[Jalview-discuss] editing and autoscrolling

Jim Procter foreveremain at gmail.com
Mon Mar 30 12:26:09 BST 2015


Hello Rob.

Perhaps we could Skype about your email ?  I think there are a couple of
different things going in regarding your automatic scrolling issue.

I'm also interested in exploring different alignment tools for RNA and
would value your advice about what we could incorporate in Jalview.

Jim.
On 27 Mar 2015 11:54, "rob van nues" <rob.van-nues at ed.ac.uk> wrote:

> Hi, I have been using JalView for a couple of years now, mainly for
> manual correction of computer generated alignments of quite divergent
> RNAs (in length and sequence) that, however, share particular conserved
> elements not picked up by the alignment programs.
>
> I work mainly offline (in the train etc) and always install the program
> locally.
>
> For including spacing on particular sequences I use the editing
> function but this function is quite hidden. After right-click, it takes
> going down two drop-down menus to select this option and if one need to
> do this a lot this becomes quite tiresome. Is there a way of associating
> a key-stroke with this function? Especially as, when accidentally
> right-clicking twice, another function is activated (I see a tiny dot
> in the selected cell) but can't do anything with it.
>
> Further, once I have been scrolling to select a large stretch of
> sequence horizontally or through a large set of sequences vertically
> for editing (mainly for introducing spaces) suddenly automatic
> scrolling is activated which makes subsequent selection of a stretch of
> nucleotides impossible (one has lost control now). Turning off
> automatic scrollling does not help here and I have to close the program
> and restart it again.
>
> Further, editing at ends of a group of lines seems sometimes impossible
> (i.e. trying to extend a line can only done one-by-one when a whole
> group could be edited in one go.
>
> I do not know whether this has to do with the OpenJDK version
> 1.7.0_75 I am using on slackware linux but it is quite annoying and
> inconsistent user interface behaviour. It would be very helpful if
> local installs could be customised so that, say automatic scrolling is
> always turned off from the start, or where one can define some
> key-bindings to frequently used functions.
>
> If anyone has any tips to get this done in the meantime I will be very
> grateful. It's a great program to use for this, but one could speed up
> the work-flow immensely with such customisation.
>
> Best regards
>
> --
> Dr. R.W. van Nues
>
> SYNTHETIC and SYSTEMS BIOLOGY at EDINBURGH (SynthSys)
>
> The University of Edinburgh
> CH Waddington Building
> Max Born Crescent
> Edinburgh EH9 3BF
>
> Telephone +44 (0)131 651 9018
> E-mail:rob.van-nues at ed.ac.uk
>
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> Scotland, with registration number SC005336.
>
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