HierarchicalBCEngine (interruptible-weka 0.1.4 API)

java.lang.Object
- weka.gui.graphvisualizer.HierarchicalBCEngine

All Implemented Interfaces:

GraphConstants, LayoutEngine
```
public class HierarchicalBCEngine
extends java.lang.Object
implements GraphConstants, LayoutEngine
```
This class lays out the vertices of a graph in a hierarchy of vertical levels, with a number of nodes in each level. The number of levels is the depth of the deepest child reachable from some parent at level 0. It implements a layout technique as described by K. Sugiyama, S. Tagawa, and M. Toda. in "Methods for visual understanding of hierarchical systems", IEEE Transactions on Systems, Man and Cybernetics, SMC-11(2):109-125, Feb. 1981.
There have been a few modifications made, however. The crossings function is changed as it was non-linear in time complexity. Furthermore, we don't have any interconnection matrices for each level, instead we just have one big interconnection matrix for the whole graph and a int[][] array which stores the vertices present in each level.

Field Summary

Fields
Modifier and Type	Field and Description
`protected int[][]`	`graphMatrix` Interconnection matrix for the graph
`protected java.util.ArrayList<LayoutCompleteEventListener>`	`layoutCompleteListeners` FastVector containing listeners for layoutCompleteEvent generated by this LayoutEngine
`protected boolean`	`m_completeReLayout` This tells the the LayoutGraph method if a completeReLayout should be performed when it is called.
`protected javax.swing.JPanel`	`m_controlsPanel` The panel containing extra options, specific to this LayoutEngine, for greater control over layout of the graph
`protected java.util.ArrayList<GraphEdge>`	`m_edges`
`protected javax.swing.JCheckBox`	`m_jCbEdgeConcentration` controls edge concentration by concentrating multilple singular dummy child nodes into one plural dummy child node
`protected javax.swing.JRadioButton`	`m_jRbBottomup`
`protected javax.swing.JRadioButton`	`m_jRbNaiveLayout`
`protected javax.swing.JRadioButton`	`m_jRbPriorityLayout`
`protected javax.swing.JRadioButton`	`m_jRbTopdown`
`protected int`	`m_nodeHeight` The nodeWidth and nodeHeight
`protected java.util.ArrayList<GraphNode>`	`m_nodes` FastVector containing nodes and edges
`protected int`	`m_nodeWidth` The nodeWidth and nodeHeight
`protected javax.swing.JProgressBar`	`m_progress` The progress bar to show the progress of the layout process
`protected int[][]`	`nodeLevels` Array containing the indices of nodes in each level.

Fields inherited from interface weka.gui.graphvisualizer.GraphConstants
DIRECTED, DOUBLE, NORMAL, PLURAL_DUMMY, REVERSED, SINGULAR_DUMMY

