[Biojava-l] SubstitutionMatrix

[Richard Holland]

I've found the problem already - the SubstitutionMatrix class has a few inconsistencies in the use of trimmed and untrimmed versions of lines. The guessAlphabet() method in this case is falling over because of an unchecked blank line in the matrix file.

I've submitted a patch to trunk which fixes all the inconsistencies and should also fix this problem with the NUC files.


On 7 Apr 2010, at 14:32, Andreas Dräger wrote:

> Hi Stefan,
> 
> Thank you for this hint. I don't know what the problem is. Recently, I tested it and it worked. I'll have a look on it tomorrow and come back to you with an answer pretty soon!
> 
> Cheers
> Andreas
> 
> Dipl.-Bioinform. Andreas Dräger
> Eberhard Karls University Tübingen
> Center for Bioinformatics (ZBIT)
> Sand 1
> 72076 Tübingen
> Germany
> 
> Phone: +49-7071-29-70436
> Fax:   +49-7071-29-5091
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/