|
Cytoscape 2.6.2 (c) 2006,2007 ISB, MSKCC, UCSD | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
public interface GraphPerspective
Method Summary | |
---|---|
void |
addGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener)
|
Object |
clone()
|
boolean |
containsEdge(Edge edge)
Return true if the given Edge is in this GraphPerspective. |
boolean |
containsEdge(Edge edge,
boolean recurse)
Return true if the given Edge is in this GraphPerspective. |
boolean |
containsNode(Node node)
Return true if the given Node is in this GraphPerspective. |
boolean |
containsNode(Node node,
boolean recurse)
Return true if the given Node is in this GraphPerspective. |
GraphPerspective |
createGraphPerspective(Filter filter)
Create a new GraphPerspective with all of the Nodes from this one that pass the given filter and all of the Edges from this one that pass the filter (and all Nodes incident on those edges). |
GraphPerspective |
createGraphPerspective(int[] node_indices)
Create a new GraphPerspective given a list of Nodes. |
GraphPerspective |
createGraphPerspective(int[] node_indices,
int[] edge_indices)
Deprecated. Use RootGraph.createGraphPerspective(int[], int[]) instead. |
GraphPerspective |
createGraphPerspective(Node[] nodes,
Edge[] edges)
Deprecated. Use RootGraph.createGraphPerspective(int[], int[]) instead. |
boolean |
edgeExists(int from_node_index,
int to_node_index)
This method returns true if and only if either 1) there exists a directed edge E in this GraphPerspective such that from_node_index is E's source node's index and to_node_index is E's target node's index or 2) there exists an undirected edge E in this GraphPerspective such that E's endpoint nodes have indices from_node_index and to_node_index. |
boolean |
edgeExists(Node from,
Node to)
This method returns true if and only if either 1) there exists a directed edge E in this GraphPerspective such that the from node specified is E's source node and the target node specified is E's target node or 2) there exists an undirected edge E in this GraphPerspective such that E's endpoints are the from and to nodes specified. |
List |
edgeMetaChildrenList(int node_index)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
List |
edgeMetaChildrenList(Node node)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
List |
edgeMetaParentsList(int edge_index)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
Iterator |
edgesIterator()
|
List |
edgesList()
Returns a list of Edge objects. |
List |
edgesList(int from_node_index,
int to_node_index,
boolean include_undirected_edges)
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead. |
List |
edgesList(Node from,
Node to)
Return a new List of the Edges in this GraphPerspective from the first given Node to the second given Node. |
int[] |
getAdjacentEdgeIndicesArray(int node_index,
boolean undirected_edges,
boolean incoming_directed_edges,
boolean outgoing_directed_edges)
Returns [RootGraph] indices of all Edges in this GraphPerspective adjacent to the Node at specified [RootGraph] index. |
List |
getAdjacentEdgesList(Node node,
boolean include_undirected_edges,
boolean incoming_edges,
boolean outgoing_edges)
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead. |
int[] |
getConnectingEdgeIndicesArray(int[] node_indices)
This will return an array of Edge indices that are the Edges between Nodes. |
List |
getConnectingEdges(List nodes)
This will return a List of giny.model.Edge objects that are the Edges between Nodes. |
int[] |
getConnectingNodeIndicesArray(int[] edge_indices)
Deprecated. Use getEdgeSourceIndex(int) and getEdgeTargetIndex(int) instead. |
int |
getDegree(int node_index)
Return the number of distinct Edges in this GraphPerspective incident on the Node with the given index. |
int |
getDegree(Node node)
Return the number of distinct Edges in this GraphPerspective incident on the given Node. |
Edge |
getEdge(int index)
Return an Edge which is in this GraphPerspective. |
int |
getEdgeCount()
Returns number of active edges in this perspective. |
int |
getEdgeCount(int from_node_index,
int to_node_index,
boolean count_undirected_edges)
