph>();
RunUI(() =>
{
allChromGraph.Left = SkylineWindow.Right + 20;
allChromGraph.Activate();
});
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 13);
WaitForDocumentChangeLoaded(doc, 8 * 60 * 1000); // 10 minutes
var libraryExplorer = ShowDialog <ViewLibraryDlg>(() => SkylineWindow.OpenLibraryExplorer(documentBaseName));
var matchedPepModsDlg = WaitForOpenForm <AddModificationsDlg>();
PauseForScreenShot <AddModificationsDlg>("Add mods alert", 14);
RunUI(() =>
{
Assert.AreEqual(13, matchedPepModsDlg.NumMatched);
Assert.AreEqual(0, matchedPepModsDlg.NumUnmatched);
matchedPepModsDlg.CancelDialog();
});
RunUI(() =>
{
libraryExplorer.GraphSettings.ShowBIons = true;
libraryExplorer.GraphSettings.ShowYIons = true;
libraryExplorer.GraphSettings.ShowCharge1 = true;
libraryExplorer.GraphSettings.ShowCharge2 = true;
libraryExplorer.GraphSettings.ShowPrecursorIon = true;
});
PauseForScreenShot <ViewLibraryDlg>("Spectral Library Explorer", 15);
RunUI(() =>
{
const string sourceFirst = "100803_0005b_MCF7_TiTip3.wiff";
const double timeFirst = 35.2128;
Assert.AreEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreEqual(timeFirst, libraryExplorer.RetentionTime, 0.01);
libraryExplorer.SelectedIndex++;
Assert.AreNotEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreNotEqual(timeFirst, libraryExplorer.RetentionTime, 0.01);
});
OkDialog(libraryExplorer, libraryExplorer.CancelDialog);
const int TIB_L = 0; // index for Tib_L
const int TIP3 = 1; // index for Tip3
AssertEx.IsDocumentState(SkylineWindow.Document, null, 11, 51, 52, 156);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIB_L]), 51, 52, 0, 156, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIP3]), 51, 52, 0, 156, 0);
string Tib_LFilename = searchFiles[TIB_L].Replace(".group.xml", PreferedExtAbWiff);
string Tip3Filename = searchFiles[TIP3].Replace(".group.xml", PreferedExtAbWiff);
// Select the first transition group.
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedPath =
SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
SkylineWindow.GraphSpectrumSettings.ShowAIons = true;
SkylineWindow.GraphSpectrumSettings.ShowBIons = true;
SkylineWindow.GraphSpectrumSettings.ShowYIons = true;
SkylineWindow.GraphSpectrumSettings.ShowPrecursorIon = true;
SkylineWindow.ExpandPrecursors();
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RunDlg <SpectrumChartPropertyDlg>(SkylineWindow.ShowSpectrumProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
const int skylineWindowWidth = 1160;
const int skylineWindowHeight = 792;
RunUI(() =>
{
// Make window screenshot size
if (IsPauseForScreenShots && SkylineWindow.WindowState != FormWindowState.Maximized)
{
SkylineWindow.Width = skylineWindowWidth;
SkylineWindow.Height = skylineWindowHeight;
}
});
RestoreViewOnScreen(13);
PauseForScreenShot("Main window with imported data", 16);
// RunUIWithDocumentWait(() =>
// {
// SkylineWindow.ToggleIntegrateAll(); // TODO: No longer necessary. Change in tutorial
// });
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.NONE);
Settings.Default.ShowDotProductPeakArea = true;
Settings.Default.ShowLibraryPeakArea = true;
});
RunUI(() =>
{
SkylineWindow.Width = 500;
var peakAreas = SkylineWindow.GraphPeakArea;
var peakAreasFloating = peakAreas.Parent.Parent;
peakAreasFloating.Left = SkylineWindow.Right + 20;
peakAreasFloating.Top = SkylineWindow.Top;
peakAreasFloating.Size = new Size(504, 643);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas view (show context menu)", 18);
RunUI(() => SkylineWindow.Width = skylineWindowWidth);
RestoreViewOnScreen(15);
RunUI(() =>
{
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowChromatogramLegends(false);
});
PauseForScreenShot("Main window layout", 19);
int atest = 0;
CheckAnnotations(TIB_L, 0, atest++);
int pepIndex = 3;
RunUI(() => SkylineWindow.CollapsePeptides());
RunUI(() => SkylineWindow.ShowAlignedPeptideIDTimes(true));
ChangePeakBounds(TIB_L, pepIndex, 38.79, 39.385);
PauseForScreenShot("Chromatogram graphs clipped from main window", 21);
CheckAnnotations(TIB_L, pepIndex, atest++);
var alignmentForm = ShowDialog <AlignmentForm>(() => SkylineWindow.ShowRetentionTimeAlignmentForm());
const int skylineWindowNarrowWidth = 788;
RunUI(() =>
{
SkylineWindow.Width = skylineWindowNarrowWidth;
alignmentForm.Width = 660;
alignmentForm.Height = 561;
alignmentForm.Left = SkylineWindow.Right + 20;
alignmentForm.Splitter.SplitterDistance = 75;
alignmentForm.ComboAlignAgainst.SelectedIndex = 0; // to match what's in the tutorial doc
});
PauseForScreenShot <AlignmentForm>("Retention time alignment form", 22);
