Fix alignment-light matrix quant access

tests/MSDIAL5/MsdialCoreTestApp/MsdialCoreTestApp.csproj

@@ -29,6 +29,10 @@
     <PackageReference Include="System.CommandLine" Version="2.0.8" />
   </ItemGroup>
 
+  <ItemGroup>
+    <InternalsVisibleTo Include="MsdialCoreTestAppTests" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\..\..\src\Common\CommonStandard\CommonStandard.csproj" />
     <ProjectReference Include="..\..\..\src\MSDIAL5\MsdialCore\MsdialCore.csproj" />

tests/MSDIAL5/MsdialCoreTestApp/Process/LcmsProcess.cs

@@ -301,10 +301,9 @@ IQuantValueAccessor CreateQuantAccessor(string exportType) => alignmentLightPeak
                 foreach (var (_, exportType, suffix) in requestedMatrices.Where(item => item.Requested)) {
                     var matrixFile = Path.Combine(matrixFolder, alignmentFile.FileName + suffix);
                     using (var matrixStream = File.Open(matrixFile, FileMode.Create, FileAccess.Write)) {
-                        new AlignmentCSVExporter().Export(
+                        ExportAlignmentMatrix(
                             matrixStream, result.AlignmentSpotProperties, align_decResults, files,
-                            new MulticlassFileMetaAccessor(0), align_accessor,
-                            new LegacyQuantValueAccessor(exportType, storage.Parameter), matrixStats);
+                            align_accessor, exportType, storage.Parameter, alignmentLightPeakStore, matrixStats);
                     }
                     Console.WriteLine($"{exportType} matrix: {matrixFile}");
                 }
@@ -412,6 +411,24 @@ private static void CollectAlignmentLightExportGarbage(bool isAlignmentLightMode
         GC.Collect(2, GCCollectionMode.Forced, blocking: true, compacting: true);
     }
 
+    internal static void ExportAlignmentMatrix(
+        Stream stream,
+        IReadOnlyList<AlignmentSpotProperty> spots,
+        IReadOnlyList<MSDecResult> msdecResults,
+        IReadOnlyList<AnalysisFileBean> files,
+        IMetadataAccessor metadataAccessor,
+        string exportType,
+        ParameterBase parameter,
+        AlignmentLightPeakStore? alignmentLightPeakStore,
+        IReadOnlyList<StatsValue> stats) {
+        IQuantValueAccessor quantAccessor = alignmentLightPeakStore is null
+            ? new LegacyQuantValueAccessor(exportType, parameter)
+            : new AlignmentLightQuantValueAccessor(exportType, parameter, alignmentLightPeakStore);
+        new AlignmentCSVExporter().Export(
+            stream, spots, msdecResults, files,
+            new MulticlassFileMetaAccessor(0), metadataAccessor, quantAccessor, stats);
+    }
+
     private static IEnumerable<MSDecResult> LoadRepresentativeDeconvolutions(IMsdialDataStorage<MsdialLcmsParameter> storage, IReadOnlyList<AlignmentSpotProperty>? spots) {
         var files = storage.AnalysisFiles;
 

