Class SequenceFunctionRefiner

  • All Implemented Interfaces:
    SymmetryRefiner

    public class SequenceFunctionRefiner
    extends java.lang.Object
    implements SymmetryRefiner
    Creates a refined alignment with the CE-Symm alternative self-alignment. Needs the order of symmetry and assumes that the last repeat aligns with the first, being thus a CLOSE symmetry.
    Since:
    4.2.0
    Author:
    Spencer Bliven, Aleix Lafita
    • Method Summary

      All Methods Static 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.
      static java.util.Map<java.lang.Integer,​java.lang.Integer> refineSymmetry​(java.util.Map<java.lang.Integer,​java.lang.Integer> alignment, int k)
      Refines a CE-Symm alignment so that it is perfectly symmetric.
      static AFPChain refineSymmetry​(AFPChain afpChain, Atom[] ca1, Atom[] ca2, int k)
      Refines a CE-Symm alignment so that it is perfectly symmetric.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • SequenceFunctionRefiner

        public SequenceFunctionRefiner()
    • Method Detail

      • refineSymmetry

        public static AFPChain refineSymmetry​(AFPChain afpChain,
                                              Atom[] ca1,
                                              Atom[] ca2,
                                              int k)
                                       throws StructureException,
                                              RefinerFailedException
        Refines a CE-Symm alignment so that it is perfectly symmetric. The resulting alignment will have a one-to-one correspondance between aligned residues of each symmetric part.
        Parameters:
        afpChain - Input alignment from CE-Symm
        k - Symmetry order. This can be guessed by CeSymm#getSymmetryOrder(AFPChain)
        Returns:
        The refined alignment
        Throws:
        StructureException
        RefinerFailedException
      • refineSymmetry

        public static java.util.Map<java.lang.Integer,​java.lang.Integer> refineSymmetry​(java.util.Map<java.lang.Integer,​java.lang.Integer> alignment,
                                                                                              int k)
                                                                                       throws StructureException
        Refines a CE-Symm alignment so that it is perfectly symmetric. The resulting alignment will have a one-to-one correspondance between aligned residues of each symmetric part.
        Parameters:
        alignment - The input alignment, as a map. This will be modified.
        k - Symmetry order. This can be guessed by CeSymm#getSymmetryOrder(AFPChain)
        Returns:
        A modified map with the refined alignment
        Throws:
        StructureException