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Cytoscape 2.5.1 (c) 2006,2007 ISB, MSKCC, UCSD | ||||||||
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java.lang.Objectfing.model.FingExtensibleRootGraph
cytoscape.giny.CytoscapeFingRootGraph
public class CytoscapeFingRootGraph
| Field Summary |
|---|
| Fields inherited from interface cytoscape.graph.dynamic.DynamicGraph |
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DIRECTED_EDGE, UNDIRECTED_EDGE |
| Constructor Summary | |
|---|---|
CytoscapeFingRootGraph()
Creates a new CytoscapeFingRootGraph object. |
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| Method Summary | |
|---|---|
boolean |
addEdgeMetaChild(int arg0,
int arg1)
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boolean |
addMetaChild(Node arg0,
Edge arg1)
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boolean |
addMetaChild(Node arg0,
Node arg1)
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boolean |
addNodeMetaChild(int arg0,
int arg1)
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boolean |
containsEdge(Edge arg0)
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boolean |
containsNode(Node arg0)
|
int |
createEdge(int arg0,
int arg1)
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int |
createEdge(int arg0,
int arg1,
boolean arg2)
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int |
createEdge(Node arg0,
Node arg1)
|
int |
createEdge(Node arg0,
Node arg1,
boolean arg2)
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int[] |
createEdges(int[] arg0,
int[] arg1,
boolean arg2)
|
GraphPerspective |
createGraphPerspective(int[] arg0,
int[] arg1)
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GraphPerspective |
createGraphPerspective(Node[] arg0,
Edge[] arg1)
|
CyNetwork |
createNetwork(Collection nodes,
Collection edges)
DOCUMENT ME! |
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()
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int |
createNode(GraphPerspective arg0)
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int |
createNode(int[] arg0,
int[] arg1)
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int |
createNode(Node[] arg0,
Edge[] arg1)
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int[] |
createNodes(int arg0)
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int |
edgeCreate(int arg0,
int arg1,
boolean arg2)
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boolean |
edgeExists(int arg0,
int arg1)
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boolean |
edgeExists(Node arg0,
Node arg1)
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List |
edgeMetaChildrenList(int arg0)
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List |
edgeMetaChildrenList(Node arg0)
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List |
edgeMetaParentsList(int arg0)
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boolean |
edgeRemove(int arg0)
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cytoscape.util.intr.IntEnumerator |
edges()
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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)
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int |
edgeSource(int arg0)
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int |
edgeTarget(int arg0)
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byte |
edgeType(int arg0)
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void |
ensureCapacity(int arg0,
int arg1)
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int[] |
getAdjacentEdgeIndicesArray(int arg0,
boolean arg1,
boolean arg2,
boolean arg3)
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int[] |
getChildlessMetaDescendants(int arg0)
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int[] |
getConnectingEdgeIndicesArray(int[] arg0)
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int[] |
getConnectingNodeIndicesArray(int[] arg0)
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int |
getDegree(int arg0)
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int |
getDegree(Node arg0)
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Edge |
getEdge(int arg0)
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CyEdge |
getEdge(String identifier)
DOCUMENT ME! |
int |
getEdgeCount()
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int |
getEdgeCount(int arg0,
int arg1,
boolean arg2)
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int |
getEdgeCount(Node arg0,
Node arg1,
boolean arg2)
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int[] |
getEdgeIndicesArray()
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int[] |
getEdgeIndicesArray(int arg0,
int arg1,
boolean arg2)
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int[] |
getEdgeIndicesArray(int arg0,
int arg1,
boolean arg2,
boolean arg3)
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int[] |
getEdgeMetaChildIndicesArray(int arg0)
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int[] |
getEdgeMetaParentIndicesArray(int arg0)
