new header and xlink psmtsv reader unit tests

smith-chem-wisc · Nov 20, 2023 · 382c0da · 382c0da
1 parent 81f9338
commit 382c0da
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Showing 6 changed files with 2,852 additions and 5 deletions.
diff --git a/mzLib/Omics/SpectrumMatch/SpectrumMatchFromTsvHeader.cs b/mzLib/Omics/SpectrumMatch/SpectrumMatchFromTsvHeader.cs
@@ -49,7 +49,7 @@ public class SpectrumMatchFromTsvHeader
         public const string Contaminant = "Contaminant";
         public const string Decoy = "Decoy";
         public const string Description = "Description";
-        public const string StartAndEndResiduesInFullSequence = "Start and End Residues In Protein";
+        public const string StartAndEndResiduesInFullSequence = "Start and End Residues In Full Sequence";
         public const string PreviousResidue = "Previous Residue";
         public const string NextResidue = "Next Residue";
         public const string TheoreticalsSearched = "Theoreticals Searched";

diff --git a/mzLib/Test/FileReadingTests/SearchResults/NewHeader.psmtsv b/mzLib/Test/FileReadingTests/SearchResults/NewHeader.psmtsv
diff --git a/mzLib/Test/FileReadingTests/SearchResults/XLink.psmtsv b/mzLib/Test/FileReadingTests/SearchResults/XLink.psmtsv
diff --git a/mzLib/Test/FileReadingTests/TestPsmFromTsv.cs b/mzLib/Test/FileReadingTests/TestPsmFromTsv.cs
@@ -324,5 +324,32 @@ public static void TestPsmFiles(string fileLoadingType)
             Assert.That(loadedFile.FileType == SupportedFileType.psmtsv);
             Assert.Throws<NotImplementedException>(() => { loadedFile.WriteResults(""); });
         }
+
+        [Test]
+        public static void ReadPsmFromTsvWithNewHeaderTerms()
+        {
+            string psmTsvPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"FileReadingTests\SearchResults\NewHeader.psmtsv");
+            List<PsmFromTsv> psms = SpectrumMatchTsvReader.ReadPsmTsv(psmTsvPath, out var warnings);
+            Assert.That(warnings.Count == 2);
+
+            IResultFile loadedFile = null;
+            var file = FileReader.ReadFile<PsmFromTsvFile>(psmTsvPath);
+            file.LoadResults();
+            Assert.That(file.Results.Count == psms.Count);
+            loadedFile = file;
+        }
+
+        [Test]
+        public static void ReadXLinkPsmFromTsv()
+        {
+            string psmTsvPath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"FileReadingTests\SearchResults\XLink.psmtsv");
+            List<PsmFromTsv> psms = SpectrumMatchTsvReader.ReadPsmTsv(psmTsvPath, out var warnings);
+
+            IResultFile loadedFile = null;
+            var file = FileReader.ReadFile<PsmFromTsvFile>(psmTsvPath);
+            file.LoadResults();
+            Assert.That(file.Results.Count == psms.Count);
+            loadedFile = file;
+        }
     }
 }
diff --git a/mzLib/Test/FileReadingTests/TestSupportedFileExtensions.cs b/mzLib/Test/FileReadingTests/TestSupportedFileExtensions.cs
@@ -1,9 +1,5 @@
 using System;
-using System.Collections.Generic;
 using System.Diagnostics.CodeAnalysis;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
 using MzLibUtil;
 using NUnit.Framework;
 using Readers;

diff --git a/mzLib/Test/Test.csproj b/mzLib/Test/Test.csproj
@@ -385,6 +385,12 @@
     <None Update="DoubleProtease.tsv">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
+    <None Update="FileReadingTests\SearchResults\NewHeader.psmtsv">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+    <None Update="FileReadingTests\SearchResults\XLink.psmtsv">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
     <None Update="ModificationTests\CommonArtifacts.txt">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>