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FlashLFQ refactoring to enable generic peak operations #837

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@Alexander-Sol Alexander-Sol commented Feb 13, 2025

Added an interface, ISingleScanDatum and and abstract class, TraceablePeak, to enable the generic use of pre-existing FlashLFQ functions.

ISingleScanDatum

  • Defines the behaviour that a single datapoint is expected to have, e.g., mz, index, separation (retention time)
  • Examples are IndexedMassSpectralPeak, IsotopicEnvelope

TraceablePeak

  • Contains a list of ISingleScanDatum object
  • Implements a default CutPeak method
  • Provides a static FindPeakBoundaries method that should be useful

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codecov bot commented Feb 14, 2025

Codecov Report

Attention: Patch coverage is 89.65517% with 9 lines in your changes missing coverage. Please review.

Project coverage is 77.77%. Comparing base (e4dda42) to head (2711f04).

Files with missing lines Patch % Lines
mzLib/FlashLFQ/Interfaces/TraceablePeak.cs 90.19% 4 Missing and 1 partial ⚠️
mzLib/FlashLFQ/IndexedMassSpectralPeak.cs 66.66% 2 Missing ⚠️
mzLib/FlashLFQ/ChromatographicPeak.cs 96.00% 0 Missing and 1 partial ⚠️
mzLib/FlashLFQ/IsotopicEnvelope.cs 66.66% 1 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #837      +/-   ##
==========================================
- Coverage   77.78%   77.77%   -0.02%     
==========================================
  Files         230      231       +1     
  Lines       34152    34170      +18     
  Branches     3538     3540       +2     
==========================================
+ Hits        26566    26576      +10     
- Misses       6983     6990       +7     
- Partials      603      604       +1     
Files with missing lines Coverage Δ
mzLib/FlashLFQ/FlashLfqEngine.cs 92.18% <100.00%> (-0.29%) ⬇️
mzLib/FlashLFQ/ChromatographicPeak.cs 97.90% <96.00%> (-0.39%) ⬇️
mzLib/FlashLFQ/IsotopicEnvelope.cs 81.48% <66.66%> (-1.86%) ⬇️
mzLib/FlashLFQ/IndexedMassSpectralPeak.cs 92.00% <66.66%> (-8.00%) ⬇️
mzLib/FlashLFQ/Interfaces/TraceablePeak.cs 90.19% <90.19%> (ø)

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@nbollis nbollis left a comment

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I wonder if these interfaces should be in projects above FlashLFQ so that packages that FlashLFQ uses could implement these interfaces for use in FlashLFQ functions

/// The position of the datum in the separation domain,
/// e.g., retention time, ion mobility
/// </summary>
public double RelativeSeparationValue { get; }
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Should we use retention time here instead?

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3 participants