protected override void DoTest()
{
// Configuring Peptide settings p. 4
PeptideSettingsUI peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Modifications);
PauseForScreenShot();
var modHeavyK = new StaticMod(HEAVY_K, "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15, // Not L10N
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUI, "Edit Isotope Modification form");
var modHeavyR = new StaticMod(HEAVY_R, "R", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15, // Not L10N
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyR, peptideSettingsUI, "Edit Isotope Modification form");
RunUI(() => peptideSettingsUI.PickedHeavyMods = new[] { HEAVY_K, HEAVY_R });
PauseForScreenShot();
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
SetTransitionClipboardText(new[] { 0, 1, 7, 8 });
RunUI(() =>
{
SkylineWindow.Paste();
SkylineWindow.CollapsePeptides();
});
PauseForScreenShot();
const string peptideStandardsName = "Tr_peps_set2";
FindNode(peptideStandardsName);
RunUI(() =>
{
SkylineWindow.Cut();
SkylineWindow.SelectedPath = new IdentityPath(SequenceTree.NODE_INSERT_ID);
SkylineWindow.Paste();
});
// Create auto-calculate regression RT predictor, p. 10
const string irtPredictorName = "iRT-OC-Study"; // Not L10N
{
var peptideSettingsUI2 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI2.SelectedTab = PeptideSettingsUI.TABS.Prediction);
var regressionDlg = ShowDialog <EditRTDlg>(peptideSettingsUI2.AddRTRegression);
const string irtCalcName = "iRT-OC-Study";
var editIrtCalcDlg = ShowDialog <EditIrtCalcDlg>(regressionDlg.AddCalculator);
RunUI(() =>
{
editIrtCalcDlg.CalcName = irtCalcName;
editIrtCalcDlg.CreateDatabase(GetOcRawTestPath("iRT-OC-Study.irtdb")); // Not L10N
SetTransitionClipboardText(new[] { 15, 17 }, c =>
{
if (string.Equals(c[8], "protein_name"))
{
return(null);
}
// c[17] = double.Parse(c[17], CultureInfo.InvariantCulture).ToString(LocalizationHelper.CurrentCulture);
return(string.Equals(c[8], peptideStandardsName) ? c : null);
});
editIrtCalcDlg.DoPasteStandard();
});
PauseForScreenShot();
RunUI(() =>
{
string carbC = string.Format("C[+{0:F01}]", 57.0);
SetTransitionClipboardText(new[] { 15, 17 }, c =>
{
if (string.Equals(c[8], peptideStandardsName) || string.Equals(c[8], "protein_name"))
{
return(null);
}
c[15] = c[15].Replace("[C160]", carbC).Replace("C[160]", carbC);
// c[17] = double.Parse(c[17], CultureInfo.InvariantCulture).ToString(LocalizationHelper.CurrentCulture);
return(c);
});
});
var addPeptidesDlg = ShowDialog <AddIrtPeptidesDlg>(editIrtCalcDlg.DoPasteLibrary);
PauseForScreenShot(); // Add Peptides form
RunUI(() =>
{
Assert.AreEqual(71, addPeptidesDlg.PeptidesCount);
Assert.AreEqual(0, addPeptidesDlg.RunsConvertedCount);
Assert.AreEqual(0, addPeptidesDlg.RunsFailedCount);
addPeptidesDlg.OkDialog();
});
WaitForClosedForm(addPeptidesDlg);
PauseForScreenShot(); // Edit iRT Calculator form
RunUI(() => Assert.AreEqual(71, editIrtCalcDlg.LibraryPeptideCount));
OkDialog(editIrtCalcDlg, editIrtCalcDlg.OkDialog);
RunUI(() =>
{
regressionDlg.SetRegressionName(irtPredictorName);
regressionDlg.ChooseCalculator(irtCalcName);
regressionDlg.SetAutoCalcRegression(true);
regressionDlg.SetTimeWindow(3);
});
PauseForScreenShot(); // Edit retention time predictor form
OkDialog(regressionDlg, regressionDlg.OkDialog);
PauseForScreenShot(); // Prediction tab
RunUI(() => peptideSettingsUI2.SelectedTab = PeptideSettingsUI.TABS.Library);
var editLibListUI = ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(peptideSettingsUI2.EditLibraryList);
var addLibUI = ShowDialog <EditLibraryDlg>(editLibListUI.AddItem);
RunUI(() => addLibUI.LibrarySpec =
new BiblioSpecLibSpec(HUMAN_MINI, GetOcRawTestPath("h130kdp_consensus.blib"))); // Not L10N
PauseForScreenShot();
OkDialog(addLibUI, addLibUI.OkDialog);
OkDialog(editLibListUI, editLibListUI.OkDialog);
RunUI(() => peptideSettingsUI2.PickedLibraries = new[] { HUMAN_MINI });
PauseForScreenShot();
OkDialog(peptideSettingsUI2, peptideSettingsUI2.OkDialog);
}
RunUI(() => SkylineWindow.SaveDocument(GetOcRawTestPath("OC-study.sky")));
// Importing Data
ImportResultsFiles(GetOcRawTestPath(), ExtAbWiff,
IsFullData ? "R201217" : "R201217_plasma_revision_A", true);
WaitForCondition(5 * 60 * 1000, () =>
SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
ImportResultsFiles(GetOcRawTestPath(), ExtAbWiff,
IsFullData ? "R201203" : "R201203_plasma_revision_F", true);
WaitForCondition(2 * 60 * 1000, () =>
SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot();
}