[Biojava-l] sequence masking?

[Douglas Hoen]

Hi,

I want to mask out DNA subsequences, such as repetitive DNA. I have  
been unable to find any APIs for this. I did find  
SequenceTools.maskSequence(), but this method masks the region  
outside an indicated location rather than inside it and it also uses  
gaps as the mask symbol, whereas I would like to use N or lowercase.  
Another related API is SoftMaskedAlphabet class, which seems useful  
but I can't find any utilities that take advantage of it.

Any help would be appreciated. Thanks,
Doug