[Biojava-l] Nearing biojava 1.3.1 release

[Schreiber, Mark]

Hi -

There have been a lot of calls for a biojava 1.3.1 maintenance release. The good news is I'm just about ready. I just need to sort out some merging of the DP code from the biojava-live version.

Before I put it out I would really like to get something resolved. Currenlty DNATools.a() == RNATools.a(). This is due to the way that the Symbols are declared in AlphabetManager.xml. I personally think this is counter intuitive and wrong. It is very easily fixable (if it needs fixing). Unless anybody disagrees I would like to make it so they are not canonical. Note that this has implications for the NUCLEOTIDE alphabet which might mean such a move is not desriable so please speak now or forever hold your peace.

There have been a lot of bug fixes and minimal API breakage, there was a little bit although it is unlikely to be noticed by most people. I don't think I will be putting out a version for Java1.3 either.

- Mark

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