FlashDeconv reverse engineer

mzLib/Development/DeconvolutionDevelopment/StandardDeconvolutionTest.cs

@@ -1,5 +1,6 @@
 using System.Diagnostics.CodeAnalysis;
 using MassSpectrometry;
+using MassSpectrometry.Deconvolution.Parameters;
 using NUnit.Framework;
 using UsefulProteomicsDatabases;
 
@@ -47,13 +48,15 @@ static StandardDeconvolutionTest()
             List<DeconvolutionParameters> topDownDeconvolutionParametersToTest =
             [
                 new ClassicDeconvolutionParameters(1, 60, 4, 3),
-                new IsoDecDeconvolutionParameters()
+                new IsoDecDeconvolutionParameters(),
+                new FlashDeconvDeconvolutionParameters(1, 60, Polarity.Positive)
             ];
 
             List<DeconvolutionParameters> bottomUpDeconvolutionParametersToTest =
             [
                 new ClassicDeconvolutionParameters(1, 12, 4, 3),
-                new IsoDecDeconvolutionParameters()
+                new IsoDecDeconvolutionParameters(),
+                new FlashDeconvDeconvolutionParameters(1, 60, Polarity.Positive)
             ];
 
 

mzLib/Development/DeconvolutionDevelopment/TestCases/SinglePeakDeconvolutionTestCase.cs

@@ -1,4 +1,5 @@
 using MassSpectrometry;
+using MassSpectrometry.Deconvolution.Parameters;
 using MzLibUtil;
 using Readers;
 
@@ -34,8 +35,11 @@ public SinglePeakDeconvolutionTestCase(DeconvolutionParameters deconParameters,
                 .GetAllScansList()
                 .First(p => p.OneBasedScanNumber == scanNumber).MassSpectrum;
 
-            // 8.5 was selected as this is the magic number found in Classic Deconvolution
-            RangeToDeconvolute = new MzRange(selectedIonMz - 8.5, selectedIonMz + 8.5);
+            if (deconParameters is FlashDeconvDeconvolutionParameters)
+                RangeToDeconvolute = null!;
+            else
+                // 8.5 was selected as this is the magic number found in Classic Deconvolution
+                RangeToDeconvolute = new MzRange(selectedIonMz - 8.5, selectedIonMz + 8.5);
         }
 
         /// <summary>

mzLib/MassSpectrometry/Deconvolution/Deconvoluter.cs

@@ -1,5 +1,6 @@
 using System.Collections.Generic;
 using Chemistry;
+using MassSpectrometry.Deconvolution.Algorithms;
 using MzLibUtil;
 
 namespace MassSpectrometry
@@ -58,6 +59,7 @@ private static DeconvolutionAlgorithm CreateAlgorithm(DeconvolutionParameters pa
             {
                 DeconvolutionType.ClassicDeconvolution => new ClassicDeconvolutionAlgorithm(parameters),
                 DeconvolutionType.ExampleNewDeconvolutionTemplate => new ExampleNewDeconvolutionAlgorithmTemplate(parameters),
+                DeconvolutionType.FlashDeconv2 => new FlashDeconv2(parameters),
                 DeconvolutionType.IsoDecDeconvolution => new IsoDecAlgorithm(parameters),
                 _ => throw new MzLibException("DeconvolutionType not yet supported")
             };

mzLib/MassSpectrometry/Deconvolution/DeconvolutionType.cs

@@ -4,6 +4,7 @@ public enum DeconvolutionType
     {
         ClassicDeconvolution,
         ExampleNewDeconvolutionTemplate,
+        FlashDeconv2,
         IsoDecDeconvolution,
     }
 }

mzLib/MassSpectrometry/Deconvolution/Parameters/FlashDeconvDeconvolutionParameters.cs

@@ -0,0 +1,20 @@
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Runtime.InteropServices;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace MassSpectrometry.Deconvolution.Parameters
+{
+    internal class FlashDeconvDeconvolutionParameters : DeconvolutionParameters
+    {
+        public override DeconvolutionType DeconvolutionType { get; protected set; } = DeconvolutionType.FlashDeconv2;
+
+        public FlashDeconvDeconvolutionParameters(int minCharge, int maxCharge, Polarity polarity = Polarity.Positive)
+            : base(minCharge, maxCharge, polarity)
+        {
+
+        }
+    }
+}

mzLib/Test/DataFiles/4734.304mZchargeOneProteoformSpectrum.txt

@@ -0,0 +1,271 @@
+278.55257	5.82
+278.61156	14.79
+278.67052	20.59
+278.72946	20.46
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+278.90623	6.1
+278.96515	3.1
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+296.7757	0
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