[Biojava-l] Getting a Slice of an Alignment

[Dexter Riley]

Thanks for looking at the method!  I'll give your improved version a try.

subAlignment does return a slice of the Alignment; a horizontal slice.  I
need a vertical slice at a given location.  In other words,
subAlignment: 
if sequence in alignment has symbols at location, return entire sequence
get(Vertical)Slice:
for sequence in alignment, return subsequence at location

I use slices for primer design, where I have a candidate primer location and
want to see the list of different target sequences in the alignment at that
position (so I can consider possible mismatches, Tm, etc.)  
It would also be handy for the GUI, to say, "give me a view of bases
2000-2567 for every sequence in this really long alignment".

Thanks,
Ed
-- 
View this message in context: http://www.nabble.com/Getting-a-Slice-of-an-Alignment-tf1849222.html#a5066891
Sent from the BioJava forum at Nabble.com.