public override IonMobilityAndCCS GetIonMobilityInfo(LibKey key, ChargeRegressionLine regressionLine)
{
if (_database != null)
{
return(_database.GetDriftTimeInfo(key, regressionLine));
}
return(null);
}
public override DriftTimeInfo GetDriftTimeInfo(String seq, ChargeRegressionLine regressionLine)
{
if (_database != null)
{
return(_database.GetDriftTimeInfo(seq, regressionLine));
}
return(null);
}
// TODO(bspratt) either upgrade this for all ion mobility types, or rip out this code altogether
public IonMobilityAndCCS GetDriftTimeInfo(LibKey key, ChargeRegressionLine regression)
{
DbIonMobilityPeptide pep;
if (DictLibrary.TryGetValue(key, out pep))
{
return(IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(regression.GetY(pep.CollisionalCrossSection), eIonMobilityUnits.drift_time_msec), pep.CollisionalCrossSection, pep.HighEnergyDriftTimeOffsetMsec));
}
return(null);
}
public DriftTimeInfo GetDriftTimeInfo(string seq, ChargeRegressionLine regression)
{
DbIonMobilityPeptide pep;
if (DictLibrary.TryGetValue(seq, out pep))
{
return(new DriftTimeInfo(regression.GetY(pep.CollisionalCrossSection), pep.HighEnergyDriftTimeOffsetMsec));
}
return(null);
}
protected override void DoTest()
{
// Lest we get "To export a scheduled method, you must first choose a retention time predictor in Peptide Settings / Prediction, or import results for all peptides in the document."
TestSmallMolecules = false;
// Skyline Collision Energy Optimization
RunUI(() => SkylineWindow.OpenFile(GetTestPath("CE_Vantage_15mTorr.sky"))); // Not L10N
if (AsSmallMolecules)
{
var doc = WaitForDocumentLoaded();
var refine = new RefinementSettings();
SkylineWindow.SetDocument(refine.ConvertToSmallMolecules(doc), doc);
}
// Deriving a New Linear Equation, p. 2
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
var editList =
ShowDialog <EditListDlg <SettingsListBase <CollisionEnergyRegression>, CollisionEnergyRegression> >
(transitionSettingsUI.EditCEList);
RunUI(() => editList.SelectItem("Thermo")); // Not L10N
EditCEDlg editItem = ShowDialog <EditCEDlg>(editList.EditItem);
PauseForScreenShot <EditCEDlg>("Edit Collision Energy Equation form", 3);
ChargeRegressionLine regressionLine2 = new ChargeRegressionLine(2, 0.034, 3.314);
ChargeRegressionLine regressionLine3 = new ChargeRegressionLine(3, 0.044, 3.314);
CheckRegressionLines(new[] { regressionLine2, regressionLine3 }, editItem.Regression.Conversions);
RunUI(() =>
{
editItem.DialogResult = DialogResult.OK;
editList.DialogResult = DialogResult.Cancel;
transitionSettingsUI.DialogResult = DialogResult.Cancel;
});
WaitForClosedForm(transitionSettingsUI);
// Measuring Retention Times for Method Scheduling, p. 3
{
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 form", 4);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr_unscheduled.csv"))); // Not L10N
WaitForClosedForm(exportMethodDlg);
}
string filePathTemplate = GetTestPath("CE_Vantage_15mTorr_unscheduled.csv"); // Not L10N
CheckTransitionList(filePathTemplate, 1, 6);
const string unscheduledName = "Unscheduled"; // Not L10N
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg =>
{
importResultsDlg.RadioAddNewChecked = true;
var path =
new[] { new KeyValuePair <string, MsDataFileUri[]>(unscheduledName,
// This is not actually a valid file path (missing OptimizeCE)
// but Skyline should correctly find the file in the same folder
// as the document.