Constructor Summary

Constructors
Constructor and Description
`HierarchicalBCEngine()` SimpleConstructor If we want to instantiate the class first, and if information for nodes and edges is not available.
`HierarchicalBCEngine(java.util.ArrayList<GraphNode> nodes, java.util.ArrayList<GraphEdge> edges, int nodeWidth, int nodeHeight)` Constructor - takes in FastVectors of nodes and edges, and the initial width and height of a node
`HierarchicalBCEngine(java.util.ArrayList<GraphNode> nodes, java.util.ArrayList<GraphEdge> edges, int nodeWidth, int nodeHeight, boolean edgeConcentration)` Constructor - takes in FastVectors of nodes and edges, the initial width and height of a node, and a boolean value to indicate if the edges should be concentrated.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addLayoutCompleteEventListener(LayoutCompleteEventListener l)` Method to add a LayoutCompleteEventListener
`protected void`	`assignLevels(int[] levels, int depth, int i, int j)` This method assigns a vertical level to each node.
`protected float[]`	`calcColBC(int lindex, int[][] levels)` See Sugiyama et al. 1981 (full reference give at top)
`protected float[]`	`calcRowBC(int lindex, int[][] levels)` See Sugiyama et al. 1981 (full reference give at top)
`protected void`	`clearTemps_and_EdgesFromNodes()` This method removes the temporary nodes that were added to fill in the gaps, and removes all edges from all nodes in their edges[][] array
`protected void`	`copy2DArray(int[][] from, int[][] to)` Copies one array of type int[][] to another.
`protected void`	`copyMatrix(int[][] from, int[][] to)` Copies one Matrix of type int[][] to another.
`protected int`	`crossings(int[][] levels)` Computes the number of edge crossings in the whole graph Takes as an argument levels of nodes.
`void`	`fireLayoutCompleteEvent(LayoutCompleteEvent e)` Fires a LayoutCompleteEvent.
`javax.swing.JPanel`	`getControlPanel()` This method returns a handle to the extra controls panel, so that the visualizing class can add it to some of it's own gui panel.
`java.util.ArrayList<GraphNode>`	`getNodes()` give access to set of graph nodes
`javax.swing.JProgressBar`	`getProgressBar()` Returns a handle to the progressBar of this LayoutEngine.
`protected static void`	`isort(int[] level, float[] BC)` This methods sorts the vertices in level[] according to their barycenters in BC[], using insertion sort.
`void`	`layoutGraph()` This method does a complete layout of the graph which includes removing cycles, assigning levels to nodes, reducing edge crossings and laying out the vertices horizontally for better visibility.
`protected int`	`lBCenter(int lindex, int eindex, int[] horPositions)`
`protected int`	`lConnectivity(int lindex, int eindex)`
`protected void`	`makeGUIPanel(boolean edgeConc)` This methods makes the gui extra controls panel "m_controlsPanel"
`protected void`	`makeProperHierarchy()`
`protected void`	`naiveLayout()` This method lays out the vertices horizontally, in each level.
`protected void`	`phaseID(int lindex, int[][] levels)` See Sugiyama et al. 1981 (full reference give at top) lindex is the index of the level we want to process.
`void`	`phaseIID(int lindex, int[][] levels)` See Sugiyama et al. 1981 (full reference give at top)
`void`	`phaseIIU(int lindex, int[][] levels)` See Sugiyama et al. 1981 (full reference give at top)
`void`	`phaseIU(int lindex, int[][] levels)` See Sugiyama et al. 1981 (full reference give at top) lindex is the index of the level we want to process.
`protected void`	`printMatrices(int[][] levels)` Prints out the interconnection matrix at each level.
`protected void`	`priorityLayout1()` This method lays out the vertices horizontally, in each level.
`protected void`	`processGraph()` This method makes the "graphMatrix" interconnection matrix for the graph given by m_nodes and m_edges vectors.
`protected void`	`removeCycles()` The following two methods remove cycles from the graph.
`void`	`removeLayoutCompleteEventListener(LayoutCompleteEventListener e)` Method to remove a LayoutCompleteEventListener.
`void`	`setNodesEdges(java.util.ArrayList<GraphNode> nodes, java.util.ArrayList<GraphEdge> edges)` Sets the nodes and edges for this LayoutEngine.
`void`	`setNodeSize(int nodeWidth, int nodeHeight)` Sets the size of a node.
`protected int`	`uBCenter(int lindex, int eindex, int[] horPositions)`
`protected int`	`uConnectivity(int lindex, int eindex)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - m_nodes
```
protected java.util.ArrayList<GraphNode> m_nodes
```
    FastVector containing nodes and edges
  - m_edges
```
protected java.util.ArrayList<GraphEdge> m_edges
```
  - layoutCompleteListeners
```
protected java.util.ArrayList<LayoutCompleteEventListener> layoutCompleteListeners
```
    FastVector containing listeners for layoutCompleteEvent generated by this LayoutEngine
  - graphMatrix
```
protected int[][] graphMatrix
```
    Interconnection matrix for the graph
  - nodeLevels
```
protected int[][] nodeLevels
```
    Array containing the indices of nodes in each level. The nodeLevels.length is equal to the number of levels
  - m_nodeWidth
```
protected int m_nodeWidth
```
    The nodeWidth and nodeHeight
  - m_nodeHeight
```
protected int m_nodeHeight
```
    The nodeWidth and nodeHeight
  - m_jRbNaiveLayout
```
protected javax.swing.JRadioButton m_jRbNaiveLayout
```
  - m_jRbPriorityLayout
```
protected javax.swing.JRadioButton m_jRbPriorityLayout
```
  - m_jRbTopdown
```
protected javax.swing.JRadioButton m_jRbTopdown
```
  - m_jRbBottomup
```
protected javax.swing.JRadioButton m_jRbBottomup
```
  - m_jCbEdgeConcentration
```
protected javax.swing.JCheckBox m_jCbEdgeConcentration
```
    controls edge concentration by concentrating multilple singular dummy child nodes into one plural dummy child node
  - m_controlsPanel
```
protected javax.swing.JPanel m_controlsPanel
```
    The panel containing extra options, specific to this LayoutEngine, for greater control over layout of the graph
  - m_progress
```
protected javax.swing.JProgressBar m_progress
```
    The progress bar to show the progress of the layout process
  - m_completeReLayout
```
protected boolean m_completeReLayout
```
    This tells the the LayoutGraph method if a completeReLayout should be performed when it is called.
- Constructor Detail
  - HierarchicalBCEngine
```
public HierarchicalBCEngine(java.util.ArrayList<GraphNode> nodes,
                            java.util.ArrayList<GraphEdge> edges,
                            int nodeWidth,
                            int nodeHeight)
```
    Constructor - takes in FastVectors of nodes and edges, and the initial width and height of a node
  - HierarchicalBCEngine
```
public HierarchicalBCEngine(java.util.ArrayList<GraphNode> nodes,
                            java.util.ArrayList<GraphEdge> edges,
                            int nodeWidth,
                            int nodeHeight,
                            boolean edgeConcentration)
```
    Constructor - takes in FastVectors of nodes and edges, the initial width and height of a node, and a boolean value to indicate if the edges should be concentrated.
    
