So myself & Chris have discussed this off list & we believe it's because of a NULL compound element in the Sequence given to the SequenceMixin method.
Does anyone on list know how the AlignedSequence code encodes gaps & the alike? Andy On 6 Dec 2010, at 13:50, Andy Yates wrote: > Hi Chris, > > Well that's going into my toStringBuilder() method & that particular line is > concerned with asking a compound for its String representation. How often do > we get nulls in our Sequences and how to deal with them. After all the > Sequence AGTCNULLAGTC is probably more harmful then helpful > > Andy > > On 6 Dec 2010, at 12:45, Chris Friedline wrote: > >> Hello, >> >> Found another potential error case, this time in beta2 (fresh pull >> from git last evening). For more info, please see >> http://pastie.org/1351388 for test case and stack trace. The JUnit >> test passes simply because the pair object is not null, but fails when >> trying to extract any information from the pair itself (toString(), >> getIdenticals(), etc). The substitution matrix file is from >> ftp://ftp.ncbi.nih.gov/blast/matrices. I'm doing large numbers of >> pairwise alignments, which do not all fail, but most do with this same >> error. >> >> Thanks, >> Chris >> >> -- >> PhD Candidate, Integrative Life Sciences >> Virginia Commonwealth University >> Richmond, VA >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Andrew Yates Ensembl Genomes Engineer EMBL-EBI Tel: +44-(0)1223-492538 Wellcome Trust Genome Campus Fax: +44-(0)1223-494468 Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
