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Add the comment on glyco-searching and the search summary on the result file #2367

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@RayMSMS RayMSMS commented May 28, 2024

  1. Add lei's comment on the coding of o-pair searching.

  2. Try to add the search summary information (PSMs, protein group, glycoPsms, Level1-glycoPsms) into the "AllResult.txt" file for glycoSearch
    (1) Text function in PostGlycoSearchAnalysisTask class
    (2) Tester in TestOGlyco class (make sure we parse the certain value)
    (3) revise the "readCsv", and enable it to read the allPSMs file smoothly.

@RayMSMS RayMSMS added the WIP Work in progress, not ready for review label May 28, 2024
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codecov bot commented May 28, 2024

Codecov Report

Attention: Patch coverage is 89.67972% with 29 lines in your changes missing coverage. Please review.

Project coverage is 93.73%. Comparing base (7dab370) to head (64f6bc4).

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2367      +/-   ##
==========================================
+ Coverage   92.97%   93.73%   +0.75%     
==========================================
  Files         139      139              
  Lines       21668    21704      +36     
  Branches     2983     3001      +18     
==========================================
+ Hits        20146    20344     +198     
+ Misses       1043      903     -140     
+ Partials      479      457      -22     
Files Coverage Δ
MetaMorpheus/EngineLayer/GlycoSearch/AdjNode.cs 80.00% <ø> (ø)
MetaMorpheus/EngineLayer/GlycoSearch/GlycanBox.cs 96.59% <100.00%> (+14.77%) ⬆️
...pheus/EngineLayer/GlycoSearch/LocalizationGraph.cs 100.00% <100.00%> (ø)
MetaMorpheus/EngineLayer/GlycoSearch/ModBox.cs 90.90% <ø> (ø)
MetaMorpheus/EngineLayer/GlycoSearch/Node.cs 88.00% <ø> (+21.33%) ⬆️
MetaMorpheus/EngineLayer/PsmTsv/PsmFromTsv.cs 97.74% <100.00%> (+0.04%) ⬆️
...pheus/TaskLayer/GlycoSearchTask/GlycoSearchTask.cs 97.59% <100.00%> (ø)
MetaMorpheus/EngineLayer/GlycoSearch/Glycan.cs 97.00% <96.66%> (+0.21%) ⬆️
...aMorpheus/EngineLayer/GlycoSearch/GlycoPeptides.cs 88.03% <94.11%> (ø)
...eus/EngineLayer/ModernSearch/ModernSearchEngine.cs 74.54% <85.71%> (ø)
... and 4 more

... and 2 files with indirect coverage changes

…Psms, Level1-glycoPsms) into the "AllResult.txt" file for glycoSearch

(1) adding text function in PostGlycoSearchAnalysisTask class
(2) adding tester in TestOGlyco class (make sure we parse the certain value)
(3) revise the "readCsv", enable to read the allPSMs file smoothly.
@RayMSMS RayMSMS added ready for review and removed WIP Work in progress, not ready for review labels Jun 4, 2024
@RayMSMS RayMSMS changed the title The lie's comment about the glyco-searching Add the comment on glyco-searching and the search summary on the result file Jun 4, 2024
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@nbollis nbollis left a comment

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lgtm

nbollis and others added 12 commits June 13, 2024 17:45
(1) Rewrite the Summary writing function
(2)Add the <summary> comment in the fuction header
1. add new tester model for "OGlycanCompositionFragments"
1. add the tester for writing function, in different search type
2. glycoBox tester for decoy glycanBox
1. delete the bin and retry to pass the tester
deleted the duplicate tester
@RayMSMS RayMSMS requested a review from elaboy August 6, 2024 19:11
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4 participants