Digestion Consolidation and Optimization #823
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Added `using` directive for `MzLibUtil`. Introduced a static readonly `HashSetPool<int>` named `HashSetPool` to manage a pool of hash sets. Updated `DigestionAgent` constructor to initialize `HashSetPool`. Refactored `GetDigestionSiteIndices` to use a hash set from `HashSetPool` for storing indices, ensuring no duplicates. Explicitly added start and end of protein sequence as cleavage sites. Implemented `try-finally` block to return hash set to pool after use. Final list of indices is now sorted before returning.
- Simplified initial check for `possibleVariableModifications.Count` and replaced `yield return null` with `yield break`. - Adjusted indentation and loop structure for clarity. - Refactored nested loop to remove unnecessary braces and streamline logic. - Simplified construction of `modificationPattern` dictionary by removing redundant checks and directly using `modIndex`.
…into DigestionFixedFix
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Maintenance
Alexander-Sol
previously approved these changes
Jan 16, 2025
trishorts
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Jan 16, 2025
trishorts
previously approved these changes
Jan 16, 2025
trishorts
approved these changes
Jan 16, 2025
Alexander-Sol
approved these changes
Jan 16, 2025
zhuoxinshi
approved these changes
Jan 17, 2025
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PR Classification
Code cleanup and performance optimization
Consolidated the code so that Transcriptomics and Proteomics are based upon the same functions.
Pull request was loaded into MetaMorpheus 1.0.6 and profiled using Jenkins Data.
This PR reduces:
PR Summary
This pull request focuses on improving code readability, performance, and maintainability by optimizing methods, refactoring logic, and removing unused code.
BioPolymerWithSetModsExtensionsto use nullableModification?type and string interpolation.DetermineFullSequencemethod by initializingStringBuilderwith an initial capacity.SetFixedModsOneIsNorFivePrimeTerminusmethod to use arefparameter and simplified logic.ProteolyticPeptide.csandNucleolyticOligo.cs.try-finallyblocks to ensure pooled objects are returned after use inProteolyticPeptide.csandNucleolyticOligo.cs.