Merge branch 'master' into GetModificationMethod

mzLib/MassSpectrometry/Deconvolution/Algorithms/ClassicDeconvolutionAlgorithm.cs

@@ -1,20 +1,17 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
 using Chemistry;
-using Easy.Common.Extensions;
 using MathNet.Numerics.Statistics;
 using MzLibUtil;
 
 namespace MassSpectrometry
 {
-    public class ClassicDeconvolutionAlgorithm : DeconvolutionAlgorithm
+    internal class ClassicDeconvolutionAlgorithm : DeconvolutionAlgorithm
     {
         private MzSpectrum spectrum;
 
-        public ClassicDeconvolutionAlgorithm(DeconvolutionParameters deconParameters) : base(deconParameters)
+        internal ClassicDeconvolutionAlgorithm(DeconvolutionParameters deconParameters) : base(deconParameters)
         {
 
         }
@@ -25,7 +22,7 @@ public ClassicDeconvolutionAlgorithm(DeconvolutionParameters deconParameters) :
         /// <param name="spectrumToDeconvolute">spectrum to deconvolute</param>
         /// <param name="range">Range of peaks to deconvolute</param>
         /// <returns></returns>
-        public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrumToDeconvolute, MzRange range)
+        internal override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrumToDeconvolute, MzRange range)
         {
             var deconParams = DeconvolutionParameters as ClassicDeconvolutionParameters ?? throw new MzLibException("Deconvolution params and algorithm do not match");
             spectrum = spectrumToDeconvolute;
@@ -205,7 +202,7 @@ private IsotopicEnvelope FindIsotopicEnvelope(int massIndex, double candidateFor
                 }
             }
 
-            return new IsotopicEnvelope(listOfObservedPeaks, monoisotopicMass, chargeState, totalIntensity, Statistics.StandardDeviation(listOfRatios), massIndex);
+            return new IsotopicEnvelope(listOfObservedPeaks, monoisotopicMass, chargeState, totalIntensity, listOfRatios.StandardDeviation());
         }
 
         private int ObserveAdjacentChargeStates(IsotopicEnvelope originalEnvelope, double mostIntensePeakMz, int massIndex, double deconvolutionTolerancePpm, double intensityRatioLimit, double minChargeToLookFor, double maxChargeToLookFor, List<double> monoisotopicMassPredictions)

mzLib/MassSpectrometry/Deconvolution/Algorithms/DeconvolutionAlgorithm.cs

@@ -8,6 +8,9 @@
 
 namespace MassSpectrometry
 {
+    /// <summary>
+    /// Parent class defining minimum requirement to be used <see cref="Deconvoluter"/> 
+    /// </summary>
     public abstract class DeconvolutionAlgorithm
     {
         // For ClassicDeconv. If not used elsewhere, move to that class
@@ -79,6 +82,6 @@ protected DeconvolutionAlgorithm(DeconvolutionParameters deconParameters)
         /// <param name="spectrum">spectrum to be deconvoluted</param>
         /// <param name="range">Range of peaks to deconvolute</param>
         /// <returns></returns>
-        public abstract IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum, MzRange range);
+        internal abstract IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum, MzRange range);
     }
 }

mzLib/MassSpectrometry/Deconvolution/Algorithms/ExampleNewDeconvolutionAlgorithmTemplate.cs

@@ -1,22 +1,19 @@
 using System;
 using System.Collections.Generic;
 using System.Diagnostics.CodeAnalysis;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
 using MzLibUtil;
 
 namespace MassSpectrometry
 {
     [ExcludeFromCodeCoverage]
-    public class ExampleNewDeconvolutionAlgorithmTemplate : DeconvolutionAlgorithm
+    internal class ExampleNewDeconvolutionAlgorithmTemplate : DeconvolutionAlgorithm
     {
-        public ExampleNewDeconvolutionAlgorithmTemplate(DeconvolutionParameters deconParameters) : base(deconParameters)
+        internal ExampleNewDeconvolutionAlgorithmTemplate(DeconvolutionParameters deconParameters) : base(deconParameters)
         {
 
