Class ResidueGroup

  • public class ResidueGroup
    extends 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.

    Aleix Lafita
    • Constructor Detail

      • ResidueGroup

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

      • order

        public int order()
        The order of symmetry of the group is the number of connected residues.
        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.
        c2 - second maximally connected component
        true if compatible, false otherwise
      • combineWith

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