[Biojava-l] SequenceMixin Error in BioJava3 Alignment

[Andy Yates]

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
>> 
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> 
> 
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-- 
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/