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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
90 stars 45 forks source link

#3 -Spectral Match Generalization #2340

Closed nbollis closed 3 months ago

nbollis commented 4 months ago

Generalized the PeptideSpectralMatch class to a generic SpectralMatch class. This enables OligoSpectralMatch to use all of the same Writing classes and a vast majority of the FDR calculations. Also added some tests to the Bin class for test coverage

codecov[bot] commented 4 months ago

Codecov Report

Attention: Patch coverage is 92.72503% with 59 lines in your changes are missing coverage. Please review.

Project coverage is 92.67%. Comparing base (8ab02bc) to head (11c8e82).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340/graphs/tree.svg?width=650&height=150&src=pr&token=m0HXyK8tFy&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) ```diff @@ Coverage Diff @@ ## master #2340 +/- ## ========================================== + Coverage 92.65% 92.67% +0.02% ========================================== Files 136 137 +1 Lines 21243 21259 +16 Branches 2930 2939 +9 ========================================== + Hits 19682 19702 +20 + Misses 1083 1077 -6 - Partials 478 480 +2 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [...ineLayer/Calibration/DataPointAquisitionResults.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0NhbGlicmF0aW9uL0RhdGFQb2ludEFxdWlzaXRpb25SZXN1bHRzLmNz) | `80.43% <100.00%> (ø)` | | | [...rpheus/EngineLayer/Calibration/LabeledDataPoint.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0NhbGlicmF0aW9uL0xhYmVsZWREYXRhUG9pbnQuY3M=) | `100.00% <100.00%> (ø)` | | | [...s/EngineLayer/ClassicSearch/ClassicSearchEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0NsYXNzaWNTZWFyY2gvQ2xhc3NpY1NlYXJjaEVuZ2luZS5jcw==) | `97.84% <100.00%> (ø)` | | | [...gineLayer/CrosslinkSearch/CrosslinkSearchEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0Nyb3NzbGlua1NlYXJjaC9Dcm9zc2xpbmtTZWFyY2hFbmdpbmUuY3M=) | `91.08% <100.00%> (ø)` | | | [...EngineLayer/CrosslinkSearch/CrosslinkedPeptides.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0Nyb3NzbGlua1NlYXJjaC9Dcm9zc2xpbmtlZFBlcHRpZGVzLmNz) | `100.00% <100.00%> (ø)` | | | [...aMorpheus/EngineLayer/GlycoSearch/GlycoPeptides.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0dseWNvUGVwdGlkZXMuY3M=) | `88.03% <100.00%> (ø)` | | | [...pheus/EngineLayer/GlycoSearch/GlycoSearchEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0dseWNvU2VhcmNoRW5naW5lLmNz) | `92.67% <100.00%> (ø)` | | | [MetaMorpheus/EngineLayer/Gptmd/GptmdEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dwdG1kL0dwdG1kRW5naW5lLmNz) | `89.34% <100.00%> (ø)` | | | [...eus/EngineLayer/Localization/LocalizationEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0xvY2FsaXphdGlvbi9Mb2NhbGl6YXRpb25FbmdpbmUuY3M=) | `98.36% <100.00%> (ø)` | | | [...eus/EngineLayer/ModernSearch/ModernSearchEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL01vZGVyblNlYXJjaC9Nb2Rlcm5TZWFyY2hFbmdpbmUuY3M=) | `74.54% <100.00%> (ø)` | | | ... and [35 more](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2340?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | |
trishorts commented 4 months ago

wonder about switching from psm to sm for all things. would be a big change.