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int |
getEdgeSourceIndex(int arg0)
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int |
getEdgeTargetIndex(int arg0)
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int |
getInDegree(int arg0)
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int |
getInDegree(int arg0,
boolean arg1)
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int |
getInDegree(Node arg0)
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int |
getInDegree(Node arg0,
boolean arg1)
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int |
getIndex(Edge arg0)
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int |
getIndex(Node arg0)
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Node |
getNode(int arg0)
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CyNode |
getNode(String identifier)
DOCUMENT ME! |
int |
getNodeCount()
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int[] |
getNodeIndicesArray()
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int[] |
getNodeMetaChildIndicesArray(int arg0)
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int[] |
getNodeMetaChildIndicesArray(int arg0,
boolean arg1)
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int[] |
getNodeMetaParentIndicesArray(int arg0)
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int |
getOutDegree(int arg0)
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int |
getOutDegree(int arg0,
boolean arg1)
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int |
getOutDegree(Node arg0)
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int |
getOutDegree(Node arg0,
boolean arg1)
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boolean |
isEdgeDirected(int arg0)
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boolean |
isEdgeMetaChild(int arg0,
int arg1)
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boolean |
isEdgeMetaParent(int arg0,
int arg1)
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boolean |
isMetaChild(Node arg0,
Edge arg1)
|
boolean |
isMetaChild(Node arg0,
Node arg1)
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boolean |
isMetaParent(Edge arg0,
Node arg1)
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boolean |
isMetaParent(Node arg0,
Node arg1)
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boolean |
isNeighbor(int arg0,
int arg1)
|
boolean |
isNeighbor(Node arg0,
Node arg1)
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boolean |
isNodeMetaChild(int arg0,
int arg1)
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boolean |
isNodeMetaChild(int arg0,
int arg1,
boolean arg2)
|
boolean |
isNodeMetaParent(int arg0,
int arg1)
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List |
metaParentsList(Edge arg0)
|
List |
metaParentsList(Node arg0)
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List |
neighborsList(Node arg0)
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int |
nodeCreate()
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boolean |
nodeExists(int arg0)
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List |
nodeMetaChildrenList(int arg0)
|
List |
nodeMetaChildrenList(Node arg0)
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List |
nodeMetaParentsList(int arg0)
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boolean |
nodeRemove(int arg0)
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cytoscape.util.intr.IntEnumerator |
nodes()
|
Iterator |
nodesIterator()
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List |
nodesList()
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Edge |
removeEdge(Edge arg0)
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int |
removeEdge(int arg0)
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boolean |
removeEdgeMetaChild(int arg0,
int arg1)
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int[] |
removeEdges(int[] arg0)
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List |
removeEdges(List arg0)
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int |
removeNode(int arg0)
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Node |
removeNode(Node arg0)
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boolean |
removeNodeMetaChild(int arg0,
int arg1)
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int[] |
removeNodes(int[] arg0)
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List |
removeNodes(List arg0)
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void |
setEdgeIdentifier(String identifier,
int index)
DOCUMENT ME! |
void |
setNodeIdentifier(String identifier,
int index)
DOCUMENT ME! |
| Methods inherited from class java.lang.Object |
|---|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Constructor Detail |
|---|
public CytoscapeFingRootGraph()
| Method Detail |
|---|
public CyNetwork createNetwork(Collection nodes,
Collection edges)
createNetwork in interface CytoscapeRootGraphnodes - DOCUMENT ME!edges - DOCUMENT ME!
public CyNetwork createNetwork(Node[] nodes,
Edge[] edges)
createNetwork in interface CytoscapeRootGraph
