I’m attempting to label a series of sequences with some User-defined Sequence Features, which I am creating as I go along.
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:
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.
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…
On 11/10/2012 06:57, Nicole Norris wrote: