adder intralink support

smith-chem-wisc · Oct 23, 2024 · 351e9f0 · 351e9f0
1 parent f24ddef
commit 351e9f0
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Showing 7 changed files with 24 additions and 3 deletions.
diff --git a/mzLib/Readers/Readers.csproj b/mzLib/Readers/Readers.csproj
@@ -17,6 +17,7 @@
 	<ItemGroup>
 		<ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj" />
 		<ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj" />
+		<ProjectReference Include="..\Transcriptomics\Transcriptomics.csproj" />
 		<ProjectReference Include="..\UsefulProteomicsDatabases\UsefulProteomicsDatabases.csproj" />
 	</ItemGroup>
 

diff --git a/mzLib/Readers/SearchResults/SpectrumMatchTsvReader.cs b/mzLib/Readers/SearchResults/SpectrumMatchTsvReader.cs
@@ -54,10 +54,12 @@ public static List<SpectrumMatchFromTsv> ReadTsv(string filePath, out List<strin
                     switch (filePath.ParseFileType())
                     {
                         case SupportedFileType.psmtsv:
+                        case SupportedFileType.IntralinkResults:
                             psms.Add(new PsmFromTsv(line, Split, parsedHeader));
                             break;
-
-                        // TODO: Create an osmtsv case when transcriptomics is merged
+                        //case SupportedFileType.osmtsv:
+                        //    psms.Add(new OsmFromTsv(line, Split, parsedHeader));
+                        //    break;
 
                         default:
                             throw new ArgumentOutOfRangeException();

diff --git a/mzLib/Readers/Util/SupportedFileTypes.cs b/mzLib/Readers/Util/SupportedFileTypes.cs
@@ -14,7 +14,8 @@ public enum SupportedFileType
         Mgf,
         BrukerD,
         psmtsv,
-        //osmtsv
+        IntralinkResults,
+        //osmtsv,
         ToppicPrsm,
         ToppicPrsmSingle,
         ToppicProteoform,
@@ -51,6 +52,7 @@ public static string GetFileExtension(this SupportedFileType type)
                 SupportedFileType.Mgf => ".mgf",
                 SupportedFileType.BrukerD => ".d",
                 SupportedFileType.psmtsv => ".psmtsv",
+                SupportedFileType.IntralinkResults => "Intralinks.tsv",
                 //SupportedFileType.osmtsv => ".osmtsv",
                 SupportedFileType.ToppicPrsm => "_prsm.tsv",
                 SupportedFileType.ToppicPrsmSingle => "_prsm_single.tsv",
@@ -116,6 +118,8 @@ public static SupportedFileType ParseFileType(this string filePath)
                         return SupportedFileType.MsPathFinderTDecoys;
                     if (filePath.EndsWith(SupportedFileType.MsPathFinderTAllResults.GetFileExtension(), StringComparison.InvariantCultureIgnoreCase))
                         return SupportedFileType.MsPathFinderTAllResults;
+                    if (filePath.EndsWith(SupportedFileType.IntralinkResults.GetFileExtension(), StringComparison.InvariantCultureIgnoreCase))
+                        return SupportedFileType.IntralinkResults;
 
                     // these tsv cases are just .tsv and need an extra step to determine the type
                     // currently need to distinguish between FlashDeconvTsv and MsFraggerPsm

diff --git a/mzLib/Test/FileReadingTests/SearchResults/XL_Intralinks.tsv b/mzLib/Test/FileReadingTests/SearchResults/XL_Intralinks.tsv
diff --git a/mzLib/Test/FileReadingTests/TestPsmFromTsv.cs b/mzLib/Test/FileReadingTests/TestPsmFromTsv.cs
@@ -22,6 +22,8 @@ public static class TestPsmFromTsv
         [TestCase("oglycoSinglePsms.psmtsv", 2)] // oglyco
         [TestCase("nglyco_f5.psmtsv", 5)] // nglyco
         [TestCase("VariantCrossTest.psmtsv", 15)] // variant crossing
+        [TestCase("XL_Intralinks.tsv", 6)] // variant crossing
+        [TestCase("XLink.psmtsv", 19)] // variant crossing
         public static void TestPsmReaderWithMultipleEntryPoints(string path, int expected)
         {
             string psmFilePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"FileReadingTests\SearchResults",

diff --git a/mzLib/Test/FileReadingTests/TestSupportedFileExtensions.cs b/mzLib/Test/FileReadingTests/TestSupportedFileExtensions.cs
@@ -37,6 +37,8 @@ internal class TestSupportedFileExtensions
         [TestCase(@"FileReadingTests\ExternalFileTypes\MsPathFinderT_DecoyResults_IcDecoy.tsv", SupportedFileType.MsPathFinderTDecoys)]
         [TestCase(@"FileReadingTests\ExternalFileTypes\MsPathFinderT_AllResults_IcTda.tsv", SupportedFileType.MsPathFinderTAllResults)]
         [TestCase(@"FileReadingTests\ExternalFileTypes\crux.txt", SupportedFileType.CruxResult)]
+        [TestCase(@"FileReadingTests\ExternalFileTypes\XL_Intralinks.tsv", SupportedFileType.IntralinkResults)]
+        [TestCase(@"FileReadingTests\ExternalFileTypes\XLink.psmtsv", SupportedFileType.psmtsv)]
         public static void TestSupportedFileTypeExtensions(string filePath, SupportedFileType expectedType)
         {
             var supportedType = filePath.ParseFileType();

diff --git a/mzLib/Test/Test.csproj b/mzLib/Test/Test.csproj
@@ -447,6 +447,9 @@
     <None Update="FileReadingTests\SearchResults\XLink.psmtsv">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>
+    <None Update="FileReadingTests\SearchResults\XL_Intralinks.tsv">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
     <None Update="ModificationTests\CommonArtifacts.txt">
       <CopyToOutputDirectory>Always</CopyToOutputDirectory>
     </None>