limit scope of variable mods to a subset of proteins

[jke000]

Extend the variable mod support to allow the user to specify a list of protein identifiers that the modification(s) would only apply to. For example, apply a list of variable mods to just histone proteins and not all proteins in the database.

[jke000]

Completed with commits fd4d7fdf and 55d75c6 by adding parameter "protein_modlist_file". This parameter points to a file containing lists of a modification number and protein accession string, one pair per line, which will apply that variable modification only to db entries that match that protein string.