Immunogenicity ligandome

Instead of trying to model the space of immunogenic epitope strings directly, instead let's model immunogenicity by only keeping track of which patterns *can't* be recognized by T-cells. These are epitopes which overlap with the set of "self" peptides used for negative selection in the thymus. 
I had more complex logic in the None branch before but then moved it out of the initializer. I'm going with your suggestion and just making DEFAULT_PEPTIDE_DIR the default value.