fr.curie.BiNoM.pathways.analysis.structure
Class Graph

java.lang.Object
  fr.curie.BiNoM.pathways.analysis.structure.Graph

Direct Known Subclasses:

BiographUtils, BipartiteGraph

public class Graph
extends java.lang.Object

Field Summary

static java.util.Vector	allGraphs
static boolean	countGraphs
java.util.HashMap	EdgeHash
java.util.Vector	Edges
java.lang.String	globalComment
java.util.Vector	metaNodes
java.lang.String	name
java.util.HashMap	NodeHash
java.util.HashMap	NodeIndexHash
java.util.Vector	Nodes
java.util.HashSet	selectedIds
java.lang.String	startId
boolean	useIDsForOutput
boolean	writeHangingNodes

Constructor Summary

Graph()

Method Summary

void	addConnections(Graph gr)
void	addEdge(Edge e)
void	addEdgeIdUnique(Edge e)
void	addEdges(Graph gr)
void	addMetanodeConnections(Graph gr, boolean nodeIntersectionView, boolean showIntersections)
void	addNode(Node n)
void	addNodes(Graph gr)
void	addNodesFromEdges()
void	assignEdgeIds()
void	calcNodesInOut()
void	createIndexNodeHash()
java.util.Vector	edgesConnectingSubGraphs(Graph meta1, Graph meta2, Graph grglobal, boolean nodeIntersectionView)
Edge	getCreateEdge(java.lang.String id)
Node	getCreateNode(java.lang.String id)
java.util.Vector<Edge>	getEdge(Node source, Node target, boolean directedGraph)
Edge	getEdge(java.lang.String id)
Edge	getEdgeByLabel(java.lang.String label)
int	getEdgeIndex(java.lang.String id)
Graph	getHangingNodes()
Node	getNode(java.lang.String id)
Node	getNodeByLabel(java.lang.String label)
int	getNodeIndex(java.lang.String id)
Graph	getNodesByLabelInclusion(java.lang.String label)
Graph	getSelectedNodes()
boolean	identicalNodes(Graph gr)
java.util.Vector	includesNodes(Graph gr)
float	includesNodesPercentage(Graph gr)
Graph	intersection(Graph gr)
static void	main(java.lang.String[] args)
Graph	makeCopy()
void	makeEdgeDoubleSense(java.lang.String edgeId) Add an edge from edgeId.Target to edgeId.Source.
static void	printGraphList()
void	removeNode(java.lang.String id)
void	removeNodes(Graph gr)
void	removeObsoleteEdges()
void	saveAsCytoscapeGML(java.lang.String fn)
void	saveAsCytoscapeSif(java.lang.String fn)
void	saveAsCytoscapeXGMML(java.lang.String fn)
void	subtractNodes(Graph gr)

Methods inherited from class java.lang.Object

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

Field Detail

name

public java.lang.String name

useIDsForOutput

public boolean useIDsForOutput

writeHangingNodes

public boolean writeHangingNodes

startId

public java.lang.String startId

globalComment

public java.lang.String globalComment

Nodes

public java.util.Vector Nodes

Edges

public java.util.Vector Edges

NodeHash

public java.util.HashMap NodeHash

NodeIndexHash

public java.util.HashMap NodeIndexHash

EdgeHash

public java.util.HashMap EdgeHash

selectedIds

public java.util.HashSet selectedIds

countGraphs

public static boolean countGraphs

allGraphs

public static java.util.Vector allGraphs

metaNodes

public java.util.Vector metaNodes

Constructor Detail

Graph

public Graph()

Method Detail

main

public static void main(java.lang.String[] args)

saveAsCytoscapeSif

public void saveAsCytoscapeSif(java.lang.String fn)

saveAsCytoscapeXGMML

public void saveAsCytoscapeXGMML(java.lang.String fn)

saveAsCytoscapeGML

public void saveAsCytoscapeGML(java.lang.String fn)

getNode

public Node getNode(java.lang.String id)

getEdge

public Edge getEdge(java.lang.String id)

getEdge

public java.util.Vector<Edge> getEdge(Node source,
                                      Node target,
                                      boolean directedGraph)

getNodeByLabel

public Node getNodeByLabel(java.lang.String label)

getNodesByLabelInclusion

public Graph getNodesByLabelInclusion(java.lang.String label)

getNodeIndex

public int getNodeIndex(java.lang.String id)

getEdgeIndex

public int getEdgeIndex(java.lang.String id)

getCreateNode

public Node getCreateNode(java.lang.String id)

getCreateEdge

public Edge getCreateEdge(java.lang.String id)

makeCopy

public Graph makeCopy()

subtractNodes

public void subtractNodes(Graph gr)

addNodes

public void addNodes(Graph gr)

addNode

public void addNode(Node n)

addEdge

public void addEdge(Edge e)

addEdgeIdUnique

public void addEdgeIdUnique(Edge e)

removeNodes

public void removeNodes(Graph gr)

removeNode

public void removeNode(java.lang.String id)

addEdges

public void addEdges(Graph gr)

removeObsoleteEdges

public void removeObsoleteEdges()

addNodesFromEdges

public void addNodesFromEdges()

addConnections

public void addConnections(Graph gr)

addMetanodeConnections

public void addMetanodeConnections(Graph gr,
                                   boolean nodeIntersectionView,
                                   boolean showIntersections)

getEdgeByLabel

public Edge getEdgeByLabel(java.lang.String label)

edgesConnectingSubGraphs

public java.util.Vector edgesConnectingSubGraphs(Graph meta1,
                                                 Graph meta2,
                                                 Graph grglobal,
                                                 boolean nodeIntersectionView)

assignEdgeIds

public void assignEdgeIds()

getHangingNodes

public Graph getHangingNodes()

calcNodesInOut

public void calcNodesInOut()

identicalNodes

public boolean identicalNodes(Graph gr)

includesNodes

public java.util.Vector includesNodes(Graph gr)

intersection

public Graph intersection(Graph gr)

includesNodesPercentage

public float includesNodesPercentage(Graph gr)

getSelectedNodes

public Graph getSelectedNodes()

printGraphList

public static void printGraphList()

makeEdgeDoubleSense

public void makeEdgeDoubleSense(java.lang.String edgeId)

Add an edge from edgeId.Target to edgeId.Source. Requires method calcInOut pre-calculated.

Parameters:

edgeId -

createIndexNodeHash

public void createIndexNodeHash()