pcruzparri

Requesting a second round of reviews! The second to last commit contains a little more in detail most changes. Currently pending work is to create a small enough subset of...

Some pending changes: Potentially modify the input to ProteinGroupsOccupancyByPeptide() be some object and create an interface rather than a list. Remove occupancy additions to FlashLFQ. These additions have been moved...

Stale and updated in new branch with updated and clean commit history. Pull request addressing these changes (and more) is now #955.

The only failing integration error is the following: ```Error: D:\a\mzLib\mzLib\MetaMorpheus\MetaMorpheus\EngineLayer\Silac\SilacConversions.cs(659,130): error CS1061: 'IIndexedMzPeak' does not contain a definition for 'ZeroBasedMs1ScanIndex' and no accessible extension method 'ZeroBasedMs1ScanIndex' accepting a first argument...

We'll want to address ambiguous sequences in the future with these string parsing methods. Here are some non-trivial cases I saw when trying a first implementation of that in this...