Hi Nicole.
On 11/10/2012 06:57, Nicole Norris wrote:
I'm attempting to label a series of sequences with some User-defined
Sequence Features, which I am creating as I go along.
OK.
However, after I've created more than one feature, in the Create New
Sequence Feature(s) dialog box I don't get the drop-down list with
previously created features. It starts off as, and remains, a white
'text field' box, with no drop-down arrow present. This differs from
the description and screenshot of this dialog box detailed in the help
file.
The screenshot in the help file actually shows the amend feature dialog
box, which - when a location is double clicked that intersects with
several features, shows the drop down menu to let you select which
feature you want to amend (it also looks different because its from an
old version of the jalview applet!). The create new feature dialog box
will remember the last feature type and group that you used, but it
doesn't have any 'last input' history beyond this, or a menu to select
from the existing feature types on the alignment. It's a great idea to
add one, however, so I've lodged a feature request along these lines here:
http://issues.jalview.org/browse/JAL-1190
I've found a work around: if I create a 'new' feature with exactly the
same name and group as an old feature, it combines that 'new' feature
with the old, but this is a tedious work around, since I have to use
exactly the same spelling throughout.
I'm not quite sure what you are saying here. The feature type dictates
how Jalview will colour the feature, so if you use the same feature type
string then all features will be rendered in the same way (although, if
you are using a 'graduated feature colour' then the actual colour shown
for a feature might depend on the associated score or the text in the
description field). I get, however, that it's hard to get the spelling
right sometimes - the sequence feature user interface could be improved
greatly for this kind of work.
Also, is there are a way to select two separate regions of a sequence
at once? (I would like to annotate to disparate regions with the same
feature, this would save some time). I have figured out how to do this
by selecting all columns in an alignment, but I would prefer not to
select the entire column.
There isn't a way to create disparate selections at the moment that
allows multiple features to be created at the same time. The only way
you can create multiple features is via the 'Find' dialog - which
includes a 'create features' button to create a feature for every match
on the alignment for the query (such as a regular expression defining a
sequence motif).
You've unfortunately hit on an area where Jalview is more difficult to
use than it should be. We've been wanting to improve the feature
creation and editing interface for a while, but there always seems to be
another thing that needs to be done first. However, I'm hopeful that the
user interface will get reviewed in the near future since we very much
want to include support for hierarchical and multipart features to allow
Jalview to handle the annotation from databases such as Ensembl. If you
know of any java programmers who might be interested in helping out with
this - I'd be very happy to hear from them !
Sorry I can't be more help.
Jim.
ps. I might be able to squeeze the drop down menu support into the 2.8.1
release.. but this isn't a promise, unfortunately...
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