Eliminate those pesky warnings (#2421)

smith-chem-wisc · Oct 3, 2024 · 8c8fe5f · 8c8fe5f
1 parent 6dd10e0
commit 8c8fe5f
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Showing 10 changed files with 77 additions and 49 deletions.
diff --git a/MetaMorpheus/EngineLayer/PsmTsv/PsmTsvReader.cs b/MetaMorpheus/EngineLayer/PsmTsv/PsmTsvReader.cs
@@ -13,7 +13,7 @@ public static List<PsmFromTsv> ReadTsv(string filePath, out List<string> warning
             List<PsmFromTsv> psms = new List<PsmFromTsv>();
             warnings = new List<string>();
 
-            StreamReader reader = null;
+            StreamReader reader;
             try
             {
                 reader = new StreamReader(filePath);
@@ -46,7 +46,7 @@ public static List<PsmFromTsv> ReadTsv(string filePath, out List<string> warning
                 }
                 catch (Exception e)
                 {
-                    warnings.Add("Could not read line: " + lineCount);
+                    warnings.Add($"Could not read line: {lineCount} with error message: {e.Message}");
                 }
             }
 

diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/FragmentResearching/FragmentationReanalysisViewModel.cs b/MetaMorpheus/GuiFunctions/MetaDraw/FragmentResearching/FragmentationReanalysisViewModel.cs
@@ -31,7 +31,7 @@ public FragmentationReanalysisViewModel(bool isProtein = true)
             if (isProtein)
             {
                 DissociationTypes = new ObservableCollection<DissociationType>(Enum.GetValues<DissociationType>()
-                    .Where(p => p != DissociationType.AnyActivationType && Omics.Fragmentation.Peptide.DissociationTypeCollection.ProductsFromDissociationType.TryGetValue(p, out var prod) && prod.Any()));
+                    .Where(p => p != DissociationType.AnyActivationType && Omics.Fragmentation.Peptide.DissociationTypeCollection.ProductsFromDissociationType.TryGetValue(p, out var prod) && prod.Count != 0));
                 PossibleProducts = new ObservableCollection<FragmentViewModel>(GetPossibleProducts(_isProtein));
                 SelectedDissociationType = DissociationType.HCD;
             }
@@ -187,7 +187,7 @@ private void SetUseForFragmentsBasedUponDissociationType(DissociationType dissoc
                     Omics.Fragmentation.Peptide.DissociationTypeCollection.ProductsFromDissociationType[dissociationType].ToArray()
                     : Omics.Fragmentation.Oligo.DissociationTypeCollection.GetRnaProductTypesFromDissociationType(dissociationType).ToArray();
             }
-            catch (Exception e)
+            catch (Exception)
             {
                 _selectedDissociationType = DissociationType.HCD;
                 dissociationTypeProducts = isProtein ?

diff --git a/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs b/MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs
@@ -15,12 +15,12 @@ public static class MetaDrawSettings
     {
         #region Constants 
 
-        public static char[] SubScriptNumbers = {
+        public static readonly char[] SubScriptNumbers = {
             '\u2080', '\u2081', '\u2082', '\u2083', '\u2084',
             '\u2085', '\u2086', '\u2087', '\u2088', '\u2089'
         };
 
-        public static char[] SuperScriptNumbers = {
+        public static readonly char[] SuperScriptNumbers = {
             '\u2070', '\u00b9', '\u00b2', '\u00b3', '\u2074',
             '\u2075', '\u2076', '\u2077', '\u2078', '\u2079'
         }; 
@@ -509,7 +509,7 @@ public static void LoadSettings(MetaDrawSettingsSnapshot settings, out bool flag
                         throw new MetaMorpheusException("Cannot parse Product Ion Color values");
                 }
             }
-            catch (Exception e)
+            catch (Exception)
             {
                 Debugger.Break();
                 SetDefaultProductTypeColors();
@@ -546,7 +546,7 @@ public static void LoadSettings(MetaDrawSettingsSnapshot settings, out bool flag
                         throw new MetaMorpheusException("Cannot parse Beta Product Ion Color values");
                 }
             }
-            catch (Exception e)
+            catch (Exception)
             {
                 Debugger.Break();
                 SetDefaultBetaProductTypeColors();
@@ -582,7 +582,7 @@ public static void LoadSettings(MetaDrawSettingsSnapshot settings, out bool flag
                         throw new MetaMorpheusException("Cannot parse Modification Color values");
                 }
             }
-            catch (Exception e)
+            catch (Exception)
             {
                 Debugger.Break();
                 SetDefaultModificationColors();
@@ -618,7 +618,7 @@ public static void LoadSettings(MetaDrawSettingsSnapshot settings, out bool flag
 
