medusa.graph

Class Graph

java.lang.Object

medusa.graph.BasicGraph

medusa.graph.Graph

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable

public class Graph
extends BasicGraph
implements java.io.Serializable, java.lang.Cloneable

Class Graph: The Graph object is basically a collection of edges with some utilities

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
Graph()

Method Summary

Modifier and Type	Method and Description
void	addGraph(BasicGraph g)
void	assignColorByMap(java.util.Map<java.lang.String,java.awt.Color> map) Assigns colors to nodes according to a map of node labels and colors.
void	autoFixOrientation()
java.lang.Object	clone()
void	cropEdges(double confidenceCutoff)
void	defaultGraph()
void	divideNodePosition(double d) Divides node positions by a double value Useful for batch operations after using FRSpring
java.util.Iterator<Edge>	edgesIterator(java.lang.String lbl)
java.lang.StringBuffer	generalStats()
Edge	getAdjacent(java.util.ArrayList unresolved, Node node)
java.util.ArrayList<Node>	getFixed() Returns an ArrayList of the fixed nodes
java.lang.StringBuffer	getNodeList()
void	growSelection()
double	isOppositeEdge(Edge e1, Edge e2)
java.lang.StringBuffer	nodesConnectivityReport() Returns a string buffer with all the connection numbers of nodes
java.util.HashMap<java.lang.String,java.lang.Integer>	nodesMap()
void	printNodeAnnotation()
void	removeEdgeByLabel(java.lang.String lbl)
void	removeFixed()
java.lang.String	reportUnique()
void	rescaleConfidence()
void	rescaleNodePercentage() Rescales nodes to 0 to 1.0, assuming they are given in values 0 to 100 %.
void	rescaleNodes(double scale)
void	rescaleNodes(int scale)
void	rescaleNodes(int xScale, int yScale)
void	setNodeAnnotation(java.lang.String name, java.lang.String annotation)
void	setNodeColor(java.awt.Color color)
void	setNodeShape(int shape)
Graph	shrinkGraph(Graph g)
Graph	subGraph(Node node) Get the subgraph that contains this node
Graph	subGraph(Node[] nodes) Get the subgraph that contains all nodes in the array
void	subtractGraph(BasicGraph g)
void	subtractGraph(Graph g)
void	tracePath(java.util.ArrayList unresolved, Node n)

Methods inherited from class medusa.graph.BasicGraph

addComment, addEdge, addEdge, addNode, addNode, clear, copyNodeSettings, edgesIterator, getComment, getEdges, getEdgeSize, getNode, getNodes, getNodesForEdge, getNodeSize, getUniqueEdges, getUniqueEdgeSize, isPlanar, nodesIterator, removeEdge, report, setComment, setNode, uniqueEdgesIterator

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Graph

public Graph()

Method Detail

addGraph

public void addGraph(BasicGraph g)

subtractGraph

public void subtractGraph(BasicGraph g)

clone

public java.lang.Object clone()
                       throws java.lang.CloneNotSupportedException

Overrides:

clone in class java.lang.Object

Throws:

java.lang.CloneNotSupportedException

edgesIterator

public java.util.Iterator<Edge> edgesIterator(java.lang.String lbl)

Parameters:

lbl -

Returns:

getFixed

public java.util.ArrayList<Node> getFixed()

Returns an ArrayList of the fixed nodes

Returns:

removeFixed

public void removeFixed()

rescaleNodes

public void rescaleNodes(int scale)

rescaleNodes

public void rescaleNodes(int xScale,
                         int yScale)

nodesMap

public java.util.HashMap<java.lang.String,java.lang.Integer> nodesMap()

divideNodePosition

public void divideNodePosition(double d)

Divides node positions by a double value Useful for batch operations after using FRSpring

subtractGraph

public void subtractGraph(Graph g)

cropEdges

public void cropEdges(double confidenceCutoff)

removeEdgeByLabel

public void removeEdgeByLabel(java.lang.String lbl)

tracePath

public void tracePath(java.util.ArrayList unresolved,
                      Node n)

getAdjacent

public Edge getAdjacent(java.util.ArrayList unresolved,
                        Node node)

reportUnique

public java.lang.String reportUnique()

defaultGraph

public void defaultGraph()

setNodeColor

public void setNodeColor(java.awt.Color color)

setNodeShape

public void setNodeShape(int shape)

setNodeAnnotation

public void setNodeAnnotation(java.lang.String name,
                              java.lang.String annotation)

printNodeAnnotation

public void printNodeAnnotation()

getNodeList

public java.lang.StringBuffer getNodeList()

shrinkGraph

public Graph shrinkGraph(Graph g)

subGraph

public Graph subGraph(Node[] nodes)

Get the subgraph that contains all nodes in the array

Parameters:

nodes - Array of ndoes

Returns:

subgraph

subGraph

public Graph subGraph(Node node)

Get the subgraph that contains this node

Parameters:

node -

Returns:

growSelection

public void growSelection()

rescaleConfidence

public void rescaleConfidence()

rescaleNodePercentage

public void rescaleNodePercentage()

Rescales nodes to 0 to 1.0, assuming they are given in values 0 to 100 %.

autoFixOrientation

public void autoFixOrientation()

isOppositeEdge

public double isOppositeEdge(Edge e1,
                             Edge e2)

rescaleNodes

public void rescaleNodes(double scale)

Parameters:

scale -

nodesConnectivityReport

public java.lang.StringBuffer nodesConnectivityReport()

Returns a string buffer with all the connection numbers of nodes

Returns:

report

generalStats

public java.lang.StringBuffer generalStats()

assignColorByMap

public void assignColorByMap(java.util.Map<java.lang.String,java.awt.Color> map)

Assigns colors to nodes according to a map of node labels and colors. This will be used in for instance clustering

Parameters:

map - Map