Residue selection using F2 is buggy or am I doing something wrong?

Jalview Discussion
1

Hi,

I’m trying to select ranges of amino acid residues using the keyboard so that I can apply sequence features to them. However, there appears to be a number of bugs in keyboard selection of residues in Jalview - unless I am doing something wrong?

I could use the mouse to make selections instead. But, it is much trickier to use the mouse as the “end” residue number is not displayed in the status bar - only the length of the selection. However this length counts gaps in the alignment, giving an inaccurate “end” residue number. When you are working with many sequence features and long sequences this makes mouse selection arduous and time consuming.

So, I try and use the keyboard as follows: switch cursor mode (F2), then enter the first residue (e.g. 25p followed by q) then the last residue (e.g. 378p followed by m). Then right click the selection marquee and apply sequence feature. Works great the first time.

However, the problem is that this only works once. After I do this, a further selection using the keyboard (to create another sequence feature) simply does not work. Also the cursor keys stop working to move the cursor around. Also, the cursor mode cannot be switched back to normal using F2 without reloading the project. This means that between creating every new sequence feature I have to save, close and reload the project.

Unless I am missing something?

Thank you,

Michael

2

Hi Michael,

This is definitely a bug! Thanks for reporting it. I’ve opened an issue on our bug tracker which you can follow to get progress reports:
https://issues.jalview.org/browse/JAL-3975

In the meantime, I have found a (slightly odd) workaround which, whilst not super convenient, is a lot more convenient than closing and opening the project every time you want to create a new feature.

  1. Open your project/alignment file as usual.
  2. Use keyboard input to select a region and create your first feature, just as you describe.
    – this is where keyboard input breaks, as you also describe.
  3. Open the Feature Settings window (View → Feature Settings …)
  4. Close the Feature Settings window.
    – you will now have keyboard input back, but it will go again after the next created feature, unless you
  5. Open the Feature Settings window again, and leave the Feature Settings window open.
  6. You can now use keyboard input to make as many features as you want, so long as you leave the Feature Settings window open!

I haven’t explored the code yet to work out what the problem is (or why this odd workaround works), but hopefully this workaround will help for now.

Let us know how you get on,

Ben