[Biojava-dev] OrderN problem

[Schreiber, Mark]

Hi -

The following code highlights an anomaly in the treatment of Alphabets
by the OrderNDistributions

    FiniteAlphabet ordern =
        (FiniteAlphabet)AlphabetManager.alphabetForName("(DNA x DNA x
DNA x DNA)");
    FiniteAlphabet ordern2 =
        (FiniteAlphabet)AlphabetManager.alphabetForName("((DNA x DNA x
DNA) x DNA)");

    System.out.println(ordern == ordern2);

    Distribution d =
OrderNDistributionFactory.DEFAULT.createDistribution(ordern);

    Distribution d2 =
OrderNDistributionFactory.DEFAULT.createDistribution(ordern2);

    System.out.println(d.getAlphabet() == d2.getAlphabet());

    System.out.println(((OrderNDistribution)d).getConditioningAlphabet()
                       ==
((OrderNDistribution)d2).getConditioningAlphabet());

    System.out.println(((OrderNDistribution)d).getConditionedAlphabet()
                       ==
((OrderNDistribution)d2).getConditionedAlphabet());

This will return false, false, true, true which is clearly not at all
logical. The problem seems to stem from the fact that the two Alphabets
are treated somewhat equally by the OrderNDistribution factory.

Some possible solutions include:

1) Don't allow alphabets like (DNA x DNA x DNA) which don't specify the
conditioning alphabet
2) Have it convert its alphabet to make things consistent.
3) Document the anomaly!!!!
4) do something smarter than 1 to 3?

- Mark


Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

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