[gt-users] New feature announcement

[Brent Pedersen]

On Wed, Nov 26, 2008 at 11:09 AM, Sascha Steinbiss
<steinbiss at zbh.uni-hamburg.de> wrote:
> Hi everyone,
>
> I am happy to announce that there is an official beta version of the
> next GenomeTools release with some substantial improvements to the
> feature set of the AnnotationSketch library.
> It is now possible to take more control over layout details to further
> customise the output.  For example, blocks can now arbitrarily assigned
> to tracks (which can be created on the fly) based on individual block
> properties (see http://genometools.org/trackselectors.html) instead of
> just the type. Furthermore, it is possible to use the internal Graphics
> object to draw to something called custom tracks. Custom tracks (see
> http://genometools.org/customtracks.html) are an extension of a generic
> AnnotationSketch track in which free user-defined drawing of arbitrary
> shapes (e.g. generated from any data source which can be accessed from
> Python) is allowed.
> Also, there is a new 'rectangle' feature style and support for
> specifying an alpha value for every color has been added.
>
> The URLs above point to short tutorials on how to use this functionality
> in practice. I am also still working on extending the FeatureNode
> bindings to include everything in the feature_node_api.h, and more is to
> come soon.
>
> In the meantime, I will be happy to get feedback on the new features.
> Feel free to pull from the official repository at
> git://genometools.org/genometools.git and have a look at what is new.
>
> Best regards,
> Sascha Steinbiss
>
> --
> 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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>

hi, very cool.
alpha and track_selectors working great!

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 havent tried custom tracks yet. but i like the gc_content example.

i think on this page:
http://genometools.org/customtracks.html

diagram = Diagram(feature_index, seqid, range, style)
should be:
diagram = Diagram.from_index

-brentp