Package pl.poznan.put.structure.pseudoknots.dp

Class ConflictClique

  • Direct Known Subclasses:
    ImmutableConflictClique
    @Immutable
public abstract class ConflictClique
extends Object
    A collection of regions conflicting with each other. Precisely, this is not a real clique. Each region in this collection has conflict with at least one other region. It does not mean that every region conflicts with every other.

    • Constructor Detail

      • ConflictClique

        public ConflictClique()

    • Method Detail

      • regions

        @Parameter(order=1)
public abstract Set<Region> regions()
        Returns:
        The set of regions in this conflict clique.

      • findRegion

        public final Optional<Region> findRegion​(int begin,
                                         int end)
        Searches for a region given its begin and end indices.
        Parameters:
        begin - The index of beginning nucleotide.
        end - The index of ending nucleotide.
        Returns:
        The region which matches the given begin and end.

      • endpoint

        public final int endpoint​(int index)
        Returns the endpoint of the given index. An endpoint is a nucleotide index in the original BPSEQ structure which matches a 5' or 3' partner of a base pair.
        Parameters:
        index - The index of an endpoint.
        Returns:
        The nucleotide index in the original BPSEQ structure.

      • endpointCount

        public final int endpointCount()
        Returns:
        The number of endpoints (should be equal to the number of regions times two).

      • indexOfEndpoint

        public final int indexOfEndpoint​(int endpoint)
        Finds the index of an endpoint in this conflict clique.
        Parameters:
        endpoint - The value of an endpoint.
        Returns:
        The index of this endpoint in this conflict clique.

      • size

        public final int size()
        Returns:
        The number of regions.

      • sortedEndpoints

        @Lazy
protected List<Integer> sortedEndpoints()