OkDialog(alignmentForm, alignmentForm.Close);
PauseForScreenShot("Status bar clipped from main window - 4/51 pep 4/52 prec 10/156 tran", 23);
const string TIP_NAME = "5b_MCF7_TiTip3";
if (IsCoverShotMode)
{
RestoreCoverViewOnScreen();
ClickChromatogram(TIP_NAME, 34.5, 366);
TreeNode selectedNode = null;
RunUI(() => selectedNode = SkylineWindow.SequenceTree.SelectedNode);
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0]);
WaitForGraphs();
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = selectedNode);
TakeCoverShot();
return;
}
pepIndex = JumpToPeptide("SSKASLGSLEGEAEAEASSPK");
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
Assert.IsTrue(8 == pepIndex);
PauseForScreenShot("Chromatogram graph metafiles for 9th peptide", 24);
CheckAnnotations(TIB_L, pepIndex, atest++);
ZoomSingle(TIP3, 31.8, 42.2, 280); // simulate the wheel scroll described in tutorial
PauseForScreenShot("Chromatogram graph metafile showing all peaks for 1_MCF_TiB_L", 24);
CheckAnnotations(TIB_L, pepIndex, atest++);
// current TIB_L peak should have idotp .87 and ppm -6.9
Assert.AreEqual(0.87, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-10.8, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
ChangePeakBounds(TIB_L, pepIndex, 36.5, 38.0);
// now current TIB_L peak should have idotp .9 and ppm -6.5
Assert.AreEqual(0.9, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-9.4, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
CheckAnnotations(TIB_L, pepIndex, atest++);
var undoIndex = SkylineWindow.Document.RevisionIndex; // preserve for simulating ctrl-z
RunUI(() => SkylineWindow.Width = skylineWindowWidth);
PickPeakBoth(pepIndex, 40.471035, 40.8134); // select peak for both chromatograms at these respective retention times
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 25);
int[] m1Thru4 = { 1, 2, 3, 4, 5 };
PickTransitions(pepIndex, m1Thru4, "Transition pick list filtered", 26, "Transition pick list unfiltered", 26); // turn on chromatograms
PickPeakBoth(pepIndex, 36.992836, 37.3896027); // select peak for both chromatograms at these respective retention times
ZoomSingle(TIP3, 32.4, 42.2, 520); // set the view for screenshot
RunUI(() =>
{
SkylineWindow.Height = 550;
SkylineWindow.ArrangeGraphsTabbed();
});
ActivateReplicate(TIP_NAME);
PauseForScreenShot("Chromatogram graph metafile comparing 33 and 37 minute peaks", 27);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
ActivateReplicate(TIP_NAME);
ClickChromatogram(TIP_NAME, 37.3, 142);
PauseForScreenShot("MS1 spectrum graph 37.32 minutes", 28);
ClickChromatogram(TIP_NAME, 33.2, 328.1);
PauseForScreenShot("MS1 spectrum graph 33.19 minutes", 29);
RunUI(() => SkylineWindow.HideFullScanGraph());
RunUI(() =>
{
SkylineWindow.Width = skylineWindowNarrowWidth;
SkylineWindow.Height = skylineWindowHeight;
SkylineWindow.ArrangeGraphs(DisplayGraphsType.Column);
});
pepIndex = JumpToPeptide("ASLGSLEGEAEAEASSPKGK"); // Not L10N
Assert.IsTrue(10 == pepIndex);
PauseForScreenShot("Chromatogram graph meta files for peptide ASLGSLEGEAEAEASSPKGK", 30);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
PickTransitions(pepIndex, m1Thru4); // turn on M+3 and M+4
ChangePeakBounds(TIP3, pepIndex, 37.35, 38.08);
ZoomSingle(TIP3, 36.65, 39.11, 300); // simulate the wheel scroll described in tutorial
PauseForScreenShot("upper - Chromatogram graph metafile for peptide ASLGSLEGEAEAEASSPKGK with adjusted integration", 31);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("AEGEWEDQEALDYFSDKESGK"); // Not L10N
PauseForScreenShot("lower - Chromatogram graph metafiles for peptide AEGEWEDQEALDYFSDKESGK", 31);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
int[] m1Thru5 = { 1, 2, 3, 4, 5, 6 };
PickTransitions(pepIndex, m1Thru5); // turn on M+3 M+4 and M+5
PauseForScreenShot("Chromatogram graph metafiles with M+3, M+4 and M+5 added", 32);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
JumpToPeptide("ALVEFESNPEETREPGSPPSVQR"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide ALVEFESNPEETREPGSPPSVQR", 33);
pepIndex = JumpToPeptide("YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR"); // Not L10N
if (IsPauseForScreenShots)
{
RestoreViewOnScreen(34);
PauseForScreenShot("upper - Peak Areas graph metafile for peptide YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR", 34);
}
int[] m1Thru7 = { 1, 2, 3, 4, 5, 6, 7, 8 };
PickTransitions(pepIndex, m1Thru7); // enable [M+3] [M+4] [M+5] [M+6] [M+7]
PauseForScreenShot("lower - Peak Areas graph metafile with M+3 through M+7 added", 34);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
// page 36 zooming setup
