Hello,
I’m wondering if a small bug in Jalview could be fixed that tends to frustrate the heck out of our new users.
The bug seems to be specific to the Mac-platform, and can be easily replicated by:
- Right clicking on any sequence label
- [Sequence Name] ==> Edit Name/Description
In the resulting window, the Sequence Name section is highlighted in blue - if one attempts to click & drag this blue-highlighted section ==> the program will freeze with the spinning wheel of death.
We realize that no-one would actually want to drag/drop this text, but unfortunately it is very easy to accidently perform this action when solely trying to edit the sequence name.
Hope this makes sense – thanks for your help,
Eric
Hi Eric - Jalview doesn't do this at the moment, but it's a useful useful feature request - so I've added it to the list (http://issues.jalview.org/browse/JAL-684).
Jim.
ps. Just as an aside - are you annotating regions of the same sequences in different alignments ? If that is the case, then after annotating them all for one alignment using the Find/Create features button, simply export the annotation as a 'features file', and then drag it on to the next alignment to mark up the same regions again.
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On 19/10/2010 22:22, Polinko, Eric wrote:
I’m wondering if it is possible to enter a list of regular expressions for motifs I’m interested in and have them saved. This way I can then re-apply the list to my next multiple alignment without needing to manually enter the expressions one by one. I have about 10 I need to look for all the time.
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J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.
Hi Eric, once again. Sorry for the confusion - the real reply to your email is below:
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J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is a Scottish Registered Charity, No. SC015096.
ahem - another lack of coffee related mistake here. Those of you who check out the bug report might have noticed that I took a look at this bug in May after Rhein Asland reported it, but couldn’t reproduce it on OSX 10.6, which suggests its an Apple Java issue that has been resolved in the latest OS version. Do you have a Snow Leopard installation that you can verify this on, Eric ?
Jim.
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J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is a Scottish Registered Charity, No. SC015096.
Ah sweet coffee!
Yes – I have verified this happens for us on both OSX 10.5 & 10.6.
Thanks,
Eric
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On 10/20/10 3:04 AM, “Jim Procter” jprocter@compbio.dundee.ac.uk wrote:
On 20/10/2010 07:54, Jim Procter wrote:
Ah - yes, it’s a bit of a show stopper. I actually noticed it back in May but as yet, haven’t had the chance to hunt the cause down (see the bug report here: http://issues.jalview.org/browse/JAL-530 ).
ahem - another lack of coffee related mistake here. Those of you who check out the bug report might have noticed that I took a look at this bug in May after Rhein Asland reported it, but couldn’t reproduce it on OSX 10.6, which suggests its an Apple Java issue that has been resolved in the latest OS version. Do you have a Snow Leopard installation that you can verify this on, Eric ?
Jim.
–
Eric Polinko
119 Clapp Hall
Biological Sciences
University of Pittsburgh
(412) 624-0419
epolinko@pitt.edu