Count the number of edges from the Node with index from_index to the Node with index to_index (where this.getIndex( to_node ) == to_index). |
int |
getEdgeCount(Node from,
Node to,
boolean count_undirected_edges)
Count the number of edges from the first Node to the second. |
int |
getEdgeIndex(int root_graph_edge_index)
Deprecated. Use getRootGraphEdgeIndex(int), whose functionality is identical. |
int[] |
getEdgeIndicesArray()
Returns an array of length getEdgeCount(); the array contains RootGraph indices of Edge objects in this GraphPerspective, in some undefined order. |
int[] |
getEdgeIndicesArray(int from_node_index,
int to_node_index,
boolean include_undirected_edges)
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead. |
int[] |
getEdgeIndicesArray(int from_node_index,
int to_node_index,
boolean include_undirected_edges,
boolean include_both_directions)
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead. |
int[] |
getEdgeMetaChildIndicesArray(int node_index)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
int[] |
getEdgeMetaParentIndicesArray(int edge_index)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
int |
getEdgeSourceIndex(int edge_index)
Retrieve the index of the Node that is the source of the Edge in this GraphPerspective with the given index. |
int |
getEdgeTargetIndex(int edge_index)
Retrieve the index of the Node that is the target of the Edge in this GraphPerspective with the given index. |
int |
getInDegree(int node_index)
Return the number of Edges e in this GraphPerspective such that e.getTarget().equals( node ). |
int |
getInDegree(int node_index,
boolean count_undirected_edges)
Return the number of Edges e in this GraphPerspective such that e.getSource().equals( node ). |
int |
getInDegree(Node node)
Return the number of Edges e in this GraphPerspective such that e.getTarget().equals( node ). |
int |
getInDegree(Node node,
boolean count_undirected_edges)
Return the number of Edges e in this GraphPerspective such that e.getSource().equals( node ). |
int |
getIndex(Edge edge)
Return the index of the given Edge in the underlying RootGraph. |
int |
getIndex(Node node)
Return the index of the given Node in the underlying RootGraph. |
Node |
getNode(int index)
Return a Node which is in this GraphPerspective. |
int |
getNodeCount()
Returns number of active nodes in this perspective. |
int |
getNodeIndex(int root_graph_node_index)
Deprecated. Use getRootGraphNodeIndex(int), whose functionality is identical. |
int[] |
getNodeIndicesArray()
Returns an array of length getNodeCount(); the array contains RootGraph indices of Node objects in this GraphPerspective, in some undefined order. |
int[] |
getNodeMetaChildIndicesArray(int node_index)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
int[] |
getNodeMetaParentIndicesArray(int node_index)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
int |
getOutDegree(int node_index)
Return the number of Edges e in this GraphPerspective such that e.getSource().equals( node ). |
int |
getOutDegree(int node_index,
boolean count_undirected_edges)
Return the number of Edges e in this GraphPerspective such that e.getSource().equals( node ). |
int |
getOutDegree(Node node)
Return the number of Edges e in this GraphPerspective such that e.getSource().equals( node ). |
int |
getOutDegree(Node node,
boolean count_undirected_edges)
Return the number of Edges e in this GraphPerspective such that e.getSource().equals( node ). |
RootGraph |
getRootGraph()
Return the root Graph for this GraphPerspective |
int |
getRootGraphEdgeIndex(int root_graph_edge_index)
This method returns the input parameter if and only if an Edge at the specified RootGraph index exists in this GraphPerspective; otherwise 0 is returned. |
int |
getRootGraphNodeIndex(int root_graph_node_index)
This method returns the input parameter if and only if a Node at the specified RootGraph index exists in this GraphPerspective; otherwise 0 is returned. |
Edge |
hideEdge(Edge edge)
If this GraphPerspective does not hide the given Edge, change it so that it does hide the edge. |
int |
hideEdge(int edge_index)
If this GraphPerspective does not hide the Edge with the given index in the RootGraph, change it so that it does hide the edge. |
int[] |
hideEdges(int[] edge_indices)
