hi,
i am now using biojava, and i think it is quite good, especially the modeling and statistics class, but on data manipulation, it seems somewhat complex. if she is like bioperl in seqio or searchio, she will be more beautiful i think. so i want the design goal of biojava, for biologist or programmer?
I agree with you about the complexity. If you can think of a cleaner and simpler API and have the time or can motivate others then feel free to tackle this. I think this happened because the early developers where all using BioJava as a library for developing compute-intensive applications, rather than as a scripting environment for running external anaysis programs. Obviously, now it would be good to address this.
Matthew
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