Hi all,
I am trying to turn a GenBank file to a Sequence object using
sequenceIterator interface in org.biojava.bio.seq package. However, one line
in the file cannot be parsed. The problem is information after that
unparsable line in the GenBank file are missing from the return Sequence
object. I
Hi everyone,
I think that there might be a problem with AnnotationBuilder (parsing
off Kegg for the curious).
With the following parser:
LineSplitParser tvp = new LineSplitParser();
tvp.setEndOfRecord("///");
tvp.setSplitOffset(12);
tvp.setContinueOnEmptyTag(true);
t
Hi -
Below is the method that is being called (copied from DistributionTools). I cannot see
anything obvious such as a memory leak but there could be one, can anybody else spot
anything?
Maybe if someone has a fancy profilling utility they could try it and let us know
where the slow down is oc
Hi folks,
I now received the answer from [EMAIL PROTECTED] (see below).
For my purposes, I conclude that don't need the "frame" value, especially
since I use "blastn" as a program. It seems save to construct the
(SeqSimilaritySearchSubHit's) query- and subject-strand values from the way
the f
I apologize, the line:
Distribution[] dists = distOverAlignment2(align, false, 0.01);
should actually be:
Distribution[] dists = DistributionTools.distOverAlignment(align,
false, 0.01);
Thank you.
Alberto Ambesi
On 3 Dec 2003, at 09:55, David Huen wrote:
On Tuesday 02 Dec 2003 4:49 pm, Alberto
On Tuesday 02 Dec 2003 4:49 pm, Alberto Ambesi wrote:
> hi, I found this bug when using Distrubutions iteratively many times.
> The problem is that when creating Distrubution objects iteratively
> computation time for each iteration increases with time.
>
> this is a piece of code that demonstrates
