Catch and warn if SFF files are missing null padding at end

Thanks for Martin Mokrejš for sample data and emails about this issue.
Warn if SFF files are missing null padding at end

Thanks for Martin Mokrejš for sample data and emails about this issue.
More useful error message from Bio.TogoWS.search_count(...)

This seems to be returning XHTML for several people over
multiple operating systems, and may be due to a change or
temporary problem with TogoWS.
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