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Usi downloader

Open Alexander-Sol opened this issue 1 year ago • 1 comments

Implemented UsiLoader class that downloads spectra from various databases as JSON, then converts them into a lightweight UsiSpectrumFromJSON class. Conversion from JSON object is done using Newtonsoft, which is a nuget package that this PR adds to the UsefulProteomicsDatabases dependencies.

MzSpectrum objects can be extracted from UsiSpectrumFromJSON objects.

UsiSpectrumFromJSON spectra could have many possible attributes, of which and isolation window and peptide base sequence can currently be accessed.

Alexander-Sol avatar Jan 09 '24 00:01 Alexander-Sol

Codecov Report

Attention: Patch coverage is 40.86022% with 55 lines in your changes are missing coverage. Please review.

Project coverage is 74.79%. Comparing base (cf854ac) to head (7396dbe).

:exclamation: Current head 7396dbe differs from pull request most recent head c4b6396. Consider uploading reports for the commit c4b6396 to get more accurate results

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #755      +/-   ##
==========================================
- Coverage   75.06%   74.79%   -0.28%     
==========================================
  Files         189      187       -2     
  Lines       30235    30165      -70     
  Branches     3035     3014      -21     
==========================================
- Hits        22697    22562     -135     
- Misses       7024     7083      +59     
- Partials      514      520       +6     
Files Coverage Δ
mzLib/UsefulProteomicsDatabases/UsiLoader.cs 65.51% <65.51%> (ø)
mzLib/Test/DatabaseTests/TestUsiDownload.cs 0.00% <0.00%> (ø)

... and 21 files with indirect coverage changes

codecov[bot] avatar Jan 09 '24 00:01 codecov[bot]