/**
* Guesses the order of symmetry in an alignment
*
* <p>Uses {@link #getSymmetryOrder(Map alignment, Map identity, int, float)} to determine the the
* symmetry order. For the identity alignment, sorts the aligned residues of each protein
* sequentially, then defines the ith residues of each protein to be equivalent.
*/
public static int getSymmetryOrder(AFPChain afpChain, int maxSymmetry, float minimumMetricChange)
throws StructureException {
// alignment comes from the afpChain alignment
Map<Integer, Integer> alignment = AlignmentTools.alignmentAsMap(afpChain);
// Now construct identity to map aligned residues in sequential order
Map<Integer, Integer> identity = guessSequentialAlignment(alignment, true);
return AlignmentTools.getSymmetryOrder(alignment, identity, maxSymmetry, minimumMetricChange);
}
