feat: add toggle for 2 or 3 class epitope predictions

[jeffreyHoelzel]

Summary:

• currently, PepSeqPred can only predict if a residue is or is not an epitope (i.e., 1 for yes, 0 for no)
• to encode some level of uncertainty in the predictions, it would be helpful to add a 3rd uncertain class which is toggleable
• for example, protein ABC123 could have the predicted epitopes: 000011122221111222001010101222000, where 0=not epitope, 1=yes epitope, and 2=uncertain

Done when:

1. logic is cleanly integrated into existing training and inference scripts
2. logic is toggleable via the CLI scripts
3. appropriate unit, integration, and E2E tests are implemented and pass locally