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 _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