tests/MSDIAL5/MsdialCoreTestAppTests/Process/LcmsProcessTests.cs

@@ -0,0 +1,89 @@
+using CompMs.App.MsdialConsole.Process;
+using CompMs.Common.Interfaces;
+using CompMs.MsdialCore.DataObj;
+using CompMs.MsdialCore.Export;
+using CompMs.MsdialCore.MSDec;
+using CompMs.MsdialCore.Parameter;
+using Microsoft.VisualStudio.TestTools.UnitTesting;
+using System;
+using System.Collections.Generic;
+using System.Collections.ObjectModel;
+using System.IO;
+
+namespace MsdialCoreTestAppTests.Process;
+
+[TestClass]
+public sealed class LcmsProcessTests
+{
+    [TestMethod]
+    public void LightModeHeightMatrixContainsAValueForEveryAnalysisFile()
+    {
+        var scratch = Path.Combine(Path.GetTempPath(), $"msdial-light-matrix-{Guid.NewGuid():N}");
+        Directory.CreateDirectory(scratch);
+        try {
+            var files = new[] {
+                new AnalysisFileBean {
+                    AnalysisFileId = 0,
+                    AnalysisFileName = "sample-a",
+                    AnalysisFileClass = "sample",
+                    AnalysisFileAnalyticalOrder = 1,
+                    AnalysisBatch = 1,
+                },
+                new AnalysisFileBean {
+                    AnalysisFileId = 1,
+                    AnalysisFileName = "sample-b",
+                    AnalysisFileClass = "sample",
+                    AnalysisFileAnalyticalOrder = 2,
+                    AnalysisBatch = 1,
+                },
+            };
+            using var store = AlignmentLightPeakStore.CreateTemp();
+            store.Initialize(1, files);
+            store.WriteSpotPeaks(0, [
+                new AlignmentChromPeakFeature { FileID = 0, FileName = "sample-a", PeakHeightTop = 125d },
+                new AlignmentChromPeakFeature { FileID = 1, FileName = "sample-b", PeakHeightTop = 250d },
+            ]);
+            var spot = new AlignmentSpotProperty { MasterAlignmentID = 0 };
+            var output = Path.Combine(scratch, "height.txt");
+            var parameter = new ParameterBase {
+                FileID_ClassName = new Dictionary<int, string> {
+                    [0] = "sample",
+                    [1] = "sample",
+                },
+            };
+
+            using (var stream = File.Create(output)) {
+                LcmsProcess.ExportAlignmentMatrix(
+                    stream,
+                    [spot],
+                    [new MSDecResult()],
+                    files,
+                    new MinimalMetadataAccessor(),
+                    "Height",
+                    parameter,
+                    store,
+                    [StatsValue.Average]);
+            }
+
+            var text = File.ReadAllText(output);
+            StringAssert.Contains(text, "sample-a\tsample-b");
+            StringAssert.Contains(text, "125\t250");
+        }
+        finally {
+            Directory.Delete(scratch, recursive: true);
+        }
+    }
+
+    private sealed class MinimalMetadataAccessor : IMetadataAccessor
+    {
+        public IReadOnlyDictionary<string, string> GetContent(AlignmentSpotProperty spot, IMSScanProperty msdec) {
+            return new ReadOnlyDictionary<string, string>(new Dictionary<string, string> {
+                ["ID"] = spot.MasterAlignmentID.ToString(),
+            });
+        }
+
+        public string[] GetHeaders() {
+            return ["ID"];
+        }
+    }
+}

tests/MSDIAL5/MsdialCoreTests/Export/AlignmentLightQuantValueAccessorTests.cs

@@ -0,0 +1,35 @@
+using CompMs.MsdialCore.DataObj;
+using CompMs.MsdialCore.Export;
+using CompMs.MsdialCore.Parameter;
+using Microsoft.VisualStudio.TestTools.UnitTesting;
+
+namespace CompMs.MsdialCoreTests.Export;
+
+[TestClass]
+public class AlignmentLightQuantValueAccessorTests
+{
+    [TestMethod]
+    public void GetQuantValuesUsesFileBackedRowsWhenSpotDoesNotHoldPeakProperties()
+    {
+        var files = new[] {
+            new AnalysisFileBean { AnalysisFileId = 0, AnalysisFileName = "sample-a" },
+            new AnalysisFileBean { AnalysisFileId = 1, AnalysisFileName = "sample-b" },
+        };
+        using var store = AlignmentLightPeakStore.CreateTemp();
+        store.Initialize(1, files);
+        store.WriteSpotPeak(0, new AlignmentChromPeakFeature {
+            FileID = 1,
+            FileName = "sample-b",
+            PeakHeightTop = 1234d,
+        });
+        var spot = new AlignmentSpotProperty { MasterAlignmentID = 0 };
+        var accessor = new AlignmentLightQuantValueAccessor("Height", new ParameterBase(), store);
+
+        var headers = accessor.GetQuantHeaders(files);
+        var values = accessor.GetQuantValues(spot);
+
+        CollectionAssert.AreEqual(new[] { "sample-a", "sample-b" }, headers);
+        Assert.AreEqual("0", values["sample-a"]);
+        Assert.AreEqual("1234", values["sample-b"]);
+    }
+}