[Ignore Coverage] #4 - Digestion params generalization

[nbollis]

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]

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).
Report is 32 commits behind head on master.

Files with missing lines	Patch %	Lines
...etaMorpheus/EngineLayer/Indexing/IndexingEngine.cs	66.66%	1 Missing and 3 partials ⚠️
MetaMorpheus/TaskLayer/MetaMorpheusTask.cs	90.00%	1 Missing and 2 partials ⚠️
...pheus/TaskLayer/CalibrationTask/CalibrationTask.cs	71.42%	0 Missing and 2 partials ⚠️
MetaMorpheus/TaskLayer/GPTMDTask/GPTMDTask.cs	71.42%	0 Missing and 2 partials ⚠️
...pheus/TaskLayer/GlycoSearchTask/GlycoSearchTask.cs	85.71%	0 Missing and 1 partial ⚠️
...us/TaskLayer/MbrAnalysis/SpectralRecoveryRunner.cs	0.00%	0 Missing and 1 partial ⚠️
...eus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs	83.33%	0 Missing and 1 partial ⚠️
MetaMorpheus/TaskLayer/SearchTask/SearchTask.cs	87.50%	0 Missing and 1 partial ⚠️
...etaMorpheus/TaskLayer/XLSearchTask/XLSearchTask.cs	85.71%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            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 with missing lines	Coverage Δ
MetaMorpheus/EngineLayer/CommonParameters.cs	95.28% <100.00%> (-0.24%)	⬇️
...gineLayer/CrosslinkSearch/CrosslinkSearchEngine.cs	91.10% <100.00%> (+0.01%)	⬆️
...pheus/EngineLayer/FdrAnalysis/FdrAnalysisEngine.cs	96.50% <100.00%> (ø)
...EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs	96.10% <100.00%> (ø)
MetaMorpheus/EngineLayer/GlycoSearch/Node.cs	88.00% <ø> (+21.33%)	⬆️
...cificEnzymeSearch/NonSpecificEnzymeSearchEngine.cs	87.47% <100.00%> (ø)
...neLayer/ProteinParsimony/ProteinParsimonyEngine.cs	98.83% <100.00%> (ø)
MetaMorpheus/EngineLayer/Silac/SilacConversions.cs	97.83% <ø> (ø)
MetaMorpheus/EngineLayer/SpectralMatch.cs	99.71% <100.00%> (ø)
...GuiFunctions/ViewModels/ModTypeForTreeViewModel.cs	100.00% <100.00%> (+48.00%)	⬆️
... and 13 more

... and 1 file with indirect coverage changes

[trishorts]

wherein nic embraces the var side