Is there a java implementation of protein sequence ambiguous searching

[adele]

  I am a software developer in a microbiology lab. EMBOSS has functions 
such as DREG, PREG to do the regular expression search of a nucleotide 
sequence. Since most of our own softwares are programmed in JAVA, I am 
trying to find the JAVA implementation of DREG, PREG, and FUZZNUC and 
FUZZPRO so that we can import these ambiguity sequence searching 
functions into our own softwares.

Thanks for any help!

Adele

Biochemistry and Microbiology
University of Victoria
BC, Canada

adelej at uvic.ca