That does help, thanks. However, when calling getAsList() on the aligned sequences and printing, this is what I see. Something seems wrong. It does appear as though null is being inserted where there should be gaps
seq = [A, A, C, A, C, T, T, G, A, C, A, T, G, T, T, C, null, G, T, C, G, C, A, A, C, T, T, T, T, A, A, G, A, G, A, T, T, A, G, A, G, T, T, T, T, C, G, G, T, T, C, G, G, C, C, G, G, A, C, G, A, A, A, C, A, C, null, null, null, null, null, null] seq = [T, A, C, C, C, T, T, A, A, C, A, T, null, null, T, C, A, G, T, G, A, C, A, A, C, C, T, C, null, null, A, G, A, G, A, T, G, A, G, null, G, C, T, T, T, C, T, C, T, T, C, G, G, null, null, null, null, null, null, null, A, G, A, C, A, C, T, G, G, G, A, T] Chris On Mon, Dec 6, 2010 at 12:22 PM, Andreas Prlic <[email protected]> wrote: > 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 > -- 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
