Package pl.poznan.put.structure.pseudoknots

Class 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 Detail

      • ConflictGraph

        public ConflictGraph()

    • Method Detail

      • 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.