new[] { MsDataFileUri.Parse(GetTestPath("CE_Vantage_15mTorr_unscheduled" + ExtThermoRaw)) }) }; // Not L10N
importResultsDlg.NamedPathSets = path;
importResultsDlg.OkDialog();
});
WaitForCondition(5 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 5 minutes
AssertEx.IsDocumentState(SkylineWindow.Document, null, 7, 27, 30, 120);
var docUnsched = SkylineWindow.Document;
AssertResult.IsDocumentResultsState(SkylineWindow.Document,
unscheduledName,
docUnsched.MoleculeCount,
docUnsched.MoleculeTransitionGroupCount, 0,
docUnsched.MoleculeTransitionCount - 1, 0);
RunUI(() =>
{
SkylineWindow.ExpandProteins();
SkylineWindow.ExpandPeptides();
});
PauseForScreenShot("Main Skyline window", 5);
// Creating Optimization Methods, p. 5
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO;
exportMethodDlg.ExportStrategy = ExportStrategy.Buckets;
exportMethodDlg.MaxTransitions = 110;
exportMethodDlg.IgnoreProteins = true;
exportMethodDlg.OptimizeType = ExportOptimize.CE;
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 6);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr.csv"))); // Not L10N
WaitForClosedForm(exportMethodDlg);
}
string filePathTemplate1 = GetTestPath("CE_Vantage_15mTorr_000{0}.csv"); // Not L10N
CheckTransitionList(filePathTemplate1, 5, 9);
var filePath = GetTestPath("CE_Vantage_15mTorr_0001.csv"); // Not L10N
CheckCEValues(filePath, 11);
// Analyze Optimization Data, p. 7
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg =>
{
importResultsDlg.RadioAddNewChecked = true;
importResultsDlg.OptimizationName = ExportOptimize.CE;
importResultsDlg.NamedPathSets = DataSourceUtil.GetDataSourcesInSubdirs(TestFilesDirs[0].FullPath).ToArray();
importResultsDlg.NamedPathSets[0] =
new KeyValuePair <string, MsDataFileUri[]>("Optimize CE", importResultsDlg.NamedPathSets[0].Value.Take(5).ToArray()); // Not L10N
importResultsDlg.OkDialog();
});
RunUI(() =>
{
SkylineWindow.ShowSingleTransition();
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ShowPeakAreaReplicateComparison();
});
WaitForDocumentLoaded(15 * 60 * 1000); // 10 minutes
if (AsSmallMolecules)
{
return; // Too peptide-centric from here to end of test
}
FindNode("IHGFDLAAINLQR");
RestoreViewOnScreen(8);
PauseForScreenShot("Main Skyline window", 8);
// p. 8
// Not L10N
RemovePeptide("EGIHAQQK");
FindNode("IDALNENK");
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view));
PauseForScreenShot("Main Skyline window", 9);
RunUI(SkylineWindow.EditDelete);
RemovePeptide("LICDNTHITK");
// Creating a New Equation for CE, p. 9
var transitionSettingsUI1 = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
var editCEDlg1 = ShowDialog <EditListDlg <SettingsListBase <CollisionEnergyRegression>, CollisionEnergyRegression> >(transitionSettingsUI1.EditCEList);
var addItem = ShowDialog <EditCEDlg>(editCEDlg1.AddItem);
RunUI(() =>
{
addItem.RegressionName = "Thermo Vantage Tutorial"; // Not L10N
addItem.UseCurrentData();
});
var graphRegression = ShowDialog <GraphRegression>(addItem.ShowGraph);
PauseForScreenShot <GraphRegression>("Collision Energy Regression graphs", 10);
var graphDatas = graphRegression.RegressionGraphDatas.ToArray();
Assert.AreEqual(2, graphDatas.Length);
ChargeRegressionLine regressionLine21 = new ChargeRegressionLine(2, 0.0305, 2.5061);
ChargeRegressionLine regressionLine31 = new ChargeRegressionLine(3, 0.0397, 1.4217);
var expectedRegressions = new[] { regressionLine21, regressionLine31 };
CheckRegressionLines(expectedRegressions, new[]
{
new ChargeRegressionLine(2,
Math.Round(graphDatas[0].RegressionLine.Slope, 4),
Math.Round(graphDatas[0].RegressionLine.Intercept, 4)),
new ChargeRegressionLine(3,
Math.Round(graphDatas[1].RegressionLine.Slope, 4),
Math.Round(graphDatas[1].RegressionLine.Intercept, 4)),
});
RunUI(graphRegression.CloseDialog);
WaitForClosedForm(graphRegression);
RunUI(addItem.OkDialog);
WaitForClosedForm(addItem);
RunUI(editCEDlg1.OkDialog);
WaitForClosedForm(editCEDlg1);
RunUI(transitionSettingsUI1.OkDialog);
WaitForClosedForm(transitionSettingsUI1);
// Optimizing Each Transition, p. 10
RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI2 =>
{
transitionSettingsUI2.UseOptimized = true;
transitionSettingsUI2.OptimizeType = OptimizedMethodType.Transition.GetLocalizedString();
transitionSettingsUI2.OkDialog();
});
RunDlg <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List), exportMethodDlg =>
{
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr_optimized.csv")); // Not L10N
});
var filePathTemplate2 = GetTestPath("CE_Vantage_15mTorr_optimized.csv"); // Not L10N
CheckTransitionList(filePathTemplate2, 1, 9);
RunUI(() => SkylineWindow.SaveDocument());
WaitForConditionUI(() => !SkylineWindow.Dirty);
}
public DriftTimeInfo GetDriftTimeInfo(string seq, ChargeRegressionLine regression)
{
DbIonMobilityPeptide pep;
if (DictLibrary.TryGetValue(seq, out pep))
return new DriftTimeInfo(regression.GetY(pep.CollisionalCrossSection), pep.HighEnergyDriftTimeOffsetMsec);
return null;
}
public static void CheckRegressionLines(ChargeRegressionLine[] lines1, ChargeRegressionLine[] lines2)
{
Assert.IsTrue(ArrayUtil.EqualsDeep(lines1, lines2));
}
protected override void DoTest()
{
// Lest we get "To export a scheduled method, you must first choose a retention time predictor in Peptide Settings / Prediction, or import results for all peptides in the document."
