Set AlignmentChromPeakFeature quant mass in gap filling

src/MSDIAL5/MsdialGcMsApi/Algorithm/Alignment/GcmsGapFiller.cs

@@ -46,6 +46,7 @@ public void GapFill(Ms1Spectra ms1Spectra, RawSpectra rawSpectra, IReadOnlyList<
         var chromXCenter = GetCenter(spot, detected);
         var peakWidth = GetPeakWidth(detected);
         var peaklist = GetPeaks(rawSpectra, chromXCenter, peakWidth, fileID, _smoothingMethod, _smoothingLevel);
+        target.Mass = spot.QuantMass;
         GapFillCore(peaklist, chromXCenter, AxTol, target);
     }
 
@@ -58,6 +59,7 @@ public void UpdateQuantMass(RawSpectra rawSpectra, AlignmentSpotProperty spot, i
         var chromXCenter = GetCenter(spot, detected);
         var peakWidth = GetPeakWidth(detected);
         var peaklist = GetPeaks(rawSpectra, chromXCenter, peakWidth, fileID, _smoothingMethod, _smoothingLevel);
+        target.Mass = spot.QuantMass;
         GapFillCore(peaklist, chromXCenter, AxTol, target);
     }
 

tests/MSDIAL5/MsdialGcMsApiTests/Algorithm/Alignment/GcmsGapFillerTests.cs

@@ -0,0 +1,61 @@
+using CompMs.Common.Components;
+using CompMs.Common.Enum;
+using CompMs.MsdialCore.DataObj;
+using CompMs.MsdialGcMsApi.Parameter;
+using Microsoft.VisualStudio.TestTools.UnitTesting;
+using System.Collections.Generic;
+
+namespace CompMs.MsdialGcMsApi.Algorithm.Alignment.Tests {
+    [TestClass()]
+    public class GcmsGapFillerTests {
+        [TestMethod()]
+        public void UpdateQuantMassSetsTargetMassToSpotQuantMass() {
+            var filler = new StubGcmsGapFiller(new MsdialGcmsParameter());
+
+            var target = new AlignmentChromPeakFeature {
+                FileID = 0,
+                MasterPeakID = -1,
+                PeakID = -1,
+                Mass = 999d,
+            };
+            var detected = new AlignmentChromPeakFeature {
+                FileID = 1,
+                MasterPeakID = 1,
+                PeakID = 1,
+                ChromXsLeft = new ChromXs(0.9d, ChromXType.RT, ChromXUnit.Min),
+                ChromXsTop = new ChromXs(1.0d, ChromXType.RT, ChromXUnit.Min),
+                ChromXsRight = new ChromXs(1.1d, ChromXType.RT, ChromXUnit.Min),
+            };
+            var spot = new AlignmentSpotProperty {
+                QuantMass = 123.456d,
+                AlignedPeakProperties = new List<AlignmentChromPeakFeature> { target, detected },
+            };
+
+            filler.UpdateQuantMass(rawSpectra: null, spot, fileID: target.FileID);
+
+            Assert.AreEqual(spot.QuantMass, target.Mass);
+        }
+
+        private sealed class StubGcmsGapFiller : GcmsGapFiller {
+            public StubGcmsGapFiller(MsdialGcmsParameter parameter) : base(parameter) {
+            }
+
+            protected override double AxTol => 0.05d;
+
+            protected override ChromXs GetCenter(AlignmentSpotProperty spot, IEnumerable<AlignmentChromPeakFeature> peaks) {
+                return new ChromXs(1.0d, ChromXType.RT, ChromXUnit.Min) {
+                    Mz = new MzValue(spot.QuantMass),
+                    RI = new RetentionIndex(1000d),
+                };
+            }
+
+            protected override double GetPeakWidth(IEnumerable<AlignmentChromPeakFeature> peaks) {
+                return 0.1d;
+            }
+
+            protected override List<ChromatogramPeak> GetPeaks(RawSpectra rawSpectra, ChromXs center, double peakWidth, int fileID, SmoothingMethod smoothingMethod, int smoothingLevel) {
+                return new List<ChromatogramPeak>();
+            }
+        }
+    }
+}

tests/MSDIAL5/MsdialGcMsApiTests/MsdialGcMsApiTests.csproj

@@ -22,8 +22,4 @@
     <ProjectReference Include="..\..\..\src\MSDIAL5\MsdialGcMsApi\MsdialGcMsApi.csproj" />
   </ItemGroup>
 
-  <ItemGroup>
-    <Folder Include="Algorithm\Alignment\" />
-  </ItemGroup>
-
 </Project>