[Biojava-l] blast parsing and empty hits

[Doug Rusch]

Hi all,

I am relatively new to the biojava community and I had a question about the blast parser in biojava. While looking at the code and judging from its behavior, the blast parser has no way to deal with empty blast reports (where no hit was found). My questions are : Am I missing something obvious? If not, are people really using this blast parser? If so, how do you handle this behavior? If not, what do people actually use to parse blast output?

Thank you for your help.

Cheers!
Doug Rusch
TCAG.org