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

Class ConflictClique

java.lang.Object
pl.poznan.put.structure.pseudoknots.dp.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 Details

    • ConflictClique

      public ConflictClique()

  • Method Details

    • 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()