[Biojava-l] Sequence logo

[mark.schreiber at novartis.com]

Hi -

There is some code for a Swing component in one of the GUI packages. It is 
useful for making a single position but not an entire logo.

In the past I have used the code that does the drawing and modified it to 
work on a Distribution[]. The code shouldn't really be in a Swing 
component it should be in a class that generates drawing instructions for 
a Graphics2D object. This is a lot more flexible because you can then draw 
into a Frame or Canvas if you want a GUI, or a BufferedImage if you want a 
graphics file, or a Batik Graphics2D object if you want to make an SVG 
file.

Also the code in BioJava doesn't let you modify the g2 object at all so 
you can't turn on anti-aliasing (highly recommended).

The idea of separating BioJava's graphics and GUI capabilities has been on 
the cards for a while. If you do this for the Sequence Logo it would be 
great to feed it back to the group as an example of how it should be done.

- Mark


biojava-l-bounces at lists.open-bio.org wrote on 08/05/2009 01:05:34 AM:

> Dear all,
> 
> Just a question: I assume you all know this visualization of position 
> frequency matrices, in which A, T, G, and C appear according to their 
> frequency within the matrix with different sizes and all letters are 
> colored differently (green, red, blue, yellow).
> 
> Is there a class in BioJava that produces this kind of visualization?
> 
> Cheers
> Andreas
> 
> -- 
> Dipl.-Bioinform. Andreas Dräger
> Eberhard Karls University Tübingen
> Center for Bioinformatics (ZBIT)
> Sand 1
> 72076 Tübingen
> Germany
> 
> Phone: +49-7071-29-70436
> Fax:   +49-7071-29-5091
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

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