[gt-users] New feature announcement

[Brent Pedersen]

On Sun, Dec 14, 2008 at 2:59 PM, Sascha Steinbiss
<steinbiss at zbh.uni-hamburg.de> wrote:
> Brent Pedersen wrote:
>>>> 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?
>
> I have found the time to work further on these suggestions and completed
> a first implementation of the ideas. It can be found in my 'barheight'
> branch in github (git://github.com/satta/genometools.git) and brings the
> following additions:
>
> - it is now possible to assign the bar_height to each type separately
> (and, of course, still globally in the 'format' section), and
>
> - each type can now have a 'z_index' style option (which is an integer).
> The z-indices of collapsed types determine the order in which features
> are drawn. Particularly, types with higher index numbers are drawn on
> top of types with lower numbers. Types with no z-index numbers are
> always drawn below those with indices and their internal ordering is
> determined alphabetically.
>
> Up to now, tracks are also ordered alphabetically by their track
> identifier, except custom tracks which are always drawn in the order
> they were added to the diagram, and below all type tracks. However, am
> planning to introduce an interface in which tracks (including custom
> tracks) can be reordered using diagram_* methods like a list. I will be
> able to do this if I find the time (at the moment, I need to dedicate
> more time to other projects which were neglected prior to revision
> submission).
>
> Feel free to test the new features, and let me know if problems arise or
> in case you have any more suggestions.
>
> 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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thanks! is the z_index going into the main repo soon?

also, a couple stylistic questions.
1) would you accept a patch that switches the use of e.g.
Feature.create() and Feature.__init__() i think it's more idiomatic to
be able to do
>>> f = FeatureNode(seqid, "gene", 100, 900, "+")
and then
>>> f = FeatureNode.create(ptr)

than vice-versa and it could rename to FeatureNode.create_from_ptr()

2) would you accept a patch that implements python descriptors so one can use:

>>> fnode.strand
'+'
>>> fnode.strand = '-'

instead of fnode.get/set_strand() ?

if either both of those seem reasonable, i'll upload a patch to the tracker.
-brent