                 }
             }
-            catch (Exception e)
+            catch (Exception)
             {
                 Debugger.Break(); 
                 SetDefaultCoverageTypeColors();
@@ -627,7 +627,7 @@ public static void LoadSettings(MetaDrawSettingsSnapshot settings, out bool flag
 
             try // Spectrum Descriptors
             {
-                if (!settings.SpectrumDescriptionValues.Any())
+                if (settings.SpectrumDescriptionValues.Count == 0)
                     throw new MetaMorpheusException("Cannot parse Spectrum Descriptor values");
 
                 var firstSplit = settings.SpectrumDescriptionValues.First().Split(',');
@@ -657,7 +657,7 @@ public static void LoadSettings(MetaDrawSettingsSnapshot settings, out bool flag
                         throw new MetaMorpheusException("Cannot parse Spectrum Descriptor values");
                 }
             }
-            catch (Exception e)
+            catch (Exception)
             {
                 Debugger.Break();
                 SetDefaultProductTypeColors();

diff --git a/MetaMorpheus/GuiFunctions/ViewModels/SpectralAveragingParametersViewModel.cs b/MetaMorpheus/GuiFunctions/ViewModels/SpectralAveragingParametersViewModel.cs
@@ -18,9 +18,7 @@ public class SpectralAveragingParametersViewModel : BaseViewModel, IEquatable<Sp
     {
         #region Private Members
 
-        private SpectralAveragingParameters spectralAveragingParameters;
-        private int previousOverlap;
-        private string? savedPath;
+        private SpectralAveragingParameters _spectralAveragingParameters;
 
         #endregion
 
@@ -35,79 +33,79 @@ enum PresetAveragingParameters
 
         public SpectralAveragingParameters SpectralAveragingParameters
         {
-            get => spectralAveragingParameters;
-            set { spectralAveragingParameters = value; OnPropertyChanged(nameof(SpectralAveragingParameters)); UpdateVisualRepresentation(); }
+            get => _spectralAveragingParameters;
+            set { _spectralAveragingParameters = value; OnPropertyChanged(nameof(SpectralAveragingParameters)); UpdateVisualRepresentation(); }
         }
 
         public OutlierRejectionType RejectionType
         {
-            get => spectralAveragingParameters.OutlierRejectionType;
-            set { spectralAveragingParameters.OutlierRejectionType = value; OnPropertyChanged(nameof(RejectionType)); }
+            get => _spectralAveragingParameters.OutlierRejectionType;
+            set { _spectralAveragingParameters.OutlierRejectionType = value; OnPropertyChanged(nameof(RejectionType)); }
         }
 
         public SpectraWeightingType WeightingType
         {
-            get => spectralAveragingParameters.SpectralWeightingType;
-            set { spectralAveragingParameters.SpectralWeightingType = value; OnPropertyChanged(nameof(WeightingType)); }
+            get => _spectralAveragingParameters.SpectralWeightingType;
+            set { _spectralAveragingParameters.SpectralWeightingType = value; OnPropertyChanged(nameof(WeightingType)); }
         }
 
         public SpectraFileAveragingType SpectraFileAveragingType
         {
-            get => spectralAveragingParameters.SpectraFileAveragingType;
-            set { spectralAveragingParameters.SpectraFileAveragingType = value; OnPropertyChanged(nameof(SpectraFileAveragingType)); }
+            get => _spectralAveragingParameters.SpectraFileAveragingType;
+            set { _spectralAveragingParameters.SpectraFileAveragingType = value; OnPropertyChanged(nameof(SpectraFileAveragingType)); }
         }
 
         public bool PerformNormalization
         {
-            get => spectralAveragingParameters.NormalizationType == NormalizationType.RelativeToTics ? true : false;
+            get => _spectralAveragingParameters.NormalizationType == NormalizationType.RelativeToTics ? true : false;
             set
             {
-                spectralAveragingParameters.NormalizationType = value == true ? NormalizationType.RelativeToTics : NormalizationType.NoNormalization;
+                _spectralAveragingParameters.NormalizationType = value ? NormalizationType.RelativeToTics : NormalizationType.NoNormalization;
                 OnPropertyChanged(nameof(PerformNormalization));
             }
         }
 
