…lignIO, Graphics, HMM, KEGG, and PDB

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Addresses #2236

Added type annotations to most getter functions in Align, AlignIO, Graphics, HMM, KEGG, and PDB modules. While this is not a completed effort, it will hopefully be useful to people who use these modules and like type hints. Since no added functionality was added and very little actual logic was changed, no additional tests were created, but all existing tests were ran.