Package org.cytoscape.view.layout

Class LayoutNode

java.lang.Object
org.cytoscape.view.layout.LayoutNode
All Implemented Interfaces:
Comparable<LayoutNode>
public final class LayoutNode extends Object implements Comparable<LayoutNode>
The LayoutNode class. This class is used as a container for information about the nodes in a layout. In particular, it provides a convenient handle to information about position, the node itself, the node view. Many of the methods of this class are wrappers for Node or View methods, and these are often wrapped by LayoutPartition methods.

Cytoscape Backwards Compatibility (Final Class): This class is final and therefore can't be extended by users. This means that we may add methods for minor version updates. Methods will only be removed for major version updates.

Module: layout-api

To use this in your app, include the following dependency in your POM:

<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>layout-api</artifactId>
</dependency>

  • Constructor Summary

    Constructors
    Constructor
    Description
    LayoutNode(View<CyNode> nodeView, int index, CyRow row)
    The main constructor for a LayoutNode.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addNeighbor(LayoutNode v)
    Convenience function to keep track of neighbors of this node.
    int
    compareTo(LayoutNode nodeView)
     
    void
    decrement(double x, double y)
    Decrement the location of this node by (x,y).
    void
    decrement(double x, double y, double z)
    Decrement the location of this node by (x,y,z).
    void
    decrementDisp(double x, double y)
    Decrement the displacement recorded for this node by (x,y).
    void
    decrementDisp(double x, double y, double z)
    Decrement the displacement recorded for this node by (x,y,z).
    double
    distance(double uX, double uY)
    Return the Euclidean distance (in 2D) between this node and a location.
    double
    distance(LayoutNode otherNode)
    Return the Euclidean distance (in 2D) between this node and another node.
    double
    distance3D(double uX, double uY, double uZ)
    Return the Euclidean distance (in 3D) between this node and a location.
    double
    distance3D(LayoutNode otherNode)
    Return the Euclidean distance (in 3D) between this node and another node.
    int
    getDegree()
    Return the node's degree (i.e.
    double
    getDepth()
    Return the height of this node
    double
    getHeight()
    Return the height of this node
    String
    getIdentifier()
    Return the node's identifier.
    int
    getIndex()
    Returns the index of this LayoutNode.
    List<LayoutNode>
    getNeighbors()
    Convenience function to return the list of neighbors (connected nodes) of this node.
    CyNode
    getNode()
    Accessor function to return the Node associated with this LayoutNode.
    View<CyNode>
    getNodeView()
    Accessor function to return the View associated with this LayoutNode.
    CyRow
    getRow()
    Accessor function to return the CyRow associated with this LayoutNode.
    double
    getWidth()
    Return the width of this node
    double
    getX()
    Return the current X value for this LayoutNode.
    double
    getXDisp()
    Return the current X displacement value for this LayoutNode.
    double
    getY()
    Return the current Y value for this LayoutNode.
    double
    getYDisp()
    Return the current Y displacement value for this LayoutNode.
    double
    getZ()
    Return the current Z value for this LayoutNode.
    double
    getZDisp()
    Return the current Z displacement value for this LayoutNode.
    void
    increment(double x, double y)
    Increment the location of this node by (x,y).
    void
    increment(double x, double y, double z)
    Increment the location of this node by (x,y,z).
    void
    incrementDisp(double x, double y)
    Increment the displacement recorded for this node by (x,y).
    void
    incrementDisp(double x, double y, double z)
    Increment the displacement recorded for this node by (x,y,z).
    boolean
    isLocked()
    Returns "true" if this node is locked, false otherwise.
    void
    lock()
    Register this node as being "locked".
    void
    moveToLocation()
    Move the node to its current x,y coordinate (ignores the value of the z coordinate).
    void
    moveToLocation3D()
    Move the node to its current x,y,z coordinate.
    String
    printDisp()
    Return a string representation of the node's displacement
    String
    printLocation()
    Return a string representation of the node's location
    void
    setDisp(double x, double y)
    Set the 2D displacement of this LayoutNode.
    void
    setDisp(double x, double y, double z)
    Set the 3D displacement of this LayoutNode.
    void
    setLocation(double x, double y)
    Set the 2D location of this LayoutNode.
    void
    setLocation(double x, double y, double z)
    Set the 3D location of this LayoutNode.
    void
    setX(double x)
    Set the X location of this LayoutNode.
    void
    setY(double y)
    Set the Y location of this LayoutNode.
    void
    setZ(double z)
    Set the Z location of this LayoutNode.
    String
    toString()
    Return a string representation of the node
    void
    unLock()
    Register this node as being "unlocked".

