cytoscape.giny
Class CytoscapeFingRootGraph

java.lang.Object
  fing.model.FingExtensibleRootGraph
      cytoscape.giny.CytoscapeFingRootGraph

All Implemented Interfaces:

CytoscapeRootGraph, cytoscape.graph.dynamic.DynamicGraph, cytoscape.graph.fixed.FixedGraph, RootGraph

public class CytoscapeFingRootGraph
extends fing.model.FingExtensibleRootGraph
implements CytoscapeRootGraph

Field Summary

Fields inherited from interface cytoscape.graph.dynamic.DynamicGraph

DIRECTED_EDGE, UNDIRECTED_EDGE

Constructor Summary

CytoscapeFingRootGraph()

Method Summary

boolean	addEdgeMetaChild(int arg0, int arg1)
boolean	addMetaChild(Node arg0, Edge arg1)
boolean	addMetaChild(Node arg0, Node arg1)
boolean	addNodeMetaChild(int arg0, int arg1)
boolean	containsEdge(Edge arg0)
boolean	containsNode(Node arg0)
int	createEdge(int arg0, int arg1)
int	createEdge(int arg0, int arg1, boolean arg2)
int	createEdge(Node arg0, Node arg1)
int	createEdge(Node arg0, Node arg1, boolean arg2)
int[]	createEdges(int[] arg0, int[] arg1, boolean arg2)
GraphPerspective	createGraphPerspective(int[] arg0, int[] arg1)
GraphPerspective	createGraphPerspective(Node[] arg0, Edge[] arg1)
CyNetwork	createNetwork(Collection nodes, Collection edges)
CyNetwork	createNetwork(int[] nodeInx, int[] edgeInx) Uses Code copied from ColtRootGraph to create a new Network.
CyNetwork	createNetwork(Node[] nodes, Edge[] edges) Creates a new Network
int	createNode()
int	createNode(GraphPerspective arg0)
int	createNode(int[] arg0, int[] arg1)
int	createNode(Node[] arg0, Edge[] arg1)
int[]	createNodes(int arg0)
int	edgeCreate(int arg0, int arg1, boolean arg2)
boolean	edgeExists(int arg0, int arg1)
boolean	edgeExists(Node arg0, Node arg1)
List	edgeMetaChildrenList(int arg0)
List	edgeMetaChildrenList(Node arg0)
List	edgeMetaParentsList(int arg0)
boolean	edgeRemove(int arg0)
cytoscape.util.intr.IntEnumerator	edges()
cytoscape.util.intr.IntEnumerator	edgesAdjacent(int arg0, boolean arg1, boolean arg2, boolean arg3)
cytoscape.util.intr.IntIterator	edgesConnecting(int arg0, int arg1, boolean arg2, boolean arg3, boolean arg4)
Iterator	edgesIterator()
List	edgesList()
List	edgesList(int arg0, int arg1, boolean arg2)
List	edgesList(Node arg0, Node arg1)
int	edgeSource(int arg0)
int	edgeTarget(int arg0)
byte	edgeType(int arg0)
void	ensureCapacity(int arg0, int arg1)
int[]	getAdjacentEdgeIndicesArray(int arg0, boolean arg1, boolean arg2, boolean arg3)
int[]	getChildlessMetaDescendants(int arg0)
int[]	getConnectingEdgeIndicesArray(int[] arg0)
int[]	getConnectingNodeIndicesArray(int[] arg0)
int	getDegree(int arg0)
int	getDegree(Node arg0)
Edge	getEdge(int arg0)
CyEdge	getEdge(String identifier)
int	getEdgeCount()
int	getEdgeCount(int arg0, int arg1, boolean arg2)
int	getEdgeCount(Node arg0, Node arg1, boolean arg2)
int[]	getEdgeIndicesArray()
int[]	getEdgeIndicesArray(int arg0, int arg1, boolean arg2)
int[]	getEdgeIndicesArray(int arg0, int arg1, boolean arg2, boolean arg3)
int[]	getEdgeMetaChildIndicesArray(int arg0)
int[]	getEdgeMetaParentIndicesArray(int arg0)
int	getEdgeSourceIndex(int arg0)
int	getEdgeTargetIndex(int arg0)
int	getInDegree(int arg0)
int	getInDegree(int arg0, boolean arg1)
int	getInDegree(Node arg0)
int	getInDegree(Node arg0, boolean arg1)
int	getIndex(Edge arg0)
int	getIndex(Node arg0)
Node	getNode(int arg0)
CyNode	getNode(String identifier)
int	getNodeCount()
int[]	getNodeIndicesArray()
int[]	getNodeMetaChildIndicesArray(int arg0)
int[]	getNodeMetaChildIndicesArray(int arg0, boolean arg1)
int[]	getNodeMetaParentIndicesArray(int arg0)
int	getOutDegree(int arg0)
int	getOutDegree(int arg0, boolean arg1)
int	getOutDegree(Node arg0)
int	getOutDegree(Node arg0, boolean arg1)
boolean	isEdgeDirected(int arg0)
boolean	isEdgeMetaChild(int arg0, int arg1)
boolean	isEdgeMetaParent(int arg0, int arg1)
boolean	isMetaChild(Node arg0, Edge arg1)
boolean	isMetaChild(Node arg0, Node arg1)
boolean	isMetaParent(Edge arg0, Node arg1)
boolean	isMetaParent(Node arg0, Node arg1)
boolean	isNeighbor(int arg0, int arg1)
boolean	isNeighbor(Node arg0, Node arg1)
boolean	isNodeMetaChild(int arg0, int arg1)
boolean	isNodeMetaChild(int arg0, int arg1, boolean arg2)
boolean	isNodeMetaParent(int arg0, int arg1)
List	metaParentsList(Edge arg0)
List	metaParentsList(Node arg0)
List	neighborsList(Node arg0)
int	nodeCreate()
boolean	nodeExists(int arg0)
List	nodeMetaChildrenList(int arg0)
List	nodeMetaChildrenList(Node arg0)
List	nodeMetaParentsList(int arg0)
boolean	nodeRemove(int arg0)
cytoscape.util.intr.IntEnumerator	nodes()
Iterator	nodesIterator()
List	nodesList()
Edge	removeEdge(Edge arg0)
int	removeEdge(int arg0)
boolean	removeEdgeMetaChild(int arg0, int arg1)
int[]	removeEdges(int[] arg0)
List	removeEdges(List arg0)
int	removeNode(int arg0)
Node	removeNode(Node arg0)
boolean	removeNodeMetaChild(int arg0, int arg1)
int[]	removeNodes(int[] arg0)
List	removeNodes(List arg0)
void	setEdgeIdentifier(String identifier, int index)
void	setNodeIdentifier(String identifier, int index)

