[DAS] DASSequence.java behaves somehow strange

[Thomas Down]

On Thu, Nov 28, 2002 at 12:08:06PM +0100, Thorsten Jansen wrote:
> Hi,
> testing my dasclient classes I recognized that the actual build from biojava
> and the build from 18.10.2002 show different behaviour in loading the
> sequence string using the DASSequence class (used method:
> dasSeq.subList(startPos,stopPos).seqString()). Using the ensembl (homo
> sapiens 8.30) data as reference server the following happens:
> 
> Using new build: Loading the sequence for chromosome 1 from position 30001
> to 40000 results in a "normal" sequence string from 30001 to 33556. From
> 33557 to 40000 only "N"s are listed. This is somehow related to the shown
> features "AC114498 (1 to 33556)" and "AL669831 (33557 to 212222)".

Okay, this is definitely wrong.  The reason why the first
clone worth of sequence is okay but the second fails is that
AL669831 is longer than a particular threshold (100000) which
causes its seqeunce to be fetched in tiles rather than in a single
request.  Something must have broken in the code which stitches
these tiles back together.  Looking now...

    Thomas.