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Eliminate those pesky warnings #2421

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merged 18 commits into from
Oct 3, 2024
Merged

Eliminate those pesky warnings #2421

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8be2574
Updated to MzLib 1.0.548 and fixed custom ions in search tasks
nbollis May 21, 2024
a00af8a
reverted calibration task change
nbollis May 21, 2024
22c60ba
merged in master
nbollis May 30, 2024
f4695bb
merged in master bbbyy
nbollis Jun 10, 2024
d4f8b9d
Merge branch 'smith-chem-wisc:master' into master
nbollis Jun 19, 2024
1f0dc48
merged in master
nbollis Jun 21, 2024
5c0268b
idkman
nbollis Jul 3, 2024
b7e6a0f
merged in master
nbollis Jul 16, 2024
6446d89
Merge remote-tracking branch 'upstream/master'
nbollis Jul 24, 2024
322235d
Spectral Library from Command Line (#2386)
nbollis Jul 23, 2024
8b48c95
merged in master
nbollis Aug 6, 2024
2ef973f
Merge branch 'master' of https://github.com/nbollis/MetaMorpheus
nbollis Aug 6, 2024
0abcd9b
Merge branch 'master' of https://github.com/nbollis/MetaMorpheus
nbollis Aug 7, 2024
f9030f9
merged in master
nbollis Sep 4, 2024
046067e
merged in master
nbollis Sep 17, 2024
c38f081
Merge remote-tracking branch 'upstream/master'
nbollis Oct 3, 2024
bc83198
Dealt with all of the warnings we get every pull request
nbollis Oct 3, 2024
cca22e6
removed more warnings
nbollis Oct 3, 2024
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4 changes: 2 additions & 2 deletions MetaMorpheus/EngineLayer/PsmTsv/PsmTsvReader.cs
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Expand Up @@ -13,7 +13,7 @@
List<PsmFromTsv> psms = new List<PsmFromTsv>();
warnings = new List<string>();

StreamReader reader = null;
StreamReader reader;
try
{
reader = new StreamReader(filePath);
Expand Down Expand Up @@ -46,7 +46,7 @@
}
catch (Exception e)
{
warnings.Add("Could not read line: " + lineCount);
warnings.Add($"Could not read line: {lineCount} with error message: {e.Message}");

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}
}

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4 changes: 2 additions & 2 deletions MetaMorpheus/GuiFunctions/MetaDraw/FragmentResearching/FragmentationReanalysisViewModel.cs
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Expand Up @@ -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;
}
Expand Down Expand Up @@ -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 ?
Expand Down
16 changes: 8 additions & 8 deletions MetaMorpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs
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Expand Up @@ -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'
};
Expand Down Expand Up @@ -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();
Expand Down Expand Up @@ -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();
Expand Down Expand Up @@ -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();
Expand Down Expand Up @@ -618,7 +618,7 @@ public static void LoadSettings(MetaDrawSettingsSnapshot settings, out bool flag

}
}
catch (Exception e)
catch (Exception)
{
Debugger.Break();
SetDefaultCoverageTypeColors();
Expand All @@ -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(',');
Expand Down Expand Up @@ -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();
Expand Down
54 changes: 26 additions & 28 deletions MetaMorpheus/GuiFunctions/ViewModels/SpectralAveragingParametersViewModel.cs
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Expand Up @@ -18,9 +18,7 @@
{
#region Private Members

private SpectralAveragingParameters spectralAveragingParameters;
private int previousOverlap;
private string? savedPath;
private SpectralAveragingParameters _spectralAveragingParameters;

#endregion

Expand All @@ -35,79 +33,79 @@

public SpectralAveragingParameters SpectralAveragingParameters
{
get => spectralAveragingParameters;
set { spectralAveragingParameters = value; OnPropertyChanged(nameof(SpectralAveragingParameters)); UpdateVisualRepresentation(); }
get => _spectralAveragingParameters;
set { _spectralAveragingParameters = value; OnPropertyChanged(nameof(SpectralAveragingParameters)); UpdateVisualRepresentation(); }

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}

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));
}
}
Expand All @@ -123,7 +121,7 @@
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};
Expand Down Expand Up @@ -180,7 +178,7 @@
throw new ArgumentException("This should never be hit!");
}

spectralAveragingParameters = parameters;
_spectralAveragingParameters = parameters;
UpdateVisualRepresentation();
}

Expand Down
34 changes: 34 additions & 0 deletions MetaMorpheus/MetaMorpheus.sln.DotSettings
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@@ -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>
5 changes: 2 additions & 3 deletions MetaMorpheus/TaskLayer/AveragingTask/SpectralAveragingTask.cs
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Expand Up @@ -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 });
Expand Down
2 changes: 0 additions & 2 deletions MetaMorpheus/TaskLayer/GlycoSearchTask/PostGlycoSearchAnalysisTask.cs
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Expand Up @@ -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);
Expand Down
1 change: 0 additions & 1 deletion MetaMorpheus/Test/SpectralRecoveryTest.cs
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Expand Up @@ -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
{
Expand Down
2 changes: 1 addition & 1 deletion MetaMorpheus/Test/TestDataFile.cs
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Expand Up @@ -419,7 +419,7 @@ public TestDataFile(PeptideWithSetModifications pepWithSetMods)
Scans = ScansHere.ToArray();
}

public string FilePath
public new string FilePath
{
get
{
Expand Down
4 changes: 2 additions & 2 deletions MetaMorpheus/Test/XLTest.cs
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Expand Up @@ -1636,7 +1636,7 @@ internal class XLTestDataFile : MsDataFile
Scans = ScansHere.ToArray();
}

public static string FilePath
public new static string FilePath
{
get
{
Expand Down Expand Up @@ -1718,7 +1718,7 @@ internal class XLTestDataFileDiffSite : MsDataFile
Scans = ScansHere.ToArray();
}

public string FilePath
public new string FilePath
{
get
{
Expand Down