         }
 
-        public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum, MzRange range = null)
+        internal override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum, MzRange range = null)
         {
             var deconParams = DeconvolutionParameters as ExampleNewDeconvolutionParametersTemplate ?? throw new MzLibException("Deconvolution params and algorithm do not match");
             range ??= spectrum.Range;

mzLib/MassSpectrometry/Deconvolution/Deconvoluter.cs

@@ -1,10 +1,5 @@
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
-using Easy.Common.Extensions;
-using Easy.Common.Interfaces;
+using System.Collections.Generic;
+using Chemistry;
 using MzLibUtil;
 
 namespace MassSpectrometry
@@ -30,27 +25,11 @@ public static class Deconvoluter
         public static IEnumerable<IsotopicEnvelope> Deconvolute(MsDataScan scan,
             DeconvolutionParameters deconvolutionParameters, MzRange rangeToGetPeaksFrom = null)
         {
-            rangeToGetPeaksFrom ??= scan.MassSpectrum.Range;
+            // set any specific deconvolution parameters found only in the MsDataScan
 
-            // set deconvolution algorithm and any specific deconvolution parameters found in the MsDataScan
-            DeconvolutionAlgorithm deconAlgorithm;
-            switch (deconvolutionParameters.DeconvolutionType)
-            {
-                case DeconvolutionType.ClassicDeconvolution:
-                    deconAlgorithm = new ClassicDeconvolutionAlgorithm(deconvolutionParameters);
-                    break;
-
-                case DeconvolutionType.ExampleNewDeconvolutionTemplate:
-                    deconAlgorithm = new ExampleNewDeconvolutionAlgorithmTemplate(deconvolutionParameters);
-                    break;
-
-                default: throw new MzLibException("DeconvolutionType not yet supported");
-            }
-
-            return deconAlgorithm.Deconvolute(scan.MassSpectrum, rangeToGetPeaksFrom);
+            foreach (var isotopicEnvelope in Deconvolute(scan.MassSpectrum, deconvolutionParameters, rangeToGetPeaksFrom)) 
+                yield return isotopicEnvelope;
         }
-
-
 
         /// <summary>
         /// Static deconvolution of an MzSpectrum that does not require Deconvoluter construction
@@ -79,7 +58,22 @@ public static IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum,
                 default: throw new MzLibException("DeconvolutionType not yet supported");
             }
 
-            return deconAlgorithm.Deconvolute(spectrum, rangeToGetPeaksFrom);
+            // Short circuit deconvolution if it is called on a neutral mass spectrum
+            if (spectrum is NeutralMassSpectrum newt)
+            {
+                for (int i = 0; i < newt.XArray.Length; i++)
+                {
+                    // skip this peak if it's outside the range of interest (e.g. if we're only interested in deconvoluting a small m/z range)
+                    if (!rangeToGetPeaksFrom.Contains(newt.XArray[i].ToMz(newt.Charges[i])))
+                        continue; 
+                    yield return new IsotopicEnvelope(newt.XArray[i], newt.YArray[i], newt.Charges[i]);
+                }
+            }
+            else
+            {
+                foreach (var isotopicEnvelope in deconAlgorithm.Deconvolute(spectrum, rangeToGetPeaksFrom)) 
+                    yield return isotopicEnvelope;
+            }
         }
     }
 }

mzLib/MassSpectrometry/MassSpectrometry.csproj

@@ -20,4 +20,8 @@
     <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj" />
   </ItemGroup>
 
+	<ItemGroup>
+		<InternalsVisibleTo Include="Development" />
+		<InternalsVisibleTo Include="Test" />
+	</ItemGroup>
 </Project>

mzLib/MassSpectrometry/MsDataFile.cs

@@ -23,9 +23,6 @@
 
 namespace MassSpectrometry
 {
-    // TODO: Define scope of class 
-    // Class scope is to provide to the data loaded from the DataFile. 
-
     /// <summary>
     /// A class for interacting with data collected from a Mass Spectrometer, and stored in a file
     /// </summary>

mzLib/MassSpectrometry/MzSpectra/IsotopicEnvelope.cs

@@ -14,40 +14,47 @@ public class IsotopicEnvelope : IHasMass
         /// <summary>
         /// Mass of most abundant observed isotopic peak, not accounting for addition or subtraction or protons due to ESI charge state induction
         /// </summary>
-        public double MostAbundantObservedIsotopicMass { get; private set; }
+        internal double MostAbundantObservedIsotopicMass { get; private set; }
         public readonly int Charge;
         public readonly double TotalIntensity;
-        public readonly double StDev;
-        public readonly int MassIndex;
 
