Change object names and adds the CodonArray object
Change object names and adds the CodonArray object

NucleotideSequenceArray and ProteinSequenceArray are renamed to NucleotideArray
and ProteinArray. Also to match the Array naming scheme, GenericAlignment is
renamed to SequenceAlignment.

Addition of CodonArray object means that some methods in NucleotideArray were
moved because they dealt with protein-coding sequences and therefore are not
general for all nucleotides sequences.

kentwait/bioseq