RunUI(() =>
{
SkylineWindow.SynchronizeZooming(true);
SkylineWindow.LockYChrom(false);
SkylineWindow.AlignToFile = GetGraphChromatogram(TIP3).GetChromFileInfoId(); // align to Tip3
});
ZoomBoth(36.5, 39.5, 1600); // simulate the wheel scroll described in tutorial
RunUI(() =>
{
SkylineWindow.ShowChromatogramLegends(false);
SkylineWindow.Width = skylineWindowWidth;
SkylineWindow.Height = 720;
});
PauseForScreenShot("Chromatogram graphs clipped from main window with synchronized zooming", 35);
ClickChromatogram(TIP_NAME, 37.5, 1107.3);
PauseForScreenShot("MS1 spectrum graph 37.50 minutes", 36);
RunUI(() => SkylineWindow.HideFullScanGraph());
RunUI(() =>
{
SkylineWindow.ShowChromatogramLegends(true);
SkylineWindow.Width = skylineWindowNarrowWidth;
SkylineWindow.Height = skylineWindowHeight;
});
RestoreViewOnScreen(36); // float the Library Match window
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tip3Filename), 37.6076f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 5b_MCF7_TiTip3 (37.61 Min)", 37);
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tib_LFilename), 37.0335f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 1_MCF_TiB_L (37.03 min)", 37);
RestoreViewOnScreen(37); // back to normal view
/* pepIndex = */ JumpToPeptide("DQVANSAFVER"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide DQVANSAFVER", 38);
// int[] m1 = {2};
// PickTransitions(pepIndex, m1); // enable [M+1] only
// // Measured times in TIB_L are different from displayed times, because of alignment
// ChangePeakBounds(TIB_L, pepIndex, 23.99, 25.29);
// ChangePeakBounds(TIP3, pepIndex, 23.81, 25.21);
// // First transition selected for screenshot
// RunUI(() =>
// {
// var pathPep = SkylineWindow.SelectedPath;
// var nodePep = ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode;
// var nodeGroup = nodePep.TransitionGroups.First();
// var nodeTran = nodeGroup.Transitions.First();
// SkylineWindow.SelectedPath = new IdentityPath(
// new IdentityPath(pathPep, nodeGroup.TransitionGroup), nodeTran.Transition);
// });
// PauseForScreenShot("page 36 - M+1 only, with adjusted integration");
// CheckAnnotations(TIB_L, pepIndex, atest++);
// CheckAnnotations(TIP3, pepIndex, EXPECTED_ANNOTATIONS[atest]);
var docAfter = WaitForProteinMetadataBackgroundLoaderCompletedUI();
// Minimizing a chromatogram cache file.
RunUI(SkylineWindow.CollapsePeptides);
for (int i = 0; i < 5; i++) // just do the first 5
{
int iPeptide = i;
var path = docAfter.GetPathTo((int)SrmDocument.Level.Molecules, iPeptide);
RunUI(() =>
{
SkylineWindow.SelectedPath = path;
});
WaitForGraphs();
}
// Eliminate extraneous chromatogram data.
doc = WaitForProteinMetadataBackgroundLoaderCompletedUI();
var minimizedFile = GetTestPath("Ms1FilteringTutorial-2min.sky"); // Not L10N
var cacheFile = Path.ChangeExtension(minimizedFile, ChromatogramCache.EXT);
{
// TODO: Figure out why the minimize fails to unlock the .skyd file, if not minimized to current file
RunUI(() => SkylineWindow.SaveDocument(minimizedFile));
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
var minimizeResultsDlg = ShowDialog <MinimizeResultsDlg>(manageResultsDlg.MinimizeResults);
RunUI(() =>
{
minimizeResultsDlg.LimitNoiseTime = true;
minimizeResultsDlg.NoiseTimeRange = 2; // Not L10N
});
PauseForScreenShot <MinimizeResultsDlg>("Minimize Results form (percentages vary slightly)", 39); // old p. 23
OkDialog(minimizeResultsDlg, () => minimizeResultsDlg.MinimizeToFile(minimizedFile));
WaitForCondition(() => File.Exists(cacheFile));
WaitForClosedForm(manageResultsDlg);
}
WaitForDocumentChange(doc);
// Inclusion list method export for MS1 filtering
doc = SkylineWindow.Document;
RunDlg <PeptideSettingsUI>(() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction), dlg =>
{
dlg.IsUseMeasuredRT = true;
dlg.TimeWindow = 10;
dlg.OkDialog();
});
doc = WaitForDocumentChangeLoaded(doc);
// Now deviating from the tutorial script for a moment to make sure we can choose a Scheduled export method.
// CONSIDER: This refinement seems to be a no-op. Not sure why it is here.
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, dlg =>
{
dlg.MinPeptides = 1; // This would get rid of proteins with no peptides (none exist)
const double minPeakFoundRatio = 0.1;
dlg.MinPeakFoundRatio = minPeakFoundRatio; // This would get rid of undetected transitions (none exist)
dlg.OkDialog(); // Will not change the document or add an Undo entry
});
// Nothing should have changed on the UI thread
RunUI(() => Assert.AreSame(doc, SkylineWindow.DocumentUI));
// Ready to export, although we will just cancel out of the dialog.
