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Scattered Optimizations #815

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Scattered Optimizations #815

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@nbollis nbollis commented Dec 13, 2024 •
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This pull request optimizes memory usage and performance across several files by introducing object pooling and other efficiency improvements.

  • Added DictionaryPool.cs and HashSetPool.cs for pooling Dictionary and HashSet instances.
  • ClassicDeconvolutionAlgorithm.cs: Reused HashSet instances from pools to reduce memory allocations.
  • DeconvolutionAlgorithm.cs: Added HashSetPool<int> and HashSetPool<double> for pooling hash sets.
  • PpmTolerance.cs: Optimized methods using a precomputed _factor field.
  • PeptideWithSetModifications.cs: Enabled nullable reference types and optimized memory usage with StringBuilder and HashSetPool<double>.
  • BioPolymerWithSetModsExtensions.cs: Implemented string interpolation instead of concatenation and optimized memory usage with StringBuilder
  • Digestion:
    • DigestionAgent.cs: Reused HashSet instances from pools to reduce memory allocations
    • DigestionProduct.cs: Reduced calls to ModFits by altering boolean check order
    • Protease.cs Reduced list creation events
    • ProteolyticPeptide.cs Reused Dictionary instances from pools to reduce memory allocations
  • IBioPolymerWithSetMods:
    • Removed unnecessary IEquatable<> reference in interface
    • PeptideWithSetModifications.cs: Reused HashSet instances from pools to reduce memory allocations.

@nbollis
PpmTolerance Optimization
738cdd8
@nbollis
Added HashSetPool and reduced runtime of Digestion
1d9bd59
@nbollis
Reduced conditional checks in ModificaitonLocalization and stringbuil…
4ea1843 
…der simplificaiton in BioPolymerWithSetModsExtensions
@nbollis
Reduced Runtime of Peptide with set modificaitons and parent classes
0c340cf
@nbollis
Increase StringBuilder capacity, add ObjectPool tests
6a43a42 
Modified DetermineFullSequence to reduce StringBuilder resizes.
Added Microsoft.Extensions.ObjectPool dependency.
Introduced ObjectPoolTests for DictionaryPool and HashSetPool.
@nbollis
Implemented pools in classic deconv
197ae90
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codecov bot commented Dec 13, 2024 •
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Codecov Report

Attention: Patch coverage is 91.24424% with 19 lines in your changes missing coverage. Please review.

Project coverage is 77.25%. Comparing base (21c1702) to head (0575432).

Files with missing lines Patch % Lines
mzLib/Omics/IBioPolymerWithSetMods.cs 60.00% 0 Missing and 4 partials ⚠️
mzLib/Proteomics/Protein/Protein.cs 20.00% 4 Missing ⚠️
...zLib/Transcriptomics/Digestion/OligoWithSetMods.cs 42.85% 2 Missing and 2 partials ⚠️
...ib/Omics/Modifications/ModificationLocalization.cs 93.75% 0 Missing and 2 partials ⚠️
...roteolyticDigestion/PeptideWithSetModifications.cs 94.87% 1 Missing and 1 partial ⚠️
...lution/Algorithms/ClassicDeconvolutionAlgorithm.cs 92.85% 0 Missing and 1 partial ⚠️
mzLib/Omics/BioPolymerWithSetModsExtensions.cs 94.44% 1 Missing ⚠️
mzLib/Omics/IBioPolymer.cs 85.71% 0 Missing and 1 partial ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #815      +/-   ##
==========================================
+ Coverage   77.23%   77.25%   +0.01%     
==========================================
  Files         218      220       +2     
  Lines       33014    33081      +67     
  Branches     3422     3436      +14     
==========================================
+ Hits        25499    25556      +57     
- Misses       6942     6949       +7     
- Partials      573      576       +3
Files with missing lines Coverage Δ
...Deconvolution/Algorithms/DeconvolutionAlgorithm.cs 100.00% <100.00%> (ø)
mzLib/MzLibUtil/DictionaryPool.cs 100.00% <100.00%> (ø)
mzLib/MzLibUtil/HashSetPool.cs 100.00% <100.00%> (ø)
mzLib/MzLibUtil/PpmTolerance.cs 100.00% <100.00%> (ø)
mzLib/Omics/Digestion/DigestionAgent.cs 90.90% <100.00%> (+0.52%) ⬆️
mzLib/Omics/Digestion/DigestionProduct.cs 95.65% <100.00%> (+0.87%) ⬆️
mzLib/Proteomics/ProteolyticDigestion/Protease.cs 95.17% <100.00%> (ø)
...teomics/ProteolyticDigestion/ProteolyticPeptide.cs 92.03% <100.00%> (+0.14%) ⬆️
mzLib/Transcriptomics/NucleicAcid.cs 92.70% <100.00%> (-0.31%) ⬇️
...lution/Algorithms/ClassicDeconvolutionAlgorithm.cs 96.55% <92.85%> (-0.38%) ⬇️
... and 7 more

... and 1 file with indirect coverage changes

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