Merge branch 'MsPathFindertResultReading' of https://github.com/nboll…

…is/mzLib into MsPathFindertResultReading
smith-chem-wisc · May 7, 2024 · 30a8d34 · 30a8d34
2 parents 38a82dc + 2e0627c
commit 30a8d34
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Showing 9 changed files with 322 additions and 313 deletions.
diff --git a/.github/workflows/dotnet.yml b/.github/workflows/dotnet.yml
@@ -32,8 +32,9 @@ jobs:
       run: cd mzLib && dotnet test --no-build --verbosity normal --collect:"XPlat Code Coverage" /p:CoverletOutputFormat=cobertura ./Test/Test.csproj
     - name: TestFlashLFQ
       run: cd mzLib && dotnet test --no-build --verbosity normal --collect:"XPlat Code Coverage" /p:CoverletOutputFormat=cobertura ./TestFlashLFQ/TestFlashLFQ.csproj
-    - name: Codecov
-      uses: codecov/codecov-action@v2
-      with:
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         verbose: true
         files: mzLib/Test*/TestResults/*/coverage.cobertura.xml
diff --git a/mzLib/MassSpectrometry/MzSpectra/SpectralSimilarity.cs b/mzLib/MassSpectrometry/MzSpectra/SpectralSimilarity.cs
diff --git a/mzLib/Omics/SpectrumMatch/LibrarySpectrum.cs b/mzLib/Omics/SpectrumMatch/LibrarySpectrum.cs
@@ -50,9 +50,9 @@ public string CalculateSpectralAngleOnTheFly(List<MatchedFragmentIon> spectrumMa
                 spectrumMatchFragments.Select(f => f.Intensity).ToArray(),
                 MatchedFragmentIons.Select(f => f.Mz).ToArray(),
                 MatchedFragmentIons.Select(f => f.Intensity).ToArray(),
-                SpectralSimilarity.SpectrumNormalizationScheme.mostAbundantPeak,
+                SpectralSimilarity.SpectrumNormalizationScheme.MostAbundantPeak,
                 toleranceInPpm: 20,
-                allPeaks: true);
+                keepAllExperimentalPeaks: true);
             double? spectralContrastAngle = spectraComparison.SpectralContrastAngle();
 
             return spectralContrastAngle == null

diff --git a/mzLib/Proteomics/RetentionTimePrediction/SSRCalc3.cs b/mzLib/Proteomics/RetentionTimePrediction/SSRCalc3.cs
@@ -568,9 +568,11 @@ public double UnknownScore
             get { return 0; }
         }
 
-        public double ScoreSequence(PeptideWithSetModifications item)
+        public double ScoreSequence(PeptideWithSetModifications item) => ScoreSequence(item.BaseSequence);
+
+        public double ScoreSequence(string baseSequence)
         {
-            var seq = item.BaseSequence; //PTMs are not yet implemented
+            var seq = baseSequence; //PTMs are not yet implemented
             double tsum3 = 0.0;
             int i;
 

diff --git a/mzLib/Readers/Util/Software.cs b/mzLib/Readers/Util/Software.cs
@@ -1,5 +1,4 @@
-
-namespace Readers
+namespace Readers
 {
     public enum Software
     {

diff --git a/mzLib/Readers/Util/SupportedFileTypes.cs b/mzLib/Readers/Util/SupportedFileTypes.cs
@@ -85,7 +85,7 @@ public static SupportedFileType ParseFileType(this string filePath)
                         return SupportedFileType.Mzrt_TopFd;
                     throw new MzLibException("Csv file type not supported");
 
-                case ".tsv": 
+                case ".tsv":
                 {
                     // these tsv cases have a specialized ending before the .tsv
                     if (filePath.EndsWith(SupportedFileType.Ms1Tsv_FlashDeconv.GetFileExtension(), StringComparison.InvariantCultureIgnoreCase))

diff --git a/mzLib/Test/FileReadingTests/TestSupportedFileExtensions.cs b/mzLib/Test/FileReadingTests/TestSupportedFileExtensions.cs
@@ -35,7 +35,6 @@ internal class TestSupportedFileExtensions
         [TestCase(@"FileReadingTests\ExternalFileTypes\MsPathFinderT_TargetResults_IcTarget.tsv", SupportedFileType.MsPathFinderTTargets)]
         [TestCase(@"FileReadingTests\ExternalFileTypes\MsPathFinderT_DecoyResults_IcDecoy.tsv", SupportedFileType.MsPathFinderTDecoys)]
         [TestCase(@"FileReadingTests\ExternalFileTypes\MsPathFinderT_AllResults_IcTda.tsv", SupportedFileType.MsPathFinderTAllResults)]
-
         public static void TestSupportedFileTypeExtensions(string filePath, SupportedFileType expectedType)
         {
             var supportedType = filePath.ParseFileType();
@@ -91,7 +90,5 @@ public static void TestGetFileExtension_Errors()
             Assert.That(e?.Message,
                 Is.EqualTo($"File type not supported"));
         }
-
-
     }
 }
diff --git a/mzLib/Test/TestRetentionTimePrediction.cs b/mzLib/Test/TestRetentionTimePrediction.cs
@@ -657,6 +657,7 @@ public void SSRCalc3_100A_Test()
                 object obj = _peptides100A[i, 1];
                 double expected = (double)_peptides100A[i, 1];
                 double actual = calc.ScoreSequence(peptide);
+                double actualString = calc.ScoreSequence(peptide.BaseSequence);
 
                 // Round the returned value to match the values presented
                 // in the supporting information of the SSRCalc 3 publication.
@@ -665,11 +666,13 @@ public void SSRCalc3_100A_Test()
                 // instead of 12.81.  When diffed with 12.81 the result was
                 // 0.005000000000002558.
                 double actualRound = Math.Round((float)actual, 2);
+                double actualStringRound = Math.Round((float)actualString, 2);
 
                 // Extra conditional added to improve debugging of issues.
                 if (Math.Abs(expected - actual) > 0.005)
                 {
                     Assert.AreEqual(expected, actualRound, "Peptide {0}", peptide);
+                    Assert.AreEqual(expected, actualStringRound, "Peptide {0}", peptide);
                 }
             }
         }