A new feature of the editing features of Jalview is to lock regions for editing using the existing red selection area. Any edits made with the mouse in this area will not affect the alignment outside the group.
An existing request on the Jalview todo list was to have keyboard editing. This would require the addition of a cursor to the Jalview interface, not a problem.
What editing capabilities would people want to do with the keyboard?
I thought editing similar to Vi editor would make sense.
Use cursor keys to move the cursor around the alignment.
Press "I" to insert a gap. If you enter a number after "I", that many gaps will be inserted.
Press "X" to delete a gap. If you enter a number after the "X", that many gaps will be deleted.
Group editing would need to lock the top left and bottom right of the selection area, suitable keys are required to do this.
Or Geoffs idea,
"........... I'd like to be able to use the arrow keys to move around the alignment and then, maybe control-rightarrow to edit to the right, and likewise to the left. At the moment, the arrow keys move the current sequence up and down the list. This is useful too, so it would also be necessary to have some quick way to switch between editing modes"
Any thoughts?
A new feature of the editing features of Jalview is to lock regions
for editing using the existing red selection area. Any edits made
with the mouse in this area will not affect the alignment outside the group.
An existing request on the Jalview todo list was to have keyboard
editing. This would require the addition of a cursor to the Jalview
interface, not a problem.
What editing capabilities would people want to do with the keyboard?
I thought editing similar to Vi editor would make sense.
OK so far
Use cursor keys to move the cursor around the alignment.
Press "I" to insert a gap. If you enter a number after "I", that many
gaps will be inserted.
And just how long will it take to insert 1000 gaps? It would be better to do
the vi thing and have number then command.
Either that or a command line where it waits for an [ENTER] after each
command.
Press "X" to delete a gap. If you enter a number after the "X", that
many gaps will be deleted.
See previous comment.
Group editing would need to lock the top left and bottom right of the
selection area, suitable keys are required to do this.
Q and M being the top left/bottom right keys on the keyboard?
The idea of having a 'command mode' is good, possibly toggled by a click
button.
Or Geoffs idea,
"........... I'd like to be able to use the arrow keys to move around
the alignment and then, maybe control-rightarrow to edit to the
right, and likewise to the left. At the moment, the arrow keys move
the current sequence up and down the list. This is useful too, so it
would also be necessary to have some quick way to switch between editing
modes"
:/[esc]?
..d
···
On 21/3/06 11:06 am, "Andrew Waterhouse" <andrew@compbio.dundee.ac.uk> wrote:
Any thoughts?
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Hi Andrew,
Thanks for looking at this.
Good to see that you can lock a region for editing, but I still think we need a general "move between gaps" editing style as well. This should work either on a complete alignment, or in a locked region.
With regard to keyboard editing: I don't like the VI-style suggestion, though I could live with it I doubt it would be generally popular. I think having a key that modifies the behaviour of the arrow keys would be a better solution. Alternatively, a hybrid of the two ideas would also work.
i.e.
1. Press "i" to insert gap at the point. Pressing "i" multiple times or holding down "i" would insert multiple gaps. Typing a number before pressing "i" would insert that many gaps.
2. To delete gaps Press "d" - similar behaviour to I except that D would only ever delete gaps.
It will be important to have a visual indication that shows what mode you are in. view mode, edit mode, locked region edit mode etc...
With regard to the cursor. This would be a useful addition in the view mode as well. i.e. I would like to be able to move around the alignment with the arrow keys and so explore the features that have been annotated on the alignment.
Geoff.
···
On Tue, 21 Mar 2006, Andrew Waterhouse wrote:
A new feature of the editing features of Jalview is to lock regions for editing using the existing red selection area. Any edits made with the mouse in this area will not affect the alignment outside the group.
An existing request on the Jalview todo list was to have keyboard editing. This would require the addition of a cursor to the Jalview interface, not a problem.
What editing capabilities would people want to do with the keyboard?
I thought editing similar to Vi editor would make sense.
Use cursor keys to move the cursor around the alignment.
Press "I" to insert a gap. If you enter a number after "I", that many gaps will be inserted.
Press "X" to delete a gap. If you enter a number after the "X", that many gaps will be deleted.
Group editing would need to lock the top left and bottom right of the selection area, suitable keys are required to do this.
Or Geoffs idea,
"........... I'd like to be able to use the arrow keys to move around the alignment and then, maybe control-rightarrow to edit to the right, and likewise to the left. At the moment, the arrow keys move the current sequence up and down the list. This is useful too, so it would also be necessary to have some quick way to switch between editing modes"
Any thoughts? _______________________________________________
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------------------
Geoff Barton, Professor of Bioinformatics, School of Life Sciences
University of Dundee, Scotland, UK. geoff@compbio.dundee.ac.uk
Tel:+44 1382 385860/345843 (Fax:345764) www.compbio.dundee.ac.uk