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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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#2- Deconvolution Generalization #2339

Closed nbollis closed 4 months ago

nbollis commented 4 months ago

Enables the generalization of deconvolution to other deconvolution types in MetaMorpheus. This is necessary for if/when Decharge is added to MzLib.

Created separate deconvolution parameters for product and precursor scans. Removed deocn tolerance and intensity ratio from toml. Added negative mode deconvolution tests.

Updated custom fragment ion window to only display Protein products with ability to do RNA once implemented in MzLib. This eliminates a crash

codecov[bot] commented 4 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 92.64%. Comparing base (0e81697) to head (3454066).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2339/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/2339?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 #2339 +/- ## ======================================= Coverage 92.64% 92.64% ======================================= Files 136 136 Lines 21211 21229 +18 Branches 2923 2928 +5 ======================================= + Hits 19650 19668 +18 Misses 1083 1083 Partials 478 478 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2339?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/2339?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0NvbW1vblBhcmFtZXRlcnMuY3M=) | `95.52% <100.00%> (+0.46%)` | :arrow_up: | | [...etaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2339?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL01zMlNjYW5XaXRoU3BlY2lmaWNNYXNzLmNz) | `96.96% <100.00%> (-0.07%)` | :arrow_down: | | [MetaMorpheus/TaskLayer/MetaMorpheusTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2339?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9NZXRhTW9ycGhldXNUYXNrLmNz) | `88.59% <100.00%> (+0.01%)` | :arrow_up: |