[Jalview-discuss] editing and autoscrolling

rob van nues rob.van-nues at ed.ac.uk
Fri Mar 27 11:54:13 GMT 2015


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

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



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