[Biojava-l] expression browser

[Matthew Pocock]

Hi all,

I've recently received a steady stream of requests for informaton about 
my old expression browser application. It is hideously un-maintained. 
I've just looked at the code for the first thing since 1999, and am 
embarased by it.

http://www.sanger.ac.uk/Users/mrp/java/ExpressionBrowser/, 
http://www.sanger.ac.uk/Users/mrp/java/ExpressionBrowser/browser-src.jar, 
http://www.sanger.ac.uk/Users/mrp/java/ExpressionBrowser/lib.jar

It may be worth picking through the entrales of this code base and 
pulling out stuff we don't want to implement again. From my point of 
view the natty things are:

   * Tree rendering - rooted and unrooted as well as arbitrary layouts
     - tools can be registered to handle tree selection

   * Matrix/Tables that can be manipulated by row/column labels
     - views can be built that don't copy the underlying data

   * Some simple tree/cluster APIs and algorithms

   * A graphics scein-graph layered on top of graphics 2d
     - you can do lots of the normal vector graphics stuff
     - swing components can be embedded
     - data can be associated with rendered glyphs

It may be worth laughing at:

   * some archealogical code that became the beginnings of BioJava

   * my use of XML-DOM as a data model

   * an early (and incomplete and buggy) implementation of xlink/xpointer

I realise that there are now java standards or libraries for some of 
this stuff, and don't want to see any of it make it onto the bio servers 
unless it has merit in its own right. I was sort of thinking of 
re-writing expression browser, and making it a seperate biojava package 
(like the GUI das client).

Thoughts?

Matthew