Site-determining ion assistant for modification localization

pwiz_tools/Skyline/Controls/ControlsResources.resx

@@ -154,6 +154,12 @@
   <data name="MessageBoxHelper_ValidateNumberListTextBox__0__must_contain_a_comma_separated_list_of_integers_from__1__to__2__" xml:space="preserve">
     <value>{0} must contain a comma separated list of integers from {1} to {2}.</value>
   </data>
+  <data name="PopupPickList_SiteDetermining_NoneFound" xml:space="preserve">
+    <value>No ions uniquely localize this modification</value>
+  </data>
+  <data name="PopupPickList_SiteDetermining_ToolTip" xml:space="preserve">
+    <value>Show only ions that uniquely localize modifications</value>
+  </data>
   <data name="PopupPickList_UpdateAutoManageUI_Auto_select_filtered__0_" xml:space="preserve">
     <value>Auto-select filtered {0}</value>
   </data>

pwiz_tools/Skyline/Controls/PopupPickList.cs

@@ -45,6 +45,7 @@ public partial class PopupPickList : FormEx, ITipDisplayer
         private bool _closing;
         private bool _autoManageChildren;
         private bool _selectalInternalChange;
+        private bool _siteDeterminingOnly;
 
         private int _leftText;
 
@@ -99,6 +100,11 @@ public PopupPickList(IChildPicker picker, string childHeading, bool okOnDeactiva
             _autoManageChildren = _picker.AutoManageChildren;
             UpdateAutoManageUI();
 
+            // Show the site-determining ions toggle only for localizable peptides.
+            bool canSd = _picker is ISiteDeterminingIonPicker sd && sd.CanShowSiteDeterminingIons;
+            tbbSiteDetermining.Visible = canSd;
+            tbbSiteDetermining.ToolTipText = ControlsResources.PopupPickList_SiteDetermining_ToolTip;
+
             // Hide the synchronize checkbox, or set its label correctly
             string synchLabelText = _picker.SynchSiblingsLabel;
             if (string.IsNullOrEmpty(synchLabelText))
@@ -116,6 +122,13 @@ public PopupPickList(IChildPicker picker, string childHeading, bool okOnDeactiva
                 cbSynchronize.Text = synchLabelText;
                 cbSynchronize.Checked = _picker.IsSynchSiblings;
             }
+
+            // Overlay the empty-state hint on the choices list. Shown only when the
+            // site-determining filter is on but no ion uniquely localizes the modification.
+            lblSiteDeterminingEmpty.Text = ControlsResources.PopupPickList_SiteDetermining_NoneFound;
+            lblSiteDeterminingEmpty.Bounds = pickListMulti.Bounds;
+            lblSiteDeterminingEmpty.Anchor = pickListMulti.Anchor;
+            lblSiteDeterminingEmpty.BringToFront();
         }
 
         public IEnumerable<string> ItemNames
@@ -127,6 +140,54 @@ public IEnumerable<string> ItemNames
             }
         }
 
+        /// <summary>
+        /// Test support: the <see cref="DocNode"/> behind each currently visible choice, in
+        /// display order. Lets a test map a visible pick to its underlying identity (e.g. a
+        /// <see cref="Transition"/>) rather than relying on the (localized) label.
+        /// </summary>
+        public IEnumerable<DocNode> VisibleChoices
+        {
+            get
+            {
+                for (int i = 0; i < pickListMulti.Items.Count; i++)
+                    yield return GetVisibleChoice(i).Choice;
+            }
+        }
+
+        /// <summary>
+        /// Test support: toggles the "site-determining ions only" filter the same way the
+        /// <see cref="tbbSiteDetermining"/> toolbar button does.
+        /// </summary>
+        public bool SiteDeterminingFilter
+        {
+            get { return _siteDeterminingOnly; }
+            set
+            {
+                _siteDeterminingOnly = value;
+                if (tbbSiteDetermining.Visible)
+                    tbbSiteDetermining.Checked = value;
+                ShowChoices();
+            }
+        }
+
+        /// <summary>
+        /// Test support: whether the site-determining ions toggle button is showing (only for
+        /// localizable peptides).
+        /// </summary>
+        public bool SiteDeterminingButtonVisible
+        {
+            get { return tbbSiteDetermining.Visible; }
+        }
+
+        /// <summary>
+        /// Test support: whether the empty-state hint (shown when the site-determining filter
+        /// leaves no visible choices) is currently displayed.
+        /// </summary>
+        public bool SiteDeterminingEmptyHintVisible
+        {
+            get { return lblSiteDeterminingEmpty.Visible; }
+        }
+
         public Rectangle GetItemTextRectangle(int i)
         {
             var rect = pickListMulti.GetItemRectangle(i);
@@ -246,12 +307,20 @@ private void ShowChoices()
             for (int i = 0; i < _choices.Count; i++)
             {
                 var choice = _choices[i];
+                if (_siteDeterminingOnly && _picker is ISiteDeterminingIonPicker sd2 &&
+                    !sd2.IsSiteDeterminingChoice(choice.Choice))
+                    continue;
                 if (!textSearch.Visible || AcceptChoice(choice, searches))
                 {
                     pickListMulti.Items.Add(choice);
                 }
             }
             pickListMulti.EndUpdate();
+
+            // Show the empty-state hint when the site-determining filter is on and it left the
+            // choices list empty (no ion uniquely localizes the modification).
+            lblSiteDeterminingEmpty.Visible = _siteDeterminingOnly && pickListMulti.Items.Count == 0;
+
             UpdateSelectAll();
         }
 
