[Biojava-l] GenBank files and weight matrices

[mmatilai at hytti.uku.fi]

Hi,

I'd like to search a GenBank file with a weight matrix. My idea was to create a simple 
weight matrix and then iterate through the file using a sequence iterator moving forward 
with the hasNext command. At each iteration the  new sequence would then be 
annotated with the weightmatrix method annotate(seq) and the positions and scores of 
matches reported in a for loop.

Apparently this is not as straight-forward since i get a match from beginning of the 
sequence file until end and a bioexception is declared before the score is reported.

I found also the Cookbook recipe and tried the exact code from this just with the 
modification that i was using a genbank file with sequence iterator to get the sequences 
and i have the same problem.

Should I do sth different to annotate the sequence in a GenBank file with my weight 
matrix? Is the sequence iterator the problem? How is it working actually, what part of the 
file does it read at one iteration?

Best regards
Merja