[gt-users] New feature announcement

[Brent Pedersen]

On Thu, Dec 4, 2008 at 4:03 AM, Sascha Steinbiss
<steinbiss at zbh.uni-hamburg.de> wrote:
> Brent Pedersen wrote:
>> hi, very cool.
>
> Hi Brent,
>
>> alpha and track_selectors working great!
>
> Good to hear that.
>
>> is it possible to specify the "z-index" of each feature type for
>> stacked/collapsed features? it seems to know to draw CDS on top,
>> but is there any way to specify the order explicitly -- and/or to
>> specify the bar_height per-feature_type, rather than per-image.
>> how does it determine from the track_selector_func what y-order the
>> features are drawn in?
>
> Right now, this is done by drawing elements in alphabetical order
> according to their type. One could think about making this configurable by
>
>   a) determining the order dynamically from the graph structure
> (elements for child nodes are always drawn on top of their parents'
> elements) or

i dont know if that's enough resolution for cases where you have multiple
feature types at the same level but want to specify that one is on top.

>
>   b) making it possible to specify a per-type z-index in the style file
> to facilitate arbitrary orderings. Any type with undefined ordering is
> then added in alphabetical order (or another sensible default).
>
> What do you think is more appropriate? The first option would be more
> intuitive, while the second option leaves more room for customisation.
>

yes, i like b) because it allows more customization. could be as you
suggest z-index per layer,
or a maybe a list in the format section that specifies order:
   draw_order = { 'gene', mRNA', 'CDS', ... }



>> i think on this page:
>> http://genometools.org/customtracks.html
>> diagram = Diagram(feature_index, seqid, range, style)
>> should be:
>> diagram = Diagram.from_index
>
> Thanks. I'll change this right away.
>
>> -brentp
>
> -Sascha
>
> --
> Sascha Steinbiss
> Zentrum für Bioinformatik
> Universität Hamburg
> Bundesstr. 43
> 20146 Hamburg
> Germany
>
> Email:  steinbiss at zbh.uni-hamburg.de
> URL:    http://www.zbh.uni-hamburg.de/steinbiss
> Phone:  +49 (40) 42838 7322
> FAX:    +49 (40) 42838 7312
>
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