Added form fields to handle new alignment processing options.

Added the second HMM conversion method and fragment handling options.
Prep. for adding additional flags to hmm build.
Letter Height radio now retains state on results page

The letter height radio button was returning to the default state after
each search. This was not ideal now that we are allowing people to reuse
their previously updated sequences. This change makes sure that the last
selected state is maintained across browser loads.
Adds alignment processing and fragment handling functionality.