editing and autoscrolling

Jalview Discussion
1

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@ed.ac.uk

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

2

Hello Dr van Nues,

Let me try to address some of your issues...

1) editing: the context menu to Edit an alignment is indeed quite hidden, but is only meant as a 'last resort' for editing residues. It sounds like you are wanting to edit/remove gaps. This can be done using mouse and/or cursor operations much more easily. Please take a look at the help for Editing Alignments, in the tool or online at
http://www.jalview.org/help/html/editing/index.html
http://www.jalview.org/help/html/features/cursorMode.html

2) double-right-click behaviour - I am puzzled by this, as I can't reproduce it. Can you describe in any more detail how/when this happens?

3) behaviour of scrolling: there are some known issues with this, but 'turning on automatic scrolling' doesn't seem to have been reported before.
You may find that working in cursor mode (using Q and M to mark regions) lets you avoid this issue.
If it continues to be a problem please describe a reproducible example if possible, and we'll look into it.

4) editing at end of sequences - I'll get back to you on that...

5) you are correct that there is no Preference setting to turn off automatic scrolling on startup; I can raise a feature request for this. Note that if you save and later reload a Jalview project, the state of this option is preserved. But this setting relates to following a mouseover of a linked alignment or structure, which doesn't sound quite like your problem if you are working in a single alignment.

Best regards,

Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
www.jalview.org
www.compbio.dundee.ac.uk

···

From: Mungo Carstairs (Staff)
Sent: 30 March 2015 08:49
To: rob van nues
Subject: Re: [Jalview-discuss] editing and autoscrolling

________________________________________
From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of rob van nues <rob.van-nues@ed.ac.uk>
Sent: 27 March 2015 11:54
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] editing and autoscrolling

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@ed.ac.uk

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

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

The University of Dundee is a registered Scottish Charity, No: SC015096

3

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@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@ed.ac.uk

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

Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss