Merge remote-tracking branch 'upstream/master'

.github/workflows/dotnet.yml

@@ -25,15 +25,16 @@ jobs:
     - name: Build (TestFlashLFQ)
       run: cd mzLib && dotnet build --no-restore ./TestFlashLFQ/TestFlashLFQ.csproj
     - name: Add coverlet collector (Test)
-      run: cd mzLib && dotnet add Test/Test.csproj package coverlet.collector
+      run: cd mzLib && dotnet add Test/Test.csproj package coverlet.collector -v 6.0.0
     - name: Add coverlet collector (TestFlashLFQ)
-      run: cd mzLib && dotnet add TestFlashLFQ/TestFlashLFQ.csproj package coverlet.collector
+      run: cd mzLib && dotnet add TestFlashLFQ/TestFlashLFQ.csproj package coverlet.collector -v 6.0.0
     - name: Test
       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

mzLib/Omics/Digestion/DigestionProduct.cs

@@ -1,5 +1,6 @@
 using System;
 using System.Collections.Generic;
+using System.ComponentModel;
 using System.Linq;
 using System.Text;
 using System.Threading.Tasks;
@@ -28,9 +29,11 @@ protected DigestionProduct(IBioPolymer parent, int oneBasedStartResidue, int one
         public int OneBasedStartResidue { get; }// the residue number at which the peptide begins (the first residue in a protein is 1)
         public int OneBasedEndResidue { get; }// the residue number at which the peptide ends
         public int MissedCleavages { get; } // the number of missed cleavages this peptide has with respect to the digesting protease
-        public virtual char PreviousResidue => OneBasedStartResidue > 1 ? Parent[OneBasedStartResidue - 2] : '-';
 
-        public virtual char NextResidue => OneBasedEndResidue < Parent.Length ? Parent[OneBasedEndResidue] : '-';
+        public virtual char PreviousResidue => Parent is null ? '-' : OneBasedStartResidue > 1 ? Parent[OneBasedStartResidue - 2] : '-';
+
+        public virtual char NextResidue => Parent is null ? '-' : OneBasedEndResidue < Parent.Length ? Parent[OneBasedEndResidue] : '-';
+
         public string BaseSequence =>
             _baseSequence ??= Parent.BaseSequence.Substring(OneBasedStartResidue - 1,
                 OneBasedEndResidue - OneBasedStartResidue + 1);

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

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;
 

mzLib/Readers/ExternalResults/IndividualResultRecords/MsFraggerPeptide.cs

@@ -0,0 +1,95 @@
+using CsvHelper.Configuration.Attributes;
+using CsvHelper.Configuration;
+using System;
+using System.Collections.Generic;
+using System.Globalization;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using Easy.Common.Extensions;
+
+namespace Readers
+{
+    public class MsFraggerPeptide
+    {
+        public static CsvConfiguration CsvConfiguration = new CsvConfiguration(CultureInfo.InvariantCulture)
+        {
+            Delimiter = "\t",
+            HasHeaderRecord = true,
+            IgnoreBlankLines = true,
+            TrimOptions = TrimOptions.Trim,
+            BadDataFound = null,
+            MissingFieldFound = null,
+            HeaderValidated = null,
+        };
+
+        [Name("Peptide", "Sequence")] public string BaseSequence { get; set; }
+
+        [Name("Prev AA")] [Optional] public char PreviousAminoAcid { get; set; }
+
+        [Name("Next AA")] [Optional] public char NextAminoAcid { get; set; }
+
+        [Ignore] private int _peptideLength;
+
+        [Name("Peptide Length")]
+        [Optional]
+        public int PeptideLength
+        {
+            get => _peptideLength.IsDefault() ? BaseSequence.Length : _peptideLength;
+            set => _peptideLength = value;
+        }
+
+        [Name("Protein Start")] [Optional] public int OneBasedStartResidueInProtein { get; set; }
+
+        [Name("Protein End")] [Optional] public int OneBasedEndResidueInProtein { get; set; }
+
+        [Name("Charges", "Charge States")]
+        [TypeConverter(typeof(CommaDelimitedToIntegerArrayTypeConverter))]
+        public int[] Charge { get; set; }
+
+        [Name("Probability")] public double Probability { get; set; }
+
+        [Name("Spectral Count")] [Optional] public int SpectralCount { get; set; }
+
+        [Name("Intensity")] [Optional] public double Intensity { get; set; }
+
+        [Name("Assigned Modifications")]
+        [TypeConverter(typeof(CommaDelimitedToStringArrayTypeConverter))]
+        public string[] AssignedModifications { get; set; }
+
+        [Name("Observed Modifications")]
+        [Optional]
+        [TypeConverter(typeof(CommaDelimitedToStringArrayTypeConverter))]
+        public string[] ObservedModifications { get; set; }
+
+        [Name("Protein")] public string Protein { get; set; }
+
+        [Name("Protein ID")] [Optional] public string ProteinAccession { get; set; }
+
+        [Ignore] private string _proteinName;
+
+        [Name("Entry Name")]
+        [Optional]
+        public string ProteinName
+        {
+            get => _proteinName.IsDefault() ? Protein.Split('|').Last().Trim() : _proteinName;
+            set => _proteinName = value;
+        }
+
+        [Name("Gene")]
+        public string Gene { get; set; }
+
+        [Name("Protein Description")]
+        public string ProteinDescription { get; set; }
+
+        [Name("Mapped Genes")]
+        [Optional]
+        [TypeConverter(typeof(CommaDelimitedToStringArrayTypeConverter))]
+        public string[] MappedGenes { get; set; }
+
+        [Name("Mapped Proteins")]
+        [Optional]
+        [TypeConverter(typeof(CommaDelimitedToStringArrayTypeConverter))]
+        public string[] MappedProteins { get; set; }
+    }
+}

