[Biojava-dev] Biojava3-Core

[Scooter Willis]

I just committed a fairly significant number of changes into BioJava3-core. If you don't have any code changes in core then probably better to delete the core package and check out again o avoid resolving lots of conflicts.

I also checked in the beginning of biojava3-genome which makes significant use of biojava3-core. The code is being used to take gene predictions from GeneMarkHMM, GeneID and GeneMark which all have their own version of gff, gff3 and gtf output. The code will take features from the predictions and maps them onto DNASequences and allows you to get ProteinSequence for each prediction. It is very much a work in progress and will be adding additional features in the next 30 days for a gene annotation project that is part of the day job.

Let me know if you have any comments or suggestions. I promise better java docs, test cases and wiki overview soon.

Scooter