If this GraphPerspective does not hide any of the Edges corresponding to the indices in the given array, change it so that it does hide those edges. |
List |
hideEdges(List edges)
Deprecated. Use hideEdge(Edge) or hideEdges(int[]) instead. |
int |
hideNode(int node_index)
If this GraphPerspective does not hide the Node with the given index in the underlying RootGraph, change it so that it does hide the node and all of its incident edges. |
Node |
hideNode(Node node)
If this GraphPerspective does not hide the given Node, change it so that it does hide the node and all of its incident edges. |
int[] |
hideNodes(int[] node_indices)
If this GraphPerspective does not hide any of the Nodes corresponding to the indices in the given array, change it so that it does hide those nodes and all Edges incident on them. |
List |
hideNodes(List nodes)
Deprecated. Use hideNode(Node) or hideNodes(int[]) instead. |
boolean |
isEdgeDirected(int edge_index)
Retrieve the directedness of the Edge in this GraphPerspective with the given [RootGraph] index. |
boolean |
isEdgeMetaChild(int parent_index,
int child_edge_index)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
boolean |
isEdgeMetaParent(int child_edge_index,
int parent_index)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
boolean |
isMetaChild(Node parent,
Edge child)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
boolean |
isMetaChild(Node parent,
Node child)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
boolean |
isMetaParent(Edge child,
Node parent)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
boolean |
isMetaParent(Node child,
Node parent)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
boolean |
isNeighbor(int a_node_index,
int another_node_index)
Please note that the definition of "node neighbor" is such: Node A is a "node neighbor" of node B if and only if there exists an edge [directed or undirected] E such that A is E's target and B is E's source, or A is E's source and B is E's target; this method then returns true if and only if node at index a_node_index is a "node neighbor" of node at index another_node_index in this GraphPerspective. |
boolean |
isNeighbor(Node a_node,
Node another_node)
Please note that the definition of "node neighbor" is such: Node A is a "node neighbor" of node B if and only if there exists an edge [directed or undirected] E such that A is E's target and B is E's source, or A is E's source and B is E's target; this method then returns true if and only if a_node is a "node neighbor" of another_node in this GraphPerspective. |
boolean |
isNodeMetaChild(int parent_index,
int child_node_index)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
boolean |
isNodeMetaParent(int child_node_index,
int parent_index)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
GraphPerspective |
join(GraphPerspective peer)
Creates a union GraphPerspective. |
List |
metaParentsList(Edge edge)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
List |
metaParentsList(Node node)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
int[] |
neighborsArray(int node_index)
Please note that the definition of "node neighbor" is such: Node A is a "node neighbor" of node B if and only if there exists an edge [directed or undirected] E such that A is E's target and B is E's source, or A is E's source and B is E's target; this method then returns a non-repeating list of indices of all nodes N in this GraphPerspective such that N is a "node neighbor" of the node at specified index, or null if no node at specified index exists in this GraphPerspective. |
List |
neighborsList(Node node)
Deprecated. Use neighborsArray(int) instead; |
List |
nodeMetaChildrenList(int parent_index)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
List |
nodeMetaChildrenList(Node node)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
List |
nodeMetaParentsList(int node_index)
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges. |
Iterator |
nodesIterator()
Returns an Iterator over all giny.model.Node objects in this GraphPerspective. |
List |
nodesList()
Returns a list of Node objects. |
void |
removeGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener)