TestSmallMolecules = false;
// Skyline Collision Energy Optimization
RunUI(() => SkylineWindow.OpenFile(GetTestPath("CE_Vantage_15mTorr.sky"))); // Not L10N
if (AsSmallMolecules)
{
var doc = WaitForDocumentLoaded();
var refine = new RefinementSettings();
SkylineWindow.SetDocument(refine.ConvertToSmallMolecules(doc), doc);
}
// Deriving a New Linear Equation, p. 2
var transitionSettingsUI = ShowDialog<TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
var editList =
ShowDialog<EditListDlg<SettingsListBase<CollisionEnergyRegression>, CollisionEnergyRegression>>
(transitionSettingsUI.EditCEList);
RunUI(() => editList.SelectItem("Thermo")); // Not L10N
EditCEDlg editItem = ShowDialog<EditCEDlg>(editList.EditItem);
PauseForScreenShot<EditCEDlg>("Edit Collision Energy Equation form", 3);
ChargeRegressionLine regressionLine2 = new ChargeRegressionLine(2, 0.034, 3.314);
ChargeRegressionLine regressionLine3 = new ChargeRegressionLine(3, 0.044, 3.314);
CheckRegressionLines(new[] {regressionLine2, regressionLine3}, editItem.Regression.Conversions);
RunUI(() =>
{
editItem.DialogResult = DialogResult.OK;
editList.DialogResult = DialogResult.Cancel;
transitionSettingsUI.DialogResult = DialogResult.Cancel;
});
WaitForClosedForm(transitionSettingsUI);
// Measuring Retention Times for Method Scheduling, p. 3
{
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 form", 4);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr_unscheduled.csv"))); // Not L10N
WaitForClosedForm(exportMethodDlg);
}
string filePathTemplate = GetTestPath("CE_Vantage_15mTorr_unscheduled.csv"); // Not L10N
CheckTransitionList(filePathTemplate, 1, 6);
const string unscheduledName = "Unscheduled"; // Not L10N
RunDlg<ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg =>
{
importResultsDlg.RadioAddNewChecked = true;
var path =
new[] {new KeyValuePair<string, MsDataFileUri[]>(unscheduledName,
// This is not actually a valid file path (missing OptimizeCE)
// but Skyline should correctly find the file in the same folder
// as the document.