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Constructor Details

    • LayoutNode

      public LayoutNode(View<CyNode> nodeView, int index, CyRow row)
      The main constructor for a LayoutNode.
      Parameters:
      nodeView - The View of this node
      index - The index (usually in a node array) of this node

  • Method Details

    • getNode

      public CyNode getNode()
      Accessor function to return the Node associated with this LayoutNode.
      Returns:
      Node that is associated with this LayoutNode

    • getRow

      public CyRow getRow()
      Accessor function to return the CyRow associated with this LayoutNode.
      Returns:
      CyRow that is associated with this LayoutNode

    • getNodeView

      public View<CyNode> getNodeView()
      Accessor function to return the View associated with this LayoutNode.
      Returns:
      View that is associated with this LayoutNode

    • setLocation

      public void setLocation(double x, double y)
      Set the 2D location of this LayoutNode. Note that this only sets the location -- it does not actually move the node to that location. Users should call moveToLocation to actually accomplish the move.
      Parameters:
      x - Double representing the new X coordinate of this node
      y - Double representing the new Y coordinate of this node

    • setLocation

      public void setLocation(double x, double y, double z)
      Set the 3D location of this LayoutNode. Note that this only sets the location -- it does not actually move the node to that location. Users should call moveToLocation to actually accomplish the move.
      Parameters:
      x - Double representing the new X coordinate of this node
      y - Double representing the new Y coordinate of this node
      z - Double representing the new Z coordinate of this node

    • setX

      public void setX(double x)
      Set the X location of this LayoutNode. Note that this only sets the location -- it does not actually move the node to that location. Users should call moveToLocation to actually accomplish the move.
      Parameters:
      x - Double representing the new X coordinate of this node

    • setY

      public void setY(double y)
      Set the Y location of this LayoutNode. Note that this only sets the location -- it does not actually move the node to that location. Users should call moveToLocation to actually accomplish the move.
      Parameters:
      y - Double representing the new Y coordinate of this node

    • setZ

      public void setZ(double z)
      Set the Z location of this LayoutNode. Note that this only sets the location -- it does not actually move the node to that location. Users should call moveToLocation to actually accomplish the move.
      Parameters:
      z - Double representing the new Z coordinate of this node

    • setDisp

      public void setDisp(double x, double y)
      Set the 2D displacement of this LayoutNode. The displacement is a little different than the location in that it records an offset from the current location. This is useful for algorithms such as Kamada Kawai and Fructerman Rheingold, which update positions iteratively.
      Parameters:
      x - Double representing the amount to offset in the x direction
      y - Double representing the amount to offset in the y direction

    • setDisp

      public void setDisp(double x, double y, double z)
      Set the 3D displacement of this LayoutNode. The displacement is a little different than the location in that it records an offset from the current location. This is useful for algorithms such as Kamada Kawai and Fructerman Rheingold, which update positions iteratively.
      Parameters:
      x - Double representing the amount to offset in the x direction
      y - Double representing the amount to offset in the y direction
      z - Double representing the amount to offset in the y direction

    • addNeighbor

      public void addNeighbor(LayoutNode v)
      Convenience function to keep track of neighbors of this node. This can be used to improve the performance of algorithms that try to determine the edge partners of nodes.
      Parameters:
      v - LayoutNode that is a neighbor of this LayoutNode

    • getNeighbors

      public List<LayoutNode> getNeighbors()
      Convenience function to return the list of neighbors (connected nodes) of this node.
      Returns:
      List of all of the neighbors (nodes with shared edges) of this node.

    • getIndex

      public int getIndex()
      Returns the index of this LayoutNode. This is not the same as the rootGraphIndex of the node. Its primarily used by LayoutPartition to keep track of the offset in the node array that holds this LayoutNode.
      Returns:
      The index of this node
      See Also:

    • lock

      public void lock()
      Register this node as being "locked". Locked nodes are exempt from being moved during layout. Usually, these are the unselected nodes when a selected-only layout is being executed.

    • unLock

      public void unLock()
      Register this node as being "unlocked". Locked nodes are exempt from being moved during layout. Usually, these are the unselected nodes when a selected-only layout is being executed. The "unlocked" state is the default.

    • isLocked

      public boolean isLocked()
      Returns "true" if this node is locked, false otherwise.
      Returns:
      true if locked, false if unlocked.