@@ -362,6 +431,12 @@ private void tbbAutoManageChildren_Click(object sender, EventArgs e)
             ToggleAutoManageChildren();
         }
 
+        private void tbbSiteDetermining_Click(object sender, EventArgs e)
+        {
+            _siteDeterminingOnly = tbbSiteDetermining.Checked;
+            ShowChoices();
+        }
+
         public void ToggleAutoManageChildren()
         {
             AutoManageChildren = tbbAutoManageChildren.Checked;

pwiz_tools/Skyline/Controls/SeqNode/SrmTreeNode.cs

@@ -844,6 +844,33 @@ public interface IShowPicker
         bool Filtered { get; set; }
     }
 
+    /// <summary>
+    /// Optional capability a child picker may implement to expose a "site-determining
+    /// ions" filter in the <see cref="PopupPickList"/>, for peptides that carry an
+    /// ambiguous (localizable) modification.
+    /// </summary>
+    public interface ISiteDeterminingIonPicker
+    {
+        /// <summary>
+        /// True when the picker's peptide is localizable, so the site-determining
+        /// ions toggle should be offered.
+        /// </summary>
+        bool CanShowSiteDeterminingIons { get; }
+
+        /// <summary>
+        /// True when the given choice is a product ion that uniquely localizes the modification
+        /// (no other positional placement produces it). May match nothing when the placement is
+        /// unresolvable, in which case the filtered list is legitimately empty.
+        /// </summary>
+        bool IsSiteDeterminingChoice(DocNode choice);
+
+        /// <summary>
+        /// The resolved modification's name for the given choice, or null when the
+        /// choice is not site-determining.
+        /// </summary>
+        string GetSiteDeterminingTip(DocNode choice);
+    }
+
     /// <summary>
     /// Implement to support the <see cref="PopupPickList"/> user interface for
     /// picking children of a <see cref="SrmTreeNode"/>.

pwiz_tools/Skyline/Controls/SeqNode/TransitionGroupTreeNode.cs

@@ -29,6 +29,7 @@
 using pwiz.Skyline.Model.Databinding.Entities;
 using pwiz.Skyline.Model.DocSettings;
 using pwiz.Skyline.Model.Lib;
+using pwiz.Skyline.Model.Localization;
 using pwiz.Skyline.Model.Results.Spectra;
 using pwiz.Skyline.Properties;
 using pwiz.Skyline.Util;
@@ -37,8 +38,9 @@
 
 namespace pwiz.Skyline.Controls.SeqNode
 {
-    public class TransitionGroupTreeNode : SrmTreeNodeParent
+    public class TransitionGroupTreeNode : SrmTreeNodeParent, ISiteDeterminingIonPicker
     {
+        private SiteDeterminingIonAnalyzer _siteDeterminingAnalyzer;
         public static TransitionGroupTreeNode CreateInstance(SequenceTree tree, DocNode nodeDoc)
         {
             Debug.Assert(nodeDoc is TransitionGroupDocNode);
@@ -356,6 +358,53 @@ private bool IsSynchable()
 
         #endregion
 
+        #region ISiteDeterminingIonPicker Members
+
+        private SiteDeterminingIonAnalyzer SiteDeterminingAnalyzer
+        {
+            get
+            {
+                var nodePep = PepNode;
+                if (nodePep == null)
+                    return null;
+                return _siteDeterminingAnalyzer ??
+                       (_siteDeterminingAnalyzer = new SiteDeterminingIonAnalyzer(DocSettings, nodePep));
+            }
+        }
+
+        public bool CanShowSiteDeterminingIons
+        {
+            get
+            {
+                var analyzer = SiteDeterminingAnalyzer;
+                return analyzer != null && analyzer.CanLocalize;
+            }
+        }
+
+        /// <summary>
+        /// True when the given choice is an ion that <em>uniquely localizes</em> the modification,
+        /// i.e. no other positional placement produces it (producing-set size == 1). For placements
+        /// that cannot be resolved (e.g. the interior of a serine run) no ion is unique, so the
+        /// filtered list is legitimately empty.
+        /// </summary>
+        public bool IsSiteDeterminingChoice(DocNode choice)
+        {
+            var analyzer = SiteDeterminingAnalyzer;
+            return analyzer != null && choice.Id is Transition transition &&
+                   analyzer.IsUniqueToPrecursor(transition);
+        }
+
+        public string GetSiteDeterminingTip(DocNode choice)
+        {
+            var analyzer = SiteDeterminingAnalyzer;
+            if (analyzer == null || !(choice.Id is Transition transition))
+                return null;
+            var mod = analyzer.GetResolvedModification(transition);
+            return mod?.Name;
+        }
+
+        #endregion
+
         #region ITipProvider Members
 
         public override bool HasTip { get { return base.HasTip || !ShowAnnotationTipOnly; } }

pwiz_tools/Skyline/Model/Databinding/Entities/ColumnCaptions.resx

@@ -738,6 +738,9 @@
   <data name="LinearFit">
     <value>Linear Fit</value>
   </data>
+  <data name="LocalizationIsomerCount">
+    <value>Localization Isomer Count</value>
+  </data>
   <data name="Log2FoldChange">
     <value>Log 2 Fold Change</value>
   </data>
@@ -855,6 +858,9 @@
   <data name="ModelScore">
     <value>Model Score</value>
   </data>
+  <data name="ModificationLocalizationGroup">
+    <value>Modification Localization Group</value>
+  </data>
   <data name="ModifiedAreaProportion">
     <value>Modified Area Proportion</value>
   </data>