UGENE Forum - Search window

Oct 23^rd, 2012 at 2:38am

Malvolio Offline
YaBB Newbies

Posts: 12

Hello!
I recently started using version 1.11.2 (universal Linux binary, full version) and definitely Ugene is getting better with every version, however I didn't like the behaviour of search function in this version. In older ones (like 1.9.3 from ubuntu repo) search appears as a separate window, and when it finds the requested sequence you can easily select the sequence and manipulate it as you please (copy, annotate etc). In newer versions search is available as a side panel and it automatically creates annotations for found sequences. It took me a while to figure out how it functions and in my view this way of highlighting search results only creates a mess in the sequence viewer. So is there a way to enable old-style search function in newer versions?
Thank you very much for your great job!

Back to top

IP Logged

Reply #1 - Oct 23^rd, 2012 at 7:09pm

Mikhail Fursov Offline
YaBB Administrator

Gender:
Posts: 162

Hi Malvolio,

Removing blocking dialogs and replacing them with a tabbed/docked windows is a one of the targets of further UGENE GUI development.

Having no blocking dialogs is better in many ways, for example you can start filling search parameters, switch to sequence back, return to filling search parameters again from the point you stopped before without loosing data filled initially.

But you are correct that we should keep all the functions we had before and here we need details from you what function is lost in Find Dialog. I think you can do the same and even more with results marked as annotations.

Here is examples:

1) When you click an annotation you automatically select the sequence under the annotation. So you can export, copy the sequence;

2) If you do not need this result (annotation) - just delete it by pressing Del button;

3) You can navigate multiple find result sets at once - just store them in different groups or use different annotation names;

4) You can disable highlighting for the annotation with a specified name. In this case a sequence will be highlighted only when you select the annotation. So you will not see a mess on the screen;

---
UGENE team

Back to top

IP Logged

Reply #2 - Oct 24^th, 2012 at 5:20am

Malvolio Offline
YaBB Newbies

Posts: 12

I absolutely agree that tabs and docks are better than popups and dialogs, so it's great that they're being implemented. Actually I got used to viewing search results as annotations and sometimes it may come in handy. However, I still think it may be confusing for beginners, so maybe there should be a special type of annotation for search results (by default it is "misc_feature").
Anyway I'll try to figure out more precisely what I miss in the current find tab and post a more detailed message later.
Good luck to you and looking forward to November, 1 release!

Back to top

IP Logged

Reply #3 - Nov 1^st, 2012 at 8:18pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Quote:

In newer versions search is available as a side panel and it automatically creates annotations for found sequences. It took me a while to figure out how it functions and in my view this way of highlighting search results only creates a mess in the sequence viewer. So is there a way to enable old-style search function in newer versions?

I think the new behavior of Find Pattern is non-intuitive and sometimes misleading.

Why is this an issue? Here's an example. Let's assume I search for some pattern and it is automatically saved as annotation. After that I would like to search for another pattern or maybe I want to search for the same pattern, but with slightly different settings (for me it happens quite a lot). This creates a mess: since I didn't change the name of the feature I end up with more annotations with the same name, and I can not distinguish among new and old search results. So, I have to delete all annotations and search again. Moreover, if I accidentally search for the same pattern without changing settings, identical annotations will be created.

I really miss the old search behaviour, which was very similar to what we have in a web-browser or a text editor: we search for some pattern, we iterate over this pattern and if it's intersting we save it as annotation. I would suggest that this mode should be available along with new behavior. Another possible solution: every new search cleans up the previous search results (auto-annotation like behaviour).

Back to top

IP Logged

Reply #4 - Nov 2^nd, 2012 at 5:29am

Agu Offline
Junior Member
(Argentinian)

Gender:
Posts: 63

Hi!
I was also surprised with the change, but agree that the side bar is a good direction.
One feature that was lost with the new bar is the ability to search for ambiguous bases.
Besides that, I think some feedback to the user will make it much more intuitive. For example, after you press the search button nothing happens, so if you were not closely watching the annotations (thing that you need to know in advance), you won't know if something was found or not. Something like "Your pattern was found 35 times and annotated as 'misc_feature'" or "Your pattern was not found" would be very useful (it could be part of the bar, not a new dialog).

In my experience, most of the searches are to check something, but not intended to make a permanent annotation, so I think the user should have the option to use "temporary" (default) or "permanent" annotations.
This auto-annotation-like, as Konstantin suggested, would also solve the problem of the mess, as you wouldn't care if too many thing got annotated, just re-open and is clean again. Deleting is not an option when your pattern was found too many times and you don't have a clue which ones are supposed to be deleted (for example after decreasing the percentage of identity too much).

Then, It would be a nice feature to be able to drag and drop annotations from the temporary to the permanent table.

Back to top

IP Logged

Reply #5 - Nov 2^nd, 2012 at 2:37pm

Yuriy Vaskin Offline
Global Moderator

Gender:
Posts: 138

The ambiguous bases search hasn't been lost. It's available when the "Substitute" algorithm type is selected.

In UGENE 1.11.3 an interesting Find Pattern feature is available. You can input multiple sequences in the patter field in FASTA format and use names of the sequences as the names of corresponding annotations.

I agree that creating permanent "misc_feature" annotation by default isn't a good idea. I talked to local biologists recently and they point to the same Find Patter usability issues as Agu does.

I'm thinking of how it should look like that's why there is no issue in the tracker yet. But thanks for your comment, I'll try to fix it asap since Find Pattern is on the most popular tool in UGENE.

Back to top

IP Logged

	Welcome, Guest. Please Login or Register
	Welcome to our forum.