JavaGenes, NASA Ames. Written largely by Al Globus

gov.nasa.javaGenes.graph
Class GraphLayout

java.lang.Object
  extended bygov.nasa.javaGenes.graph.GraphLayout
All Implemented Interfaces:
java.io.Serializable

public class GraphLayout
extends java.lang.Object
implements java.io.Serializable

this class is an interface to the jiggle package that does graph layout for viewing.

See Also:
Serialized Form

Nested Class Summary
protected  class GraphLayout.CoordinateProvider
           
 
Field Summary
 double accuracyOfLineSearch
           
 double BarnesHutTheta
           
 double border
           
 double edgeLength
           
 int iterations
           
 int maxLineSearchIterations
           
 double restartThreshold
           
 double vertexSize
           
 
Constructor Summary
GraphLayout()
           
 
Method Summary
protected  void grid(jiggle.Graph graph, double size)
          put the xy is the locations of each vertex near the points in a three-dimensional grid
 void layout2d(Graph graph)
          provided xyz locations for every vertex in the graph in such a way that the graph looks ok in two dimensions
protected  jiggle.ForceModel makeForceModel(jiggle.Graph graph)
           
protected  jiggle.Graph makeGraph(Graph graph)
          used before layout to turn a JavaGenes graph into a jiggle graph
protected  jiggle.FirstOrderOptimizationProcedure makeOptimization(jiggle.Graph graph, jiggle.ForceModel model)
           
protected  void scramble(jiggle.Graph graph, double size)
          set the xyz locations of vertices in a graph to random values
 java.lang.String toString()
           
protected  void updatePositions(jiggle.Graph from, Graph to)
          called after layout to move xyz locations to a JavaGenes graph
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

iterations

public int iterations

maxLineSearchIterations

public int maxLineSearchIterations

vertexSize

public double vertexSize

edgeLength

public double edgeLength

border

public double border

BarnesHutTheta

public double BarnesHutTheta

accuracyOfLineSearch

public double accuracyOfLineSearch

restartThreshold

public double restartThreshold
Constructor Detail

GraphLayout

public GraphLayout()
Method Detail

toString

public java.lang.String toString()

layout2d

public void layout2d(Graph graph)
provided xyz locations for every vertex in the graph in such a way that the graph looks ok in two dimensions


makeGraph

protected jiggle.Graph makeGraph(Graph graph)
used before layout to turn a JavaGenes graph into a jiggle graph


makeForceModel

protected jiggle.ForceModel makeForceModel(jiggle.Graph graph)

makeOptimization

protected jiggle.FirstOrderOptimizationProcedure makeOptimization(jiggle.Graph graph,
                                                                  jiggle.ForceModel model)

scramble

protected void scramble(jiggle.Graph graph,
                        double size)
set the xyz locations of vertices in a graph to random values

Parameters:
size - edge length of the cube within which all vertices will fall

grid

protected void grid(jiggle.Graph graph,
                    double size)
put the xy is the locations of each vertex near the points in a three-dimensional grid


updatePositions

protected void updatePositions(jiggle.Graph from,
                               Graph to)
called after layout to move xyz locations to a JavaGenes graph


JavaGenes, NASA Ames. Written largely by Al Globus