vn.edu.tlu.hatrang.autoRWRMTN.internal.model

Class CyNetworkUtils

java.lang.Object

vn.edu.tlu.hatrang.autoRWRMTN.internal.model.CyNetworkUtils

public class CyNetworkUtils
extends Object

Constructor Summary

Constructors

Constructor and Description
CyNetworkUtils()

Method Summary

Modifier and Type	Method and Description
static Set<org.cytoscape.model.CyEdge>	getAllConnectingEdges(org.cytoscape.model.CyNetwork aNetwork, Collection<org.cytoscape.model.CyNode> nodes) Checks the specified network has values for the given node attributes.
static Map<org.cytoscape.model.CyNode,MutInteger>	getNeighborMap(org.cytoscape.model.CyNetwork aNetwork, org.cytoscape.model.CyNode aNode) Gets all the neighbors of the given node and their frequencies.
static Map<org.cytoscape.model.CyNode,MutInteger>	getNeighborMap(org.cytoscape.model.CyNetwork aNetwork, org.cytoscape.model.CyNode aNode, List<org.cytoscape.model.CyEdge> aIncEdges) Gets all the neighbors of the given node and their frequencies.
static Set<org.cytoscape.model.CyNode>	getNeighbors(org.cytoscape.model.CyNetwork aNetwork, org.cytoscape.model.CyNode aNode) Gets all the neighbors of the given node.
static Set<org.cytoscape.model.CyNode>	getNeighbors(org.cytoscape.model.CyNetwork aNetwork, org.cytoscape.model.CyNode aNode, List<org.cytoscape.model.CyEdge> aIncEdges) Gets all the neighbors of the given node.
static int	getPairConnCount(org.cytoscape.model.CyNetwork aNetwork, Collection<org.cytoscape.model.CyNode> aNodeIndices, boolean aIgnoreDir) Gets the number of pair connections between the given set of nodes.
static int	removeSelfLoops(org.cytoscape.model.CyNetwork aNetwork) Removes all self-loops in a network and returns the number of removed self-loops.

Methods inherited from class java.lang.Object

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

Constructor Detail

CyNetworkUtils

public CyNetworkUtils()

Method Detail

getAllConnectingEdges

public static Set<org.cytoscape.model.CyEdge> getAllConnectingEdges(org.cytoscape.model.CyNetwork aNetwork,
                                                                    Collection<org.cytoscape.model.CyNode> nodes)

Checks the specified network has values for the given node attributes.

Parameters:

aNetwork - Network of interest.

nodes - Collection of CyNode Cytoscape

Returns:

Array of all attributes for which all nodes in aNetwork have values; an empty set if no such attributes are found.

getPairConnCount

public static int getPairConnCount(org.cytoscape.model.CyNetwork aNetwork,
                                   Collection<org.cytoscape.model.CyNode> aNodeIndices,
                                   boolean aIgnoreDir)

Gets the number of pair connections between the given set of nodes.

This method effectively counts the number of edges between nodes in the given set, ignoring self-loops and multiple edges.

Parameters:

aNetwork - Network containing the nodes of interest.

aNodeIndices - Indices of the nodes to be examined.

aIgnoreDir - Flag indicating if connections are undirected.

Returns:

Number of pair connections between the nodes in the given node set. The returned value is always in the range [0, n(n-1)/2] for undirected networks ( aIgnoreDir == true) and [0, n(n-1)] for directed networks ( aIgnoreDir == true).

getNeighbors

public static Set<org.cytoscape.model.CyNode> getNeighbors(org.cytoscape.model.CyNetwork aNetwork,
                                                           org.cytoscape.model.CyNode aNode)

Gets all the neighbors of the given node. All types of edges incident on the node are considered - incoming, outgoing and undirected.

Note that the node itself is never returned as its neighbor.

Parameters:

aNetwork - Network that contains the node of interest - aNode.

aNode - CyNode , whose neighbors are to be found.

Returns:

Set of Node instances, containing all the neighbors of aNode; empty set if the node specified is an isolated vertex.

See Also:

getNeighbors(CyNetwork, CyNode)

getNeighbors

public static Set<org.cytoscape.model.CyNode> getNeighbors(org.cytoscape.model.CyNetwork aNetwork,
                                                           org.cytoscape.model.CyNode aNode,
                                                           List<org.cytoscape.model.CyEdge> aIncEdges)

Gets all the neighbors of the given node.

Note that the node itself is never returned as its neighbor.

Parameters:

aNetwork - Network that contains the node of interest - aNode.

aNode - CyNode , whose neighbors are to be found.

aIncEdges - Array of all the edges incident on aNode.

Returns:

Set of Node instances, containing all the neighbors of aNode; empty set if the node specified is an isolated vertex.

getNeighborMap

public static Map<org.cytoscape.model.CyNode,MutInteger> getNeighborMap(org.cytoscape.model.CyNetwork aNetwork,
                                                                        org.cytoscape.model.CyNode aNode)

Gets all the neighbors of the given node and their frequencies. All types of edges incident on the node are considered - incoming, outgoing and undirected.

Note that the node itself is never counted as its neighbor.

Parameters:

aNetwork - Network that contains the node of interest - aNode.

aNode - CyNode , whose neighbors are to be found.

Returns:

Map of Node instances as keys, containing all the neighbors of aNode and the number of their occurrences as the values, encapsulated in MutInteger instances.

See Also:

getNeighborMap(CyNetwork, CyNode )

getNeighborMap

public static Map<org.cytoscape.model.CyNode,MutInteger> getNeighborMap(org.cytoscape.model.CyNetwork aNetwork,
                                                                        org.cytoscape.model.CyNode aNode,
                                                                        List<org.cytoscape.model.CyEdge> aIncEdges)

Gets all the neighbors of the given node and their frequencies.

All types of edges incident on the node are considered - incoming, outgoing and undirected.

Note that the node itself is never counted as its neighbor.

Parameters:

aNetwork - Network that contains the node of interest - aNode.

aNode - CyNode , whose neighbors are to be found.

aIncEdges - Array of all the edges incident on aNode.

Returns:

Map of Node instances as keys, containing all the neighbors of aNode and the number of their occurrences as values, encapsulated in MutInteger instances.

removeSelfLoops

public static int removeSelfLoops(org.cytoscape.model.CyNetwork aNetwork)

Removes all self-loops in a network and returns the number of removed self-loops. All types of edges are considered - incoming, outgoing and undirected.

Parameters:

aNetwork - Network from which self-loops are to be removed.

Returns:

Number of removed self-loops.