Stability Update

[Alexander-Sol]

This PR is intended to address longstanding instability in MetaMorpheus results. Specifically, Calibration can produce different outputs with identical inputs.

Unfortunately, even with this PR, variable results from Calibration were observed

Changes

• Fixed locks in DataPointAcquisitionEngine

  • I believe this is the main issue. Previously, improper locking led to race conditions when adding to the lists of LabeledDataPoint

• Created a Resolve method for List and call it in SpectralMatch.ResolveAllAmbiguities

  • Previously, the first element of the BioPolymerWithSetModsToMatchingFragments dictionary was used. As dictionaries aren't ordered, this could lead to stochastic results
  • CrosslinkSpectralMatch keeps the legacy version of ResolveAllAmbiguities because I don't understand how XL search works and the new method broke things

• Changed MsDataFileManager to use ConcurrentDictionary to eliminate warnings about race conditions caused by asynchronous loading

  • (To be clear, I don't think race conditions could have arisen with how FileManagers are currently used, but better safe than sorry)

[codecov]

Codecov Report

Attention: Patch coverage is 95.34884% with 4 lines in your changes missing coverage. Please review.

Project coverage is 93.90%. Comparing base (e6cf8e7) to head (8833d48).

Files with missing lines	Patch %	Lines
...ineLayer/CrosslinkSearch/CrosslinkSpectralMatch.cs	92.30%	0 Missing and 3 partials ⚠️
MetaMorpheus/TaskLayer/MetaMorpheusTask.cs	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #2455   +/-   ##
=======================================
  Coverage   93.89%   93.90%           
=======================================
  Files         146      146           
  Lines       22206    22255   +49     
  Branches     3059     3067    +8     
=======================================
+ Hits        20851    20898   +47     
  Misses        906      906           
- Partials      449      451    +2     

Files with missing lines	Coverage Δ
...ineLayer/Calibration/DataPointAcquisitionEngine.cs	94.84% <100.00%> (ø)
...heus/EngineLayer/FdrAnalysis/SpectralMatchGroup.cs	86.66% <100.00%> (+0.95%)	⬆️
MetaMorpheus/EngineLayer/PsmTsv/PsmTsvWriter.cs	97.62% <100.00%> (+0.08%)	⬆️
.../SpectralLibrarySearch/CrosslinkLibrarySpectrum.cs	94.38% <100.00%> (ø)
MetaMorpheus/EngineLayer/SpectralMatch.cs	97.83% <100.00%> (+0.01%)	⬆️
...pheus/TaskLayer/CalibrationTask/CalibrationTask.cs	88.73% <100.00%> (ø)
MetaMorpheus/TaskLayer/MyFileManager.cs	96.55% <100.00%> (+0.89%)	⬆️
MetaMorpheus/TaskLayer/SearchTask/SearchTask.cs	95.84% <100.00%> (+0.01%)	⬆️
MetaMorpheus/TaskLayer/MetaMorpheusTask.cs	89.13% <0.00%> (ø)
...ineLayer/CrosslinkSearch/CrosslinkSpectralMatch.cs	95.98% <92.30%> (-0.38%)	⬇️