Add "Library Retention Times" column to the Document Grid

pwiz_tools/Skyline/Controls/Databinding/SkylineViewContext.cs

@@ -493,6 +493,8 @@ public static ViewInfo GetDefaultViewInfo(ColumnDescriptor columnDescriptor)
                     columnsToRemove.Add(PropertyPath.Root.Property("NormalizationMethod"));
                     columnsToRemove.Add(PropertyPath.Root.Property(nameof(Model.Databinding.Entities.Peptide.AutoSelectPrecursors)));
                     columnsToRemove.Add(PropertyPath.Root.Property(nameof(Model.Databinding.Entities.Peptide.AttributeGroupId)));
+                    columnsToRemove.Add(
+                        PropertyPath.Root.Property(nameof(Model.Databinding.Entities.Peptide.LibraryRetentionTimes)));
                     columnsToRemove.Add(PropertyPath.Root.Property(nameof(Model.Databinding.Entities.Peptide.SurrogateExternalStandard)));
                     foreach (var prop in MoleculeAccessionNumbers.PREFERRED_ACCESSION_TYPE_ORDER)
                         columnsToRemove.Add(PropertyPath.Root.Property(prop)); // By default don't show CAS, InChI etc

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

@@ -606,6 +606,9 @@
   <data name="LibraryRank">
     <value>Library Rank</value>
   </data>
+  <data name="LibraryRetentionTimes">
+    <value>Library Retention Times</value>
+  </data>
   <data name="LibraryScore1">
     <value>Library Score1</value>
   </data>
@@ -669,6 +672,9 @@
   <data name="MaxHeight">
     <value>Max Height</value>
   </data>
+  <data name="MaxLibraryRetentionTime">
+    <value>Max Library Retention Time</value>
+  </data>
   <data name="MaxRetentionTime">
     <value>Max Retention Time</value>
   </data>
@@ -690,6 +696,9 @@
   <data name="MeanFwhm">
     <value>Mean Fwhm</value>
   </data>
+  <data name="MeanLibraryRetentionTime">
+    <value>Mean Library Retention Time</value>
+  </data>
   <data name="MeanMaxFwhm">
     <value>Mean Max Fwhm</value>
   </data>
@@ -732,6 +741,9 @@
   <data name="MinFoldChange">
     <value>Min Fold Change</value>
   </data>
+  <data name="MinLibraryRetentionTime">
+    <value>Min Library Retention Time</value>
+  </data>
   <data name="MinRetentionTime">
     <value>Min Retention Time</value>
   </data>

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

@@ -635,6 +635,9 @@ spectrum is associated with the precursor ion.</value>
     <value>The rank based on LibraryIntensity of this transition among all transitions
 allowed by the transition Filter settings, shown in the user interface as “(rank #)”.</value>
   </data>
+  <data name="LibraryRetentionTimes">
+    <value>Comma separated list of the retention times for the peptide or molecule found in any spectral library.</value>
+  </data>
   <data name="LibraryScore1">
     <value>Raw peptide library score that may or may not be used to rank among
 precursors of a protein.</value>
@@ -707,6 +710,9 @@ precursor.</value>
   <data name="MaxHeight">
     <value>Max Height</value>
   </data>
+  <data name="MaxLibraryRetentionTime">
+    <value>Maximum retention time for the peptide or molecule found in any spectral library</value>
+  </data>
   <data name="MaxRetentionTime">
     <value>Maximum of the transition RetentionTime values.</value>
   </data>
@@ -728,6 +734,9 @@ precursor.</value>
   <data name="MeanFwhm">
     <value>Mean of the transition Fwhm (peak width) values.</value>
   </data>
+  <data name="MeanLibraryRetentionTime">
+    <value>Average of the retention times for the peptide or molecule found in any spectral library</value>
+  </data>
   <data name="MeanMaxFwhm">
     <value>Mean of the precursor MaxFwhm (peak width) values.</value>
   </data>
@@ -773,6 +782,9 @@ If there are no internal standard peak areas, then the median transition peak ar
   <data name="MinFoldChange">
     <value>The lower bound of the confidence interval of the fold change.</value>
   </data>
+  <data name="MinLibraryRetentionTime">
+    <value>Minimum retention time for the peptide or molecule found in any spectral library</value>
+  </data>
   <data name="MinRetentionTime">
     <value>Minimum of the transition RetentionTime values.</value>
   </data>

