Class ResidueGroup


  • public class ResidueGroup
    extends java.lang.Object
    A ResidueGroup is a set of residues that are part of a maximally connected component of the self-Alignment Graph in symmetry analysis.

    This class provides an interface for comparing and combining them to refine self-Alignments into consistent MultipleAlignments of repeats.

    Since:
    4.2.0
    Author:
    Aleix Lafita
    • Constructor Summary

      Constructors 
      Constructor Description
      ResidueGroup​(java.util.Set<java.lang.Integer> component)
      Create a ResidueGroup object from a maximally connected component.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void combineWith​(java.util.List<java.util.List<java.lang.Integer>> alignRes)
      Combine the ResidueGroup with the alignment block.
      boolean isCompatible​(ResidueGroup other)
      Determine if two Residuegroups (maximally connected components of the alignment Graph) are compatible, based in the following criterion:
      int order()
      The order of symmetry of the group is the number of connected residues.
      • Methods inherited from class java.lang.Object

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

      • ResidueGroup

        public ResidueGroup​(java.util.Set<java.lang.Integer> component)
        Create a ResidueGroup object from a maximally connected component.
        Parameters:
        component - set of residues connected
    • Method Detail

      • order

        public int order()
        The order of symmetry of the group is the number of connected residues.
        Returns:
        size of residues List
      • isCompatible

        public boolean isCompatible​(ResidueGroup other)
        Determine if two Residuegroups (maximally connected components of the alignment Graph) are compatible, based in the following criterion:
         Two maximally connected components of the self-alignment Graph are
         compatible if they can be combined in a consistent multiple alignment
         of repeats, i.e.there exists one residue in c1 between each sorted
         pair of residues in c2.
         
        Compatibility is an intransitive relation, which means that for three ResidueGroups {A,B,C}, if A is compatible with B and B is compatible with C, then A is not necessarily compatible with C.
        Parameters:
        c2 - second maximally connected component
        Returns:
        true if compatible, false otherwise
      • combineWith

        public void combineWith​(java.util.List<java.util.List<java.lang.Integer>> alignRes)
        Combine the ResidueGroup with the alignment block.
        Parameters:
        alignRes - the alignment block, will be modified.