diff --git a/pwiz_tools/Skyline/TestTutorial/TargetedMSMSTutorialTest.cs b/pwiz_tools/Skyline/TestTutorial/TargetedMSMSTutorialTest.cs index 582599374f..7d8e9eac02 100644 --- a/pwiz_tools/Skyline/TestTutorial/TargetedMSMSTutorialTest.cs +++ b/pwiz_tools/Skyline/TestTutorial/TargetedMSMSTutorialTest.cs @@ -104,12 +104,13 @@ public void DoTestTargetedMSMSTutorial(RefinementSettings.ConvertToSmallMolecule LinkPdf = "https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/PRM-22_2.pdf"; TestFilesZipPaths = new[] - { - UseRawFiles - ? @"http://skyline.ms/tutorials/TargetedMSMS_2.zip" - : @"http://skyline.ms/tutorials/TargetedMSMSMzml_2.zip", - @"TestTutorial\TargetedMSMSViews.zip" - }; + { + UseRawFiles + ? @"http://skyline.ms/tutorials/TargetedMSMS_2.zip" + : @"http://skyline.ms/tutorials/TargetedMSMSMzml_2.zip", + @"TestTutorial\TargetedMSMSViews.zip", + @"TestTutorial\TargetedMSMS_2_Extras.zip" + }; RunFunctionalTest(); } @@ -202,7 +203,7 @@ private void LowResTestPartOne(RefinementSettings.ConvertToSmallMoleculesMode as Assert.IsTrue(ArrayUtil.ContainsAll(new[] {IonType.y, IonType.b, IonType.precursor}, tranSettingsFullScan.Filter.PeptideIonTypes)); Assert.IsTrue(ArrayUtil.ContainsAll(new[] { IonType.custom, IonType.precursor }, - tranSettingsFullScan.Filter.SmallMoleculeIonTypes)); + tranSettingsFullScan.Filter.SmallMoleculeIonTypes)); } RunUI(() => SkylineWindow.ExpandPrecursors()); @@ -383,7 +384,7 @@ private void LowResTest() }); WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled); PauseForScreenShot("Import Peptide Search Build Spectral Library with files page", 16); - + RunDlg(importPeptideSearchDlg.ClickNextButtonNoCheck, dlg => dlg.OkDialog()); doc = WaitForDocumentChangeLoaded(doc, WAIT_TIME*2); // double wait time, becuase of intermittent failures on nightly runs if (AsSmallMolecules) @@ -568,25 +569,41 @@ private void LowResTest() Assert.AreEqual(AsSmallMoleculeMasses ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count()); // Library and two replicates Assert.AreEqual(6, SkylineWindow.GraphPeakArea.CurveCount); + + SkylineWindow.ActivateReplicate("20fmol"); }); // Graph p.23 PauseForPeakAreaGraphScreenShot("Peak Areas Replicate Comparison graph metafile"); if (!AsSmallMoleculeMasses) VerifyDotProducts(0.99, 0.98); - // Screenshot of full 5-point dilution curve - // TODO: Open saved document with 5-point calibration curve with data not available to this test. Meantime, use a placeholder. - PauseForPeakAreaGraphScreenShot( - "PLACEHOLDER. Saved screenshot was manually generated. See todo in test for more info", - processShot: MarkBitmapAsPlaceholder); + // Switch documents for the next screenshot with all 5 runs + RunUI(() => SkylineWindow.SaveDocument()); + + var fiveRunFile = TestFilesDirs[2].GetTestPath(@"BSA_Protea_label_free_20100323_meth3_long_all.sky"); + RunUI(() => SkylineWindow.OpenFile(fiveRunFile)); + FindNode("K.LVNELTEFAK.T [66, 75]"); + + RunUI(() => + { + SkylineWindow.ShowReplicateOrder(SummaryReplicateOrder.time); + SkylineWindow.GraphPeakArea.TryGetGraphPane(out AreaReplicateGraphPane pane); + pane.GraphSummary.ActiveLibrary = true; + }); + + PauseForPeakAreaGraphScreenShot("Peak Areas five point calibration curve"); // Check graph p23. (checked) - RunUI(() => - { - SkylineWindow.ShowAllTransitions(); - if (!IsCoverShotMode) - SkylineWindow.ShowSplitChromatogramGraph(true); - }); + RunUI(() => + { + // Restore PRM tutorial to its state prior to taking the 5-point calibration curve screenshot + SkylineWindow.OpenFile(GetTestPath(@"Low Res\BSA_Protea_label_free_meth3.sky")); + WaitForDocumentLoaded(); + + SkylineWindow.ShowAllTransitions(); + if (!IsCoverShotMode) + SkylineWindow.ShowSplitChromatogramGraph(true); + }); // Select precursor if (!AsSmallMoleculeMasses) @@ -640,11 +657,13 @@ private void LowResTest() // PeakAreaGraph Normalize to total p.27. RunUI(() => - { - SkylineWindow.ShowPeakAreaReplicateComparison(); - SkylineWindow.ShowProductTransitions(); - SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL); - }); + { + SkylineWindow.ShowPeakAreaReplicateComparison(); + SkylineWindow.ShowProductTransitions(); + SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL); + + Settings.Default.PeakAreaDotpDisplay = DotProductDisplayOption.none.ToString(); + }); // Ensure graph looks like p27. if (!AsSmallMoleculeMasses) @@ -936,6 +955,8 @@ private void TofTest() var graph = SkylineWindow.GraphPeakArea.GraphControl; var scale = graph.GraphPane.YAxis.Scale; scale.Max = 25000000; + + Settings.Default.PeakAreaDotpDisplay = DotProductDisplayOption.label.ToString(); }); PauseForPeakAreaGraphScreenShot("Peak Areas Replicate Comparison graph metafile"); WaitForDotProducts(); diff --git a/pwiz_tools/Skyline/TestTutorial/TargetedMSMS_2_Extras.zip b/pwiz_tools/Skyline/TestTutorial/TargetedMSMS_2_Extras.zip new file mode 100644 index 0000000000..a7622dd1c0 Binary files /dev/null and b/pwiz_tools/Skyline/TestTutorial/TargetedMSMS_2_Extras.zip differ