|
Edge |
restoreEdge(Edge edge)
If this GraphPerspective hides the given Edge, change it so that it does not hide the edge or the Nodes on which the edge is incident. |
int |
restoreEdge(int edge_index)
If this GraphPerspective hides the Edge with the given index in the underlying RootGraph, change it so that it does not hide the edge or the Nodes on which the edge is incident. |
int[] |
restoreEdges(int[] edge_indices)
If this GraphPerspective hides any of the Edges corresponding to the indices in the given array, change it so that it does not hide those edges or any of the Nodes on which they are incident. |
List |
restoreEdges(List edges)
Deprecated. Use restoreEdges(int[]) instead. |
int |
restoreNode(int node_index)
If this GraphPerspective hides the Node with the given index in the underlying RootGraph, change it so that it does not hide the node. |
Node |
restoreNode(Node node)
If this GraphPerspective hides the given Node, change it so that it does not hide the node. |
int[] |
restoreNodes(int[] node_indices)
If this GraphPerspective hides any of the Nodes corresponding to the indices in the given array, change it so that it does not hide those nodes. |
int[] |
restoreNodes(int[] node_indices,
boolean restore_incident_edges)
Deprecated. Use restoreNodes(int[]) and restoreEdges(int[]) instead; to get edges incident to specified nodes, use RootGraph.getConnectingEdgeIndicesArray(int[]). |
List |
restoreNodes(List nodes)
Deprecated. Use restoreNode(Node) restoreNodes(int[]) instead. |
List |
restoreNodes(List nodes,
boolean restore_incident_edges)
Deprecated. Use restoreNodes(int[]) and restoreEdges(int[]) instead; to get edges incident to specified nodes, use RootGraph.getConnectingEdgeIndicesArray(int[]). |
Method Detail |
---|
void addGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener)
void removeGraphPerspectiveChangeListener(GraphPerspectiveChangeListener listener)
Object clone()
RootGraph getRootGraph()
int getNodeCount()
int getEdgeCount()
Iterator nodesIterator()
TECHNICAL DETAIL: Iterating over the set of all nodes in a GraphPerspective and manipulating a GraphPerspective's topology (by calling hideXXX() and restoreXXX() methods) concurrently will have undefined effects on the returned Iterator.
List nodesList()
nodesIterator()
int[] getNodeIndicesArray()
nodesIterator()
,
GraphObject.getRootGraphIndex()
Iterator edgesIterator()
List edgesList()
edgesIterator()
int[] getEdgeIndicesArray()
edgesIterator()
,
GraphObject.getRootGraphIndex()
int[] getEdgeIndicesArray(int from_node_index, int to_node_index, boolean include_undirected_edges, boolean include_both_directions)
getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
Node hideNode(Node node)
node
- The Node to hide.
int hideNode(int node_index)
node_index
- The index in the underlying RootGraph of the Node to hide.
List hideNodes(List nodes)
hideNode(Node)
,
hideNodes(int[])
int[] hideNodes(int[] node_indices)
node_indices
- The int array of indices in the underlying RootGraph of
the Nodes to hide.
Node restoreNode(Node node)
node
- The Node to restore.
int restoreNode(int node_index)
node_index
- The index in the underlying RootGraph of the Node to
restore.
List restoreNodes(List nodes)
restoreNode(Node)
,
restoreNodes(int[])
List restoreNodes(List nodes, boolean restore_incident_edges)
restoreNodes(int[])
,
restoreEdges(int[])
,
RootGraph.getConnectingEdgeIndicesArray(int[])
int[] restoreNodes(int[] node_indices, boolean restore_incident_edges)
node_indices
- The Node indices.restore_incident_edges
- Whether or not the incident edges to the
restored nodes should also be restored.
restoreNodes(int[])
,
restoreEdges(int[])
,
RootGraph.getConnectingEdgeIndicesArray(int[])
int[] restoreNodes(int[] node_indices)
node_indices
- The int array of indices in the underlying RootGraph
of the Nodes to restore.
Edge hideEdge(Edge edge)
edge
- The Edge to hide.
int hideEdge(int edge_index)
edge_index
- The index in the underlying RootGraph of the Edge to
hide.
List hideEdges(List edges)
hideEdge(Edge)
,
hideEdges(int[])
int[] hideEdges(int[] edge_indices)
edge_indices
- The int array of indices in the underlying RootGraph of
the Edges to hide.