         public double Percentile
         {
-            get => spectralAveragingParameters.Percentile;
-            set { spectralAveragingParameters.Percentile = value; OnPropertyChanged(nameof(Percentile)); }
+            get => _spectralAveragingParameters.Percentile;
+            set { _spectralAveragingParameters.Percentile = value; OnPropertyChanged(nameof(Percentile)); }
         }
 
         public double MinSigmaValue
         {
-            get => spectralAveragingParameters.MinSigmaValue;
-            set { spectralAveragingParameters.MinSigmaValue = value; OnPropertyChanged(nameof(MinSigmaValue)); }
+            get => _spectralAveragingParameters.MinSigmaValue;
+            set { _spectralAveragingParameters.MinSigmaValue = value; OnPropertyChanged(nameof(MinSigmaValue)); }
         }
 
         public double MaxSigmaValue
         {
-            get => spectralAveragingParameters.MaxSigmaValue;
-            set { spectralAveragingParameters.MaxSigmaValue = value; OnPropertyChanged(nameof(MaxSigmaValue)); }
+            get => _spectralAveragingParameters.MaxSigmaValue;
+            set { _spectralAveragingParameters.MaxSigmaValue = value; OnPropertyChanged(nameof(MaxSigmaValue)); }
         }
 
         public double BinSize
         {
-            get => spectralAveragingParameters.BinSize;
-            set { spectralAveragingParameters.BinSize = value; OnPropertyChanged(nameof(BinSize)); }
+            get => _spectralAveragingParameters.BinSize;
+            set { _spectralAveragingParameters.BinSize = value; OnPropertyChanged(nameof(BinSize)); }
         }
 
         public int NumberOfScansToAverage
         {
-            get => spectralAveragingParameters.NumberOfScansToAverage;
+            get => _spectralAveragingParameters.NumberOfScansToAverage;
             set 
             { 
-                spectralAveragingParameters.NumberOfScansToAverage = value;
-                spectralAveragingParameters.ScanOverlap = value - 1;
+                _spectralAveragingParameters.NumberOfScansToAverage = value;
+                _spectralAveragingParameters.ScanOverlap = value - 1;
                 OnPropertyChanged(nameof(NumberOfScansToAverage));
             }
         }
 
         public int MaxThreads
         {
-            get => spectralAveragingParameters.MaxThreadsToUsePerFile;
+            get => _spectralAveragingParameters.MaxThreadsToUsePerFile;
             set
             {
-                spectralAveragingParameters.MaxThreadsToUsePerFile = value;
+                _spectralAveragingParameters.MaxThreadsToUsePerFile = value;
                 OnPropertyChanged(nameof(MaxThreads));
             }
         }
@@ -123,7 +121,7 @@ public int MaxThreads
         public SpectralAveragingParametersViewModel(SpectralAveragingParameters parameters)
         {
             // value initialization
-            spectralAveragingParameters = parameters;
+            _spectralAveragingParameters = parameters;
             RejectionTypes = (OutlierRejectionType[])Enum.GetValues(typeof(OutlierRejectionType));
             WeightingTypes = new [] { SpectraWeightingType.WeightEvenly, SpectraWeightingType.TicValue};
             SpectraFileAveragingTypes = new[] { SpectraFileAveragingType.AverageAll, SpectraFileAveragingType.AverageDdaScans, SpectraFileAveragingType.AverageEverynScansWithOverlap};
@@ -180,7 +178,7 @@ public void SetOtherParameters(object settingsNameToSet)
                     throw new ArgumentException("This should never be hit!");
             }
 
-            spectralAveragingParameters = parameters;
+            _spectralAveragingParameters = parameters;
             UpdateVisualRepresentation();
         }
 