    • incrementDisp

      public void incrementDisp(double x, double y)
      Increment the displacement recorded for this node by (x,y).
      Parameters:
      x - the additional amount to displace in the x direction
      y - the additional amount to displace in the y direction

    • incrementDisp

      public void incrementDisp(double x, double y, double z)
      Increment the displacement recorded for this node by (x,y,z).
      Parameters:
      x - the additional amount to displace in the x direction
      y - the additional amount to displace in the y direction
      z - the additional amount to displace in the z direction

    • increment

      public void increment(double x, double y)
      Increment the location of this node by (x,y). Note that location values are merely recorded until moveToLocation is called.
      Parameters:
      x - the amount to move in the x direction
      y - the amount to move in the y direction

    • increment

      public void increment(double x, double y, double z)
      Increment the location of this node by (x,y,z). Note that location values are merely recorded until moveToLocation is called.
      Parameters:
      x - the amount to move in the x direction
      y - the amount to move in the y direction
      z - the amount to move in the z direction

    • decrementDisp

      public void decrementDisp(double x, double y)
      Decrement the displacement recorded for this node by (x,y).
      Parameters:
      x - the additional amount to displace in the -x direction
      y - the additional amount to displace in the -y direction

    • decrementDisp

      public void decrementDisp(double x, double y, double z)
      Decrement the displacement recorded for this node by (x,y,z).
      Parameters:
      x - the additional amount to displace in the -x direction
      y - the additional amount to displace in the -y direction
      z - the additional amount to displace in the -z direction

    • decrement

      public void decrement(double x, double y)
      Decrement the location of this node by (x,y). Note that location values are merely recorded until moveToLocation is called.
      Parameters:
      x - the amount to move in the -x direction
      y - the amount to move in the -y direction

    • decrement

      public void decrement(double x, double y, double z)
      Decrement the location of this node by (x,y,z). Note that location values are merely recorded until moveToLocation is called.
      Parameters:
      x - the amount to move in the -x direction
      y - the amount to move in the -y direction
      z - the amount to move in the -z direction

    • getX

      public double getX()
      Return the current X value for this LayoutNode.
      Returns:
      current X value

    • getY

      public double getY()
      Return the current Y value for this LayoutNode.
      Returns:
      current Y value

    • getZ

      public double getZ()
      Return the current Z value for this LayoutNode.
      Returns:
      current Z value

    • getXDisp

      public double getXDisp()
      Return the current X displacement value for this LayoutNode.
      Returns:
      current X displacement value

    • getYDisp

      public double getYDisp()
      Return the current Y displacement value for this LayoutNode.
      Returns:
      current Y displacement value

    • getZDisp

      public double getZDisp()
      Return the current Z displacement value for this LayoutNode.
      Returns:
      current Z displacement value

    • getWidth

      public double getWidth()
      Return the width of this node
      Returns:
      width of this node

    • getHeight

      public double getHeight()
      Return the height of this node
      Returns:
      height of this node

    • getDepth

      public double getDepth()
      Return the height of this node
      Returns:
      height of this node

    • distance

      public double distance(LayoutNode otherNode)
      Return the Euclidean distance (in 2D) between this node and another node. This method only considers the X and Y coordinates of the nodes.
      Parameters:
      otherNode - the node to measure the distance to
      Returns:
      the Euclidean distance from this node to otherNode

    • distance3D

      public double distance3D(LayoutNode otherNode)
      Return the Euclidean distance (in 3D) between this node and another node. This method considers the X, Y and Z coordinates of the nodes.
      Parameters:
      otherNode - the node to measure the distance to
      Returns:
      the Euclidean distance from this node to otherNode

    • distance

      public double distance(double uX, double uY)
      Return the Euclidean distance (in 2D) between this node and a location. This method only considers the X and Y coordinates of the nodes.
      Parameters:
      uX - the X location to measure the distance to
      uY - the Y location to measure the distance to
      Returns:
      the Euclidean distance from this node to (uX,uY)

    • distance3D

      public double distance3D(double uX, double uY, double uZ)
      Return the Euclidean distance (in 3D) between this node and a location. This method considers the X, Y and Z coordinates of the nodes.
      Parameters:
      uX - the X location to measure the distance to
      uY - the Y location to measure the distance to
      uZ - the Z location to measure the distance to
      Returns:
      the Euclidean distance from this node to (uX,uY,uZ)

    • moveToLocation

      public void moveToLocation()
      Move the node to its current x,y coordinate (ignores the value of the z coordinate).

    • moveToLocation3D

      public void moveToLocation3D()
      Move the node to its current x,y,z coordinate.

    • getIdentifier

      public String getIdentifier()
      Return the node's identifier.
      Returns:
      String containing the node's identifier

    • getDegree

      public int getDegree()
      Return the node's degree (i.e. number of nodes it's connected to).
      Returns:
      Degree of this node

    • toString

      public String toString()
      Return a string representation of the node
      Overrides:
      toString in class Object
      Returns:
      String containing the node's identifier and location

    • printDisp

      public String printDisp()
      Return a string representation of the node's displacement
      Returns:
      String containing the node's X,Y displacement

    • printLocation

      public String printLocation()
      Return a string representation of the node's location
      Returns:
      String containing the node's X,Y location

    • compareTo

      public int compareTo(LayoutNode nodeView)
      Specified by:
      compareTo in interface Comparable<LayoutNode>