Edge restoreEdge(Edge edge)
edge
- The Edge to restore.
int restoreEdge(int edge_index)
edge_index
- The index in the underlying RootGraph of the Edge to
restore.
List restoreEdges(List edges)
restoreEdges(int[])
int[] restoreEdges(int[] edge_indices)
edge_indices
- An array of indices in the underlying RootGraph of
the Edges to restore.
boolean containsNode(Node node)
containsNode(Node, boolean)
boolean containsNode(Node node, boolean recurse)
boolean containsEdge(Edge edge)
containsEdge( Edge,
boolean )
with a true recurse boolean argument.
boolean containsEdge(Edge edge, boolean recurse)
GraphPerspective join(GraphPerspective peer)
GraphPerspective createGraphPerspective(Node[] nodes, Edge[] edges)
nodes
- A [possibly null] array of Nodes in this GraphPerspective to
include in the new GraphPerspective.edges
- A [possibly null] array of Edges in this GraphPerspective to
include in the new GraphPerspective.
RootGraph.createGraphPerspective(int[], int[])
GraphPerspective createGraphPerspective(int[] node_indices, int[] edge_indices)
node_indices
- A [possibly null] array of [RootGraph] indices
of Nodes in this GraphPerspective to include in the new GraphPerspective.edge_indices
- A [possibly null] array of [RootGraph] indices
of Edges in this GraphPerspective to include in the new GraphPerspective.
RootGraph.createGraphPerspective(int[], int[])
GraphPerspective createGraphPerspective(Filter filter)
List neighborsList(Node node)
neighborsArray(int)
int[] neighborsArray(int node_index)
node_index
- The node whose neighbors you're looking for.boolean isNeighbor(Node a_node, Node another_node)
a_node
- Source node.another_node
- Possible target node.boolean isNeighbor(int a_node_index, int another_node_index)
a_node_index
- Source node index.another_node_index
- Possible target node index.boolean edgeExists(Node from, Node to)
from
- Source node.to
- Possible target node.boolean edgeExists(int from_node_index, int to_node_index)
from_node_index
- Source node index.to_node_index
- Possible target node index.int getEdgeCount(Node from, Node to, boolean count_undirected_edges)
from
- the Node in this GraphPerspective that is the source of the
edges to be counted.to
- the Node in this GraphPerspective that is the target of the
edges to be counted.count_undirected_edges
- Undirected edges will be included in the
count iff count_undirected_edges is true.
int getEdgeCount(int from_node_index, int to_node_index, boolean count_undirected_edges)
from_node_index
- the index in this GraphPerspective of the Node to
count edges from.to_node_index
- the index in this GraphPerspective of the Node to
find edges to.count_undirected_edges
- Undirected edges will be included in the
count iff count_undirected_edges is true.
List edgesList(Node from, Node to)
from
- the Node in this GraphPerspective that is the source of the
Edges to be returned.to
- the Node in this GraphPerspective that is the target of the
Edges to be returned.
List edgesList(int from_node_index, int to_node_index, boolean include_undirected_edges)
from_node_index
- the index in this GraphPerspective of the Node to
return edges from.to_node_index
- the index in this GraphPerspective of the Node to
return edges to.include_undirected_edges
- Undirected edges will be included in the
List iff include_undirected_edges is true.
getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
int[] getEdgeIndicesArray(int from_node_index, int to_node_index, boolean include_undirected_edges)
from_node_index
- the index in this GraphPerspective of the Node to
return edges from.to_node_index
- the index in this GraphPerspective of the Node to
return edges to.include_undirected_edges
- Undirected edges will be included in the
array iff include_undirected_edges is true.
getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
int getInDegree(Node node)
node
- the Node to count in-edges of.
int getInDegree(int node_index)
node_index
- the index of the Node to count in-edges of.
