I have re-written the feature projection code. This has made things much cleaner, and hopefully understandable to mortals. Also, the projection APIs now have documentation! If you are interested, look at the javadocs for org.biojava.bio.seq.project, and in particular, ProjectionContext and ProjectedFeatureHolder.
This has hit loads of files (the cvs log was 77 lines long before I added comments!). So, I've put in a branch tag PROJECTION_CHANGE to cvs. If in the future, you wish to work with the old projection code, you will need to check out that branch. The cvs HEAD is going to contain the new projection code.
At the same time, I've been sorting out some of the package structure under .seq - this may break code that directly uses classes like SubSequence, but will leave code unaffected that uses SequenceTools.
As a side-effect of this, the bytecode package has gained a load of documentation and some bug fixes. Accordingly, there is a new bytecode.jar under biojava-live.
I have made no attempt to roll these changes over to other packages, such as the ensembl code. You have been warned. If you run production code from the biojava-live head, then you will get what you deserve :)
Matthew
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