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