public CyNetwork createNetwork(int[] nodeInx,
int[] edgeInx)
createNetwork in interface CytoscapeRootGraphpublic CyNode getNode(String identifier)
getNode in interface CytoscapeRootGraphidentifier - DOCUMENT ME!
public CyEdge getEdge(String identifier)
getEdge in interface CytoscapeRootGraphidentifier - DOCUMENT ME!
public void setNodeIdentifier(String identifier,
int index)
setNodeIdentifier in interface CytoscapeRootGraphidentifier - DOCUMENT ME!index - DOCUMENT ME!
public void setEdgeIdentifier(String identifier,
int index)
setEdgeIdentifier in interface CytoscapeRootGraphidentifier - DOCUMENT ME!index - DOCUMENT ME!public cytoscape.util.intr.IntEnumerator nodes()
nodes in interface cytoscape.graph.dynamic.DynamicGraphnodes in interface cytoscape.graph.fixed.FixedGraphpublic cytoscape.util.intr.IntEnumerator edges()
edges in interface cytoscape.graph.dynamic.DynamicGraphedges in interface cytoscape.graph.fixed.FixedGraphpublic int nodeCreate()
nodeCreate in interface cytoscape.graph.dynamic.DynamicGraphpublic boolean nodeRemove(int arg0)
nodeRemove in interface cytoscape.graph.dynamic.DynamicGraph
public int edgeCreate(int arg0,
int arg1,
boolean arg2)
edgeCreate in interface cytoscape.graph.dynamic.DynamicGraphpublic boolean edgeRemove(int arg0)
edgeRemove in interface cytoscape.graph.dynamic.DynamicGraphpublic boolean nodeExists(int arg0)
nodeExists in interface cytoscape.graph.dynamic.DynamicGraphnodeExists in interface cytoscape.graph.fixed.FixedGraphpublic byte edgeType(int arg0)
edgeType in interface cytoscape.graph.dynamic.DynamicGraphedgeType in interface cytoscape.graph.fixed.FixedGraphpublic int edgeSource(int arg0)
edgeSource in interface cytoscape.graph.dynamic.DynamicGraphedgeSource in interface cytoscape.graph.fixed.FixedGraphpublic int edgeTarget(int arg0)
edgeTarget in interface cytoscape.graph.dynamic.DynamicGraphedgeTarget in interface cytoscape.graph.fixed.FixedGraph
public cytoscape.util.intr.IntEnumerator edgesAdjacent(int arg0,
boolean arg1,
boolean arg2,
boolean arg3)
edgesAdjacent in interface cytoscape.graph.dynamic.DynamicGraphedgesAdjacent in interface cytoscape.graph.fixed.FixedGraph
public cytoscape.util.intr.IntIterator edgesConnecting(int arg0,
int arg1,
boolean arg2,
boolean arg3,
boolean arg4)
edgesConnecting in interface cytoscape.graph.dynamic.DynamicGraphedgesConnecting in interface cytoscape.graph.fixed.FixedGraph
public GraphPerspective createGraphPerspective(Node[] arg0,
Edge[] arg1)
createGraphPerspective in interface RootGraph
public GraphPerspective createGraphPerspective(int[] arg0,
int[] arg1)
createGraphPerspective in interface RootGraph
public void ensureCapacity(int arg0,
int arg1)
ensureCapacity in interface RootGraphpublic int getNodeCount()
getNodeCount in interface RootGraphpublic int getEdgeCount()
getEdgeCount in interface RootGraphpublic Iterator nodesIterator()
nodesIterator in interface RootGraphpublic List nodesList()
nodesList in interface RootGraphpublic int[] getNodeIndicesArray()
getNodeIndicesArray in interface RootGraphpublic Iterator edgesIterator()
edgesIterator in interface RootGraphpublic List edgesList()
edgesList in interface RootGraphpublic int[] getEdgeIndicesArray()
getEdgeIndicesArray in interface RootGraphpublic Node removeNode(Node arg0)
removeNode in interface RootGraphpublic int removeNode(int arg0)
removeNode in interface RootGraphpublic List removeNodes(List arg0)
removeNodes in interface RootGraphpublic int[] removeNodes(int[] arg0)
removeNodes in interface RootGraphpublic int createNode()
createNode in interface RootGraph
public int createNode(Node[] arg0,
Edge[] arg1)
createNode in interface RootGraphpublic int createNode(GraphPerspective arg0)
createNode in interface RootGraph
public int createNode(int[] arg0,
int[] arg1)
createNode in interface RootGraphpublic int[] createNodes(int arg0)
createNodes in interface RootGraphpublic Edge removeEdge(Edge arg0)
removeEdge in interface RootGraphpublic int removeEdge(int arg0)
removeEdge in interface RootGraphpublic List removeEdges(List arg0)
removeEdges in interface RootGraphpublic int[] removeEdges(int[] arg0)
removeEdges in interface RootGraph
public int createEdge(Node arg0,
Node arg1)
createEdge in interface RootGraph
public int createEdge(Node arg0,
Node arg1,
boolean arg2)
createEdge in interface RootGraph
public int createEdge(int arg0,
int arg1)
createEdge in interface RootGraph
public int createEdge(int arg0,
int arg1,
boolean arg2)
createEdge in interface RootGraph
public int[] createEdges(int[] arg0,
int[] arg1,
boolean arg2)
createEdges in interface RootGraphpublic boolean containsNode(Node arg0)
containsNode in interface RootGraphpublic boolean containsEdge(Edge arg0)
containsEdge in interface RootGraphpublic List neighborsList(Node arg0)
neighborsList in interface RootGraph
public boolean isNeighbor(Node arg0,
Node arg1)
isNeighbor in interface RootGraph
public boolean isNeighbor(int arg0,
int arg1)
isNeighbor in interface RootGraph
public boolean edgeExists(Node arg0,
Node arg1)
edgeExists in interface RootGraph