    Parameters:
    
    nodes - - FastVector containing all the nodes
    
    edges - - FastVector containing all the edges
    
    nodeWidth - - A node's allowed width
    
    nodeHeight - - A node's allowed height
    
    edgeConcentration - - True: if want to concentrate edges, False: otherwise
  - HierarchicalBCEngine
```
public HierarchicalBCEngine()
```
    SimpleConstructor If we want to instantiate the class first, and if information for nodes and edges is not available. However, we would have to manually provide all the information later on by calling setNodesEdges and setNodeSize methods
- Method Detail
  - makeGUIPanel
```
protected void makeGUIPanel(boolean edgeConc)
```
    This methods makes the gui extra controls panel "m_controlsPanel"
  - getNodes
```
public java.util.ArrayList<GraphNode> getNodes()
```
    give access to set of graph nodes
    
    Specified by:
    
    getNodes in interface LayoutEngine
  - getControlPanel
```
public javax.swing.JPanel getControlPanel()
```
    This method returns a handle to the extra controls panel, so that the visualizing class can add it to some of it's own gui panel.
    
    Specified by:
    
    getControlPanel in interface LayoutEngine
  - getProgressBar
```
public javax.swing.JProgressBar getProgressBar()
```
    Returns a handle to the progressBar of this LayoutEngine.
    
    Specified by:
    
    getProgressBar in interface LayoutEngine
  - setNodesEdges
```
public void setNodesEdges(java.util.ArrayList<GraphNode> nodes,
                          java.util.ArrayList<GraphEdge> edges)
```
    Sets the nodes and edges for this LayoutEngine. Must be used if the class created by simple HierarchicalBCEngine() constructor.
    
    Specified by:
    
    setNodesEdges in interface LayoutEngine
    
    Parameters:
    
    nodes - - FastVector containing all the nodes
    
    edges - - FastVector containing all the edges
  - setNodeSize
```
public void setNodeSize(int nodeWidth,
                        int nodeHeight)
```
    Sets the size of a node. This method must be used if the class created by simple HierarchicalBCEngine() constructor.
    
    Specified by:
    
    setNodeSize in interface LayoutEngine
    
    Parameters:
    
    nodeWidth - - A node's allowed width
    
    nodeHeight - - A node's allowed height
  - addLayoutCompleteEventListener
```
public void addLayoutCompleteEventListener(LayoutCompleteEventListener l)
```
    Method to add a LayoutCompleteEventListener
    
    Specified by:
    
    addLayoutCompleteEventListener in interface LayoutEngine
    
    Parameters:
    
    l - - Listener to receive the LayoutCompleteEvent by this class.
  - removeLayoutCompleteEventListener
```
public void removeLayoutCompleteEventListener(LayoutCompleteEventListener e)
```
    Method to remove a LayoutCompleteEventListener.
    
    Specified by:
    
    removeLayoutCompleteEventListener in interface LayoutEngine
    
    Parameters:
    
    e - - The LayoutCompleteEventListener to remove.
  - fireLayoutCompleteEvent
```
public void fireLayoutCompleteEvent(LayoutCompleteEvent e)
```
    Fires a LayoutCompleteEvent.
    
    Specified by:
    
    fireLayoutCompleteEvent in interface LayoutEngine
    
    Parameters:
    
    e - - The LayoutCompleteEvent to fire
  - layoutGraph
```
public void layoutGraph()
```
    This method does a complete layout of the graph which includes removing cycles, assigning levels to nodes, reducing edge crossings and laying out the vertices horizontally for better visibility. The removing of cycles and assignment of levels is only performed if hasn't been performed earlier or if some layout option has been changed and it is necessary to do so. It is necessary to do so, if the user selects/deselects edge concentration or topdown/bottomup options.
    The layout is performed in a separate thread and the progress bar of the class is updated for each of the steps as the process continues.
    