         public double Score { get; private set; }
 
-        public IsotopicEnvelope(List<(double mz, double intensity)> bestListOfPeaks, double bestMonoisotopicMass, int bestChargeState, double bestTotalIntensity, double bestStDev, int bestMassIndex)
+        /// <summary>
+        /// Used for an isotopic envelope that mzLib deconvoluted (e.g., from a mass spectrum)
+        /// </summary>
+        public IsotopicEnvelope(List<(double mz, double intensity)> bestListOfPeaks, double bestMonoisotopicMass, int bestChargeState, double bestTotalIntensity, double bestStDev)
         {
             Peaks = bestListOfPeaks;
             MonoisotopicMass = bestMonoisotopicMass;
-            MostAbundantObservedIsotopicMass = GetMostAbundantObservedIsotopicMass(bestListOfPeaks, bestChargeState);
+            MostAbundantObservedIsotopicMass = bestListOfPeaks.MaxBy(p => p.intensity).mz * Math.Abs(bestChargeState);
             Charge = bestChargeState;
             TotalIntensity = bestTotalIntensity;
-            StDev = bestStDev;
-            MassIndex = bestMassIndex;
-            Score = ScoreIsotopeEnvelope();
+            Score = ScoreIsotopeEnvelope(bestStDev);
         }
 
-        public double GetMostAbundantObservedIsotopicMass(List<(double mz, double intensity)> peaks, int charge)
+        /// <summary>
+        /// Used for a neutral mass read in from a deconvoluted file
+        /// Assumes the mass is correct: score is max value
+        /// </summary>
+        public IsotopicEnvelope(double monoisotopicMass, double intensity, int charge)
         {
-            return peaks.MaxBy(p => p.intensity).mz * Math.Abs(charge);
+            MonoisotopicMass = monoisotopicMass;
+            Charge = charge;
+            TotalIntensity = intensity;
+            Score = double.MaxValue;
+            Peaks = [(monoisotopicMass.ToMz(charge), intensity)];
         }
 
         public override string ToString()
         {
             return Charge + "\t" + Peaks[0].mz.ToString("G8") + "\t" + Peaks.Count + "\t" + TotalIntensity;
         }
 
-        private double ScoreIsotopeEnvelope() //likely created by Stefan Solntsev using peptide data
+        private double ScoreIsotopeEnvelope(double stDev) //likely created by Stefan Solntsev using peptide data
         {
             return Peaks.Count >= 2 ?
-                TotalIntensity / Math.Pow(StDev, 0.13) * Math.Pow(Peaks.Count, 0.4) / Math.Pow(Math.Abs(Charge), 0.06) :
+                TotalIntensity / Math.Pow(stDev, 0.13) * Math.Pow(Peaks.Count, 0.4) / Math.Pow(Math.Abs(Charge), 0.06) :
                 0;
         }
 
@@ -60,6 +67,5 @@ public void SetMedianMonoisotopicMass(List<double> monoisotopicMassPredictions)
         {
             MonoisotopicMass = monoisotopicMassPredictions.Median();
         }
-
     }
 }

mzLib/MassSpectrometry/MzSpectra/MzSpectrum.cs

@@ -22,10 +22,8 @@
 using System;
 using System.Collections;
 using System.Collections.Generic;
-using System.Diagnostics;
 using System.IO;
 using System.Linq;
-using System.Text.Json;
 
 namespace MassSpectrometry
 {
@@ -126,7 +124,7 @@ public MzRange Range
             }
         }
 
-        public double? FirstX
+        public virtual double? FirstX
         {
             get
             {
@@ -138,7 +136,7 @@ public double? FirstX
             }
         }
 
-        public double? LastX
+        public virtual double? LastX
         {
             get
             {
@@ -373,7 +371,7 @@ public IsotopicEnvelope FindIsotopicEnvelope(int massIndex, double candidateForM
                 }
             }
 
-            return new IsotopicEnvelope(listOfObservedPeaks, monoisotopicMass, chargeState, totalIntensity, Statistics.StandardDeviation(listOfRatios), massIndex);
+            return new IsotopicEnvelope(listOfObservedPeaks, monoisotopicMass, chargeState, totalIntensity, listOfRatios.StandardDeviation());
         }
 
