Class GraphComponentRefiner

  • All Implemented Interfaces:
    SymmetryRefiner

    public class GraphComponentRefiner
    extends java.lang.Object
    implements SymmetryRefiner
    The GraphRefiner transforms the self-alignment into a Graph and extracts its maximally connected Components. It then refines the alignment by combining the compatible Components with the following heuristic:
     Given a set of components and their pairwise compatibilities, iteratively
     add the most compatible component, which is compatible to all the components
     already added, to the final alignment.
     
    Author:
    Aleix Lafita
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      MultipleAlignment refine​(AFPChain selfAlignment, Atom[] atoms, int order)
      Returns a refined symmetry alignment, where the repeat residues are aligned consistently in a MultipleAlignment.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait