[Biojava-dev] IsoelectricPointCalc bug?

[Pjm]

> Ah, OK.  I think the problem arises from a very small error in FP 
> computations.  The binary search algorithm that solves the isoelectric 
> point equation expects and requires that successive bounds of the search 
> fall on either side of zero.  I think what has happened is the small error 
> in computation has put both bounds on the same side of zero causing it to 
> foobar.
> 
> I think we can prevent it by increasing the termination tolerance for the pI 
> computation.  Try changing in 
> org.biojava.bio.proteomics.IsoelectricPointCalc the line:-
> double pI = BinarySearch.solve(1.0, 13.0, 0.001, computeObj);
> 
> to:-
> double pI = BinarySearch.solve(1.0, 13.0, 0.005, computeObj);

Thanks for the quick reply.

The binary search does a quick check before doing anything and this is where 
the error is thrown. The tolerance is not used I'm affraid. See this from 
org/biojava/utils/math/BinarySearch.java

     public static double solve(double min, double max, double tolerance, 
ComputeObject obj)
         throws BioException
     {
         // compute initial values
         double x1 = min;
         double y1 = obj.compute(min);
         double x2 = max;
         double y2 = obj.compute(max);

         // validate that function standas some chance of monotonicity
         if ((y1 <  0.0) && (y2 < 0.0)) throw new BioException("Illegal initial 
range limits.");
         if ((y1 >  0.0) && (y2 > 0.0)) throw new BioException("Illegal initial 
range limits.");