Methods inherited from class java.lang.Object

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

Methods inherited from interface giny.model.RootGraph

addEdgeMetaChild, addMetaChild, addMetaChild, addNodeMetaChild, containsEdge, containsNode, createEdge, createEdge, createEdge, createEdge, createEdges, createGraphPerspective, createGraphPerspective, createNode, createNode, createNode, createNode, createNodes, edgeExists, edgeExists, edgeMetaChildrenList, edgeMetaChildrenList, edgeMetaParentsList, edgesIterator, edgesList, edgesList, edgesList, ensureCapacity, getAdjacentEdgeIndicesArray, getChildlessMetaDescendants, getConnectingEdgeIndicesArray, getConnectingNodeIndicesArray, getDegree, getDegree, getEdge, getEdgeCount, getEdgeCount, getEdgeCount, getEdgeIndicesArray, getEdgeIndicesArray, getEdgeIndicesArray, getEdgeMetaChildIndicesArray, getEdgeMetaParentIndicesArray, getEdgeSourceIndex, getEdgeTargetIndex, getInDegree, getInDegree, getInDegree, getInDegree, getIndex, getIndex, getNode, getNodeCount, getNodeIndicesArray, getNodeMetaChildIndicesArray, getNodeMetaChildIndicesArray, getNodeMetaParentIndicesArray, getOutDegree, getOutDegree, getOutDegree, getOutDegree, isEdgeDirected, isEdgeMetaChild, isEdgeMetaParent, isMetaChild, isMetaChild, isMetaParent, isMetaParent, isNeighbor, isNeighbor, isNodeMetaChild, isNodeMetaChild, isNodeMetaParent, metaParentsList, metaParentsList, neighborsList, nodeMetaChildrenList, nodeMetaChildrenList, nodeMetaParentsList, nodesIterator, nodesList, removeEdge, removeEdge, removeEdgeMetaChild, removeEdges, removeEdges, removeNode, removeNode, removeNodeMetaChild, removeNodes, removeNodes

