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 ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
