add codon alphabet (inherited from Bio.Alphabet.Alphabet) for CodonSeq
change __getitem__ method of CodonSeq to incorporate the step slice
add mismatch support
modify _str_line method in Generic.py for the ease of CodonAlignment __str__ method
delete _str_line method
add toSeq method for CodonSeq (helpful to write it out)
add toMultipleSeqAlignment method for CodonAlignment
fix a bug of terminal anchor checking
add code for CodonAlignment -- MultipleSeqAlignment convertion
add user specified pro-nucl correspondance support and start codon ENH
change 10s to anchor_len
add test file for CodonAlign
small revision for the test to pass

add header
add frameshift support in CodonSeq
add unittest for rf_table option in CodonSeq
fix a small bug of _str_line
reorganise slice option for CodonSeq
update CodonAlignment test
naive implementation of forward frameshift
fix a bug of get_full_rf_table() to deal with last codon