[Biojava-dev] OutOfMemory when using a big Weight Matrix to find Motifs in 1.3.1 but not in 1.3

[Bruno Aranda - e-BioIntel]

Hi Mark,

I've tried to increase the memory heap to 512 Mb but my little linux 
almost died... However I've found the origin of the problem. The class I 
tested followed the steps of your wonderful tutorial, and I used the low 
score treshold of "0.1". With the new ScoreType System I got too many 
results for my motif (every base in the sequence), so too many features 
were created and the OutOutMemoryError was raised.
Now, for instance, I can put a treshold of 4000 (?) and I get some 
results (some of them with a probability higher than 5000 (?)... but I 
don't understand why probability scores are that high. Well, I will send 
to your home a beer truck if you can explain which probability is used 
for these score matrices ;-). Thanks,

Bruno Aranda
ebioIntel