mzLib/Readers/ExternalResults/IndividualResultRecords/MsFraggerProtein.cs

@@ -0,0 +1,111 @@
+using CsvHelper.Configuration.Attributes;
+using CsvHelper.Configuration;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace Readers
+{
+    public class MsFraggerProtein
+    {
+        public static CsvConfiguration CsvConfiguration => new CsvConfiguration(System.Globalization.CultureInfo.InvariantCulture)
+        {
+            Delimiter = "\t",
+            HasHeaderRecord = true,
+            IgnoreBlankLines = true,
+            TrimOptions = TrimOptions.Trim,
+            BadDataFound = null,
+            MissingFieldFound = null,
+        };
+
+        [Name("Protein")]
+        public string Protein { get; set; }
+
+        [Name("Protein ID")]
+        public string Accession { get; set; }
+
+        [Name("Entry Name")]
+        public string AccessionOrganism { get; set; }
+
+        [Name("Gene")]
+        public string Gene { get; set; }
+
+        [Name("Length", "Protein Length")]
+        public int Length { get; set; }
+
+        [Name("Organism")]
+        public string Organism { get; set; }
+
+        [Name("Protein Description", "Description")]
+        public string Description { get; set; }
+
+        [Name("Protein Existence")]
+        public string ProteinExistence { get; set; }
+
+        [Name("Coverage")]
+        [Optional]
+        public double Coverage { get; set; }
+
+        [Name("Protein Probability")]
+        public double ProteinProbability { get; set; }
+
+        [Name("Top Peptide Probability")]
+        public double TopPeptideProbability { get; set; }
+
+        [Name("Total Peptides", "Combined Total Peptides")]
+        public int TotalPeptides { get; set; }
+
+        [Name("Unique Peptides")]
+        [Optional]
+        public int UniquePeptides { get; set; }
+
+        [Name("Razor Peptides")]
+        [Optional]
+        public int RazorPeptides { get; set; }
+
+        [Name("Total Spectral Count", "Combined Total Spectral Count")]
+        public int TotalSpectralCount { get; set; }
+
+        [Name("Unique Spectral Count", "Combined Unique Spectral Count")]
+        public int UniqueSpectralCount { get; set; }
+
+        [Name("Razor Spectral Count")]
+        [Optional]
+        public int RazorSpectralCount { get; set; }
+
+        [Name("Total Intensity")]
+        [Optional]
+        public double TotalIntensity { get; set; }
+
+        [Name("Unique Intensity")]
+        [Optional]
+        public double UniqueIntensity { get; set; }
+
+        [Name("Razor Intensity")]
+        [Optional]
+        public double RazorIntensity { get; set; }
+
+        [Name("Razor Assigned Modifications")]
+        [TypeConverter(typeof(CommaDelimitedToStringArrayTypeConverter))]
+        [Optional]
+        public string[] RazorAssignedModifications { get; set; }
+
+        [Name("Razor Observed Modifications")]
+        [Optional]
+        [TypeConverter(typeof(CommaDelimitedToStringArrayTypeConverter))]
+        public string[] RazorObservedModifications { get; set; }
+
+        [Name("Indistinguishable Proteins")]
+        [TypeConverter(typeof(CommaDelimitedToStringArrayTypeConverter))]
+        public string[] IndistinguishableProteins { get; set; }
+
+        public MsFraggerProtein()
+        {
+            RazorAssignedModifications = new string[0];
+            RazorObservedModifications = new string[0];
+            IndistinguishableProteins = new string[0];
+        }
+    }
+}