Merge branch 'master' into Skyline/work/20240905_what_is_up_with_test…

…s_on_jason_xps
ProteoWizard · Jan 10, 2025 · 19b83bc · 19b83bc
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diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/AbsoluteQuant/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/AbsoluteQuant/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/AbsoluteQuant/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/AbsoluteQuant/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/AbsoluteQuant/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/AbsoluteQuant/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/AuditLog/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/AuditLog/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/CustomReports/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/CustomReports/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/CustomReports/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/CustomReports/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/CustomReports/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/CustomReports/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DDASearch/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DDASearch/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DDASearch/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DDASearch/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DDASearch/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DDASearch/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DIA-PASEF/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DIA-PASEF/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DIA-QE/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DIA-QE/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DIA-QE/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DIA-QE/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DIA-QE/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DIA-QE/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DIA-TTOF/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DIA-TTOF/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DIA-TTOF/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DIA-TTOF/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DIA-TTOF/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DIA-TTOF/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DIA/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DIA/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DIA/en/index.html b/pwiz_tools/Skyline/Documentation/Tutorials/DIA/en/index.html
@@ -549,6 +549,7 @@ <h1>Exploring DIA Results</h1>
         <li>Right-click one of the chromatogram graphs, and click <b>Legend</b> to uncheck it.</li>
         <li>Dock the <b>Peak Areas – Replicate Comparison</b> graph to the right edge of the main window on top of the <b>Library
                 Match</b> view.</li>
+        <li>Right-click the <b>Peak Areas – Replicate Comparison</b> graph, choose <b>Show Dot Product</b>, and click <b>Labels</b>.</li>
         <li>Select the first peptide K.YALSQDV<b><u>C</u></b>TYR.D [64, 74] in the <b>Targets</b> view.</li>
     </ul>
     <p class="keep-next">

diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DIA/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DIA/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/DIA/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/DIA/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/s-24.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/s-24.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/s-25.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/s-25.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/s-30.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/s-30.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/s-31.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/s-31.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/s-34.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/s-34.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/s-36.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/en/s-36.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/s-24.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/s-24.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/s-25.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/s-25.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/s-30.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/s-30.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/s-31.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/s-31.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/s-34.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/s-34.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/s-36.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/ja/s-36.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/s-24.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/s-24.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/s-25.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/s-25.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/s-30.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/s-30.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/s-31.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/s-31.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/s-34.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/s-34.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/s-36.png b/pwiz_tools/Skyline/Documentation/Tutorials/ExistingQuant/zh-CHS/s-36.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/GroupedStudies/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/GroupedStudies/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/GroupedStudies/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/GroupedStudies/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/GroupedStudies/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/GroupedStudies/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/HiResMetabolomics/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/HiResMetabolomics/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/IMSFiltering/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/IMSFiltering/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/LibraryExplorer/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/LibraryExplorer/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/MS1Filtering/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/MS1Filtering/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/MS1Filtering/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/MS1Filtering/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/MS1Filtering/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/MS1Filtering/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/MethodEdit/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/MethodEdit/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/MethodEdit/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/MethodEdit/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/MethodEdit/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/MethodEdit/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/MethodRefine/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/MethodRefine/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/MethodRefine/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/MethodRefine/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/MethodRefine/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/MethodRefine/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/OptimizeCE/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/PRM/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/PRM/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/PRM/en/index.html b/pwiz_tools/Skyline/Documentation/Tutorials/PRM/en/index.html
@@ -483,6 +483,7 @@ <h1>Reviewing the Data</h1>
     <ul>
         <li>On the <b>View</b> menu, choose <b>Peak Areas</b> and click <b>Replicate Comparison</b> (F7).</li>
         <li>On the <b>View</b> menu, choose <b>Transitions</b> and click <b>Products</b> (Ctrl-Alt-F10).</li>
+        <li>Right-click the <b>Peak Areas – Replicate Comparison</b> graph, choose <b>Show Dot Product</b>, and click <b>Labels</b>.</li>
     </ul>
     <p class="keep-next">
         The <b>Peak Areas</b> graph should now look like this:
@@ -496,7 +497,6 @@ <h1>Reviewing the Data</h1>
     <ul>
         <li>Right-click the <b>Peak Areas</b> graph, choose <b>Normalize To</b> and click <b>None</b>.</li>
         <li>Right-click the <b>Peak Areas</b> graph, and click <b>Show Library</b>.</li>
-        <li>Right-click the <b>Peak Areas</b> graph, and click <b>Show Dot Product</b>.</li>
     </ul>
     <p>
         You can review all of the target peptides with these settings to see that they all match the search spectra very well, and that the

diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/PRM/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/PRM/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/PRM/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/PRM/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/PeakPicking/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/PeakPicking/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/SmallMolecule/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/SmallMolecule/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/SmallMolecule/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/SmallMolecule/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/SmallMolecule/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/SmallMolecule/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/SmallMoleculeIMSLibraries/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/SmallMoleculeIMSLibraries/en/cover.png
diff --git a/..._tools/Skyline/Documentation/Tutorials/SmallMoleculeMethodDevCEOpt/en/cover.png b/..._tools/Skyline/Documentation/Tutorials/SmallMoleculeMethodDevCEOpt/en/cover.png
diff --git a/..._tools/Skyline/Documentation/Tutorials/SmallMoleculeMethodDevCEOpt/ja/cover.png b/..._tools/Skyline/Documentation/Tutorials/SmallMoleculeMethodDevCEOpt/ja/cover.png
diff --git a/...ls/Skyline/Documentation/Tutorials/SmallMoleculeMethodDevCEOpt/zh-CHS/cover.png b/...ls/Skyline/Documentation/Tutorials/SmallMoleculeMethodDevCEOpt/zh-CHS/cover.png
diff --git a/..._tools/Skyline/Documentation/Tutorials/SmallMoleculeQuantification/en/cover.png b/..._tools/Skyline/Documentation/Tutorials/SmallMoleculeQuantification/en/cover.png
diff --git a/..._tools/Skyline/Documentation/Tutorials/SmallMoleculeQuantification/ja/cover.png b/..._tools/Skyline/Documentation/Tutorials/SmallMoleculeQuantification/ja/cover.png
diff --git a/...ls/Skyline/Documentation/Tutorials/SmallMoleculeQuantification/zh-CHS/cover.png b/...ls/Skyline/Documentation/Tutorials/SmallMoleculeQuantification/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/iRT/en/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/iRT/en/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/iRT/ja/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/iRT/ja/cover.png
diff --git a/pwiz_tools/Skyline/Documentation/Tutorials/iRT/zh-CHS/cover.png b/pwiz_tools/Skyline/Documentation/Tutorials/iRT/zh-CHS/cover.png
diff --git a/pwiz_tools/Skyline/SkylineTester/WindowThumbnail.cs b/pwiz_tools/Skyline/SkylineTester/WindowThumbnail.cs
@@ -56,7 +56,7 @@ private void UnregisterThumb()
         {
             if (_thumb != IntPtr.Zero)
             {
-                DwmapiTest.UnregisterThumbnail(_thumb);
+                DwmapiTest.DwmUnregisterThumbnail(_thumb);
                 _thumb = IntPtr.Zero;
             }
         }
@@ -71,7 +71,7 @@ private void RegisterThumb()
             }
 
             IntPtr newThumb;
-            DwmapiTest.RegisterThumbnail(MainWindow.Handle, window, out newThumb);
+            DwmapiTest.DwmRegisterThumbnail(MainWindow.Handle, window, out newThumb);
             if (newThumb == IntPtr.Zero)
             {
                 UnregisterThumb();
@@ -86,7 +86,7 @@ private void RegisterThumb()
             Point locationOnForm = MainWindow.PointToClient(Parent.PointToScreen(Location));
 
