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Quant interfaces#985

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Alexander-Sol wants to merge 2 commits into
smith-chem-wisc:masterfrom
Alexander-Sol:QuantInterfaces
Open

Quant interfaces#985
Alexander-Sol wants to merge 2 commits into
smith-chem-wisc:masterfrom
Alexander-Sol:QuantInterfaces

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@Alexander-Sol
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codecov Bot commented Dec 3, 2025

Codecov Report

❌ Patch coverage is 90.53118% with 41 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.08%. Comparing base (36b61b2) to head (ef4e13a).

Files with missing lines Patch % Lines
mzLib/FlashLFQ/FlashLFQResults.cs 87.17% 11 Missing and 4 partials ⚠️
mzLib/FlashLFQ/ProteinGroup.cs 33.33% 9 Missing and 1 partial ⚠️
mzLib/FlashLFQ/Peptide.cs 43.75% 8 Missing and 1 partial ⚠️
...antification/GenericProteinQuantificationEngine.cs 85.10% 2 Missing and 5 partials ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #985      +/-   ##
==========================================
- Coverage   81.09%   81.08%   -0.02%     
==========================================
  Files         271      274       +3     
  Lines       39144    39230      +86     
  Branches     4292     4303      +11     
==========================================
+ Hits        31744    31808      +64     
- Misses       6650     6667      +17     
- Partials      750      755       +5     
Files with missing lines Coverage Δ
mzLib/FlashLFQ/IntensityNormalizationEngine.cs 97.27% <ø> (-0.01%) ⬇️
...ation/MedianPolishProteinQuantificationStrategy.cs 100.00% <100.00%> (ø)
...uantification/Top3ProteinQuantificationStrategy.cs 100.00% <100.00%> (ø)
mzLib/FlashLFQ/SpectraFileInfo.cs 100.00% <ø> (ø)
...antification/GenericProteinQuantificationEngine.cs 85.10% <85.10%> (ø)
mzLib/FlashLFQ/Peptide.cs 92.78% <43.75%> (-4.09%) ⬇️
mzLib/FlashLFQ/ProteinGroup.cs 86.66% <33.33%> (-10.67%) ⬇️
mzLib/FlashLFQ/FlashLFQResults.cs 90.14% <87.17%> (-2.88%) ⬇️
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@nbollis nbollis left a comment

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What about the interface that is already in readers? How does this play into this?

/// <summary>
/// The peptide sequence
/// </summary>
string Sequence { get; }
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We should probably use BaseSequence or FullSequence so it maps better with our existing objects.

/// <summary>
/// The filename without extension
/// </summary>
string FilenameWithoutExtension { get; }
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Cap on Name

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Love the dependency injection and inversion of control here

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