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.ABI_TOF; // Not L10N
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
exportMethodDlg.CancelButton.PerformClick();
});
WaitForClosedForm(exportMethodDlg);
// Because this was showing up in the nightly test failures
WaitForConditionUI(() => exportMethodDlg.IsDisposed);
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
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);
}
private void LowResTest()
{
string documentFile = GetTestPath(@"Low Res\BSA_Protea_label_free_meth3.sky");
WaitForCondition(() => File.Exists(documentFile));
RunUI(() => SkylineWindow.OpenFile(documentFile));
bool AsSmallMolecules = AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none;
const int expectedMoleculeCount = 9;
int expectedTransitionGroupCount = 10;
int expectedTransitionCount = 78;
var document = SkylineWindow.Document;
if (AsSmallMolecules)
{
ConvertDocumentToSmallMolecules(AsSmallMoleculesTestMode);
document = SkylineWindow.Document;
Assert.AreEqual(document.PeptideTransitionGroupCount, 0);
Assert.AreEqual(document.MoleculeTransitionGroupCount, expectedTransitionGroupCount);
Assert.AreEqual(document.PeptideTransitionCount, 0);
Assert.AreEqual(document.MoleculeTransitionCount, expectedTransitionCount);
}
AssertEx.IsDocumentState(document, null, 3, expectedMoleculeCount, expectedTransitionGroupCount, expectedTransitionCount);
// p. 3 Select first peptide
RunUI(() => SkylineWindow.SelectedPath = document.GetPathTo((int)SrmDocument.Level.Molecules, 0));
PauseForScreenShot("Main window", 3);
// p. 4 Configure Document for Thermo raw files
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan);
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Peptide Settings - Full-Scan tab blank", 5);
RunUI(() =>
{
transitionSettingsUI.PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
transitionSettingsUI.PrecursorMassAnalyzer = FullScanMassAnalyzerType.qit;
transitionSettingsUI.AcquisitionMethod = FullScanAcquisitionMethod.Targeted;
});
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Peptide Settings - Full-Scan tab low res", 6);
RunUI(() =>
{
transitionSettingsUI.SetRetentionTimeFilter(RetentionTimeFilterType.ms2_ids, 2);
// p.6 - library ion match tolerance same as extraction window
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Library;
transitionSettingsUI.IonMatchTolerance = 0.7;
});
PauseForScreenShot <TransitionSettingsUI.LibraryTab>("Transition Settings - Library tab match tolerance same as MS/MS resolution", 8);
RunUI(() =>
{
// p.6
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.FragmentTypes += ", p";
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 9);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
var docFullScan = WaitForDocumentChange(document);
var tranSettingsFullScan = docFullScan.Settings.TransitionSettings;
Assert.AreEqual(FullScanPrecursorIsotopes.Count, tranSettingsFullScan.FullScan.PrecursorIsotopes);
Assert.AreEqual(FullScanMassAnalyzerType.qit, tranSettingsFullScan.FullScan.PrecursorMassAnalyzer);
Assert.AreEqual(FullScanAcquisitionMethod.Targeted, tranSettingsFullScan.FullScan.AcquisitionMethod);
Assert.IsTrue(ArrayUtil.EqualsDeep(new[] { IonType.y, IonType.b, IonType.precursor },
tranSettingsFullScan.Filter.IonTypes));
}
RunUI(() => SkylineWindow.ExpandPrecursors());
// Check all the precursors on picklists
bool pausedForScreenShot = false;
foreach (PeptideGroupTreeNode node in SkylineWindow.SequenceTree.GetSequenceNodes())
{
foreach (TreeNode child in node.Nodes)
{
foreach (SrmTreeNodeParent grandChild in child.Nodes)
{
// Because of RunUI must copy to local variable first.
SrmTreeNodeParent child1 = grandChild;
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = child1);
var picklist = ShowDialog <PopupPickList>(() => SkylineWindow.SequenceTree.ShowPickList(false));
RunUI(() =>
{
picklist.SetItemChecked(0, true);
Assert.IsTrue(picklist.GetItemLabel(0).Contains(IonType.precursor.GetLocalizedString()));
Assert.IsTrue(picklist.GetItemChecked(0));
});
if (!pausedForScreenShot)
{
PauseForScreenShot <PopupPickList>("Transitions popup pick-list", 10);
pausedForScreenShot = true;
}
OkDialog(picklist, picklist.OnOk);
}
}
}
WaitForDocumentLoaded();
if (!AsSmallMolecules) // No libraries for small molecules, yet
{
foreach (var nodeGroup in SkylineWindow.Document.MoleculeTransitionGroups)
{
Assert.IsFalse(nodeGroup.HasLibInfo && nodeGroup.Transitions.All(nodeTran => !nodeTran.HasLibInfo));
}
}
// All transition groups should now have a precursor transition
foreach (var nodeGroup in SkylineWindow.Document.MoleculeTransitionGroups)
{
Assert.AreEqual(IonType.precursor, nodeGroup.Transitions.First().Transition.IonType);
}
// p.8
ExportMethodDlg exportMethodDlg =
ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg.SetInstrument("Thermo LTQ");
Assert.AreEqual("Thermo LTQ", exportMethodDlg.InstrumentType);
exportMethodDlg.SetMethodType(ExportMethodType.Standard);
exportMethodDlg.SetTemplateFile(GetTestPath(@"Low Res\TargetedMSMS_template.meth"));
});
PauseForScreenShot <ExportMethodDlg.MethodView>("Export Method form", 11);
// p. 10 Ok the error box.
