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Update Omics to read additional SpectrumMatchFromTsv types #807

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@nbollis nbollis commented Oct 23, 2024

Library spectrum, PsmFromTsv, and PsmFromTsvReader have been moved from MetaMorpheus to Mzlib.
The files have not yet been deleted in MetaMorpheus.

This pull request prepares the PsmReader to pass all tests in MetaMorpheus.

This pull request also fixes issues with reading in XL tsv files in Mzlib

@nbollis nbollis added Maintenance The user isn't impacted by it, it's purely behind the scenes WIP labels Oct 23, 2024
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codecov bot commented Oct 23, 2024

Codecov Report

Attention: Patch coverage is 81.75182% with 25 lines in your changes missing coverage. Please review.

Project coverage is 76.46%. Comparing base (6c18e9f) to head (6ecd93d).

Files with missing lines Patch % Lines
...ib/Omics/SpectrumMatch/CrosslinkLibrarySpectrum.cs 82.50% 11 Missing and 3 partials ⚠️
mzLib/Proteomics/PSM/PsmFromTsv.cs 80.43% 7 Missing and 2 partials ⚠️
mzLib/Omics/SpectrumMatch/SpectrumMatchFromTsv.cs 50.00% 1 Missing and 1 partial ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #807      +/-   ##
==========================================
- Coverage   76.48%   76.46%   -0.03%     
==========================================
  Files         211      212       +1     
  Lines       31960    32080     +120     
  Branches     3286     3298      +12     
==========================================
+ Hits        24446    24531      +85     
- Misses       6954     6984      +30     
- Partials      560      565       +5     
Files with missing lines Coverage Δ
mzLib/Omics/SpectrumMatch/LibrarySpectrum.cs 93.22% <ø> (ø)
...ib/Readers/SearchResults/SpectrumMatchTsvReader.cs 97.45% <100.00%> (+1.65%) ⬆️
mzLib/Readers/Util/SupportedFileTypes.cs 97.59% <100.00%> (+0.09%) ⬆️
mzLib/Omics/SpectrumMatch/SpectrumMatchFromTsv.cs 92.45% <50.00%> (-4.90%) ⬇️
mzLib/Proteomics/PSM/PsmFromTsv.cs 89.16% <80.43%> (-2.96%) ⬇️
...ib/Omics/SpectrumMatch/CrosslinkLibrarySpectrum.cs 82.50% <82.50%> (ø)

Corrected the mapping of `NextResidue` and `PreviousResidue` headers in the `parsedHeader` dictionary. The headers are now correctly mapped to `SpectrumMatchFromTsvHeader.NextResidue` and `SpectrumMatchFromTsvHeader.PreviousResidue` in both conditional branches.
@nbollis nbollis changed the title Update Omics to reflect upcoming changes in MetaMorpheus Update Omics to read additional SpectrumMatchFromTsv types Oct 29, 2024
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