create alignment submodule

~~**NOT READY FOR MERGE**  Working on some doc issues, but I want travis to run the tests in the meantime.~~

Doc issues sorted out, I think this should be ready to go, but we need to remember to test install/testing with setup.py before the release since I did have to make changes to setup.py. 

Fixes #419.

I think that `StripedSmithWaterman, AlignmentStructure, align_striped_smith_waterman` should be a part of the `./ssw` directory's `__init__.py` file so that you can import like this: `from .ssw import ( ...` which is more consistent with other `__init__` imports. 

In the ssw folder I tried to treat each internal file as  a private member with the `__init__.py` creating an artificial "ssw.py" that gives us a cohesive block which can be relocated and thrown around. I feel that importing directly through the `ssw` directory breaks this cohesion.