Update Handling of Sequence Variants (Part 7): Point LoadProteinXML to new VariantApplicationMethod

[trishorts]

current LoadProteinXML has two int variables: maxVariantsForCombinatorics =4 and minAlleleDepth = 1. VariantApplication now has three consensusPlusVariantIsoforms = 1, minAlleleDepth = 0 and maxVariantsPerIsoform = 0. This PR changes LoadProteinXML to use all three variables. It also calls the new GetConsensusAndVariantBioPolymers method in VariantApplication

this may break some tests in MM where variants are expected but none are called for. The former LoadXML called for 4 with a min depth of 1. defaults now are zero.

[codecov]

Codecov Report

❌ Patch coverage is 70.18868% with 79 lines in your changes missing coverage. Please review.
✅ Project coverage is 80.91%. Comparing base (57f1327) to head (2d4af20).

Files with missing lines	Patch %	Lines
mzLib/Omics/BioPolymer/SequenceVariation.cs	56.75%	22 Missing and 10 partials ⚠️
mzLib/Omics/BioPolymer/VariantApplication.cs	65.43%	20 Missing and 8 partials ⚠️
mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs	88.54%	7 Missing and 4 partials ⚠️
...Databases/DecoyGeneration/DecoyProteinGenerator.cs	12.50%	0 Missing and 7 partials ⚠️
...micsDatabases/DecoyGeneration/RnaDecoyGenerator.cs	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #970      +/-   ##
==========================================
- Coverage   81.00%   80.91%   -0.10%     
==========================================
  Files         269      269              
  Lines       38826    38957     +131     
  Branches     4241     4272      +31     
==========================================
+ Hits        31450    31521      +71     
- Misses       6640     6678      +38     
- Partials      736      758      +22     

Files with missing lines	Coverage Δ
mzLib/Omics/BioPolymer/VariantCallFormat.cs	86.95% <ø> (ø)
mzLib/UsefulProteomicsDatabases/ProteinDbLoader.cs	96.03% <100.00%> (ø)
mzLib/UsefulProteomicsDatabases/ProteinDbWriter.cs	95.48% <100.00%> (ø)
...micsDatabases/DecoyGeneration/RnaDecoyGenerator.cs	83.72% <50.00%> (ø)
...Databases/DecoyGeneration/DecoyProteinGenerator.cs	90.79% <12.50%> (ø)
mzLib/UsefulProteomicsDatabases/ProteinXmlEntry.cs	96.78% <88.54%> (-2.75%)	⬇️
mzLib/Omics/BioPolymer/VariantApplication.cs	82.76% <65.43%> (+0.99%)	⬆️
mzLib/Omics/BioPolymer/SequenceVariation.cs	66.93% <56.75%> (-19.03%)	⬇️

... and 1 file with indirect coverage changes

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