int getInDegree(Node node, boolean count_undirected_edges)
node
- the Node to count in-edges of.count_undirected_edges
- Undirected edges will be included in the
count iff count_undirected_edges is true.
int getInDegree(int node_index, boolean count_undirected_edges)
node_index
- the index of the Node to count in-edges of.count_undirected_edges
- Undirected edges will be included in the
count iff count_undirected_edges is true.
int getOutDegree(Node node)
node
- the Node to count out-edges of.
int getOutDegree(int node_index)
node_index
- the index of the Node to count out-edges of.
int getOutDegree(Node node, boolean count_undirected_edges)
node
- the Node to count out-edges of.count_undirected_edges
- Undirected edges will be included in the
count iff count_undirected_edges is true.
int getOutDegree(int node_index, boolean count_undirected_edges)
node_index
- the index of the Node to count out-edges of.count_undirected_edges
- Undirected edges will be included in the
count iff count_undirected_edges is true.
int getDegree(Node node)
int getDegree(int node_index)
int getIndex(Node node)
node
- the Node to find a corresponding index for.
int getNodeIndex(int root_graph_node_index)
getRootGraphNodeIndex(int)
int getRootGraphNodeIndex(int root_graph_node_index)
Node getNode(int index)
index
- the index into the underlying RootGraph to find a
corresponding GraphPerspective Node for.
int getIndex(Edge edge)
edge
- the Edge to find a corresponding index for.
int getEdgeIndex(int root_graph_edge_index)
getRootGraphEdgeIndex(int)
int getRootGraphEdgeIndex(int root_graph_edge_index)
Edge getEdge(int index)
index
- the index into the underlying RootGraph to find a
corresponding GraphPerspective Edge for.
int getEdgeSourceIndex(int edge_index)
edge_index
- the [RootGraph] index of the Edge in this GraphPerspective.
int getEdgeTargetIndex(int edge_index)
edge_index
- the [RootGraph] index of the Edge in this GraphPerspective.
boolean isEdgeDirected(int edge_index)
edge_index
- the [RootGraph] index of the Edge in this GraphPerspective.
boolean isMetaParent(Node child, Node parent)
child
- the Node that is the child (the containee) in the
contains-a relationship that we are querying.parent
- the Node that is the parent (the container) in the
contains-a relationship that we are querying.
boolean isNodeMetaParent(int child_node_index, int parent_index)
child_node_index
- the index in the RootGraph of the Node
that is the child (the containee) in the contains-a relationship
that we are querying.parent_index
- the index in the RootGraph of the Node that is
the parent (the container) in the contains-a relationship that we
are querying.
List metaParentsList(Node node)
node
- the Node that is the child (the containee) in the
contains-a relationship that we are querying.
List nodeMetaParentsList(int node_index)
node_index
- the index in the RootGraph of the Node that is
the child (the containee) in the contains-a relationship that we
are querying.
int[] getNodeMetaParentIndicesArray(int node_index)
node_index
- the index in the underlying RootGraph of the Node that is
the child (the containee) in the contains-a relationship that we
are querying.
boolean isMetaChild(Node parent, Node child)
parent
- the Node that is the parent (the container) in the
contains-a relationship that we are querying.child
- the Node that is the child (the containee) in the
contains-a relationship that we are querying.
boolean isNodeMetaChild(int parent_index, int child_node_index)
parent_index
- the index in the RootGraph of the Node that is
the parent (the container) in the contains-a relationship that we
are querying.child_node_index
- the index in the RootGraph of the Node
that is the child (the containee) in the contains-a relationship
that we are querying.
List nodeMetaChildrenList(Node node)
node
- the Node that is the parent (the container) in the
contains-a relationship that we are querying.