{
var messageDlg = ShowDialog <MessageDlg>(() => exportMethodDlg.OkDialog(GetTestPath(@"Low Res\TargetedMSMS_BSA_Protea.meth")));
PauseForScreenShot <MessageDlg>("Error message (expected)", 12);
OkDialog(messageDlg, messageDlg.OkDialog);
}
// Making a report by hand p.11
ExportLiveReportDlg exportReportDlg = ShowDialog <ExportLiveReportDlg>(() => SkylineWindow.ShowExportReportDialog());
var editReportListDlg = ShowDialog <ManageViewsForm>(exportReportDlg.EditList);
var viewEditor = ShowDialog <ViewEditor>(editReportListDlg.AddView);
RunUI(() =>
{
Assert.IsTrue(viewEditor.ChooseColumnsTab.TrySelect(PropertyPath.Parse("Proteins!*.Name")));
viewEditor.ChooseColumnsTab.AddSelectedColumn();
Assert.AreEqual(1, viewEditor.ChooseColumnsTab.ColumnCount);
var columnsToAdd = new[]
{
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.ModifiedSequence"),
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.Charge"),
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.Mz"),
};
foreach (var id in columnsToAdd)
{
Assert.IsTrue(viewEditor.ChooseColumnsTab.TrySelect(id), "Unable to select {0}", id);
viewEditor.ChooseColumnsTab.AddSelectedColumn();
}
Assert.AreEqual(4, viewEditor.ChooseColumnsTab.ColumnCount);
});
PauseForScreenShot <ViewEditor>("Edit Report form", 13);
{
var previewReportDlg = ShowDialog <DocumentGridForm>(viewEditor.ShowPreview);
var expectedRows = 10 + (TestSmallMolecules ? 1 : 0);
WaitForConditionUI(() => previewReportDlg.IsComplete && previewReportDlg.RowCount == expectedRows);
RunUI(() =>
{
Assert.AreEqual(4, previewReportDlg.ColumnCount);
var precursors =
SkylineWindow.Document.MoleculeTransitionGroups.ToArray();
const int precursorIndex = 3;
for (int i = 0; i < expectedRows; i++)
{
Assert.AreEqual(precursors[i].PrecursorMz, double.Parse(previewReportDlg.DataGridView.Rows[i].Cells[precursorIndex].Value.ToString()), 0.000001);
}
var precursorMzCol = previewReportDlg.DataGridView.Columns[precursorIndex];
Assert.IsNotNull(precursorMzCol);
previewReportDlg.DataGridView.Sort(precursorMzCol, ListSortDirection.Ascending);
});
PauseForScreenShot <DocumentGridForm>("Preview New Report window", 14);
OkDialog(previewReportDlg, previewReportDlg.Close);
}
// Press the Esc key until all forms have been dismissed.
RunUI(() =>
{
viewEditor.Close();
editReportListDlg.Close();
exportReportDlg.CancelClick();
});
WaitForClosedForm(viewEditor);
WaitForClosedForm(editReportListDlg);
WaitForClosedForm(exportReportDlg);
//p. 12 Import Full-Scan Data
// Launch import peptide search wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
RunUI(() => importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.prm);
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search Build Spectral Library blank page", 15);
const int prefixLen = 35;
const string lowResDir = "Low Res";
const string searchDir = "search";
const string lowRes20Base = "klc_20100329v_Protea_Peptide_Curve_20fmol_uL_tech1";
string lowRes20File = GetTestPath(Path.Combine(lowResDir, lowRes20Base + ExtThermoRaw));
string lowRes20FileRaw = Path.ChangeExtension(lowRes20File, ExtThermoRaw);
string lowRes20Search = GetTestPath(Path.Combine(lowResDir, Path.Combine(searchDir, lowRes20Base + BiblioSpecLiteBuilder.EXT_PERCOLATOR)));
string shortLowRes20FileName = (Path.GetFileNameWithoutExtension(lowRes20File) ?? "").Substring(prefixLen);
const string lowRes80Base = "klc_20100329v_Protea_Peptide_Curve_80fmol_uL_tech1";
string lowRes80File = GetTestPath(Path.Combine(lowResDir, lowRes80Base + ExtThermoRaw));
string lowRes80Search = GetTestPath(Path.Combine(lowResDir, Path.Combine(searchDir, lowRes80Base + BiblioSpecLiteBuilder.EXT_PERCOLATOR)));
string shortLowRes80FileName = (Path.GetFileNameWithoutExtension(lowRes80File) ?? "").Substring(prefixLen);
string[] searchFiles = { lowRes20Search, lowRes80Search };
var doc = SkylineWindow.Document;
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
importPeptideSearchDlg.BuildPepSearchLibControl.CutOffScore = 0.99;
importPeptideSearchDlg.BuildPepSearchLibControl.FilterForDocumentPeptides = true;
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search Build Spectral Library with files page", 16);
RunDlg <MessageDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck, dlg => dlg.OkDialog());
doc = WaitForDocumentChangeLoaded(doc);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(documentFile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsPage>("Import Peptide Search Extract Chromatograms page", 17);
// We're on the "Extract Chromatograms" page of the wizard.
// All the test results files are in the same directory as the
// document file, so all the files should be found, and we should
// just be able to move to the next page.
TryWaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page);
var correctPage = false;
ImportPeptideSearchDlg.Pages currentPage = 0;
RunUI(() => correctPage = ImportPeptideSearchDlg.Pages.chromatograms_page == (currentPage = importPeptideSearchDlg.CurrentPage));
if (!correctPage)
{
WaitForConditionUI(1, // Immediate timeout - just want the richer error message that WaitForConditionUI provides
() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page,
string.Format("Expected to be on chromatograms_page, on {0} instead", currentPage));
}
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
// Modifications are already set up, so that page should get skipped.
// We're on the "Configure Transition Settings" page of the wizard.
// We've already set up these settings, so just click next.
WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.transition_settings_page);
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
// We're on the "Configure Full-Scan Settings" page of the wizard.
// We've already set up these settings, so just click next.
WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
doc = WaitForDocumentChange(doc);
// Add FASTA also skipped because filter for document peptides was chosen.
WaitForClosedForm(importPeptideSearchDlg);
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 18);
WaitForDocumentChangeLoaded(doc, 15 * 60 * 1000); // 15 minutes
WaitForClosedAllChromatogramsGraph();
expectedTransitionGroupCount = 10; // Expect this many with results
expectedTransitionCount = 87; // Expect this many with results
AssertResult.IsDocumentResultsState(SkylineWindow.Document, shortLowRes20FileName, expectedMoleculeCount, expectedTransitionGroupCount, 0, expectedTransitionCount, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, shortLowRes80FileName, expectedMoleculeCount, expectedTransitionGroupCount, 0, expectedTransitionCount, 0);
RunUI(() =>
{
Assert.IsTrue(SkylineWindow.IsGraphSpectrumVisible);
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.CollapsePrecursors();
SkylineWindow.Width = 1070;
});
// Select the first precursor.
