[Biojava-dev] Contributing chromatogram support to BioJava

[Rhett Sutphin]

On Wednesday, March 12, 2003, at 10:02  AM, Matthew Pocock wrote:
> The only possible gotcha with the sequence rendering API is that 
> nucleotides are evenly spaced. So, you have to scale the number of 
> samples to fit into however many pixles 'width' is reserved for one 
> nucleotide. If ChromoatogramGraphic is the same, then thunderbirds are 
> go.

Ah.  I have to withdraw my previous statement, then.  
ChromatogramGraphic is oriented towards representing the whole 
chromatogram (or a contiguous section) as it is actually sampled.  It 
provides methods for horizontal and vertical scaling, but not on a 
per-call basis.  And it can draw lines dividing the chromatogram into 
calls, but it's just an overlay -- the actual drawing of the traces is 
isolated from the calls.

FWIW, I've just finished porting it over to the biojava-style 
Chromatogram API, and I've put the javadoc up in the same place as 
before:

http://www.detailedbalance.net/~rhett/dev/biojava/chromat-contrib/doc/

It may be that an adapter could be made to fit ChromatogramGraphic into 
a SequenceRenderer, but it sounds like it would be a 
square-peg-round-hole sort of thing.  It probably would be better just 
to port AbiTraceRenderer to use the Chromatogram interface instead of 
the AbiTrace class.  The interfaces (at least the part that 
AbiTraceRenderer uses) are very similar.

Rhett
--
Rhett Sutphin
Research Assistant (Software)
Coordinated Laboratory for Computational Genomics
   and the Center for Macular Degeneration
University of Iowa - Iowa City, IA 52242 - USA
4111 MEBRF - email: rhett-sutphin at uiowa.edu