    Specified by:
    
    layoutGraph in interface LayoutEngine
  - clearTemps_and_EdgesFromNodes
```
protected void clearTemps_and_EdgesFromNodes()
```
    This method removes the temporary nodes that were added to fill in the gaps, and removes all edges from all nodes in their edges[][] array
  - processGraph
```
protected void processGraph()
```
    This method makes the "graphMatrix" interconnection matrix for the graph given by m_nodes and m_edges vectors. The matix is used by other methods.
  - makeProperHierarchy
```
protected void makeProperHierarchy()
```
  - crossings
```
protected int crossings(int[][] levels)
```
    Computes the number of edge crossings in the whole graph Takes as an argument levels of nodes. It is essentially the same algorithm provided in Universitat des Saarlandes technical report A03/94 by Georg Sander.
  - removeCycles
```
protected void removeCycles()
```
    The following two methods remove cycles from the graph.
  - assignLevels
```
protected void assignLevels(int[] levels,
                            int depth,
                            int i,
                            int j)
```
    This method assigns a vertical level to each node. See makeProperHierarchy() to see how to use it.
  - phaseID
```
protected void phaseID(int lindex,
                       int[][] levels)
```
    See Sugiyama et al. 1981 (full reference give at top) lindex is the index of the level we want to process. In this method we'll sort the vertices at the level one below lindex according to their UP-barycenters (or column barycenters).
  - phaseIU
```
public void phaseIU(int lindex,
                    int[][] levels)
```
    See Sugiyama et al. 1981 (full reference give at top) lindex is the index of the level we want to process. In this method we'll sort the vertices at the level lindex according to their DOWN-barycenters (or row barycenters).
  - phaseIID
```
public void phaseIID(int lindex,
                     int[][] levels)
```
    See Sugiyama et al. 1981 (full reference give at top)
  - phaseIIU
```
public void phaseIIU(int lindex,
                     int[][] levels)
```
    See Sugiyama et al. 1981 (full reference give at top)
  - calcRowBC
```
protected float[] calcRowBC(int lindex,
                            int[][] levels)
```
    See Sugiyama et al. 1981 (full reference give at top)
  - calcColBC
```
protected float[] calcColBC(int lindex,
                            int[][] levels)
```
    See Sugiyama et al. 1981 (full reference give at top)
  - printMatrices
```
protected void printMatrices(int[][] levels)
```
    Prints out the interconnection matrix at each level. See Sugiyama et al. 1981 (full reference give at top)
  - isort
```
protected static void isort(int[] level,
                            float[] BC)
```
    This methods sorts the vertices in level[] according to their barycenters in BC[], using insertion sort. It, however, doesn't touch the vertices with barycenter equal to zero.
  - copyMatrix
```
protected void copyMatrix(int[][] from,
                          int[][] to)
```
    Copies one Matrix of type int[][] to another.
  - copy2DArray
```
protected void copy2DArray(int[][] from,
                           int[][] to)
```
    Copies one array of type int[][] to another.
  - naiveLayout
```
protected void naiveLayout()
```
    This method lays out the vertices horizontally, in each level. It simply assings an x value to a vertex according to its index in the level.
  - uConnectivity
```
protected int uConnectivity(int lindex,
                            int eindex)
```
  - lConnectivity
```
protected int lConnectivity(int lindex,
                            int eindex)
```
  - uBCenter
```
protected int uBCenter(int lindex,
                       int eindex,
                       int[] horPositions)
```
  - lBCenter
```
protected int lBCenter(int lindex,
                       int eindex,
                       int[] horPositions)
```
  - priorityLayout1
```
protected void priorityLayout1()
```
    This method lays out the vertices horizontally, in each level. See Sugiyama et al. 1981 for full reference.

Class HierarchicalBCEngine

Field Summary

Fields inherited from interface weka.gui.graphvisualizer.GraphConstants

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

m_nodes

m_edges

layoutCompleteListeners

graphMatrix

nodeLevels

m_nodeWidth

m_nodeHeight

m_jRbNaiveLayout

m_jRbPriorityLayout

m_jRbTopdown

m_jRbBottomup

m_jCbEdgeConcentration

m_controlsPanel

m_progress

m_completeReLayout

Constructor Detail

HierarchicalBCEngine

HierarchicalBCEngine

HierarchicalBCEngine

Method Detail

makeGUIPanel

getNodes

getControlPanel

getProgressBar

setNodesEdges

setNodeSize

addLayoutCompleteEventListener

removeLayoutCompleteEventListener

fireLayoutCompleteEvent

layoutGraph

clearTemps_and_EdgesFromNodes

processGraph

makeProperHierarchy

crossings

removeCycles

assignLevels

phaseID

phaseIU

phaseIID

phaseIIU

calcRowBC

calcColBC

printMatrices

isort

copyMatrix

copy2DArray

naiveLayout

uConnectivity

lConnectivity

uBCenter

lBCenter

priorityLayout1