Protein Inference for Glyco Search (1/2)

[trishorts]

Previously, there was no protein inference for glyco search. This PR adds protein inference for the complete dataset. This PR DOES NOT have the option of writing the individual file results. That will be done in part two. I broke this down to simplify implementation and review. Once this PR is integrated, I will work on part two. After we can do both full set and individual file results I will move to LFQ.

Changes were made to: GlycoSearchParamters PostGlycoSearchAnalysisParameters PostGlycoSearchAnalysisTask.

[codecov[bot]]

Codecov Report

Merging #2232 (af96b0d) into master (57235d4) will increase coverage by 0.29%. The diff coverage is 94.21%.

@@            Coverage Diff             @@
##           master    #2232      +/-   ##
==========================================
+ Coverage   91.15%   91.44%   +0.29%     
==========================================
  Files         133      134       +1     
  Lines       20068    20167      +99     
  Branches     2798     2809      +11     
==========================================
+ Hits        18292    18441     +149     
+ Misses       1280     1237      -43     
+ Partials      496      489       -7     

Impacted Files	Coverage Δ
...yer/GlycoSearchTask/PostGlycoSearchAnalysisTask.cs	80.00% <90.66%> (+15.48%)	:arrow_up:
EngineLayer/ProteinParsimony/ProteinGroup.cs	94.29% <100.00%> (ø)
TaskLayer/GlycoSearchTask/GlycoSearchParameters.cs	100.00% <100.00%> (ø)
TaskLayer/GlycoSearchTask/GlycoSearchTask.cs	92.54% <100.00%> (+0.93%)	:arrow_up:
...ycoSearchTask/PostGlycoSearchAnalysisParameters.cs	100.00% <100.00%> (ø)
TaskLayer/XLSearchTask/WriteFile.cs	96.61% <0.00%> (+0.67%)	:arrow_up:
EngineLayer/GlycoSearch/GlycoSpectralMatch.cs	95.01% <0.00%> (+4.03%)	:arrow_up:
EngineLayer/GlycoSearch/GlycoSearchEngine.cs	81.68% <0.00%> (+6.03%)	:arrow_up:
TaskLayer/GlycoSearchTask/GlycoProteinParsimony.cs	76.36% <0.00%> (+7.27%)	:arrow_up:

[Alexander-Sol]

The appveyor build didn't fail, but it was taking longer than usual. I manually cancelled it in order to start builds related to installer issues

[lonelu]

I try to run a task in GUI. Some default values are not auto selected in GUI->GlycoSearchTaskWindow, such as O-Glycan Database. And Protein Parsimony is not selectable.

[lonelu]

It seems like one cannot select the 2nd checkbox 'Require at least two peptides...' or 3rd checkbox 'Treat modified peptides..' Also if unselect 1st checkbox 'Apply protein parsimony...', I cannot select it again.