[Biopython-dev] [Bug 2697] New: MaxEntropy calculate function assumes integer values for class and convergence criteria is hard coded

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2697

           Summary: MaxEntropy calculate function assumes integer values for
                    class and convergence criteria is hard coded
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: minor
          Priority: P3
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: bsouthey at gmail.com


The Bio.MaxEntrophy.classify() assumes that the targets are integers starting
at zero. However, a model can be trained by using character values. This
requires a simple change in a loop in that function.

Also, the convergence criteria is hard coded into the file by the following
gloable definitions:
MAX_IIS_ITERATIONS = 10000    # Maximum iterations for IIS.
IIS_CONVERGE = 1E-5           # Convergence criteria for IIS.
MAX_NEWTON_ITERATIONS = 100   # Maximum iterations on Newton's method.
NEWTON_CONVERGE = 1E-10       # Convergence criteria for Newton's method.

This makes it impossible for the user to specify their own values without
changing the actual function. This is changed by passing these values to the
train function and subfunctions. 

Both of these are fixed in an attached patch.


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