[Biojava-l] Setting weights with ambiguity

[Schreiber, Mark]

Hi -

There is a subtle bug in Distribution where the setWeight(Symbol s,
double weight) method misbehaves when setting the wieght with an
ambiguity symbol. Currently the weight is added equally to all atomic
symbols that make up the ambiguity symbol. The getWeight(Symbol s) works
as you would expect.

Discussing this with Thomas we think there are two possible solutions:

1)	Throw an exception if setWeight is given an ambiguity symbol.
2)	Divide the weight amongst the atomic symbols that make up the
ambiguity on the basis of the null model.

I prefer 2 as it is more what you would expect. The current signature of
the setWeight method doesn't suggest the requirement for an Atomic
Symbol and changing it at this stage might break some peoples programs.

Possible lesson from this, it is safer  to "set weights" through a
trainer.

If no one has a better idea I will look at implementing option 2.

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

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