Just another few questions. How long will it be before the source for your application is released and are there any plans to develop this into an applet? Also how have you drawn the base calls and mapped them to the correct peaks or is there a way of detecting this via the generated image?
I probably won't be able to release the source for the whole application. However, I will be open-sourcing the Swing components that handle the scrolling, etc., for a ChromatogramGraphic. I can't make any promises about a schedule for that -- I've got to do some refactoring to fix a bug I've found and I don't have time for it right now. Hopefully in the next month or two.
I am not planning on making an applet out this. Once I release the swing components, though, it should be straightforward to make your own. The chromatogram parsing libraries already include support for reading chromatograms from a arbitrary input stream, so loading a chromatogram via HTTP isn't a problem. (In fact, Chromatogram Viewer does this for the demo chromatogram that shows up when you first load the program.)
The basecalls are drawn into a separate panel by the higher-level swing components. If you'd like to draw the calls onto your generated image, you have a couple of options:
* Every chromatogram object contains an Alignment of basecalls to trace peaks. You can use this, plus your trace bounds and horizontal scale (if any) to figure out where the peaks are on the image.
* ChromatogramGraphic has a method ( http://biojava.org/docs/api/org/biojava/bio/chromatogram/graphic/ ChromatogramGraphic.html#getCallboxBounds(int,%20boolean) ) that will give you the bounds it has calculated for a particular call. You can draw a symbol for the base in the box however you like. (Note carefully that the index parameter is 0-based. This is different from the Alignment returned by Chromatogram.getBaseCalls() which, like most BioJava structures, uses 1-based indexing.)
Rhett
-- Rhett Sutphin Research Assistant (Software) Coordinated Laboratory for Computational Genomics and the Center for Macular Degeneration University of Iowa - Iowa City - Iowa - 52246 mailto:[EMAIL PROTECTED]
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