[Biojava-l] SearchProfile Sample App (dp package)

[Roger McIntosh]

I am experimenting with the SearchProfile sample app.
I am confused about how the "StoppingCriteria" is to be used to specify
termination conditions for the training algorithm. In my testing, most fasta
protein sequences cause the system to "hang" after one cycle of training.
Very simple sequences work (i.e. continue on through the 5 cycles specified
in the test app).
Can anyone offer a ray of enlightment here?
Also: I see no provision for specifying pseudocounts in constructing the HMM
model from the primary data. Is this correct?
R.McIntosh