I think what you're looking at here are the labels of the alignment. What you need to be looking at is a combination of the labels and the symbol lists mapped to each label by the alignment.
The getLabels() method of a sub alignment will return you all the original sequences for that alignment, full-length. The symbolListForLabel(label) method of a sub-alignment will return only the symbols of the sequence that fall within the alignment. cheers, Richard On Mon, 2006-06-26 at 07:16 -0700, Dexter Riley wrote: > Hello. I have a FlexibleAlignment of 20 sequences, and want to get a slice > of it: > >Seq1 > nactatcgg...atcagcgtatctgac > >Seq2 > nactatcgg...atcagcgtatctgac > ... > >Seq19 > nactatcgg...atcagcgtatctgac > >Seq20 > nactatcgg...atcagcgtatctgac > > So a slice of the Location(1,5) of this alignment should look like: > >Seq1 > nacta > >Seq2 > nacta > ... > >Seq19 > nacta > >Seq20 > nacta > > How to do this? Alignment.subAlignment(null, Location(1,5)) returns an > alignment containing all the full-length sequences (presumably because all > the sequences have symbols between positions 1 and 5). > > Any suggestions would be greatly appreciated. > Thanks, > Ed > -- > View this message in context: > http://www.nabble.com/Getting-a-Slice-of-an-Alignment-t1849222.html#a5047818 > Sent from the BioJava forum at Nabble.com. > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
