Ptm stoichiometry

[pcruzparri]

New PR with changes from PR #797 and more.

Description:
PTM stoichiometry classes created for each structural level (protein group -> protein -> (base) peptide - modification). Probably the most important class to understand is the QuantifiedPeptide class for which an object represents a collection of post-translationally modified variants sharing the same base sequence. This is in contrast with other Peptide classes that represent a peptide with a given full sequence. The QuantifiedProtein class, which stores the QuantifiedPeptide objects, handles peptide-to-protein indexing and obtaining of the modification stoichiometry for the protein. The QuantifiedModification class is primarily a data class, and the QuantifiedProteinGroup class is mostly a container for the different QuantifiedProtein members of the protein group. Lastly, the PositionFrequencyAnalysis class has a method to take a list of (full sequence, protein group list, intensity) tuples and create a collection of QuantifiedProteinGroup objects.

[codecov]

Codecov Report

❌ Patch coverage is 83.33333% with 37 lines in your changes missing coverage. Please review.
✅ Project coverage is 80.94%. Comparing base (54abc4c) to head (8a895de).

Files with missing lines	Patch %	Lines
...til/PositionFrequencyAnalysis/QuantifiedProtein.cs	73.80%	17 Missing and 5 partials ⚠️
...til/PositionFrequencyAnalysis/QuantifiedPeptide.cs	81.42%	12 Missing and 1 partial ⚠️
...tionFrequencyAnalysis/PositionFrequencyAnalysis.cs	97.14%	0 Missing and 1 partial ⚠️
...ositionFrequencyAnalysis/QuantifiedProteinGroup.cs	93.33%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #955      +/-   ##
==========================================
+ Coverage   80.93%   80.94%   +0.01%     
==========================================
  Files         268      273       +5     
  Lines       38495    38717     +222     
  Branches     4166     4204      +38     
==========================================
+ Hits        31155    31340     +185     
- Misses       6635     6664      +29     
- Partials      705      713       +8     

Files with missing lines	Coverage Δ
mzLib/MzLibUtil/ClassExtensions.cs	98.38% <100.00%> (+0.06%)	⬆️
...ositionFrequencyAnalysis/QuantifiedModification.cs	100.00% <100.00%> (ø)
...tionFrequencyAnalysis/PositionFrequencyAnalysis.cs	97.14% <97.14%> (ø)
...ositionFrequencyAnalysis/QuantifiedProteinGroup.cs	93.33% <93.33%> (ø)
...til/PositionFrequencyAnalysis/QuantifiedPeptide.cs	81.42% <81.42%> (ø)
...til/PositionFrequencyAnalysis/QuantifiedProtein.cs	73.80% <73.80%> (ø)

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