Refactor IsoDec classes and enhance parameters

Updated IsoDecAlgorithm to use generic DeconvolutionParameters.
Enhanced IsoDecDeconvolutionParameters with new properties.
Refactored constructor to use camelCase parameter names.
Removed unused using directives from IsoDecAlgorithm.cs.
Ensured correct casting in IsoDecAlgorithm.
Renamed Css_Threshold to CssThreshold for consistency.

mzLib/MassSpectrometry/Deconvolution/Algorithms/IsoDecAlgorithm.cs

@@ -2,18 +2,12 @@
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
-using System.Numerics;
 using System.Runtime.InteropServices;
-using System.Text;
-using System.Threading.Tasks;
-using MassSpectrometry.MzSpectra;
 using MzLibUtil;
-using MathNet.Numerics.Statistics;
-using System.Reflection.Metadata.Ecma335;
 
 namespace MassSpectrometry
 {
-    public class IsoDecAlgorithm(IsoDecDeconvolutionParameters deconParameters)
+    public class IsoDecAlgorithm(DeconvolutionParameters deconParameters)
         : DeconvolutionAlgorithm(deconParameters)
     {
         private static string _phaseModelPath;
@@ -96,7 +90,7 @@ public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum, M
                 .ToArray();
 
             IntPtr matchedPeaksPtr = Marshal.AllocHGlobal(Marshal.SizeOf(typeof(MatchedPeak)) * intensities.Length);
-            IsoSettings settings = DeconParametersToIsoSettings(deconParameters);
+            IsoSettings settings = DeconParametersToIsoSettings(DeconvolutionParameters as IsoDecDeconvolutionParameters);
             int result = process_spectrum(mzs, intensities, intensities.Length, _phaseModelPath , matchedPeaksPtr, settings);
             if(result > 0)
             {
@@ -105,7 +99,7 @@ public override IEnumerable<IsotopicEnvelope> Deconvolute(MzSpectrum spectrum, M
                 {
                     matchedpeaks[i] = Marshal.PtrToStructure<MatchedPeak>(matchedPeaksPtr + i * Marshal.SizeOf(typeof(MatchedPeak)));
                 }
-                return ConvertToIsotopicEnvelopes(deconParameters, matchedpeaks, spectrum);
+                return ConvertToIsotopicEnvelopes(DeconvolutionParameters as IsoDecDeconvolutionParameters, matchedpeaks, spectrum);
             }
 
             else return new List<IsotopicEnvelope>();

mzLib/MassSpectrometry/Deconvolution/Parameters/IsoDecDeconvolutionParameters.cs

@@ -9,50 +9,134 @@ namespace MassSpectrometry
     public class IsoDecDeconvolutionParameters : DeconvolutionParameters
     {
         public override DeconvolutionType DeconvolutionType { get; protected set; } = DeconvolutionType.IsoDecDeconvolution;
+
+        /// <summary>
+        /// Precision of encoding matrix
+        /// </summary>
         public int PhaseRes { get; protected set; } = 8;
+
+        /// <summary>
+        /// Verbose output
+        /// </summary>
         public int Verbose { get; protected set; } = 0;
+
+        /// <summary>
+        /// Peak Detection Window
+        /// </summary>
         public int PeakWindow { get; protected set; } = 80;
+
+        /// <summary>
+        /// Peak Detection Threshold
+        /// </summary>
         public float PeakThreshold { get; protected set; } = (float)0.0001;
+
+        /// <summary>
+        /// Minimum Peaks for an allowed peak
+        /// </summary>
         public int MinPeaks { get; protected set; } = 3;
-        public float Css_Threshold { get; set; } = (float)0.7;
+
+        /// <summary>
+        /// Minimum cosine similarity score for isotope distribution
+        /// </summary>
+        public float CssThreshold { get; set; } = (float)0.7;
+
+        /// <summary>
+        /// Match Tolerance for peak detection in ppm
+        /// </summary>
         public float MatchTolerance { get; set; } = (float)5;
+
+        /// <summary>
+        /// Maximum shift allowed for isotope distribution
+        /// </summary>
         public int MaxShift { get; protected set; } = 3;
+
+        /// <summary>
+        /// MZ Window for isotope distribution
+        /// </summary>
         public float[] MzWindow { get; set; } = new float[] { (float)-1.05, (float)2.05 };
+
+        /// <summary>
+        /// Plus One Intensity range. Will be used for charge state 1
+        /// </summary>
         public float[] PlusOneIntWindow { get; protected set; } = new float[] { (float)0.1, (float)0.6 };
+
+        /// <summary>
+        /// Number of knockdown rounds
+        /// </summary>
         public int KnockdownRounds { get; set; } = 5;
+
+        /// <summary>
+        /// Minimum score difference for isotope distribution to allow missed monoisotopic peaks
+        /// </summary>
         public float MinScoreDiff { get; set; } = (float)0.1;
+
+        /// <summary>
+        /// Minimum area covered by isotope distribution. Use in or with css_thresh
+        /// </summary>
         public float MinAreaCovered { get; set; } = (float)0.15;
+
+        /// <summary>
+        /// Isotope Distribution Length
+        /// </summary>
         public int IsoLength { get; protected set; } = 64;
+
+        /// <summary>
+        /// Mass difference between isotopes
+        /// </summary>
         public double MassDiffC { get; protected set; } = 1.0033;
+
+        /// <summary>
+        /// Adduct Mass
+        /// </summary>
         public float AdductMass { get; set; } = (float)1.00727276467;
+
+        /// <summary>
+        /// Use set the -1 isotope as 0 to help force better alignments
+        /// </summary>
         public int MinusOneAreasZero { get; set; } = 1;
+
+        /// <summary>
+        /// Threshold for isotope distribution. Will remove relative intensities below this.
+        /// </summary>
         public float IsotopeThreshold { get; set; } = (float)0.01;
+
+        /// <summary>
+        /// Threshold for data. Will remove relative intensities below this relative to max intensity in each cluster
+        /// </summary>
         public float DataThreshold { get; set; } = (float)0.05;
+
+        /// <summary>
+        /// Ratio above which a secondary charge state prediction will be returned.
+        /// </summary>
         public float ZScoreThreshold { get; protected set; } = (float)0.95;
+
+        /// <summary>
+        /// Report multiple monoisotopic peaks
+        /// </summary>
         public bool ReportMulitpleMonoisos { get; set; } = true;
 
         public IsoDecDeconvolutionParameters(
-            int phaseres = 8,
-            bool reportmultiplemonoisos = true,
-            float css_threshold = (float)0.7, 
-            float match_tolerance = (float)5, 
-            int maxshift = 3, 
-            float[] mzwindow = null, 
-            int knockdown_rounds = 5, 
-            float min_area_covered = (float)0.20, 
+            int phaseRes = 8,
+            bool reportMultipleMonoisos = true,
+            float cssThreshold = (float)0.7,
+            float matchTolerance = (float)5,
+            int maxShift = 3,
+            float[] mzWindow = null,
+            int knockdownRounds = 5,
+            float minAreaCovered = (float)0.20,
             float relativedatathreshold = (float)0.05)
-            : base(1,50,Polarity.Positive)
+            : base(1, 50, Polarity.Positive)
         {
-            this.PhaseRes = phaseres;
-            this.ReportMulitpleMonoisos = reportmultiplemonoisos;
-            this.Css_Threshold = css_threshold;
-            this.MatchTolerance = match_tolerance;
-            this.MaxShift = maxshift;
-            if (mzwindow != null)
-                this.MzWindow = mzwindow;
+            this.PhaseRes = phaseRes;
+            this.ReportMulitpleMonoisos = reportMultipleMonoisos;
+            this.CssThreshold = cssThreshold;
+            this.MatchTolerance = matchTolerance;
+            this.MaxShift = maxShift;
+            if (mzWindow != null)
+                this.MzWindow = mzWindow;
             else this.MzWindow = new float[] { (float)-1.05, (float)2.05 };
-            this.KnockdownRounds = knockdown_rounds;
-            this.MinAreaCovered = min_area_covered;
+            this.KnockdownRounds = knockdownRounds;
+            this.MinAreaCovered = minAreaCovered;
         }
     }
 }