[Biojava-dev] Proposal to change DP interface

[David Huen]

The training algorithm interfaces in org.biojava.bio.dp are have a method:-

public void train(SequenceDB db,
                  double nullWeight,
                  StoppingCriteria stopper)
           throws IllegalSymbolException,
                  BioException

This method is only suitable for single-head DP as it provides for only one 
SequenceDB as a source of training sequences whereas twohead DP requires 
two sequences.

I propose to change the SequenceDB to SequenceDB[]:-

public void train(SequenceDB [] db,
                  double nullWeight,
                  StoppingCriteria stopper)
           throws IllegalSymbolException,
                  BioException

This will allow the specification of multiple SequenceDBs to be used in 
tandem for training.

Comments would be welcome. 

Thanks,
David Huen