Created BenchmarkSetStats.
Fixed problem caused by recent interface change in biojava.
Just sort Differences.
Print matrices of classifier scores: rows are data points, and columns
are classifiers.
Wrote a class to find residues that are trivially aligned.
Update dependency to symmetry-0.3.2.
Sorted benchmark names by space group.
Determine "true helical" better.
Update symmetry dependency to 0.3.3.
Made Criterion, CriteriaDifferences, and ROCCurves work with changes to
Alignment.
Extracted SymD-running code from SymDResults into SymDRunner.
Fixed SampleBuilderTest.
Committing folds code.
Wrote ErrorKernel, makes a couple assumptions about CE-Symm to derive
error rates for CE-Symm finding, say, C2 symmetry instead of C6. Creates
a transition matrix that we'll use in FoldOrder. Also added Apache
Commons math to POM.
Handle inverse transitions.