Very nice to hear from you, Sebastian.
I am using Jalview now very frequently. Every tad bit I realizewhich
could improve the workflow in Jalview I will post here. Please tell
me, if this is desired.
That's fine - but I have to say that since there is no one working
full-time on Jalview, you might not always get an immediate reply to
help or questions.
I've added all your other requests in to this email, so I can address
them all at once.
Basti wrote:
I am using Jalview and I found three nice properties with which
Jalview would be much more nice (can this be?)
There is always room for improvement, however far down the asymptote it
may be (I'm afraid).
1.) I would be happy if the scope of the shifting sequence (in the
case I shift it up) would be in the displayed window. Means when I
move it up it dissapears in the hiden upper frame area.
Good point - and not too hard to fix. It will be added to the buglist.
2.) Is there a possibility to search for a name in the titles of the
sequence? So its easy to insert a new sequence right next to a similar
one.
The find function also searches sequence IDs - so you can already do
this. However, there is a bug in the current release version that
prevents case insensitive matching working correctly - so you may not
have noticed that matches to IDs occur. You can also, of course, use the
'sort by ID' to put all the sequences with similar IDs together, after
you have added the sequence.
3.) Could there be a possibility to move the whole sequence via the
mouse up and down? Just unlock (as in BIOEDIT) and click the label
(hold mouse button pressed) and move it up. When arrived at desired
position, release mouse and..here we are!
I agree that it might be a useful thing to do, and I will again add it
to the features list. I think it will require some experimentation,
though: if enabled this way, I can imagine that it would be easy to move
a sequence set up or down when you are click-dragging to select over the
alignment.
Sebastian wrote in : Sequence Labels
how can I switch off the "/1-156" behind the "normal" labels?
This is under the alignment window's format menu, which contains all of
the settings for layout control of the current view. You can also change
the default settings in your preferences (including the preferences for
adding the /start-end to the sequence ID when you write out a particular
type of file).
Sebastian wrote in : 'new query'
When switching to the keyboard mode then a black cursor appears at the
upper left in the sequence area. Even when I have a sequence selected.
Wouldn't it be better to move this activated cursor area at the
beginning of the selected sequence?
Agreed. It would.
Or if more than one sequence are selected, then it could mark the
first letter of the upper sequence.
Yes. This would be a sensible default (since it goes to the upper left
of the sequence area, it is sensible to go to the upper-left of the
selected area).
Thanks for all these comments - I think they may help Jalview to be even
nicer to use 
Jim
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J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
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