Real OpenMS FLASHDeconv using exe from provided installation path

mzLib/MassSpectrometry/Deconvolution/Deconvoluter.cs

@@ -84,6 +84,7 @@ private static DeconvolutionAlgorithm CreateAlgorithm(DeconvolutionParameters pa
                 DeconvolutionType.ClassicDeconvolution => new ClassicDeconvolutionAlgorithm(parameters),
                 DeconvolutionType.ExampleNewDeconvolutionTemplate => new ExampleNewDeconvolutionAlgorithmTemplate(parameters),
                 DeconvolutionType.IsoDecDeconvolution => new IsoDecAlgorithm(parameters),
+                DeconvolutionType.RealFLASHDeconvolution => new RealFLASHDeconvolutionAlgorithm(parameters),
                 _ => throw new MzLibException("DeconvolutionType not yet supported")
             };
         }

mzLib/MassSpectrometry/Deconvolution/DeconvolutionType.cs

@@ -5,5 +5,6 @@ public enum DeconvolutionType
         ClassicDeconvolution,
         ExampleNewDeconvolutionTemplate,
         IsoDecDeconvolution,
+        RealFLASHDeconvolution    // Wraps the official FLASHDeconv.exe from OpenMS
     }
 }

mzLib/MassSpectrometry/Deconvolution/Parameters/RealFLASHDeconvolutionParameters.cs

@@ -0,0 +1,89 @@
+#nullable enable
+using System.IO;
+
+namespace MassSpectrometry
+{
+    /// <summary>
+    /// Parameters for <see cref="RealFLASHDeconvolutionAlgorithm"/>, which wraps
+    /// the official FLASHDeconv executable from OpenMS.
+    ///
+    /// The executable is located via:
+    ///   1. <see cref="FLASHDeconvExePath"/> (explicit, highest priority)
+    ///   2. Well-known OpenMS install paths checked at runtime
+    ///   3. System PATH
+    ///
+    /// In MetaMorpheus, set <c>GlobalSettings.FLASHDeconvExecutablePath</c> once
+    /// (persisted in GlobalSettings.toml) and leave <see cref="FLASHDeconvExePath"/>
+    /// null — the algorithm will use the global setting automatically.
+    /// </summary>
+    public class RealFLASHDeconvolutionParameters : DeconvolutionParameters
+    {
+        public override DeconvolutionType DeconvolutionType { get; protected set; }
+            = DeconvolutionType.RealFLASHDeconvolution;
+
+        // ── Executable location ───────────────────────────────────────────────
+
+        /// <summary>
+        /// Full path to FLASHDeconv.exe.  Leave null to use the well-known-path
+        /// search or GlobalSettings.FLASHDeconvExecutablePath.
+        /// </summary>
+        public string? FLASHDeconvExePath { get; set; }
+
+        /// <summary>
+        /// Directory for temporary mzML / TSV files.  Defaults to system temp.
+        /// All temp files are deleted after each call.
+        /// </summary>
+        public string WorkingDirectory { get; set; } = Path.GetTempPath();
+
+        /// <summary>
+        /// Seconds to wait before killing the FLASHDeconv process.
+        /// Default: 300 s (5 minutes).
+        /// </summary>
+        public int ProcessTimeoutSeconds { get; set; } = 300;
+
+        // ── Algorithm flags (map to FLASHDeconv CLI) ──────────────────────────
+
+        /// <summary>ppm tolerance  →  -Algorithm:tol</summary>
+        public double TolerancePpm { get; set; } = 10.0;
+
+        /// <summary>Minimum neutral mass (Da)  →  -Algorithm:min_mass</summary>
+        public double MinMass { get; set; } = 50.0;
+
+        /// <summary>Maximum neutral mass (Da)  →  -Algorithm:max_mass</summary>
+        public double MaxMass { get; set; } = 100_000.0;
+
+        /// <summary>
+        /// Minimum isotope cosine similarity  →  -Algorithm:min_isotope_cosine
+        /// Default matches FLASHDeconv's own default (0.85).
+        /// </summary>
+        public double MinIsotopeCosine { get; set; } = 0.85;
+
+        // ── Constructor ───────────────────────────────────────────────────────
+
+        public RealFLASHDeconvolutionParameters(
+            int minCharge = 1,
+            int maxCharge = 60,
+            double tolerancePpm = 10.0,
+            double minMass = 50.0,
+            double maxMass = 100_000.0,
+            double minIsotopeCosine = 0.85,
+            Polarity polarity = Polarity.Positive,
+            string? flashDeconvExePath = null,
+            string? workingDirectory = null,
+            int processTimeoutSeconds = 300,
+            AverageResidue? averageResidueModel = null)
+            : base(minCharge, maxCharge, polarity, averageResidueModel)
+        {
+            TolerancePpm = tolerancePpm;
+            MinMass = minMass;
+            MaxMass = maxMass;
+            MinIsotopeCosine = minIsotopeCosine;
+            FLASHDeconvExePath = flashDeconvExePath;
+            WorkingDirectory = workingDirectory ?? Path.GetTempPath();
+            ProcessTimeoutSeconds = processTimeoutSeconds;
+        }
+
+        // Decoy deconvolution doesn't apply to the FLASHDeconv exe wrapper.
+        public override DeconvolutionParameters? ToDecoyParameters() => null;
+    }
+}