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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 |
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Fields inherited from interface cytoscape.graph.dynamic.DynamicGraph |
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DIRECTED_EDGE, UNDIRECTED_EDGE |
Constructor Summary | |
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CytoscapeFingRootGraph()
Creates a new CytoscapeFingRootGraph object. |
Method Summary | |
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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)
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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)
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int |
createEdge(Node arg0,
Node arg1,
boolean arg2)
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int[] |
createEdges(int[] arg0,
int[] arg1,
boolean arg2)
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GraphPerspective |
createGraphPerspective(int[] arg0,
int[] arg1)
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GraphPerspective |
createGraphPerspective(Node[] arg0,
Edge[] arg1)
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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)
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cytoscape.util.intr.IntIterator |
edgesConnecting(int arg0,
int arg1,
boolean arg2,
boolean arg3,
boolean arg4)
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Iterator |
edgesIterator()
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List |
edgesList()
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List |
edgesList(int arg0,
int arg1,
boolean arg2)
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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)
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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)
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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)
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boolean |
isNodeMetaParent(int arg0,
int arg1)
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List |
metaParentsList(Edge arg0)
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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)
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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()
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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 |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public CytoscapeFingRootGraph()
Method Detail |
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public CyNetwork createNetwork(Collection nodes, Collection edges)
createNetwork
in interface CytoscapeRootGraph
nodes
- 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 CytoscapeRootGraph
public CyNode getNode(String identifier)
getNode
in interface CytoscapeRootGraph
identifier
- DOCUMENT ME!
public CyEdge getEdge(String identifier)
getEdge
in interface CytoscapeRootGraph
identifier
- DOCUMENT ME!
public void setNodeIdentifier(String identifier, int index)
setNodeIdentifier
in interface CytoscapeRootGraph
identifier
- DOCUMENT ME!index
- DOCUMENT ME!public void setEdgeIdentifier(String identifier, int index)
setEdgeIdentifier
in interface CytoscapeRootGraph
identifier
- DOCUMENT ME!index
- DOCUMENT ME!public cytoscape.util.intr.IntEnumerator nodes()
nodes
in interface cytoscape.graph.dynamic.DynamicGraph
nodes
in interface cytoscape.graph.fixed.FixedGraph
public cytoscape.util.intr.IntEnumerator edges()
edges
in interface cytoscape.graph.dynamic.DynamicGraph
edges
in interface cytoscape.graph.fixed.FixedGraph
public int nodeCreate()
nodeCreate
in interface cytoscape.graph.dynamic.DynamicGraph
public 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.DynamicGraph
public boolean edgeRemove(int arg0)
edgeRemove
in interface cytoscape.graph.dynamic.DynamicGraph
public boolean nodeExists(int arg0)
nodeExists
in interface cytoscape.graph.dynamic.DynamicGraph
nodeExists
in interface cytoscape.graph.fixed.FixedGraph
public byte edgeType(int arg0)
edgeType
in interface cytoscape.graph.dynamic.DynamicGraph
edgeType
in interface cytoscape.graph.fixed.FixedGraph
public int edgeSource(int arg0)
edgeSource
in interface cytoscape.graph.dynamic.DynamicGraph
edgeSource
in interface cytoscape.graph.fixed.FixedGraph
public int edgeTarget(int arg0)
edgeTarget
in interface cytoscape.graph.dynamic.DynamicGraph
edgeTarget
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.DynamicGraph
edgesAdjacent
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.DynamicGraph
edgesConnecting
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 RootGraph
public int getNodeCount()
getNodeCount
in interface RootGraph
public int getEdgeCount()
getEdgeCount
in interface RootGraph
public Iterator nodesIterator()
nodesIterator
in interface RootGraph
public List nodesList()
nodesList
in interface RootGraph
public int[] getNodeIndicesArray()
getNodeIndicesArray
in interface RootGraph
public Iterator edgesIterator()
edgesIterator
in interface RootGraph
public List edgesList()
edgesList
in interface RootGraph
public int[] getEdgeIndicesArray()
getEdgeIndicesArray
in interface RootGraph
public Node removeNode(Node arg0)
removeNode
in interface RootGraph
public int removeNode(int arg0)
removeNode
in interface RootGraph
public List removeNodes(List arg0)
removeNodes
in interface RootGraph
public int[] removeNodes(int[] arg0)
removeNodes
in interface RootGraph
public int createNode()
createNode
in interface RootGraph
public int createNode(Node[] arg0, Edge[] arg1)
createNode
in interface RootGraph
public int createNode(GraphPerspective arg0)
createNode
in interface RootGraph
public int createNode(int[] arg0, int[] arg1)
createNode
in interface RootGraph
public int[] createNodes(int arg0)
createNodes
in interface RootGraph
public Edge removeEdge(Edge arg0)
removeEdge
in interface RootGraph
public int removeEdge(int arg0)
removeEdge
in interface RootGraph
public List removeEdges(List arg0)
removeEdges
in interface RootGraph
public 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 RootGraph
public boolean containsNode(Node arg0)
containsNode
in interface RootGraph
public boolean containsEdge(Edge arg0)
containsEdge
in interface RootGraph
public 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 RootGraph
public int[] getConnectingEdgeIndicesArray(int[] arg0)
getConnectingEdgeIndicesArray
in interface RootGraph
public 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 RootGraph
public int getInDegree(Node arg0)
getInDegree
in interface RootGraph
public 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 RootGraph
public int getOutDegree(Node arg0)
getOutDegree
in interface RootGraph
public 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 RootGraph
public int getDegree(Node arg0)
getDegree
in interface RootGraph
public int getDegree(int arg0)
getDegree
in interface RootGraph
public int getIndex(Node arg0)
getIndex
in interface RootGraph
public Node getNode(int arg0)
getNode
in interface RootGraph
public int getIndex(Edge arg0)
getIndex
in interface RootGraph
public Edge getEdge(int arg0)
getEdge
in interface RootGraph
public int getEdgeSourceIndex(int arg0)
getEdgeSourceIndex
in interface RootGraph
public int getEdgeTargetIndex(int arg0)
getEdgeTargetIndex
in interface RootGraph
public 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 RootGraph
public List metaParentsList(Node arg0)
metaParentsList
in interface RootGraph
public List nodeMetaParentsList(int arg0)
nodeMetaParentsList
in interface RootGraph
public 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 RootGraph
public List nodeMetaChildrenList(Node arg0)
nodeMetaChildrenList
in interface RootGraph
public List nodeMetaChildrenList(int arg0)
nodeMetaChildrenList
in interface RootGraph
public int[] getNodeMetaChildIndicesArray(int arg0)
getNodeMetaChildIndicesArray
in interface RootGraph
public int[] getNodeMetaChildIndicesArray(int arg0, boolean arg1)
getNodeMetaChildIndicesArray
in interface RootGraph
public 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 RootGraph
public List metaParentsList(Edge arg0)
metaParentsList
in interface RootGraph
public List edgeMetaParentsList(int arg0)
edgeMetaParentsList
in interface RootGraph
public 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 RootGraph
public List edgeMetaChildrenList(Node arg0)
edgeMetaChildrenList
in interface RootGraph
public List edgeMetaChildrenList(int arg0)
edgeMetaChildrenList
in interface RootGraph
public int[] getEdgeMetaChildIndicesArray(int arg0)
getEdgeMetaChildIndicesArray
in interface RootGraph
|
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