[Biojava-dev] abi trace viewer

[Michael L. Heuer]

All right, all these people working on drawing stuff.

At the InfoVis2002 conference, I saw a presentation "Arc Diagrams:
Visualizing structure in strings" by Martin Wattenberg (email:
mwatten@us.ibm.com).  Very generally, the idea is to find pairs of
matching substrings in a string and represent them as translucent arcs.

For fun, I wrote a version that works with existing Features on a
Sequence.  This way the substring-finding problem is decoupled from the
visualization.

> http://shore.net/~heuermh/arcdiagram.tar.gz

I started an attempt at reconciling this with the existing biojava
renderers, but to be honest I get in that code and want to rearchitect
everything.  Maybe after a few more hours I'll understand it better.  :)

   michael


On Thu, 7 Nov 2002, Matthew Pocock wrote:

> Schreiber, Mark wrote:
> > This truly is Righteous,
> shucks
> >
> > Just a few humble comments.  Color.BLACK in java 1.3 is Color.black
> > (stupid I know). I have fixed these in the CVS. Another problem is that
> > all the peaks appear to go to the top of the screen when they have no
> > signal instead of going to the bottom of the screen.
>
> My bad - I sort of forgot what coordinate system I was in. You can just
> render to depth - (What_we_had_before) for y-coordinates.
>
>   Finaly to be
> > completely pedantic the standard colour scheme (if there can be said to
> > be such a thing) is:
> >
> > C = blue
> > G = black
> > A = green
> > T = red
>
> I sort of guessed these colors. My memory is too crap and I couldn't see
> a propper abi viewer. Feel free to fix this, or use the
> org.biojava.bio.gui.SymbolStyle interface to plug this in (and fix
> DNAStyle default values to match these).
>
> > So despite my quibbling, top effort!
> >
> > - Mark
>
> Matthew
>
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