pwiz_tools/Skyline/Model/Databinding/Entities/Peptide.cs

@@ -384,6 +384,16 @@ public override string ToString()
             return DocNode.GetCrosslinkedSequence();
         }
 
+        [Format(Formats.RETENTION_TIME)]
+        [ChildDisplayName("{0}LibraryRetentionTime")]
+        public RetentionTimeValues LibraryRetentionTimes
+        {
+            get
+            {
+                return RetentionTimeValues.ForTimes(SrmDocument.Settings.GetUnalignedRetentionTimes(DocNode.Target, DocNode.ExplicitMods).Distinct());
+            }
+        }
+
         [InvariantDisplayName("PeptideDocumentLocation")]
         [Obsolete]
         public DocumentLocation DocumentLocation

pwiz_tools/Skyline/Model/Databinding/Entities/RetentionTimeValues.cs

@@ -0,0 +1,80 @@
+/*
+ * Original author: Nicholas Shulman <nicksh .at. u.washington.edu>,
+ *                  MacCoss Lab, Department of Genome Sciences, UW
+ *
+ * Copyright 2023 University of Washington - Seattle, WA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using pwiz.Common.Collections;
+using pwiz.Common.DataBinding.Attributes;
+using pwiz.Skyline.Model.Hibernate;
+using pwiz.Skyline.Util;
+
+namespace pwiz.Skyline.Model.Databinding.Entities
+{
+    /// <summary>
+    /// Formattable list of retention time values which also has "Min", "Max" and "Mean" sub-properties.
+    /// Suitable for displaying a list of retention times in the Document Grid.
+    /// </summary>
+    public class RetentionTimeValues : IFormattable
+    {
+        private ImmutableList<double> _times;
+        private RetentionTimeValues(ImmutableList<double> times)
+        {
+            _times = times;
+        }
+
+        public static RetentionTimeValues ForTimes(IEnumerable<double> times)
+        {
+            var list = ImmutableList.ValueOf(times.OrderBy(t => t));
+            if (list.Count == 0)
+            {
+                return null;
+            }
+
+            return new RetentionTimeValues(list);
+        }
+
+        [Format(Formats.RETENTION_TIME)]
+        public double Min
+        {
+            get { return _times[0]; }
+        }
+
+        [Format(Formats.RETENTION_TIME)]
+        public double Max
+        {
+            get { return _times[_times.Count - 1]; }
+        }
+
+        [Format(Formats.RETENTION_TIME)]
+        public double Mean
+        {
+            get { return _times.Average(); }
+        }
+
+        public string ToString(string format, IFormatProvider formatProvider)
+        {
+            return new FormattableList<double>(_times).ToString(format, formatProvider);
+        }
+
+        public override string ToString()
+        {
+            return new FormattableList<double>(_times).ToString();
+        }
+    }
+}

pwiz_tools/Skyline/Skyline.csproj

@@ -519,6 +519,7 @@
     </Compile>
     <Compile Include="Model\Databinding\Collections\FixedSkylineObjectList.cs" />
     <Compile Include="Model\Databinding\Entities\CalibrationCurveMetrics.cs" />
+	<Compile Include="Model\Databinding\Entities\RetentionTimeValues.cs" />
     <Compile Include="Model\Databinding\Entities\ColumnCaptions.Designer.cs">
       <AutoGen>True</AutoGen>
       <DesignTime>True</DesignTime>