Constructor Detail

CytoscapeFingRootGraph

public CytoscapeFingRootGraph()

Method Detail

createNetwork

public CyNetwork createNetwork(Collection nodes,
                               Collection edges)

Specified by:

createNetwork in interface CytoscapeRootGraph

createNetwork

public CyNetwork createNetwork(Node[] nodes,
                               Edge[] edges)

Creates a new Network

Specified by:

createNetwork in interface CytoscapeRootGraph

createNetwork

public CyNetwork createNetwork(int[] nodeInx,
                               int[] edgeInx)

Uses Code copied from ColtRootGraph to create a new Network.

Specified by:

createNetwork in interface CytoscapeRootGraph

getNode

public CyNode getNode(String identifier)

Specified by:

getNode in interface CytoscapeRootGraph

getEdge

public CyEdge getEdge(String identifier)

Specified by:

getEdge in interface CytoscapeRootGraph

setNodeIdentifier

public void setNodeIdentifier(String identifier,
                              int index)

Specified by:

setNodeIdentifier in interface CytoscapeRootGraph

setEdgeIdentifier

public void setEdgeIdentifier(String identifier,
                              int index)

Specified by:

setEdgeIdentifier in interface CytoscapeRootGraph

nodes

public cytoscape.util.intr.IntEnumerator nodes()

Specified by:

nodes in interface cytoscape.graph.dynamic.DynamicGraph

Specified by:

nodes in interface cytoscape.graph.fixed.FixedGraph

edges

public cytoscape.util.intr.IntEnumerator edges()

Specified by:

edges in interface cytoscape.graph.dynamic.DynamicGraph

Specified by:

edges in interface cytoscape.graph.fixed.FixedGraph

nodeCreate

public int nodeCreate()

Specified by:

nodeCreate in interface cytoscape.graph.dynamic.DynamicGraph

nodeRemove

public boolean nodeRemove(int arg0)

Specified by:

nodeRemove in interface cytoscape.graph.dynamic.DynamicGraph

edgeCreate

public int edgeCreate(int arg0,
                      int arg1,
                      boolean arg2)

Specified by:

edgeCreate in interface cytoscape.graph.dynamic.DynamicGraph

edgeRemove

public boolean edgeRemove(int arg0)

Specified by:

edgeRemove in interface cytoscape.graph.dynamic.DynamicGraph

nodeExists

public boolean nodeExists(int arg0)

Specified by:

nodeExists in interface cytoscape.graph.dynamic.DynamicGraph

Specified by:

nodeExists in interface cytoscape.graph.fixed.FixedGraph

edgeType

public byte edgeType(int arg0)

Specified by:

edgeType in interface cytoscape.graph.dynamic.DynamicGraph

Specified by:

edgeType in interface cytoscape.graph.fixed.FixedGraph

edgeSource

public int edgeSource(int arg0)

Specified by:

edgeSource in interface cytoscape.graph.dynamic.DynamicGraph

Specified by:

edgeSource in interface cytoscape.graph.fixed.FixedGraph

edgeTarget

public int edgeTarget(int arg0)

Specified by:

edgeTarget in interface cytoscape.graph.dynamic.DynamicGraph

Specified by:

edgeTarget in interface cytoscape.graph.fixed.FixedGraph

edgesAdjacent

public cytoscape.util.intr.IntEnumerator edgesAdjacent(int arg0,
                                                       boolean arg1,
                                                       boolean arg2,
                                                       boolean arg3)

Specified by:

edgesAdjacent in interface cytoscape.graph.dynamic.DynamicGraph

Specified by:

edgesAdjacent in interface cytoscape.graph.fixed.FixedGraph

edgesConnecting

public cytoscape.util.intr.IntIterator edgesConnecting(int arg0,
                                                       int arg1,
                                                       boolean arg2,
                                                       boolean arg3,
                                                       boolean arg4)

