public class SymmOptimizer extends Object
MultipleMCalgorithm in biojava. Another major difference is that the free Pool is shared for all repeats, so that no residue can appear to more than one repeat at a time.
This algorithm does not use a unfiform distribution for selecting moves, farther residues have more probability to be shrinked or gapped. This modification of the algorithm improves convergence and running time.
Use call method to parallelize optimizations, or use optimize method instead.
Because gaps are allowed in the repeats, a
|Constructor and Description|
Constructor with a seed MultipleAligment storing a refined symmetry alignment of the repeats.
|Modifier and Type||Method and Description|
Optimization method based in a Monte-Carlo approach.
public SymmOptimizer(CeSymmResult symmResult)
public MultipleAlignment optimize() throws StructureException, RefinerFailedException
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