Warn when ion mobility filtering is disabled but IM values are available (#4150)

pwiz_tools/Skyline/Model/Results/ResultsResources.resx

@@ -311,6 +311,15 @@ It is recommended that you delete this file so that Skyline can create a new fil
   <data name="SpectrumFilter_CalcDiaIsolationValues_Unable_to_determine_isolation_width_for_the_scan_targeted_at__0_" xml:space="preserve">
     <value>Unable to determine isolation width for the scan targeted at {0}</value>
   </data>
+  <data name="SpectrumFilter_IonMobilityFilteringDisabled_EnableSpectralLibrary" xml:space="preserve">
+    <value>Note: the spectral library has ion mobility values for "{0}", but they are being ignored because "Use spectral library ion mobility values when present" is not enabled. To apply ion mobility filtering, open Settings &gt; Transition Settings &gt; Ion Mobility and enable that option.</value>
+  </data>
+  <data name="SpectrumFilter_IonMobilityFilteringDisabled_SetWindow" xml:space="preserve">
+    <value>Note: ion mobility values are available for "{0}", but no effective filter window is configured. To apply ion mobility filtering, open Settings &gt; Transition Settings &gt; Ion Mobility and set a window type (resolving power, fixed width, or linear range) with a non-zero value.</value>
+  </data>
+  <data name="SpectrumFilter_IonMobilityFilteringDisabled_SetWindowAndEnableSpectralLibrary" xml:space="preserve">
+    <value>Note: the spectral library has ion mobility values for "{0}", but ion mobility filtering is disabled. To apply filtering, open Settings &gt; Transition Settings &gt; Ion Mobility, set a window type (resolving power, fixed width, or linear range) with a value, and enable "Use spectral library ion mobility values when present".</value>
+  </data>
   <data name="TransitionBinner_BinData_" xml:space="preserve">
     <value>Imported spectrum appears to be missing m/z or intensity values ({0} != {1})</value>
   </data>

pwiz_tools/Skyline/Model/Results/SpectrumFilter.cs

@@ -141,23 +141,19 @@ public SpectrumFilter(SrmDocument document, MsDataFileUri msDataFileUri, IFilter
             // TIC and Base peak are meaningless with FAIMS, where we can't know the actual overall ion counts -also can't reliably share times with any ion mobility scheme
             if (instrumentInfo != null && instrumentInfo.IonMobilityUnits != eIonMobilityUnits.none)
             {
-                if ((libraryIonMobilityInfo != null && !libraryIonMobilityInfo.IsEmpty) || _isWatersSonar)
+                _isIonMobilityFiltered = WouldApplyIonMobilityFiltering(
+                    document.Settings, libraryIonMobilityInfo, moleculesThisPass, ionMobilityMax);
+
+                // Issue 4150: if filtering would not apply under current settings, probe simple
+                // settings variations to see whether a specific setting change would enable it,
+                // and warn the user about the specific change. When a retention time predictor
+                // is in use, SpectrumFilter is constructed twice for the same file (first pass
+                // sees only first-pass peptides, second pass sees all molecules) - skip the
+                // first pass so the warning fires only once and with the complete molecule set.
+                if (!_isIonMobilityFiltered && (retentionTimePredictor == null || !firstPass))
                 {
-                    _isIonMobilityFiltered = true;
-                }
-                else
-                {
-                    foreach (var pair in moleculesThisPass.SelectMany(
-                        node => node.TransitionGroups.Select(nodeGroup => new PeptidePrecursorPair(node, nodeGroup))))
-                    {
-                        var ionMobility = document.Settings.GetIonMobilityFilter(
-                            pair.NodePep, pair.NodeGroup, null, libraryIonMobilityInfo, _ionMobilityFunctionsProvider, ionMobilityMax);
-                        _isIonMobilityFiltered = ionMobility.HasIonMobilityValue;
-                        if (_isIonMobilityFiltered)
-                        {
-                            break;
-                        }
-                    }
+                    WarnIfSettingsChangeWouldEnableFiltering(
+                        document.Settings, libraryIonMobilityInfo, moleculesThisPass, msDataFileUri, ionMobilityMax);
                 }
             }
 
@@ -490,6 +486,128 @@ public SpectrumFilter(SrmDocument document, MsDataFileUri msDataFileUri, IFilter
             InitIonMobilityAndRTLimits();
         }
 
+        // Representative window used solely to probe "would enabling a filter window turn
+        // filtering on for this data?" - value is arbitrary, just needs to be non-empty.
+        private const double PROBE_RESOLVING_POWER = 50;
+
+        /// <summary>
+        /// Returns true if ion mobility filtering would actually produce a filter for at least
+        /// one precursor in the document under the given settings. Used both to set
+        /// <see cref="_isIonMobilityFiltered"/> from real settings and to probe hypothetical
+        /// settings variations when diagnosing a "filtering disabled" warning (issue 4150).
+        /// </summary>
+        private bool WouldApplyIonMobilityFiltering(SrmSettings settings,
+            LibraryIonMobilityInfo libraryIonMobilityInfo,
+            IList<PeptideDocNode> molecules, double ionMobilityMax)
+        {
+            // Waters SONAR maps mz bins to IM; the "filter" is always derived from the mz filter.
+            if (_isWatersSonar)
+            {
+                return true;
+            }
+
+            foreach (var pair in molecules.SelectMany(
+                node => node.TransitionGroups.Select(nodeGroup => new PeptidePrecursorPair(node, nodeGroup))))
+            {
+                var ionMobility = settings.GetIonMobilityFilter(
+                    pair.NodePep, pair.NodeGroup, null, libraryIonMobilityInfo, _ionMobilityFunctionsProvider, ionMobilityMax);
+                if (ionMobility != null && ionMobility.HasIonMobilityValue)
+                {
+                    return true;
+                }
+            }
+            return false;
+        }
+
+        // Issue 4150: with current settings no precursor produces an ion mobility filter. Probe
+        // the obvious setting variations (add a window width, enable spectral-library IM, both)
+        // to see whether a specific change would enable filtering. If one would, emit a
+        // non-blocking notice that tells the user exactly which setting to flip. Spectral-library
+        // IM info is settings-invariant so can be reused across probes.
+        private void WarnIfSettingsChangeWouldEnableFiltering(SrmSettings settings,
+            LibraryIonMobilityInfo libraryIonMobilityInfo,
+            IList<PeptideDocNode> molecules, MsDataFileUri msDataFileUri, double ionMobilityMax)
+        {
+            bool WouldWith(SrmSettings probe) =>
+                WouldApplyIonMobilityFiltering(probe, libraryIonMobilityInfo, molecules, ionMobilityMax);
+
+            // Skip probes that can't change the outcome: if a setting is already on, the
+            // corresponding "With..." variation is a no-op, and since base filtering is already
+            // false that probe would also be false. When both are on, no setting change can
+            // enable filtering, so there's no actionable warning.
+            var imFiltering = settings.TransitionSettings.IonMobilityFiltering;
+            var existingCalc = imFiltering?.FilterWindowWidthCalculator;
+            bool hasWindow = HasUsableWindow(existingCalc);
+            bool hasSpectralLib = imFiltering?.UseSpectralLibraryIonMobilityValues ?? false;
+            if (hasWindow && hasSpectralLib)
+            {
+                return;
+            }
+
+            // Prefer the user's existing window if one is both selected and usable - probing with
+            // their real values keeps the "would this change fix it?" test faithful instead of
+            // substituting an arbitrary resolving power. Fall back to a default probe if no
+            // window type is set OR the selected type has a zero-valued primary field
+            // (e.g., fixed_width=0, linear_range widths both 0), which would produce a
+            // zero-width filter and make the probe a silent no-op.
+            var probeWindow = hasWindow
+                ? existingCalc
+                : new IonMobilityWindowWidthCalculator(PROBE_RESOLVING_POWER);
+            SrmSettings WithWindow(SrmSettings s) => s.ChangeTransitionSettings(
+                s.TransitionSettings.ChangeIonMobilityFiltering(
+                    s.TransitionSettings.IonMobilityFiltering.ChangeFilterWindowWidthCalculator(probeWindow)));
+            SrmSettings WithSpectralLib(SrmSettings s) => s.ChangeTransitionSettings(
+                s.TransitionSettings.ChangeIonMobilityFiltering(
+                    s.TransitionSettings.IonMobilityFiltering.ChangeUseSpectralLibraryIonMobilityValues(true)));
+
+            string message = null;
+            if (!hasWindow && WouldWith(WithWindow(settings)))
+            {
+                // Window alone is enough: IMSDB or explicit IM is present.
+                message = ResultsResources.SpectrumFilter_IonMobilityFilteringDisabled_SetWindow;
+            }
+            else if (!hasSpectralLib && WouldWith(WithSpectralLib(settings)))
+            {
+                // Enabling spectral-lib IM alone is enough: window is already configured.
+                message = ResultsResources.SpectrumFilter_IonMobilityFilteringDisabled_EnableSpectralLibrary;
+            }
+            else if (!hasWindow && !hasSpectralLib && WouldWith(WithSpectralLib(WithWindow(settings))))
+            {
+                // Need both: no IMSDB or explicit IM, but spectral-lib IM is usable once enabled and a window is set.
+                message = ResultsResources.SpectrumFilter_IonMobilityFilteringDisabled_SetWindowAndEnableSpectralLibrary;
+            }
+            // else: no setting change would enable filtering, so there's no actionable warning.
+
+            if (message != null)
+            {
+                var fileName = msDataFileUri?.GetFileName() ?? string.Empty;
+                Messages.WriteAsyncUserMessage(message, fileName);
+            }
+        }
+
+        // A calculator is "usable" as a probe only if its active mode has a non-zero primary
+        // field. A mode-selected-but-all-zero calculator produces a zero-width filter that makes
+        // the WithWindow probe a silent no-op, which would incorrectly suppress the warning.
+        private static bool HasUsableWindow(IonMobilityWindowWidthCalculator calc)
+        {
+            if (calc == null)
+            {
+                return false;
+            }
+            switch (calc.WindowWidthMode)
+            {
+                case IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.resolving_power:
+                    return calc.ResolvingPower > 0;
+                case IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.fixed_width:
+                    return calc.FixedWindowWidth > 0;
+                case IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.linear_range:
+                    return calc.PeakWidthAtIonMobilityValueZero > 0 ||
+                           calc.PeakWidthAtIonMobilityValueMax > 0;
+                default:
+                    return false;
+            }
+        }
+
         public bool ProvidesCollisionalCrossSectionConverter { get { return _ionMobilityFunctionsProvider != null;  } }
 
