[gt-users] New feature announcement

[Brent Pedersen]

On Fri, Jan 23, 2009 at 10:23 AM, Brent Pedersen <bpederse at gmail.com> wrote:
> 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
>

all the changes i mention above are in my fork on github (think i may
be getting the hang of git).
i've used FeatureNode.create_from_ptr()
i also added python unit tests.
-b