[Biojava-l] Multiple Sequence Viewer

[Russ Kepler]

On Thursday 12 February 2009 08:20:55 Scooter Willis wrote:
> My plan is to model the multiple sequence viewer used in JALView. Sequence
> name on the left to fire events when clicked. I also typically work with
> large sequences so need both horizontal and vertical scroll which does not
> appear to be in the current viewers. I do see support for viewing a range
> of a sequence but nothing to scroll or I could be missing something on how
> the current viewer would scroll not using a ScrollPane.

I guess I don't see the problem with using a ScrollPane, it works well in the 
app I've written.

> This should be something easy to do in BioJava based on the importance of
> viewing multiple sequence alignments.

It not all *that* hard, in my case it's a ScrollPane with a 
TranslatedSequencePanel with a MultiLineRenderer with a bunch of 
GappedRenderers containing individual sequence or other renderers.  The TSP 
holds the alignment and feeds the individual renderers with the appropriate 
sequence.

Somewhere around here I have something I scratched up in BioJava 1.4 that 
worked as a Clustal alignment viewer, I'll see if I can find it and pop it 
your way.