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "LVNELTEFAK" : "K.LVNELTEFAK.T [65, 74]");
}
else
{
FindNode(document.MoleculeTransitionGroups.First().CustomIon.DisplayName);
}
// Ensure Graphs look like p17. (checked)
WaitForGraphs();
RestoreViewOnScreen(18);
PauseForScreenShot("Main window with data imported", 19);
const double minDotp = 0.9;
foreach (var nodeGroup in SkylineWindow.Document.PeptideTransitionGroups)
{
double dotp = nodeGroup.Results[0][0].LibraryDotProduct ?? 0;
Assert.IsTrue(Math.Round(dotp, 2) >= minDotp, string.Format("Library dot-product {0} found below {1}", dotp, minDotp));
}
RunUI(() => SkylineWindow.AutoZoomBestPeak());
// Ensure Graphs look like p18. (checked)
WaitForGraphs();
PauseForScreenShot("Chromatogram graphs clipped from main window with zoomed peaks", 20);
RestoreViewOnScreen(21);
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(lowRes20FileRaw, 77.7722)));
PauseForScreenShot <GraphSpectrum>("Library Match view clipped from main window with noisy spectrum", 21);
RunUI(() =>
{
SkylineWindow.ShowGraphSpectrum(false);
Assert.IsFalse(SkylineWindow.IsGraphSpectrumVisible);
SkylineWindow.ShowPeptideIDTimes(false);
});
RunUI(() =>
{
var chromGraphs = SkylineWindow.GraphChromatograms.ToArray();
Assert.AreEqual(2, chromGraphs.Length);
Assert.AreEqual(46.8, chromGraphs[0].GraphItems.First().BestPeakTime, 0.05);
Assert.AreEqual(46.8, chromGraphs[1].GraphItems.First().BestPeakTime, 0.05);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowProductTransitions();
});
WaitForCondition(() => !SkylineWindow.GraphPeakArea.IsHidden);
if (!AsSmallMolecules) // No libraries (yet?)
{
WaitForDotProducts();
}
RunUI(() =>
{
// Graph p.15
Assert.AreEqual(AsSmallMolecules ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(6, SkylineWindow.GraphPeakArea.CurveCount);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Replicate Comparison graph metafile", 22);
if (!AsSmallMolecules) // No libraries (yet?)
{
VerifyDotProducts(0.99, 0.98);
}
// Check graph p15. (checked)
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
SkylineWindow.ShowSplitChromatogramGraph(true);
});
// p. 16 screenshot of full 5-point dilution curve
// Select precursor
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "DRVYIHPF" : "R.DRVYIHPF.- [34, 41]"); // May be localized " (missed 1)"
}
else
{
FindNode(Resources.CustomIon_DisplayName_Ion + " [1047");
}
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Replicate Comparison graph metafile with split graphs", 24);
RunUI(() =>
{
SkylineWindow.Size = new Size(990, 620);
SkylineWindow.ShowGraphPeakArea(false);
});
PauseForScreenShot("Chromatogram graphs clipped from main window with split graphs", 25);
// PeakAreaGraph Normalize to total p.20.
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowProductTransitions();
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view);
});
// Ensure graph looks like p20.
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "KNLQSLDPSH" : "R.IKNLQSLDPSH.- [80, 90]");
FindNode(AsSmallMolecules ? "KNLQSLDPSH" : "R.IKNLQSLDPSH.- [80, 90]"); // Phosphorylated
}
else
{
FindNode(Resources.CustomIon_DisplayName_Ion + " [1333");
}
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("figure 1a - Area Replicate graph metafile for IKNLQSLDPSH", 26);
RunUI(() =>
{
Assert.AreEqual(AsSmallMolecules ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(9, SkylineWindow.GraphPeakArea.CurveCount);
});
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "HLVDEPQNLIK" : "K.HLVDEPQNLIK.Q [401, 411]");
}
else
{
FindNode(Resources.CustomIon_DisplayName_Ion + " [1306");
}
WaitForGraphs();
PauseForScreenShot("figure 1b - Area replicate graph metafile for HLVDEPQNLIK", 26);
RunUI(() =>
{
Assert.AreEqual(AsSmallMolecules ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(7, SkylineWindow.GraphPeakArea.CurveCount);
});
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
WaitForCondition(() => SkylineWindow.GraphPeakArea.IsHidden);
RunUI(() => SkylineWindow.SaveDocument());
}
protected override void DoTest()
{
var folderAbsoluteQuant = UseRawFiles ? "AbsoluteQuant" : "AbsoluteQuantMzml";
// Generating a Transition List, p. 4
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI.PrecursorMassType = MassType.Monoisotopic;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.RegressionCEName = "Thermo TSQ Vantage";
transitionSettingsUI.RegressionDPName = Resources.SettingsList_ELEMENT_NONE_None;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 4);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.PrecursorCharges = "2";
transitionSettingsUI.ProductCharges = "1";
transitionSettingsUI.FragmentTypes = "y";
transitionSettingsUI.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_3;
transitionSettingsUI.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion_minus_1;
transitionSettingsUI.SpecialIons = new string[0];
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 4);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
// Configuring Peptide settings p. 4
PeptideSettingsUI peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Modifications);
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab", 5);
var modHeavyK = new StaticMod("Label:13C(6)15N(2) (C-term K)", "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15,
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUI, "Edit Isotope Modification over Transition Settings", 5);
RunUI(() => peptideSettingsUI.PickedHeavyMods = new[] { modHeavyK.Name });
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab with mod added", 5);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
// Inserting a peptide sequence p. 5
using (new CheckDocumentState(1, 1, 2, 10))
{
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pasteDlg.PastePeptides);
WaitForProteinMetadataBackgroundLoaderCompletedUI();
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 6);
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
RunUI(SkylineWindow.ExpandPrecursors);
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
WaitForCondition(() => File.Exists(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
PauseForScreenShot("Main window with Targets view", 6);
// Exporting a transition list p. 6
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO;
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.OptimizeType = ExportOptimize.NONE;
exportMethodDlg.MethodType = ExportMethodType.Standard;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List", 7);
OkDialog(exportMethodDlg, () =>
exportMethodDlg.OkDialog(TestFilesDir.GetTestPath("Quant_Abs_Thermo_TSQ_Vantage.csv")));
}
// Importing RAW files into Skyline p. 7
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
PauseForScreenShot <ImportResultsDlg>("Import Results - click OK to get shot of Import Results Files and then cancel", 8);
RunUI(() =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Skip(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg.NamedPathSets = namedPathSets.ToArray();
});
RunDlg <ImportResultsNameDlg>(importResultsDlg.OkDialog,
importResultsNameDlg => importResultsNameDlg.NoDialog());
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
Settings.Default.ArrangeGraphsOrder = GroupGraphsOrder.Document.ToString();
Settings.Default.ArrangeGraphsReversed = false;
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.AutoZoomBestPeak();
});
WaitForCondition(() => Equals(8, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden)),
"unexpected visible graphChromatogram count");
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot("Main window with imported data", 9);
// Analyzing SRM Data from FOXN1-GST Sample p. 9
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults,
importResultsDlg1 =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Take(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg1.NamedPathSets = namedPathSets.ToArray();
importResultsDlg1.OkDialog();
});
WaitForGraphs();
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
WaitForCondition(5 * 60 * 1000, // five minutes
() =>
SkylineWindow.Document.Settings.HasResults &&
SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RunUI(() =>
{
SkylineWindow.ToggleIntegrateAll();
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ShowPeakAreaReplicateComparison();
// Total normalization
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view);
});
RunUI(() => SkylineWindow.ActivateReplicate("FOXN1-GST"));
WaitForGraphs();
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 0));
WaitForGraphs();
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphPeakArea.ResultsIndex);
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphRetentionTime.ResultsIndex);
});
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.First().TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for light", 10);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 1));
WaitForGraphs();
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.ToArray()[1].TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for heavy", 10);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0));
WaitForGraphs();
// Heavy normalization
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_ratio_view));
WaitForGraphs();
RunUI(() =>
{
int transitionGroupCount = SkylineWindow.DocumentUI.Peptides.First().TransitionGroupCount;
CheckGstGraphs(transitionGroupCount, transitionGroupCount - 1);
});
PauseForScreenShot("Main window with totals graphs for light and heavy and FOXN1-GST", 11);
const int columnsToAddCount = 4;
var columnSeparator = TextUtil.CsvSeparator;
// Generating a Calibration Curve p. 11
var exportLiveReportDlg = ShowDialog <ExportLiveReportDlg>(SkylineWindow.ShowExportReportDialog);
var editReportListDlg = ShowDialog <ManageViewsForm>(exportLiveReportDlg.EditList);
const string reportName = "Peptide Ratio Results Test";
var columnsToAdd = new[]
{
PropertyPath.Parse("Proteins!*.Peptides!*.Sequence"),
PropertyPath.Parse("Proteins!*.Name"),
PropertyPath.Parse("Replicates!*.Name"),
PropertyPath.Parse("Proteins!*.Peptides!*.Results!*.Value.RatioToStandard"),
};
Assert.AreEqual(columnsToAddCount, columnsToAdd.Length);
{
var viewEditor = ShowDialog <ViewEditor>(editReportListDlg.AddView);
RunUI(() =>
{
viewEditor.ViewName = reportName;
foreach (var id in columnsToAdd)
{
Assert.IsTrue(viewEditor.ChooseColumnsTab.TrySelect(id), "Unable to select {0}", id);
viewEditor.ChooseColumnsTab.AddSelectedColumn();
}
Assert.AreEqual(columnsToAdd.Length, viewEditor.ChooseColumnsTab.ColumnCount);
});
// TODO: MultiViewProvider not yet supported in Common
PauseForScreenShot <ViewEditor>("Edit Report form", 12);
OkDialog(viewEditor, viewEditor.OkDialog);
}
RunUI(editReportListDlg.OkDialog);
WaitForClosedForm(editReportListDlg);
RunUI(() =>
{
exportLiveReportDlg.ReportName = reportName;
exportLiveReportDlg.OkDialog(TestFilesDir.GetTestPath("Calibration.csv"), columnSeparator);
});
// Check if export file is correct.
string filePath = TestFilesDir.GetTestPath("Calibration.csv");
Assert.IsTrue(File.Exists(filePath));
string[] lines = File.ReadAllLines(filePath);
string[] line0 = lines[0].Split(columnSeparator);
int count = line0.Length;
Assert.IsTrue(lines.Count() == SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Count + 1);
Assert.AreEqual(columnsToAddCount, count);
// Check export file data
double ratio1 = Double.Parse(lines[1].Split(new[] { columnSeparator }, 4)[3]);
double ratio2 = Double.Parse(lines[2].Split(new[] { columnSeparator }, 4)[3]);
double ratio3 = Double.Parse(lines[3].Split(new[] { columnSeparator }, 4)[3]);
double ratio4 = Double.Parse(lines[4].Split(new[] { columnSeparator }, 4)[3]);
double ratio5 = Double.Parse(lines[5].Split(new[] { columnSeparator }, 4)[3]);
double ratio6 = Double.Parse(lines[6].Split(new[] { columnSeparator }, 4)[3]);
double ratio7 = Double.Parse(lines[7].Split(new[] { columnSeparator }, 4)[3]);
double ratio8 = Double.Parse(lines[8].Split(new[] { columnSeparator }, 4)[3]);
double ratio9 = Double.Parse(lines[9].Split(new[] { columnSeparator }, 4)[3]);
Assert.AreEqual(21.4513, ratio1, 0.1);
Assert.AreEqual(6.2568, ratio2, 0.1);
Assert.AreEqual(2.0417, ratio3, 0.1);
Assert.AreEqual(0.8244, ratio4, 0.1);
Assert.AreEqual(0.2809, ratio5, 0.1);
Assert.AreEqual(0.1156, ratio6, 0.1);
Assert.AreEqual(0.0819, ratio7, 0.1);
Assert.AreEqual(0.0248, ratio8, 0.1);
Assert.AreEqual(0.7079, ratio9, 0.1);
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
}
protected override void DoTest()
{
var testFilesDir = TestFilesDir;
var skyFile = "test_b.sky";
var basename = "289_97";
var sourceData = TestFilesDir.GetTestPath(basename + ExtensionTestContext.ExtMzml);
string docPath;
var doc = InitHighReplicateCountDocument(testFilesDir, skyFile, out docPath);
Settings.Default.ImportResultsSimultaneousFiles =
(int)MultiFileLoader.ImportResultsSimultaneousFileOptions
.many; // use maximum threads for multiple file import
var listChromatograms = new List <ChromatogramSet>();
var filenames = new List <string>();
var TOO_MANY_FILES = Skyline.SkylineWindow.MAX_GRAPH_CHROM * 2;
int count;
for (count = 0; count < TOO_MANY_FILES; count++)
{
var fname = TestFilesDir.GetTestPath(GetReplicateNameFromIndex(count));
filenames.Add(fname);
if (count != Skyline.SkylineWindow.MAX_GRAPH_CHROM)
{
File.Copy(sourceData, fname);
}
var path = MsDataFileUri.Parse(fname);
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, path) ??
new ChromatogramSet(path.GetFileName().Replace('.', '_'), new[] { path }));
}
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(SkylineWindow.SetDocument(docResults, doc));
var document = WaitForDocumentLoaded();
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
foreach (var pair in document.MoleculePrecursorPairs)
{
for (var f = 0; f < filenames.Count; f++)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(document.Settings.MeasuredResults.TryLoadChromatogram(f, pair.NodePep, pair.NodeGroup,
tolerance,
true, out chromGroupInfo));
}
}
WaitForClosedAllChromatogramsGraph();
// We expect 0th display to be R0, then as we move on to high undisplayed chromatograms we expect r0 to be replaced with R100, R1 with R101 etc
var graphChromatograms = SkylineWindow.GraphChromatograms.ToList();
Assert.IsTrue(graphChromatograms.Any(g => g.NameSet.Equals("R0_mzML")));
var oldest = graphChromatograms[0].NameSet;
var newest = "distinct_mzML"; // This replicate should have a different peak
Assert.IsFalse(graphChromatograms.Any(g => g.NameSet.Equals(newest)));
// Now select a graph not currently displayed
RunUI(() => SkylineWindow.SelectedResultsIndex = Skyline.SkylineWindow.MAX_GRAPH_CHROM);
WaitForGraphs();
graphChromatograms = SkylineWindow.GraphChromatograms.ToList();
Assert.IsFalse(graphChromatograms.Any(g => g.NameSet.Equals(oldest)));
Assert.IsTrue(graphChromatograms.Any(g => g.NameSet.Equals(newest)));
RunUI(() => SkylineWindow.ArrangeGraphsTiled()); // Arrange so that all are fully visible, so we can use .Visible in test below
// Now close all, then open them back up again with ctrl-up/ctrl-down hotkeys, and verify that we see the ones we expect
RunUI(() => SkylineWindow.CloseAllChromatograms());
WaitForClosedAllChromatogramsGraph();
// Now run through the replicates
for (count = 0; count < TOO_MANY_FILES; count++)
{
RunUI(() => SkylineWindow.SelectedResultsIndex = count);
var name = GetReplicateNameFromIndex(count).Replace(@".", @"_");
WaitForConditionUI(() => SkylineWindow.GraphChromatograms.Any(g => g.NameSet.Equals(name) && g.Visible));
graphChromatograms = SkylineWindow.GraphChromatograms.ToList();
for (var index = 0; index < TOO_MANY_FILES; index++)
{
name = GetReplicateNameFromIndex(index).Replace(@".", @"_");
var visible = graphChromatograms.Any(g => g.NameSet.Equals(name) && g.Visible);
var shouldBeVisible = (index > count - Skyline.SkylineWindow.MAX_GRAPH_CHROM) && (index <= count);
Assert.IsTrue(visible == shouldBeVisible);
if (shouldBeVisible)
{
// Make sure it's showing the right data
Assert.IsTrue(graphChromatograms.First(g => g.NameSet.Equals(name)).FilePath.ToString().Contains(GetReplicateNameFromIndex(index)));
}
}
}
}