Re: [Gmod-ajax] Formatting using GFF notes and some other stuff

[Mitch S. <mit...@be...>]

Most of these are pretty high on the to-do list; specifically:

On 07/26/2010 11:24 PM, David Breimann wrote:
> 1. I would like to display some annotations from a GFF file on a 
> single track and control their color/glyph according to the content of 
> the note in the GFF (e.g. if 'Note=red' I would like this feature to 
> be colored red, and if 'Note=green' I would like it to be green).

Adding an option for javascript callbacks to customize feature elements 
is on the to-do list.  The way I'm currently envisioning it, you'd be 
able to specify a javascript function that would get the HTML element 
for the feature, and the feature data (including "Note" if you specified 
it in extraData).  Then you'd be able to modify that HTML element 
however you wanted based on that data.

> 2. Can  I control for the height of the tracks (I know it can be done 
> for WIG tracks, but what about normal features tracks)?

Are you seeing tracks that are too tall, or too short, or both?

On the development branch, the density histograms now have a height 
limit.  On the other hand, if the individual features are shown there's 
currently no mechanism for limiting the height of the track, although 
that's also on the to-do list.

> 3. How can I control which tracks are shown by default?

In index.html, there's a section that looks like this:

            var b = new Browser({
                                    containerID: "GenomeBrowser",
                                    refSeqs: refSeqs,
                                    trackData: trackInfo,
                                    defaultTracks: 
"DNA,gene,mRNA,noncodingRNA",
                                    location: queryParams.loc,
                                    tracks: queryParams.tracks,
                                    bookmark: bookmarkCallback
                                });

the "defaultTracks" setting is a comma-separated list of track labels; 
those tracks will be shown by default.

> 4. Suggestion: have a "reset view" in the browser (currently I have to 
> clear my browser history to return to the default view).

I don't doubt that this is useful for you, but since I don't think I've 
heard this requested before, I'm interested in the specifics of the use 
case.  What's the context where you want to do this?  And when you want 
to go back to the default view, what makes the default better than what 
you were looking at before?

For example, you might have two biological questions that you want to 
investigate, and each of them might be addressed using a different set 
of tracks.  So if you're looking at a bunch of tracks, and you decide 
you want to switch all those tracks off and go look at a different set 
of tracks, then that's one situation where I can imagine wanting to do 
have a "reset view" option.  But I'd like to hear the specifics of your 
case.

> 5. Is there any ETA for the improvement of the WIG tracks (most 
> importantly adding a scale)?

That's definitely high on the to-do list, but it's tough to estimate a 
time, because it'll involve restructuring the code a bit.  And I'm 
currently in the middle of dealing with another issue.  But the scale 
bar is probably first on the list after this current bug I'm working on.

Mitch