public boolean edgeExists(int arg0,
int arg1)
edgeExists in interface RootGraph
public int getEdgeCount(Node arg0,
Node arg1,
boolean arg2)
getEdgeCount in interface RootGraph
public int getEdgeCount(int arg0,
int arg1,
boolean arg2)
getEdgeCount in interface RootGraph
public int[] getAdjacentEdgeIndicesArray(int arg0,
boolean arg1,
boolean arg2,
boolean arg3)
getAdjacentEdgeIndicesArray in interface RootGraphpublic int[] getConnectingEdgeIndicesArray(int[] arg0)
getConnectingEdgeIndicesArray in interface RootGraphpublic int[] getConnectingNodeIndicesArray(int[] arg0)
getConnectingNodeIndicesArray in interface RootGraph
public int[] getEdgeIndicesArray(int arg0,
int arg1,
boolean arg2,
boolean arg3)
getEdgeIndicesArray in interface RootGraph
public List edgesList(Node arg0,
Node arg1)
edgesList in interface RootGraph
public List edgesList(int arg0,
int arg1,
boolean arg2)
edgesList in interface RootGraph
public int[] getEdgeIndicesArray(int arg0,
int arg1,
boolean arg2)
getEdgeIndicesArray in interface RootGraphpublic int getInDegree(Node arg0)
getInDegree in interface RootGraphpublic int getInDegree(int arg0)
getInDegree in interface RootGraph
public int getInDegree(Node arg0,
boolean arg1)
getInDegree in interface RootGraph
public int getInDegree(int arg0,
boolean arg1)
getInDegree in interface RootGraphpublic int getOutDegree(Node arg0)
getOutDegree in interface RootGraphpublic int getOutDegree(int arg0)
getOutDegree in interface RootGraph
public int getOutDegree(Node arg0,
boolean arg1)
getOutDegree in interface RootGraph
public int getOutDegree(int arg0,
boolean arg1)
getOutDegree in interface RootGraphpublic int getDegree(Node arg0)
getDegree in interface RootGraphpublic int getDegree(int arg0)
getDegree in interface RootGraphpublic int getIndex(Node arg0)
getIndex in interface RootGraphpublic Node getNode(int arg0)
getNode in interface RootGraphpublic int getIndex(Edge arg0)
getIndex in interface RootGraphpublic Edge getEdge(int arg0)
getEdge in interface RootGraphpublic int getEdgeSourceIndex(int arg0)
getEdgeSourceIndex in interface RootGraphpublic int getEdgeTargetIndex(int arg0)
getEdgeTargetIndex in interface RootGraphpublic boolean isEdgeDirected(int arg0)
isEdgeDirected in interface RootGraph
public boolean addMetaChild(Node arg0,
Node arg1)
addMetaChild in interface RootGraph
public boolean addNodeMetaChild(int arg0,
int arg1)
addNodeMetaChild in interface RootGraph
public boolean removeNodeMetaChild(int arg0,
int arg1)
removeNodeMetaChild in interface RootGraph
public boolean isMetaParent(Node arg0,
Node arg1)
isMetaParent in interface RootGraph
public boolean isNodeMetaParent(int arg0,
int arg1)
isNodeMetaParent in interface RootGraphpublic List metaParentsList(Node arg0)
metaParentsList in interface RootGraphpublic List nodeMetaParentsList(int arg0)
nodeMetaParentsList in interface RootGraphpublic int[] getNodeMetaParentIndicesArray(int arg0)
getNodeMetaParentIndicesArray in interface RootGraph
public boolean isMetaChild(Node arg0,
Node arg1)
isMetaChild in interface RootGraph
public boolean isNodeMetaChild(int arg0,
int arg1)
isNodeMetaChild in interface RootGraph
public boolean isNodeMetaChild(int arg0,
int arg1,
boolean arg2)
isNodeMetaChild in interface RootGraphpublic List nodeMetaChildrenList(Node arg0)
nodeMetaChildrenList in interface RootGraphpublic List nodeMetaChildrenList(int arg0)
nodeMetaChildrenList in interface RootGraphpublic int[] getNodeMetaChildIndicesArray(int arg0)
getNodeMetaChildIndicesArray in interface RootGraph
public int[] getNodeMetaChildIndicesArray(int arg0,
boolean arg1)
getNodeMetaChildIndicesArray in interface RootGraphpublic int[] getChildlessMetaDescendants(int arg0)
getChildlessMetaDescendants in interface RootGraph
public boolean addMetaChild(Node arg0,
Edge arg1)
addMetaChild in interface RootGraph
public boolean addEdgeMetaChild(int arg0,
int arg1)
addEdgeMetaChild in interface RootGraph
public boolean removeEdgeMetaChild(int arg0,
int arg1)
removeEdgeMetaChild in interface RootGraph
public boolean isMetaParent(Edge arg0,
Node arg1)
isMetaParent in interface RootGraph
public boolean isEdgeMetaParent(int arg0,
int arg1)
isEdgeMetaParent in interface RootGraphpublic List metaParentsList(Edge arg0)
metaParentsList in interface RootGraphpublic List edgeMetaParentsList(int arg0)
edgeMetaParentsList in interface RootGraphpublic int[] getEdgeMetaParentIndicesArray(int arg0)
getEdgeMetaParentIndicesArray in interface RootGraph
public boolean isMetaChild(Node arg0,
Edge arg1)
isMetaChild in interface RootGraph
public boolean isEdgeMetaChild(int arg0,
int arg1)
isEdgeMetaChild in interface RootGraphpublic List edgeMetaChildrenList(Node arg0)
edgeMetaChildrenList in interface RootGraphpublic List edgeMetaChildrenList(int arg0)
edgeMetaChildrenList in interface RootGraphpublic int[] getEdgeMetaChildIndicesArray(int arg0)
getEdgeMetaChildIndicesArray in interface RootGraph
|
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| SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD | ||||||||