Package pl.poznan.put.structure.pseudoknots

Class ConflictGraph

java.lang.Object
pl.poznan.put.structure.pseudoknots.ConflictGraph
Direct Known Subclasses:
ImmutableConflictGraph
@Immutable public abstract class ConflictGraph extends Object
A graph of conflicts between regions. A conflict is when one region starts/end in the middle of another region.d

  • Constructor Details

    • ConflictGraph

      public ConflictGraph()

  • Method Details

    • isConflicting

      public static boolean isConflicting(Region first, Region second)
      Checks if given regions are conflicting. A conflict is when one region starts/ends in the middle of another region.
      Parameters:
      first - The first region.
      second - The second region.
      Returns:
      True if regions are conflicting.

    • regions

      @Parameter(order=1) protected abstract List<Region> regions()

    • removeRegion

      public final void removeRegion(Region region)
      Removes region and all associated conflicts with it from the graph.
      Parameters:
      region - The region to remove.

    • conflictsWith

      public final Set<Region> conflictsWith(Region region)
      Returns all regions that conflict with a given one.
      Parameters:
      region - The region to search conflict for.
      Returns:
      A collection of regions in conflict with the given one.

    • regionsWithConflicts

      public final Set<Region> regionsWithConflicts()
      Returns all regions that are in conflict with at least one other region.
      Returns:
      A set of regions which are in at least one conflict.

    • hasConflicts

      public final boolean hasConflicts()
      Returns:
      True if at least one region has at least one conflict.

    • hasConflicts

      public final boolean hasConflicts(Region region)
      Checks if a given region has any conflicts.
      Parameters:
      region - The region to check.
      Returns:
      True if the given region has at least one conflict.

    • conflictCliques

      public final List<ConflictClique> conflictCliques()
      Searches for connected components (named conflict cliques, although they are not real cliques).
      Returns:
      The list of conflict cliques.

    • simplified

      public final ConflictGraph simplified()
      Creates a simplified copy of this instance. The simplification merges smaller region which are fully embedded into the bigger ones, if both the small and big region have exactly the same conflicts.
      Returns:
      A simplified instance of this conflict graph.

    • conflicts

      @Lazy protected Map<Region,Set<Region>> conflicts()