[WIP] Transciptomics: Digestion, Fragmentaiton, Decoy Generation

[nbollis]

to be considered after:
Transcriptomics Base is in MzLib and MetaMorpheus

** RNA Representation **
Nucleotide : INucleotide, IHasChemicalFormula

Represents a single nucleotide in an oligo
Has default implementations for all 4 common DNA and RNA bases and pseudouridine
Allows addition of custom bases

NucleicAcid : IBioPolymer

Base class which RNA inherits from. Can also be used for DNA in the future
Contains sequence information in the form of an array of nucleotides and a simple base sequence
Can be read in from one type of database so far
terminal caps are implemented as IHasChemicalFormula

** Digestion **
NucleolyticOligo

Inherits from LysisProduct akin in to ProteolyticPeptide for a protein
Handles Sequence information for digestion products

OligoWithSetMods

Inherits from NucleolyticOligo and implements interface IBioPolymerWithSetMods

Rnase

Inherits form DigestionAgent like Protease

** END WORK ON PR NOTES 11/30/23 **

NucleicAcid

Base class which RNA inherits from. Can also be used for DNA in the future
Contains sequence information in the form of an array of nucleotides and a simple base sequence

RNAFragment

Inherits from IProduct interface
Can be used in MetaMorpheus code interchangably with Proteomics.Product
Contains identical property names to the Proteomics.Product class

DissociationTypeCollection

Implements almost every function in the Proteomics.DissociationTypeCollection including

• Get Product Types based upon DissociationType (only CID and HCD are implemented)
• Get Mass shift based upon product type
• Get the terminus type based upon the fragment type
• Get Product Type based upon DissociationType and a specific Terminus (CID and HCD)

[codecov]

Codecov Report

Attention: 193 lines in your changes are missing coverage. Please review.

Comparison is base (40c4c4b) 74.90% compared to head (28bdc79) 75.46%.
Report is 3 commits behind head on master.

❗ Current head 28bdc79 differs from pull request most recent head 942ab61. Consider uploading reports for the commit 942ab61 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #744      +/-   ##
==========================================
+ Coverage   74.90%   75.46%   +0.56%     
==========================================
  Files         185      197      +12     
  Lines       30072    31025     +953     
  Branches     3006     3159     +153     
==========================================
+ Hits        22524    23414     +890     
- Misses       7036     7070      +34     
- Partials      512      541      +29     

Files	Coverage Δ
mzLib/Omics/Digestion/DigestionAgent.cs	90.38% <ø> (ø)
...ragmentation/Peptide/DissociationTypeCollection.cs	97.95% <ø> (ø)
...gmentation/Peptide/TerminusSpecificProductTypes.cs	100.00% <ø> (ø)
mzLib/Omics/IBioPolymer.cs	0.00% <ø> (ø)
mzLib/Omics/IBioPolymerWithSetMods.cs	95.23% <ø> (ø)
mzLib/Omics/SpectrumMatch/SpectrumMatchFromTsv.cs	97.34% <ø> (ø)
...Proteomics/ProteolyticDigestion/DigestionParams.cs	92.04% <100.00%> (+2.71%)	⬆️
...roteolyticDigestion/PeptideWithSetModifications.cs	96.18% <ø> (ø)
mzLib/Transcriptomics/Digestion/Rnase.cs	100.00% <100.00%> (ø)
mzLib/Transcriptomics/RNA.cs	100.00% <100.00%> (ø)
... and 11 more

... and 5 files with indirect coverage changes