List nodeMetaChildrenList(int parent_index)
parent_index
- the index in the underlying RootGraph of the Node that is
the parent (the container) in the contains-a relationship that we
are querying.
int[] getNodeMetaChildIndicesArray(int node_index)
node_index
- the index in the RootGraph of the Node that is
the parent (the containee) in the contains-a relationship that we
are querying.
boolean isMetaParent(Edge child, Node parent)
child
- the Edge that is the child (the containee) in the
contains-a relationship that we are querying.parent
- the Node that is the parent (the container) in the
contains-a relationship that we are querying.
boolean isEdgeMetaParent(int child_edge_index, int parent_index)
child_edge_index
- the index in the RootGraph of the Edge
that is the child (the containee) in the contains-a relationship
that we are querying.parent_index
- the index in the RootGraph of the Node that is
the parent (the container) in the contains-a relationship that we
are querying.
List metaParentsList(Edge edge)
edge
- the Edge that is the child (the containee) in the
contains-a relationship that we are querying.
List edgeMetaParentsList(int edge_index)
edge_index
- the index in the RootGraph of the Edge that is
the child (the containee) in the contains-a relationship that we
are querying.
int[] getEdgeMetaParentIndicesArray(int edge_index)
edge_index
- the index in the RootGraph of the Edge that is
the child (the containee) in the contains-a relationship that we
are querying.
boolean isMetaChild(Node parent, Edge child)
parent
- the Node that is the parent (the container) in the
contains-a relationship that we are querying.child
- the Edge that is the child (the containee) in the
contains-a relationship that we are querying.
boolean isEdgeMetaChild(int parent_index, int child_edge_index)
parent_index
- the index in the RootGraph of the Node that is
the parent (the container) in the contains-a relationship that we
are querying.child_edge_index
- the index in the RootGraph of the Edge
that is the child (the containee) in the contains-a relationship
that we are querying.
List edgeMetaChildrenList(Node node)
node
- the Node that is the parent (the container) in the
contains-a relationship that we are querying.
List edgeMetaChildrenList(int node_index)
node_index
- the index in the RootGraph of the Node that is
the parent (the container) in the contains-a relationship that we
are querying.
int[] getEdgeMetaChildIndicesArray(int node_index)
node_index
- the index in the RootGraph of the Node that is
the parent (the containee) in the contains-a relationship that we
are querying.
List getAdjacentEdgesList(Node node, boolean include_undirected_edges, boolean incoming_edges, boolean outgoing_edges)
node
- the nodeinclude_undirected_edges
- should we include undirected edgesincoming_edges
- Include incoming edgesoutgoing_edges
- Include outgoing edges
getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean)
int[] getAdjacentEdgeIndicesArray(int node_index, boolean undirected_edges, boolean incoming_directed_edges, boolean outgoing_directed_edges)
node_index
- the [RootGraph] index of the Node whose adjacent
Edge information we're seeking.undirected_edges
- Edge indices of all adjacent
undirected Edges are included in the return value of this
method if this value is true, otherwise not a single
index corresponding to an undirected Edge is returned;
undirected Edge E is an adjacent undirected Edge to Node N
[definition:] if and only if E's source is N or E's target
is N.incoming_directed_edges
- Edge indices of all incoming
directed Edges are included in the return value of this
method if this value is true, otherwise not a single index
corresponding to an incoming directed Edge is returned;
directed Edge E is an incoming directed Edge to Node N
[definition:] if and only if N is E's target.outgoing_directed_edges
- Edge indices of all outgoing
directed Edges are included in the return value of this
method if this value is true, otherwise not a single index
corresponding to an outgoing directed Edge is returned;
directed Edge E is an outgoing directed Edge from Node N
[definition:] if and only if N is E's source.
List getConnectingEdges(List nodes)
int[] getConnectingEdgeIndicesArray(int[] node_indices)
int[] getConnectingNodeIndicesArray(int[] edge_indices)
getEdgeSourceIndex(int)
,
getEdgeTargetIndex(int)
GraphPerspective createGraphPerspective(int[] node_indices)
|
www.cytoscape.org | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |