Package org.biopax.paxtools.query.algorithm

Class BFS

java.lang.Object
org.biopax.paxtools.query.algorithm.BFS
Direct Known Subclasses:
CycleBreaker
public class BFS extends Object
Implements breadth-first search. Takes a set of source nodes, distance limit and labels nodes towards one direction, with their breadth distances.
Author:
Ozgun Babur, Merve Cakir

  • Field Details

    • dist

      protected Map<GraphObject,Integer> dist
      Distance labels. Missing label interpreted as infinitive.

    • colors

      protected Map<GraphObject,Integer> colors
      Color labels. Missing color interpreted as white.

    • sourceSet

      protected Set<Node> sourceSet
      BFS starts from source nodes. They get the label 0.

    • stopSet

      protected Set<Node> stopSet
      BFS will not further traverse neighbors of any node in the stopSet.

    • direction

      protected Direction direction
      Whether the direction is FORWARD, it is REVERSE otherwise.

    • limit

      protected int limit
      Stop distance.

    • queue

      protected LinkedList<Node> queue
      BFS queue.

    • FORWARD

      public static final boolean FORWARD
      Forward traversal direction.
      See Also:

    • BACKWARD

      public static final boolean BACKWARD
      Backward traversal direction.
      See Also:

    • UPWARD

      public static final boolean UPWARD
      Forward traversal direction.
      See Also:

    • DOWNWARD

      public static final boolean DOWNWARD
      Backward traversal direction.
      See Also:

    • WHITE

      public static final int WHITE
      Color white indicates the node is not processed.
      See Also:

    • GRAY

      public static final int GRAY
      Color gray indicates that the node is in queue waiting to be procecessed.
      See Also:

    • BLACK

      public static final int BLACK
      Color black indicates that the node was processed.
      See Also:

  • Constructor Details

    • BFS

      public BFS(Set<Node> sourceSet, Set<Node> stopSet, Direction direction, int limit)
      Constructor with all parameters.
      Parameters:
      sourceSet - Seed of BFS
      stopSet - Nodes that won't be traversed
      direction - Direction of the traversal
      limit - Distance limit

    • BFS

      public BFS()
      Empty constructor for other possible uses.

  • Method Details

    • run

      public Map<GraphObject,Integer> run()
      Executes the algorithm.
      Returns:
      BFS tree

    • initMaps

      protected void initMaps()
      Initializes maps used during query.

    • processNode

      protected void processNode(Node current)
      Processes a node.
      Parameters:
      current - The current node

    • labelEquivRecursive

      protected void labelEquivRecursive(Node node, boolean up, int dist, boolean enqueue, boolean head)
      Labels equivalent nodes recursively.
      Parameters:
      node - Node to label equivalents
      up - Traversing direction. Up means towards parents, if false then towards children
      dist - The label
      enqueue - Whether to enqueue equivalents
      head - Where to enqueue. Head or tail.

    • isEquivalentInTheSet

      protected boolean isEquivalentInTheSet(Node node, Set<Node> set)
      Checks if an equivalent of the given node is in the set.
      Parameters:
      node - Node to check equivalents
      set - Node set
      Returns:
      true if an equivalent is in the set

    • isEquivalentInTheSet

      protected boolean isEquivalentInTheSet(Node node, boolean direction, Set<Node> set)
      Checks if an equivalent of the given node is in the set.
      Parameters:
      node - Node to check equivalents
      direction - Direction to go to get equivalents
      set - Node set
      Returns:
      true if an equivalent is in the set

    • getColor

      protected int getColor(Node node)
      Gets color tag of the node
      Parameters:
      node - Node to get color tag
      Returns:
      color tag

    • setColor

      protected void setColor(Node node, int color)
      Sets color tag
      Parameters:
      node - node to set color tag
      color - the color tag

    • getLabel

      public int getLabel(GraphObject go)
      Gets the distance label of the object.
      Parameters:
      go - object to get the distance
      Returns:
      the distance label

    • setLabel

      protected void setLabel(GraphObject go, int label)
      Sets the distance label.
      Parameters:
      go - object to set the distance label
      label - the distance label