Re: SequenceMixin Error in BioJava3 Alignment
Andreas Prlic <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Hi Andy, Check out the SimpleAlignedSequence class, for how Gaps are handled... Does that help? Andreas On Mon, Dec 6, 2010 at 7:13 AM, Andy Yates <[email protected]> wrote: > 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 > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l