[Biojava-l] SimpleAssembly.subList()

[Thomas Down]

On Fri, Apr 06, 2001 at 05:24:40PM +1200, Schreiber, Mark wrote:
> The SimpleAssembly test seems to be failing, I get the following output:
>  
> gattacannnnnnnnnnnnn
> g
> gatta
> ttacann
> ttacannnn
> tcg
> nnnn
> fragment at 1-7
>     test at 2-3
> fragment at 10-13
>     test at 9-10
>         sub-test at 9-9
> 
> I am thinking all those n's shouldn't be there (at least some of them
> anyhow)

Nope, you're right -- there was a fairly subtle bug in the
seqString/subStr optimized implementations in AssembledSymbolList.
Only really affected very short assemblies, for the most part
(which is how it went un-noticed for so long).

Hope this is fixed now -- if you still see any more problems,
AssembledSymbolList.locationUpstreamOfPoint is probably
prime suspect...

   Thomas.