[Biojava-dev] bits of information

[Schreiber, Mark]

Hi -
 
The bitsOfInformation() method from DistributionTools seems to be returning only the average weighted entropy not the actual information.
 
Eg for a distribution made thus:
 
      //set the weight of a to 0.97
      dist.setWeight(DNATools.a(), 0.97);
      //set the others to 0.01
      dist.setWeight(DNATools.c(), 0.01);
      dist.setWeight(DNATools.g(), 0.01);
      dist.setWeight(DNATools.t(), 0.01);
 
The bits of information is calculated to be: 0.24194073285321088 bits
 
This strikes me as a bit low (excuse the pun). Possibly there should be a method called totalEntropy and bits of information should return log2(alpha size) - totalEntropy.
 
- Mark
 

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