smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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Eliminate PEP from FDR analysis during calibration #2294

Closed trishorts closed 11 months ago

trishorts commented 12 months ago

I discovered that PEP analysis was automatically running during the FDRAnalysisEngine for everything. Calibration does not benefit from PEP calculations. Since they take time, and could be run several times during a calibration task, I eliminated it.

This is done by adding a bool DoPEP=true in the FDRAnalysis engine constructor. Default is true. But, when this is called during calibration I set it to false. Then I put the call to PEP inside an if clause:

if(DoPEP) { PEPAnalysis }

codecov[bot] commented 12 months ago

Codecov Report

Merging #2294 (9c2e169) into master (7dfe22b) will increase coverage by 0.00%. The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master    #2294   +/-   ##
=======================================
  Coverage   92.02%   92.02%           
=======================================
  Files         135      135           
  Lines       20602    20606    +4     
  Branches     2828     2829    +1     
=======================================
+ Hits        18958    18962    +4     
  Misses       1161     1161           
  Partials      483      483           
Impacted Files Coverage Δ
...pheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs 94.50% <100.00%> (+0.12%) :arrow_up:
...pheus/TaskLayer/CalibrationTask/CalibrationTask.cs 89.14% <100.00%> (ø)