         [Obsolete("Deconvolution Has been moved to the Deconvoluter Object")]
@@ -796,7 +794,12 @@ private MzPeak GetPeak(int index)
             return peakList[index];
         }
 
-        private MzPeak GeneratePeak(int index)
+        /// <summary>
+        /// The source of all peaks which populate the peakList
+        /// </summary>
+        /// <param name="index"></param>
+        /// <returns></returns>
+        protected virtual MzPeak GeneratePeak(int index)
         {
             return new MzPeak(XArray[index], YArray[index]);
         }

mzLib/MassSpectrometry/MzSpectra/NeutralMassSpectrum.cs

@@ -0,0 +1,65 @@
+using System;
+using Chemistry;
+
+namespace MassSpectrometry
+{
+    public class NeutralMassSpectrum : MzSpectrum
+    {
+        public int[] Charges { get; init; }
+        public NeutralMassSpectrum(double[,] monoisotopicMassesIntensities, int[] charges) : base(monoisotopicMassesIntensities)
+        {
+            if (monoisotopicMassesIntensities.GetLength(0) != charges.Length)
+                throw new ArgumentException("The lengths of monoisotopicMasses, intensities, and charges must be the same.");
+
+            Charges = charges;
+
+            double minMz = double.MaxValue;
+            double maxMz = double.MinValue;
+            for (int i = 0; i < monoisotopicMassesIntensities.GetLength(0); i++)
+            {
+                var mz = monoisotopicMassesIntensities[i,0].ToMz(charges[i]);
+                if (mz < minMz)
+                    minMz = mz;
+                if (mz > maxMz)
+                    maxMz = mz;
+            }
+
+            FirstX = minMz;
+            LastX = maxMz;
+        }
+
+        public NeutralMassSpectrum(double[] monoisotopicMasses, double[] intensities, int[] charges, bool shouldCopy)
+            : base(monoisotopicMasses, intensities, shouldCopy)
+        {
+            if (monoisotopicMasses.GetLength(0) != intensities.Length || monoisotopicMasses.Length != charges.Length)
+                throw new ArgumentException("The lengths of monoisotopicMasses, intensities, and charges must be the same.");
+
+            Charges = charges;
+
+            double minMz = double.MaxValue;
+            double maxMz = double.MinValue;
+            for (int i = 0; i < monoisotopicMasses.Length; i++)
+            {
+                var mz = monoisotopicMasses[i].ToMz(charges[i]);
+                if (mz < minMz)
+                    minMz = mz;
+                if (mz > maxMz)
+                    maxMz = mz;
+            }
+
+            FirstX = minMz;
+            LastX = maxMz;
+        }
+
+        public override double? FirstX { get; } // in m/z
+        public override double? LastX { get; } // in m/z
+
+        /// <summary>
+        /// Converts to a charged spectrum
+        /// </summary>
+        protected override MzPeak GeneratePeak(int index)
+        {
+            return new MzPeak(XArray[index].ToMz(Charges[index]), YArray[index]);
+        }
+    }
+}

mzLib/SpectralAveraging/Algorithms/SpectraFileAveraging.cs

@@ -54,7 +54,7 @@ private static MsDataScan[] AverageAll(IReadOnlyCollection<MsDataScan> scans, Sp
         // create output
         MsDataScan averagedScan = new(averagedSpectrum, 1, representativeScan.OneBasedScanNumber,
             representativeScan.IsCentroid, representativeScan.Polarity, scans.Select(p => p.RetentionTime).Average(),
-            averagedSpectrum.Range, null, representativeScan.MzAnalyzer, scans.Select(p => p.TotalIonCurrent).Average(),
+            averagedSpectrum.Range, representativeScan.ScanFilter, representativeScan.MzAnalyzer, scans.Select(p => p.TotalIonCurrent).Average(),
             representativeScan.InjectionTime, null, representativeScan.NativeId);
         MsDataScan[] msDataScans = { averagedScan };
         return msDataScans;
@@ -129,7 +129,8 @@ private static MsDataScan GetAveragedDataScanFromAveragedSpectrum(MzSpectrum ave
             centralScan.IsCentroid,
             centralScan.Polarity,
             centralScan.RetentionTime,
-            averagedSpectrum.Range, null,
+            averagedSpectrum.Range,
+            centralScan.ScanFilter,
             centralScan.MzAnalyzer,
             averagedSpectrum.SumOfAllY,
             centralScan.InjectionTime,