This modification contains a lot of changes.
- creation of a TransitionMatrix class that reads a set of inframe CDS sequences to determine the codon transitions
	It uses a pseudocount to augment transitions that do not appear in the raw CDS data
- addition of the TransitionMatrix class to Sequence class to compute likelihood (log) and graded-likelihood (log)
	Grade-likelihood is a cumulative list of transition probabilities. It will be used to compare against the
	original sequence.
- testing of CAI, GeneticCode etc.