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Improved intensity pairs trying to make spectrum library comparisons faster #765

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merged 47 commits into from
Apr 18, 2024

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@trishorts trishorts commented Feb 26, 2024

The primary purpose of this PR is to make the computation of spectrum similarity a little faster.
Overall, I attempted also to improve the code.

Some points to clarify because some changes were made:

  1. We assume in general that we'll be comparing experimental to theoretical. We wish to keep all theoretical peaks even if they are not paired to an experimental because that will lower the similarity as desired. Default is to keep all theoretical peaks.
  2. If desired, the user can choose to use all experimental peaks. Default however is to not.
  3. To enable comparison of two experimental spectra, we now have two separate bools for keeping unpaired peaks.
  4. Lots of explanations were added to unit tests so that future understanders can understand.
  5. KullbackLeibler, which should be used for isotope envelopes, is improved but unchanged.
  6. We are now officially tossing ALL zero intensity peaks from the start. doesn't matter, experimental or theoretical.

MICHAEL SHORTREED and others added 30 commits November 18, 2021 12:30
@trishorts trishorts changed the title Improved intensity pairs trying to make SLS faster Improved intensity pairs trying to make spectrum library comparisons faster Feb 28, 2024
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codecov bot commented Mar 1, 2024

Codecov Report

Attention: Patch coverage is 94.23077% with 6 lines in your changes are missing coverage. Please review.

Project coverage is 75.04%. Comparing base (cf854ac) to head (400c865).

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@@            Coverage Diff             @@
##           master     #765      +/-   ##
==========================================
- Coverage   75.06%   75.04%   -0.02%     
==========================================
  Files         189      189              
  Lines       30235    30236       +1     
  Branches     3035     3034       -1     
==========================================
- Hits        22697    22692       -5     
- Misses       7024     7029       +5     
- Partials      514      515       +1     
Files Coverage Δ
mzLib/Omics/SpectrumMatch/LibrarySpectrum.cs 93.22% <100.00%> (ø)
...b/MassSpectrometry/MzSpectra/SpectralSimilarity.cs 97.55% <94.11%> (-2.10%) ⬇️

@Alexander-Sol Alexander-Sol merged commit 855560a into smith-chem-wisc:master Apr 18, 2024
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5 participants