[Biojava-l] About ABITrace class

Russ Kepler russ at kepler-eng.com
Sun Dec 30 17:04:05 UTC 2007

On Friday 28 December 2007 01:54:30 David Bourgais wrote:
> Hello BioJava users
> I am writing a little program using BioJava 1.5 and JFreeChart 1.0.8.
> My aim is to display with JFreeChart a chromatogram by reading an ab1
> file with the BioJava help.
> Okay, I can display my chromatogram. But, my chromatogram size is 13301
> (using getTrace(AtomicSymbol base)) when my sequence size is 1110 bp
> (according to the the BufferedImage produced with BioJava).
> Why this difference ? How can I correct my program in order to see
> correctly my chromatogram ?

If I understand you correctly you're looking at the trace data (multiple 
points per peak) and comparing to the base calls (one call per peak).  In my 
experience folks interested in the chromatogram would prefer to see an image 
with the chromatogram spaced properly, those primarily interested in the base 
calls prefer to have the chromatogram scaled around a fixed width for the 
basecall.  There's code to do either in BioJava, but the former might not be 
setup to generate a BufferedImage (if you can't find it I might be able to 
help some).

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