             PInvokeCommon.SIZE size;
-            DwmapiTest.QueryThumbnailSourceSize(_thumb, out size);
+            DwmapiTest.DwmQueryThumbnailSourceSize(_thumb, out size);
 
             var props = new DwmapiTest.THUMBNAIL_PROPERTIES
             {
@@ -105,7 +105,7 @@ private void RegisterThumb()
             if (size.cy < Height)
                 props.rcDestination.bottom = props.rcDestination.top + size.cy;
 
-            DwmapiTest.UpdateThumbnailProperties(_thumb, ref props);
+            DwmapiTest.DwmUpdateThumbnailProperties(_thumb, ref props);
         }
 
         private IntPtr FindWindow(int processId)

diff --git a/pwiz_tools/Skyline/TestRunnerLib/PInvoke/DwmapiTest.cs b/pwiz_tools/Skyline/TestRunnerLib/PInvoke/DwmapiTest.cs
@@ -48,18 +48,18 @@ public struct THUMBNAIL_PROPERTIES
 
         // ReSharper disable once StringLiteralTypo
         [DllImport("dwmapi.dll")]
-        public static extern int RegisterThumbnail(IntPtr dest, IntPtr src, out IntPtr thumb);
+        public static extern int DwmRegisterThumbnail(IntPtr dest, IntPtr src, out IntPtr thumb);
 
         // ReSharper disable once StringLiteralTypo
         [DllImport("dwmapi.dll")]
-        public static extern int UnregisterThumbnail(IntPtr thumb);
+        public static extern int DwmUnregisterThumbnail(IntPtr thumb);
 
         // ReSharper disable once StringLiteralTypo
         [DllImport("dwmapi.dll")]
-        public static extern int QueryThumbnailSourceSize(IntPtr thumb, out PInvokeCommon.SIZE size);
+        public static extern int DwmQueryThumbnailSourceSize(IntPtr thumb, out PInvokeCommon.SIZE size);
 
         // ReSharper disable once StringLiteralTypo
         [DllImport("dwmapi.dll")]
-        public static extern int UpdateThumbnailProperties(IntPtr hThumb, ref THUMBNAIL_PROPERTIES props);
+        public static extern int DwmUpdateThumbnailProperties(IntPtr hThumb, ref THUMBNAIL_PROPERTIES props);
     }
 }
diff --git a/pwiz_tools/Skyline/TestTutorial/DiaTutorialTest.cs b/pwiz_tools/Skyline/TestTutorial/DiaTutorialTest.cs
@@ -319,7 +319,6 @@ protected override void DoTest()
                 SkylineWindow.ShowChromatogramLegends(false);
                 SkylineWindow.ShowPeakAreaReplicateComparison();
                 SkylineWindow.ArrangeGraphs(DisplayGraphsType.Row);
-                // TODO: Need to explain this in the tutorial
                 // CONSIDER: SkylineWindow should probably have a function for this
                 Settings.Default.PeakAreaDotpDisplay = DotProductDisplayOption.label.ToString();
                 SkylineWindow.Width = 1250;

diff --git a/pwiz_tools/Skyline/TestTutorial/ExistingExperimentsTutorialTest.cs b/pwiz_tools/Skyline/TestTutorial/ExistingExperimentsTutorialTest.cs
@@ -510,7 +510,6 @@ private void DoStudy7Test()
             FindNode("SSDLVALSGGHTFGK"); // Not L10N
             RunUI(NormalizeGraphToHeavy);
             PauseForPeakAreaGraphScreenShot("Peak Areas graph metafile");
-            Settings.Default.PeakAreaDotpDisplay = DotProductDisplayOption.none.ToString();
             FindNode((564.7746).ToString(LocalizationHelper.CurrentCulture) + "++"); // ESDTSYVSLK - Not L10N
             WaitForGraphs();
             PauseForPeakAreaGraphScreenShot("Peak Areas graph metafile");