[Biojava-dev] Proposal to change DP interface

[mark schreiber]

Hi -

Would it be possible to overload the method and keep the old one as well?
You could throw a bioexception if the old method is used for a single head
model if you wish.

- Mark
 

-----Original Message-----
From: biojava-dev-bounces at portal.open-bio.org
[mailto:biojava-dev-bounces at portal.open-bio.org] On Behalf Of David Huen
Sent: Monday, 8 December 2003 9:21 a.m.
To: biojava-dev at biojava.org
Subject: [Biojava-dev] Proposal to change DP interface

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

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