[Jalview-discuss] problems loading nhx files

jprocter at compbio.dundee.ac.uk jprocter at compbio.dundee.ac.uk
Fri Jun 10 00:45:08 BST 2011


Still slow, even with that dataset ?  What memory is being allocated ... I found it fine on an i7 mac with 128mb java heap.

J. B. Procter Jalview/enfin Barton group

-----Original Message-----
From: Albert Vilella <avilella at gmail.com>
To: Jim Procter <jprocter at compbio.dundee.ac.uk>
Cc: jalview-discuss at jalview.org
Sent: Thu, 09 Jun 2011 16:32
Subject: Re: problems loading nhx files

I tried with the latest version but still it's superslow...

On Thu, Jun 9, 2011 at 3:22 AM, Jim Procter
<jprocter at compbio.dundee.ac.uk> wrote:
> Hi Albert,
>
> On 23/07/28164 05:59, Albert Vilella wrote:
>>
>> I am loading alignments and nhx tree files associated to them (see
>> example in attachments) with Jalview 2.4.0.b2, and I getting this
>> window:
>>
>> Possible problem with tree file:
>> Tree file contained comments which may confure input algorithm.
>
> This is a warning message telling you that Jalview might not have parsed the
> comments in the NHX file correctly. Most of the time Jalview gets it right,
> but my newick tree parser has been known to get confused with trees with
> comments - however in that case, it usually results in a spectacularly
> broken tree topology, and a bunch of other problems.
>>
>> The tree loads fine, and I can sort my sequences by input tree, but
>> the whole system is sluggish, it takes seconds to transition
>> for every click...
>
> ok. tree parser is working then :)
> I tried this on my machine using the latest build of jalview (get it from
> the www.jalview.org/versions.html page), and don't seem to have a problem.
> Can you have a go with that ?
>
> Jim.
>
>
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