new[] { MsDataFileUri.Parse(GetTestPath("CE_Vantage_15mTorr_unscheduled" + ExtThermoRaw))})}; // Not L10N
importResultsDlg.NamedPathSets = path;
importResultsDlg.OkDialog();
});
WaitForCondition(5*60*1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 5 minutes
AssertEx.IsDocumentState(SkylineWindow.Document, null, 7, 27, 30, 120);
var docUnsched = SkylineWindow.Document;
AssertResult.IsDocumentResultsState(SkylineWindow.Document,
unscheduledName,
docUnsched.MoleculeCount,
docUnsched.MoleculeTransitionGroupCount, 0,
docUnsched.MoleculeTransitionCount - 1, 0);
RunUI(() =>
{
SkylineWindow.ExpandProteins();
SkylineWindow.ExpandPeptides();
});
PauseForScreenShot("Main Skyline window", 5);
// Creating Optimization Methods, p. 5
{
var exportMethodDlg = ShowDialog<ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO;
exportMethodDlg.ExportStrategy = ExportStrategy.Buckets;
exportMethodDlg.MaxTransitions = 110;
exportMethodDlg.IgnoreProteins = true;
exportMethodDlg.OptimizeType = ExportOptimize.CE;
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
});
PauseForScreenShot<ExportMethodDlg.TransitionListView>("Export Transition List form", 6);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr.csv"))); // Not L10N
WaitForClosedForm(exportMethodDlg);
}
string filePathTemplate1 = GetTestPath("CE_Vantage_15mTorr_000{0}.csv"); // Not L10N
CheckTransitionList(filePathTemplate1, 5, 9);
var filePath = GetTestPath("CE_Vantage_15mTorr_0001.csv"); // Not L10N
CheckCEValues(filePath, 11);
// Analyze Optimization Data, p. 7
RunDlg<ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg =>
{
importResultsDlg.RadioAddNewChecked = true;
importResultsDlg.OptimizationName = ExportOptimize.CE;
importResultsDlg.NamedPathSets = DataSourceUtil.GetDataSourcesInSubdirs(TestFilesDirs[0].FullPath).ToArray();
importResultsDlg.NamedPathSets[0] =
new KeyValuePair<string, MsDataFileUri[]>("Optimize CE", importResultsDlg.NamedPathSets[0].Value.Take(5).ToArray()); // Not L10N
importResultsDlg.OkDialog();
});
RunUI(() =>
{
SkylineWindow.ShowSingleTransition();
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ShowPeakAreaReplicateComparison();
});
if (AsSmallMolecules)
{
return; // Too peptide-centric from here to end of test
}
FindNode("IHGFDLAAINLQR");
RestoreViewOnScreen(8);
WaitForCondition(15*60*1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 10 minutes
PauseForScreenShot("Main Skyline window", 8);
// p. 8
// Not L10N
RemovePeptide("EGIHAQQK");
FindNode("IDALNENK");
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view));
PauseForScreenShot("Main Skyline window", 9);
RunUI(SkylineWindow.EditDelete);
RemovePeptide("LICDNTHITK");
// Creating a New Equation for CE, p. 9
var transitionSettingsUI1 = ShowDialog<TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
var editCEDlg1 = ShowDialog<EditListDlg<SettingsListBase<CollisionEnergyRegression>, CollisionEnergyRegression>>(transitionSettingsUI1.EditCEList);
var addItem = ShowDialog<EditCEDlg>(editCEDlg1.AddItem);
RunUI(() =>
{
addItem.RegressionName = "Thermo Vantage Tutorial"; // Not L10N
addItem.UseCurrentData();
});
var graphRegression = ShowDialog<GraphRegression>(addItem.ShowGraph);
PauseForScreenShot<GraphRegression>("Collision Energy Regression graphs", 10);
var graphDatas = graphRegression.RegressionGraphDatas.ToArray();
Assert.AreEqual(2, graphDatas.Length);
ChargeRegressionLine regressionLine21 = new ChargeRegressionLine(2, 0.0305, 2.5061);
ChargeRegressionLine regressionLine31 = new ChargeRegressionLine(3, 0.0397, 1.4217);
var expectedRegressions = new[] {regressionLine21, regressionLine31};
CheckRegressionLines(expectedRegressions, new[]
{
new ChargeRegressionLine(2,
Math.Round(graphDatas[0].RegressionLine.Slope, 4),
Math.Round(graphDatas[0].RegressionLine.Intercept, 4)),
new ChargeRegressionLine(3,
Math.Round(graphDatas[1].RegressionLine.Slope, 4),
Math.Round(graphDatas[1].RegressionLine.Intercept, 4)),
});
RunUI(graphRegression.CloseDialog);
WaitForClosedForm(graphRegression);
RunUI(addItem.OkDialog);
WaitForClosedForm(addItem);
RunUI(editCEDlg1.OkDialog);
WaitForClosedForm(editCEDlg1);
RunUI(transitionSettingsUI1.OkDialog);
WaitForClosedForm(transitionSettingsUI1);
// Optimizing Each Transition, p. 10
RunDlg<TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI2 =>
{
transitionSettingsUI2.UseOptimized = true;
transitionSettingsUI2.OptimizeType = OptimizedMethodType.Transition.GetLocalizedString();
transitionSettingsUI2.OkDialog();
});
RunDlg<ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List), exportMethodDlg =>
{
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr_optimized.csv")); // Not L10N
});
var filePathTemplate2 = GetTestPath("CE_Vantage_15mTorr_optimized.csv"); // Not L10N
CheckTransitionList(filePathTemplate2, 1, 9);
RunUI(() => SkylineWindow.SaveDocument());
WaitForConditionUI(() => !SkylineWindow.Dirty);
}
public override DriftTimeInfo GetDriftTimeInfo(String seq, ChargeRegressionLine regressionLine)
{
if (_database != null)
return _database.GetDriftTimeInfo(seq, regressionLine);
return null;
}
