[Biojava-l] Getting a Slice of an Alignment

[Richard Holland]

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  -  Biojava-l at lists.open-bio.org
> 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