implement simple codon alignment without mismatch and frameshift
add index seq file support and test_data
add CodonSeq object for codon slice
add __str__ method to CodonAlignment for nice output
modify unittest for CodonAlignment
replace self-defined exceptions with build-in exceptions
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 frameshift support in CodonSeq
add unittest for rf_table option in CodonSeq
fix a small bug of _str_line