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smith-chem-wisc · Sep 20, 2024 · 5a3445b · 5a3445b
1 parent f33313b
commit 5a3445b
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/MetaMorpheus/EngineLayer/Gptmd/GptmdEngine.cs b/MetaMorpheus/EngineLayer/Gptmd/GptmdEngine.cs
@@ -99,7 +99,7 @@ protected override MetaMorpheusEngineResults RunSpecific()
 
                                     if (newPeptides.Any())
                                     {
-                                        var scores = new ConcurrentBag<double>();
+                                        var scores = new List<double>();
                                         var targetFragmentsForEachDissociationType = new ConcurrentDictionary<DissociationType, List<Product>>();
 
                                         if (CommonParameters.DissociationType == DissociationType.Autodetect)
@@ -198,9 +198,9 @@ protected override MetaMorpheusEngineResults RunSpecific()
 
             return new GptmdResults(this, modDict.ToDictionary(kvp => kvp.Key, kvp => new HashSet<Tuple<int, Modification>>(kvp.Value)), modsAdded);
         }
-        private ConcurrentBag<double> CalculatePeptideScores(List<PeptideWithSetModifications> newPeptides, DissociationType dissociationType, SpectralMatch psm)
+        private List<double> CalculatePeptideScores(List<PeptideWithSetModifications> newPeptides, DissociationType dissociationType, SpectralMatch psm)
         {
-            var scores = new ConcurrentBag<double>();
+            var scores = new List<double>();
 
             foreach (var peptide in newPeptides)
             {

diff --git a/MetaMorpheus/TaskLayer/GPTMDTask/GPTMDTask.cs b/MetaMorpheus/TaskLayer/GPTMDTask/GPTMDTask.cs
@@ -39,10 +39,6 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
             nextFileLoadingTask.Start();
             LoadModifications(taskId, out var variableModifications, out var fixedModifications, out var localizeableModificationTypes);
 
-            // TODO: print error messages loading GPTMD mods
-            List<Modification> gptmdModifications = GlobalVariables.AllModsKnown.OfType<Modification>().Where(b => GptmdParameters.ListOfModsGptmd.Contains((b.ModificationType, b.IdWithMotif))).ToList();
-            IEnumerable<Tuple<double, double>> combos = LoadCombos(gptmdModifications).ToList();
-
             // start loading proteins in the background
             List<Protein> proteinList = null;
             Task<List<Protein>> proteinLoadingTask = new(() =>
@@ -55,6 +51,11 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
             });
             proteinLoadingTask.Start();
 
+            // TODO: print error messages loading GPTMD mods
+            List<Modification> gptmdModifications = GlobalVariables.AllModsKnown.OfType<Modification>().Where(b => GptmdParameters.ListOfModsGptmd.Contains((b.ModificationType, b.IdWithMotif))).ToList();
+            IEnumerable<Tuple<double, double>> combos = LoadCombos(gptmdModifications).ToList();
+
+
             List<SpectralMatch> allPsms = new List<SpectralMatch>();
 
             var numRawFiles = currentRawFileList.Count;
@@ -116,7 +117,6 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
                     nextFileLoadingTask = new Task<MsDataFile>(() => myFileManager.LoadFile(currentRawFileList[nextFileIndex], SetAllFileSpecificCommonParams(CommonParameters, fileSettingsList[nextFileIndex])));
                     nextFileLoadingTask.Start();
                 }
-                //MsDataFile myMsDataFile = myFileManager.LoadFile(origDataFile, combinedParams);
                 Status("Getting ms2 scans...", new List<string> { taskId, "Individual Spectra Files", origDataFile });
                 Ms2ScanWithSpecificMass[] arrayOfMs2ScansSortedByMass = GetMs2Scans(myMsDataFile, origDataFile, combinedParams).OrderBy(b => b.PrecursorMass).ToArray();
                 myFileManager.DoneWithFile(origDataFile);