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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
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[Ignore Coverage] #4 - Digestion params generalization #2341

Open nbollis opened 4 months ago

nbollis commented 4 months ago

Generalizes digestion parameters in common parameters to enable rna digestion and protein digestion.

In the task windows, I had to move all things dependent upon the digestion agent being a protease into an if clause that casts the IDigestionParams.DigestionAgent into a protease

Needed to improve code coverage so I found a few miscelaneous spots to do so. ModTypeForTreeViewModel and the Glyco Node class

codecov[bot] commented 4 months ago

Codecov Report

Attention: Patch coverage is 87.78626% with 16 lines in your changes missing coverage. Please review.

Project coverage is 93.00%. Comparing base (4a0a5e8) to head (1ed889e).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341/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/2341?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 #2341 +/- ## ========================================== + Coverage 92.79% 93.00% +0.20% ========================================== Files 137 137 Lines 21170 21172 +2 Branches 2924 2935 +11 ========================================== + Hits 19645 19691 +46 + Misses 1045 998 -47 - Partials 480 483 +3 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [MetaMorpheus/EngineLayer/CommonParameters.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FCommonParameters.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0NvbW1vblBhcmFtZXRlcnMuY3M=) | `95.28% <100.00%> (-0.24%)` | :arrow_down: | | [...gineLayer/CrosslinkSearch/CrosslinkSearchEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FCrosslinkSearch%2FCrosslinkSearchEngine.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0Nyb3NzbGlua1NlYXJjaC9Dcm9zc2xpbmtTZWFyY2hFbmdpbmUuY3M=) | `91.10% <100.00%> (+0.01%)` | :arrow_up: | | [...pheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FFdrAnalysis%2FFdrAnalysisEngine.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL0ZkckFuYWx5c2lzRW5naW5lLmNz) | `96.50% <100.00%> (ø)` | | | [...EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FFdrAnalysis%2FPEPValueAnalysisGeneric.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL1BFUFZhbHVlQW5hbHlzaXNHZW5lcmljLmNz) | `96.10% <100.00%> (ø)` | | | [MetaMorpheus/EngineLayer/GlycoSearch/Node.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FNode.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL05vZGUuY3M=) | `88.00% <ø> (+21.33%)` | :arrow_up: | | [...cificEnzymeSearch/NonSpecificEnzymeSearchEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FNonSpecificEnzymeSearch%2FNonSpecificEnzymeSearchEngine.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL05vblNwZWNpZmljRW56eW1lU2VhcmNoL05vblNwZWNpZmljRW56eW1lU2VhcmNoRW5naW5lLmNz) | `87.47% <100.00%> (ø)` | | | [...neLayer/ProteinParsimony/ProteinParsimonyEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FProteinParsimony%2FProteinParsimonyEngine.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1Byb3RlaW5QYXJzaW1vbnkvUHJvdGVpblBhcnNpbW9ueUVuZ2luZS5jcw==) | `98.83% <100.00%> (ø)` | | | [MetaMorpheus/EngineLayer/Silac/SilacConversions.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FSilac%2FSilacConversions.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1NpbGFjL1NpbGFjQ29udmVyc2lvbnMuY3M=) | `97.83% <ø> (ø)` | | | [MetaMorpheus/EngineLayer/SpectralMatch.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FSpectralMatch.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1NwZWN0cmFsTWF0Y2guY3M=) | `99.71% <100.00%> (ø)` | | | [...GuiFunctions/ViewModels/ModTypeForTreeViewModel.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341?src=pr&el=tree&filepath=MetaMorpheus%2FGuiFunctions%2FViewModels%2FModTypeForTreeViewModel.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0d1aUZ1bmN0aW9ucy9WaWV3TW9kZWxzL01vZFR5cGVGb3JUcmVlVmlld01vZGVsLmNz) | `100.00% <100.00%> (+48.00%)` | :arrow_up: | | ... and [13 more](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2341/indirect-changes?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 3 months ago

wherein nic embraces the var side