MsPathFinderT result reading

mzLib/Chemistry/ChemicalFormula.cs

@@ -19,9 +19,11 @@
 using MzLibUtil;
 using System;
 using System.Collections.Generic;
+using System.ComponentModel.DataAnnotations.Schema;
 using System.Globalization;
 using System.Linq;
 using System.Text;
+using System.Text.Json.Serialization;
 using System.Text.RegularExpressions;
 
 namespace Chemistry
@@ -65,7 +67,7 @@ public ChemicalFormula(IHasChemicalFormula capFormula)
             Elements = new Dictionary<Element, int>(capFormula.ThisChemicalFormula.Elements);
         }
 
-        public ChemicalFormula ThisChemicalFormula => this;
+        [JsonIgnore] public ChemicalFormula ThisChemicalFormula => this;
 
         /// <summary>
         /// Gets the average mass of this chemical formula

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];
+        }
+    }
+}

mzLib/Readers/ExternalResults/IndividualResultRecords/MsFraggerPsm.cs

@@ -0,0 +1,159 @@
+using System;
+using System.Collections.Generic;
+using System.Globalization;
+using System.Linq;
+using System.Runtime.InteropServices;
+using System.Text;
+using System.Threading.Tasks;
+using System.Xml.Linq;
+using CsvHelper.Configuration;
+using CsvHelper.Configuration.Attributes;
+using MassSpectrometry;
+using Omics.Modifications;
+using Proteomics.AminoAcidPolymer;
+using Proteomics;
+using static System.Net.Mime.MediaTypeNames;
+using ThermoFisher.CommonCore.Data.Interfaces;
+
+namespace Readers
+{
+    public class MsFraggerPsm
+    {
+        public static CsvConfiguration CsvConfiguration = new CsvConfiguration(CultureInfo.InvariantCulture)
+        {
+            Delimiter = "\t",
+            HasHeaderRecord = true,
+            IgnoreBlankLines = true,
+            TrimOptions = TrimOptions.Trim,
+            BadDataFound = null,
+        };
+
+        #region MsFragger Fields
+
+        [Name("Spectrum")]
+        public string Spectrum { get; set; }
+
+        [Name("Spectrum File")]
+        public string SpectrumFilePath { get; set; }
+
+        [Name("Peptide")]
+        public string BaseSequence { get; set; }
+
+        [Name("Modified Peptide")]
+        public string FullSequence { get; set; }
+
+        [Name("Extended Peptide")]
+        public string ExtendedSequence { get; set; }
+
+        [Name("Prev AA")]
+        public char PreviousAminoAcid { get; set; }
+
+        [Name("Next AA")]
+        public char NextAminoAcid { get; set; }
+
+        [Name("Peptide Length")]
+        public int PeptideLength { get; set; }
+
+        [Name("Charge")]
+        public int Charge { get; set; }
+
+        [Name("Retention")]
+        public double RetentionTime { get; set; }
+
+        [Name("Observed Mass")]
+        public double ObservedMass { get; set; }
+
+        [Name("Calibrated Observed Mass")]
+        public double CalibratedObservedMass { get; set; }
+
+        [Name("Observed M/Z")]
+        public double ObservedMz { get; set; }
+
+        [Name("Calibrated Observed M/Z")]
+        public double CalibratedObservedMz { get; set; }
+
+        [Name("Calculated Peptide Mass")]
+        public double CalculatedPeptideMass { get; set; }
+
+        [Name("Calculated M/Z")]
+        public double CalculatedMz { get; set; }
+
+        [Name("Delta Mass")]
+        public double DeltaMass { get; set; }
+
+        [Name("Expectation")]
+        public double Expectation { get; set; }
+
+        [Name("Hyperscore")]
+        public double HyperScore { get; set; }
+
+        [Name("Nextscore")]
+        public double NextScore { get; set; }
+
+        [Name("PeptideProphet Probability")]
+        public double PeptideProphetProbability { get; set; }
+
+        [Name("Number of Enzymatic Termini")]
+        public int NumberOfEnzymaticTermini { get; set; }
+
+        [Name("Number of Missed Cleavages")]
+        public int NumberOfMissedCleavages { get; set; }
+
+        [Name("Protein Start")]
+        public int ProteinStart { get; set; }
+
+        [Name("Protein End")]
+        public int ProteinEnd { get; set; }
+
+        [Name("Intensity")]
+        public double Intensity { get; set; }
+
+        [Name("Assigned Modifications")]
+        public string AssignedModifications { get; set; }
+
+        [Name("Observed Modifications")]
+        public string ObservedModifications { get; set; }
+
+        [Name("Purity")]
+        public double Purity { get; set; }
+
+        [Name("Is Unique")]
+        public bool IsUnique { get; set; }
+
+        [Name("Protein")]
+        public string Protein { get; set; }
+
+        [Name("Protein ID")]
+        public string ProteinAccession { get; set; }
+
+        [Name("Entry Name")]
+        public string EntryName { get; set; }
+
+        [Name("Gene")]
+        public string Gene { get; set; }
+
+        [Name("Protein Description")]
+        public string ProteinDescription { get; set; }
+
+        [Name("Mapped Genes")]
+        public string MappedGenes { get; set; }
+
+        [Name("Mapped Proteins")]
+        public string MappedProteins { get; set; }
+
+        #endregion
+
+        #region Interpreted Fields
+
+        [Ignore] private string _fileNameWithoutExtension;
+        [Ignore] public string FileNameWithoutExtension =>
+            _fileNameWithoutExtension ??= Spectrum.Split('.')[0];
+
+        [Ignore] private int? _oneBasedScanNumber;
+
+        [Ignore]
+        public int OneBasedScanNumber => _oneBasedScanNumber ??= int.Parse(Spectrum.Split('.')[1]);
+
+        #endregion
+    }
+}