diff --git a/MetaMorpheus/MetaMorpheus.sln.DotSettings b/MetaMorpheus/MetaMorpheus.sln.DotSettings
@@ -0,0 +1,34 @@
+<wpf:ResourceDictionary xml:space="preserve" xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml" xmlns:s="clr-namespace:System;assembly=mscorlib" xmlns:ss="urn:shemas-jetbrains-com:settings-storage-xaml" xmlns:wpf="http://schemas.microsoft.com/winfx/2006/xaml/presentation">
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Calib/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=coisolation/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=crosslinked/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=crosslinks/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=csms/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Cterm/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=deadend/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=fasta/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Frac/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Glyco/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Gsms/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=inframe/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=localizaiton/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=localizeable/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=missense/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Mzml/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Ngly/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=nglyco/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Nterm/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Ogly/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=oglyco/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Phospho/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=prot/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=proteingroup/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=psmtsv/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=pwsm/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Silac/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Taskconfig/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=toml/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Unimod/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=Uniprot/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=xlink/@EntryIndexedValue">True</s:Boolean>
+	<s:Boolean x:Key="/Default/UserDictionary/Words/=xlinker/@EntryIndexedValue">True</s:Boolean></wpf:ResourceDictionary>
diff --git a/MetaMorpheus/TaskLayer/AveragingTask/SpectralAveragingTask.cs b/MetaMorpheus/TaskLayer/AveragingTask/SpectralAveragingTask.cs
@@ -81,15 +81,14 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
                 }
                 catch (Exception e)
                 {
-                    Warn($"Averaging Failure! Could not average spectra for file {originalUnaveragedFilepathWithoutExtenstion}");
+                    Warn($"Averaging Failure! Could not average spectra for file {originalUnaveragedFilepathWithoutExtenstion} with exception {e.Message}");
                 }
                 myFileManager.DoneWithFile(originalUnaveragedFilepath);
 
                 // carry over file-specific parameters from the unaveraged file to the averaged one
-                var fileSpecificParams = new FileSpecificParameters();
                 if (fileSettingsList[spectraFileIndex] != null)
                 {
-                    fileSpecificParams = fileSettingsList[spectraFileIndex].Clone();// write toml settings for the averaged file if there are file specific parameters
+                    var fileSpecificParams = fileSettingsList[spectraFileIndex].Clone();// write toml settings for the averaged file if there are file specific parameters
                     var newTomlFileName = Path.Combine(OutputFolder, originalUnaveragedFilepathWithoutExtenstion + AveragingSuffix + ".toml");
                     Toml.WriteFile(fileSpecificParams, newTomlFileName, tomlConfig);
                     FinishedWritingFile(newTomlFileName, new List<string> { taskId, "Individual Spectra Files", originalUnaveragedFilepathWithoutExtenstion });

diff --git a/MetaMorpheus/TaskLayer/GlycoSearchTask/PostGlycoSearchAnalysisTask.cs b/MetaMorpheus/TaskLayer/GlycoSearchTask/PostGlycoSearchAnalysisTask.cs
@@ -31,8 +31,6 @@ protected override MyTaskResults RunSpecific(string OutputFolder, List<DbForTask
 
         public MyTaskResults Run(string OutputFolder, List<DbForTask> dbFilenameList, List<string> currentRawFileList, string taskId, FileSpecificParameters[] fileSettingsList, List<GlycoSpectralMatch> allPsms, CommonParameters commonParameters, GlycoSearchParameters glycoSearchParameters, List<Protein> proteinList, List<Modification> variableModifications, List<Modification> fixedModifications, List<string> localizeableModificationTypes, MyTaskResults MyTaskResults)
         {
-            List<ProteinGroup> proteinGroups = null;
-
             if (!Parameters.GlycoSearchParameters.WriteDecoys)
             {
                 allPsms.RemoveAll(b => b.IsDecoy);

diff --git a/MetaMorpheus/Test/SpectralRecoveryTest.cs b/MetaMorpheus/Test/SpectralRecoveryTest.cs
@@ -97,7 +97,6 @@ public void SpectralRecoveryTestSetup()
                 Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", @"SpectralRecoveryTest\K13_20ng_1min_frac1.mzML") };
             databaseList = new List<DbForTask>() {new DbForTask(
                 Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", @"SpectralRecoveryTest\HumanFastaSlice.fasta"), false) };
-            outputFolder = outputFolder;
 
             SearchTask searchTask = new SearchTask
             {

diff --git a/MetaMorpheus/Test/TestDataFile.cs b/MetaMorpheus/Test/TestDataFile.cs
@@ -419,7 +419,7 @@ public TestDataFile(PeptideWithSetModifications pepWithSetMods)
             Scans = ScansHere.ToArray();
         }
 
-        public string FilePath
+        public new string FilePath
         {
             get
             {

diff --git a/MetaMorpheus/Test/XLTest.cs b/MetaMorpheus/Test/XLTest.cs
@@ -1636,7 +1636,7 @@ internal class XLTestDataFile : MsDataFile
                 Scans = ScansHere.ToArray();
             }
 
-            public static string FilePath
+            public new static string FilePath
             {
                 get
                 {
@@ -1718,7 +1718,7 @@ internal class XLTestDataFileDiffSite : MsDataFile
                 Scans = ScansHere.ToArray();
             }
 
-            public string FilePath
+            public new string FilePath
             {
                 get
                 {