Specified by:

edgesConnecting in interface cytoscape.graph.dynamic.DynamicGraph

Specified by:

edgesConnecting in interface cytoscape.graph.fixed.FixedGraph

createGraphPerspective

public GraphPerspective createGraphPerspective(Node[] arg0,
                                               Edge[] arg1)

Specified by:

createGraphPerspective in interface RootGraph

createGraphPerspective

public GraphPerspective createGraphPerspective(int[] arg0,
                                               int[] arg1)

Specified by:

createGraphPerspective in interface RootGraph

ensureCapacity

public void ensureCapacity(int arg0,
                           int arg1)

Specified by:

ensureCapacity in interface RootGraph

getNodeCount

public int getNodeCount()

Specified by:

getNodeCount in interface RootGraph

getEdgeCount

public int getEdgeCount()

Specified by:

getEdgeCount in interface RootGraph

nodesIterator

public Iterator nodesIterator()

Specified by:

nodesIterator in interface RootGraph

nodesList

public List nodesList()

Specified by:

nodesList in interface RootGraph

getNodeIndicesArray

public int[] getNodeIndicesArray()

Specified by:

getNodeIndicesArray in interface RootGraph

edgesIterator

public Iterator edgesIterator()

Specified by:

edgesIterator in interface RootGraph

edgesList

public List edgesList()

Specified by:

edgesList in interface RootGraph

getEdgeIndicesArray

public int[] getEdgeIndicesArray()

Specified by:

getEdgeIndicesArray in interface RootGraph

removeNode

public Node removeNode(Node arg0)

Specified by:

removeNode in interface RootGraph

removeNode

public int removeNode(int arg0)

Specified by:

removeNode in interface RootGraph

removeNodes

public List removeNodes(List arg0)

Specified by:

removeNodes in interface RootGraph

removeNodes

public int[] removeNodes(int[] arg0)

Specified by:

removeNodes in interface RootGraph

createNode

public int createNode()

Specified by:

createNode in interface RootGraph

createNode

public int createNode(Node[] arg0,
                      Edge[] arg1)

Specified by:

createNode in interface RootGraph

createNode

public int createNode(GraphPerspective arg0)

Specified by:

createNode in interface RootGraph

createNode

public int createNode(int[] arg0,
                      int[] arg1)

Specified by:

createNode in interface RootGraph

createNodes

public int[] createNodes(int arg0)

Specified by:

createNodes in interface RootGraph

removeEdge

public Edge removeEdge(Edge arg0)

Specified by:

removeEdge in interface RootGraph

removeEdge

public int removeEdge(int arg0)

Specified by:

removeEdge in interface RootGraph

removeEdges

public List removeEdges(List arg0)

Specified by:

removeEdges in interface RootGraph

removeEdges

public int[] removeEdges(int[] arg0)

Specified by:

removeEdges in interface RootGraph

createEdge

public int createEdge(Node arg0,
                      Node arg1)

Specified by:

createEdge in interface RootGraph

createEdge

public int createEdge(Node arg0,
                      Node arg1,
                      boolean arg2)

Specified by:

createEdge in interface RootGraph

createEdge

public int createEdge(int arg0,
                      int arg1)

Specified by:

createEdge in interface RootGraph

createEdge

public int createEdge(int arg0,
                      int arg1,
                      boolean arg2)

Specified by:

createEdge in interface RootGraph

createEdges

public int[] createEdges(int[] arg0,
                         int[] arg1,
                         boolean arg2)

Specified by:

createEdges in interface RootGraph

containsNode

public boolean containsNode(Node arg0)

Specified by:

containsNode in interface RootGraph

containsEdge

public boolean containsEdge(Edge arg0)

Specified by:

containsEdge in interface RootGraph

neighborsList

public List neighborsList(Node arg0)

Specified by:

neighborsList in interface RootGraph

isNeighbor

public boolean isNeighbor(Node arg0,
                          Node arg1)

Specified by:

isNeighbor in interface RootGraph

isNeighbor

public boolean isNeighbor(int arg0,
                          int arg1)