         public eIonMobilityUnits IonMobilityUnits

pwiz_tools/Skyline/TestFunctional/CrosslinkImsTest.cs

@@ -18,8 +18,11 @@
  */
 using System.Linq;
 using Microsoft.VisualStudio.TestTools.UnitTesting;
+using pwiz.Skyline.Controls;
 using pwiz.Skyline.Model;
+using pwiz.Skyline.Model.DocSettings;
 using pwiz.Skyline.Model.Lib;
+using pwiz.Skyline.Model.Results;
 using pwiz.Skyline.SettingsUI;
 using pwiz.Skyline.SettingsUI.IonMobility;
 using pwiz.SkylineTestUtil;
@@ -98,6 +101,39 @@ protected override void DoTest()
                 ionMobilityLibraryDlg.OkDialog();
             });
             OkDialog(transitionSettingsUi, transitionSettingsUi.OkDialog);
+
+            VerifyIonMobilityFilteringDisabledWarning();
+        }
+
+        // Issue 4150: when re-importing data while the IM filter window is disabled but IM values
+        // remain available (here from the IMSDB created earlier in this test), Skyline should
+        // emit a non-blocking informational message to the Immediate Window naming the specific
+        // fix - in this case, setting a filter window width.
+        private void VerifyIonMobilityFilteringDisabledWarning()
+        {
+            const string fileName = "CrosslinkImsTest.mzML";
+
+            RunUI(() => SkylineWindow.ModifyDocument("Disable IM filtering window", doc =>
+                doc.ChangeSettings(doc.Settings.ChangeTransitionSettings(
+                    doc.Settings.TransitionSettings.ChangeIonMobilityFiltering(
+                        doc.Settings.TransitionSettings.IonMobilityFiltering.ChangeFilterWindowWidthCalculator(
+                            IonMobilityWindowWidthCalculator.EMPTY))))));
+            RunUI(() => SkylineWindow.ModifyDocument("Remove results",
+                doc => doc.ChangeMeasuredResults(null)));
+            // Save so the existing .skyd is rewritten and re-import doesn't trigger a confirmation dialog
+            RunUI(() => SkylineWindow.SaveDocument());
+
+            ImportResultsFile(TestFilesDir.GetTestPath(fileName));
+
+            TryWaitForOpenForm<ImmediateWindow>();
+            var immediateWindow = FindOpenForm<ImmediateWindow>();
+            Assert.IsNotNull(immediateWindow, @"Immediate window should be shown");
+
+            // The IMSDB is populated at this point, so setting a filter window alone would enable
+            // filtering. The diagnostic should pick the SetWindow-specific message, not a generic one.
+            var expected = string.Format(
+                ResultsResources.SpectrumFilter_IonMobilityFilteringDisabled_SetWindow, fileName);
+            RunUI(() => StringAssert.Contains(immediateWindow.TextContent, expected));
         }
     }
 }