[Biojava-l] force it to be dna sequence and not protein

[Guoneng Zhong]

Hi,
In the course of debugging this parser program I am doing for ClustalW 
report, I realized that all along it has been thinking that it is a 
peptide sequence alignment.  This is the code fragment:

             AlignmentFormat format = new MSFAlignmentFormat();
             Alignment alignment = format.read(reader);

Convince the program that the file that created the "reader" is an 
alignment of dna sequences?

Thanks,
G