Specified by:

isNeighbor in interface RootGraph

edgeExists

public boolean edgeExists(Node arg0,
                          Node arg1)

Specified by:

edgeExists in interface RootGraph

edgeExists

public boolean edgeExists(int arg0,
                          int arg1)

Specified by:

edgeExists in interface RootGraph

getEdgeCount

public int getEdgeCount(Node arg0,
                        Node arg1,
                        boolean arg2)

Specified by:

getEdgeCount in interface RootGraph

getEdgeCount

public int getEdgeCount(int arg0,
                        int arg1,
                        boolean arg2)

Specified by:

getEdgeCount in interface RootGraph

getAdjacentEdgeIndicesArray

public int[] getAdjacentEdgeIndicesArray(int arg0,
                                         boolean arg1,
                                         boolean arg2,
                                         boolean arg3)

Specified by:

getAdjacentEdgeIndicesArray in interface RootGraph

getConnectingEdgeIndicesArray

public int[] getConnectingEdgeIndicesArray(int[] arg0)

Specified by:

getConnectingEdgeIndicesArray in interface RootGraph

getConnectingNodeIndicesArray

public int[] getConnectingNodeIndicesArray(int[] arg0)

Specified by:

getConnectingNodeIndicesArray in interface RootGraph

getEdgeIndicesArray

public int[] getEdgeIndicesArray(int arg0,
                                 int arg1,
                                 boolean arg2,
                                 boolean arg3)

Specified by:

getEdgeIndicesArray in interface RootGraph

edgesList

public List edgesList(Node arg0,
                      Node arg1)

Specified by:

edgesList in interface RootGraph

edgesList

public List edgesList(int arg0,
                      int arg1,
                      boolean arg2)

Specified by:

edgesList in interface RootGraph

getEdgeIndicesArray

public int[] getEdgeIndicesArray(int arg0,
                                 int arg1,
                                 boolean arg2)

Specified by:

getEdgeIndicesArray in interface RootGraph

getInDegree

public int getInDegree(Node arg0)

Specified by:

getInDegree in interface RootGraph

getInDegree

public int getInDegree(int arg0)

Specified by:

getInDegree in interface RootGraph

getInDegree

public int getInDegree(Node arg0,
                       boolean arg1)

Specified by:

getInDegree in interface RootGraph

getInDegree

public int getInDegree(int arg0,
                       boolean arg1)

Specified by:

getInDegree in interface RootGraph

getOutDegree

public int getOutDegree(Node arg0)

Specified by:

getOutDegree in interface RootGraph

getOutDegree

public int getOutDegree(int arg0)

Specified by:

getOutDegree in interface RootGraph

getOutDegree

public int getOutDegree(Node arg0,
                        boolean arg1)

Specified by:

getOutDegree in interface RootGraph

getOutDegree

public int getOutDegree(int arg0,
                        boolean arg1)

Specified by:

getOutDegree in interface RootGraph

getDegree

public int getDegree(Node arg0)

Specified by:

getDegree in interface RootGraph

getDegree

public int getDegree(int arg0)

Specified by:

getDegree in interface RootGraph

getIndex

public int getIndex(Node arg0)

Specified by:

getIndex in interface RootGraph

getNode

public Node getNode(int arg0)

Specified by:

getNode in interface RootGraph

getIndex

public int getIndex(Edge arg0)

Specified by:

getIndex in interface RootGraph

getEdge

public Edge getEdge(int arg0)

Specified by:

getEdge in interface RootGraph

getEdgeSourceIndex

public int getEdgeSourceIndex(int arg0)

Specified by:

getEdgeSourceIndex in interface RootGraph

getEdgeTargetIndex

public int getEdgeTargetIndex(int arg0)

Specified by:

getEdgeTargetIndex in interface RootGraph

isEdgeDirected

public boolean isEdgeDirected(int arg0)

Specified by:

isEdgeDirected in interface RootGraph

addMetaChild

public boolean addMetaChild(Node arg0,
                            Node arg1)

Specified by:

addMetaChild in interface RootGraph

addNodeMetaChild

public boolean addNodeMetaChild(int arg0,
                                int arg1)

Specified by:

addNodeMetaChild in interface RootGraph

removeNodeMetaChild

public boolean removeNodeMetaChild(int arg0,
                                   int arg1)

