private static string GetResultsText(TransitionDocNode nodeTran, int index, int indexRatio)
{
int? rank = nodeTran.GetPeakRank(index);
string label = (rank.HasValue && rank > 0 ? string.Format(Resources.TransitionTreeNode_GetResultsText__0__, rank) : string.Empty);
float? ratio = nodeTran.GetPeakAreaRatio(index, indexRatio);
if (!ratio.HasValue)
{
return(label);
}
return(string.Format(Resources.TransitionTreeNode_GetResultsText__0__ratio__1__, label, MathEx.RoundAboveZero(ratio.Value, 2, 4)));
}
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);
}
private static string GetResultsText(TransitionDocNode nodeTran, int index, int indexRatio)
{
int? rank = nodeTran.GetPeakRank(index);
string label = (rank.HasValue && rank > 0 ? string.Format(Resources.TransitionTreeNode_GetResultsText__0__, rank) : string.Empty);
float? ratio = nodeTran.GetPeakAreaRatio(index, indexRatio);
if (!ratio.HasValue)
return label;
return string.Format(Resources.TransitionTreeNode_GetResultsText__0__ratio__1__, label, MathEx.RoundAboveZero(ratio.Value, 2, 4));
}