Specified by:

removeNodeMetaChild in interface RootGraph

isMetaParent

public boolean isMetaParent(Node arg0,
                            Node arg1)

Specified by:

isMetaParent in interface RootGraph

isNodeMetaParent

public boolean isNodeMetaParent(int arg0,
                                int arg1)

Specified by:

isNodeMetaParent in interface RootGraph

metaParentsList

public List metaParentsList(Node arg0)

Specified by:

metaParentsList in interface RootGraph

nodeMetaParentsList

public List nodeMetaParentsList(int arg0)

Specified by:

nodeMetaParentsList in interface RootGraph

getNodeMetaParentIndicesArray

public int[] getNodeMetaParentIndicesArray(int arg0)

Specified by:

getNodeMetaParentIndicesArray in interface RootGraph

isMetaChild

public boolean isMetaChild(Node arg0,
                           Node arg1)

Specified by:

isMetaChild in interface RootGraph

isNodeMetaChild

public boolean isNodeMetaChild(int arg0,
                               int arg1)

Specified by:

isNodeMetaChild in interface RootGraph

isNodeMetaChild

public boolean isNodeMetaChild(int arg0,
                               int arg1,
                               boolean arg2)

Specified by:

isNodeMetaChild in interface RootGraph

nodeMetaChildrenList

public List nodeMetaChildrenList(Node arg0)

Specified by:

nodeMetaChildrenList in interface RootGraph

nodeMetaChildrenList

public List nodeMetaChildrenList(int arg0)

Specified by:

nodeMetaChildrenList in interface RootGraph

getNodeMetaChildIndicesArray

public int[] getNodeMetaChildIndicesArray(int arg0)

Specified by:

getNodeMetaChildIndicesArray in interface RootGraph

getNodeMetaChildIndicesArray

public int[] getNodeMetaChildIndicesArray(int arg0,
                                          boolean arg1)

Specified by:

getNodeMetaChildIndicesArray in interface RootGraph

getChildlessMetaDescendants

public int[] getChildlessMetaDescendants(int arg0)

Specified by:

getChildlessMetaDescendants in interface RootGraph

addMetaChild

public boolean addMetaChild(Node arg0,
                            Edge arg1)

Specified by:

addMetaChild in interface RootGraph

addEdgeMetaChild

public boolean addEdgeMetaChild(int arg0,
                                int arg1)

Specified by:

addEdgeMetaChild in interface RootGraph

removeEdgeMetaChild

public boolean removeEdgeMetaChild(int arg0,
                                   int arg1)

Specified by:

removeEdgeMetaChild in interface RootGraph

isMetaParent

public boolean isMetaParent(Edge arg0,
                            Node arg1)

Specified by:

isMetaParent in interface RootGraph

isEdgeMetaParent

public boolean isEdgeMetaParent(int arg0,
                                int arg1)

Specified by:

isEdgeMetaParent in interface RootGraph

metaParentsList

public List metaParentsList(Edge arg0)

Specified by:

metaParentsList in interface RootGraph

edgeMetaParentsList

public List edgeMetaParentsList(int arg0)

Specified by:

edgeMetaParentsList in interface RootGraph

getEdgeMetaParentIndicesArray

public int[] getEdgeMetaParentIndicesArray(int arg0)

Specified by:

getEdgeMetaParentIndicesArray in interface RootGraph

isMetaChild

public boolean isMetaChild(Node arg0,
                           Edge arg1)

Specified by:

isMetaChild in interface RootGraph

isEdgeMetaChild

public boolean isEdgeMetaChild(int arg0,
                               int arg1)

Specified by:

isEdgeMetaChild in interface RootGraph

edgeMetaChildrenList

public List edgeMetaChildrenList(Node arg0)

Specified by:

edgeMetaChildrenList in interface RootGraph

edgeMetaChildrenList

public List edgeMetaChildrenList(int arg0)

Specified by:

edgeMetaChildrenList in interface RootGraph

getEdgeMetaChildIndicesArray

public int[] getEdgeMetaChildIndicesArray(int arg0)

Specified by:

getEdgeMetaChildIndicesArray in interface RootGraph