brain.cliqueCalculation

Class BidirectionalGraph

java.lang.Object

brain.cliqueCalculation.Graph

brain.cliqueCalculation.BidirectionalGraph

public class BidirectionalGraph
extends Graph

This class shows the application of a network generating algorithms which generate a graph out of a given distribution of cliques.

Field Summary

Fields

Modifier and Type	Field and Description
int	diameter Diameter gives the distance of the most distant vertices connected by the shortest path possible.
int	edgesCount Gives the number of edges in the graph.

Constructor Summary

Constructors

Constructor and Description
BidirectionalGraph() Standard constructor
BidirectionalGraph(double[][] _internalLinks) This constructor allows to instantiate an already constructed graph from internal links of an Module.
BidirectionalGraph(java.util.HashMap<java.lang.Integer,java.util.TreeSet<java.lang.Integer>> localpart) This constructor allows to instantiate an already constructed graph in a HashMap
BidirectionalGraph(Module module) This constructor allows to instantiate an already constructed graph from internal links of an Module.

Method Summary

Methods

Modifier and Type	Method and Description
void	addDirectedLink(java.lang.Integer nodeA, java.lang.Integer nodeB) Adds a directed Link from nodeA to nodeB.
void	addNode(java.lang.Integer node) Adds a node to the graph
void	addNodes(java.util.TreeSet<java.lang.Integer> nodes) Adds a aet of nodes to the graph.
boolean	areConnected(java.lang.Integer verticeA, java.lang.Integer verticeB) Checks wheather two vertices are connected.
boolean	areNeighbours(java.lang.Integer a, java.lang.Integer b) Check if a and b are neighbours/directly connected a---b
void	connect(java.lang.Integer nodeA, java.lang.Integer nodeB) Connects two vertices in a graph in both directions from nodeA to nodeB and from nodeB to nodeA (bidirectional)
void	connectedToClique(java.lang.Integer candidate, java.util.TreeSet<java.lang.Integer> clique) Connects a node to a node set
BidirectionalGraph	copy(java.util.TreeSet<java.lang.Integer> name)
BidirectionalGraph	createLocalNetworkPart(java.lang.Integer siteA, java.lang.Integer siteB) Creates a local part of a this graph.
java.util.Vector<java.util.TreeSet<java.lang.Integer>>	detectIndependentSets()
void	disconnect(java.lang.Integer node) Disconnects a vertice from a bidirectional graph in both directions
void	disconnect(java.lang.Integer nodeA, java.lang.Integer nodeB) Disconnects two vertices in a bidirectional graph in both directions from i to j and from j to i (bidirectional)
boolean	existsNode(int j)
java.util.HashMap<java.lang.Integer,java.lang.Integer>	getCliqueDistribution() Returns the HashMap which holds the clique distribution.
java.util.TreeSet<java.lang.Integer>	getCommonNeighbours(java.lang.Integer a, java.lang.Integer b) Gets common neighbours between two vertices.
java.util.TreeSet<java.lang.Integer>	getCommonNeighbours(java.util.TreeSet<java.lang.Integer> Vertices, java.lang.Integer can) Gets common neighbours between a pool of vertices and an additional vertice.
java.util.TreeSet<java.lang.String>	getConnections()
java.lang.Integer	getCoordinationNumber(java.lang.Integer vertice) Gets the coordination number.
int[]	getDistribution() Returns the clique distribution used to construct the graph
java.util.TreeSet<java.lang.Integer>	getLinksOfNode(java.lang.Integer vertice) Get all connections of a vertice to neighbours as a TreeSet
java.util.HashMap<java.lang.Integer,java.util.TreeSet<java.lang.Integer>>	getNetworkTreeSet() Get the network as a TreeSet
boolean	getNodeExists(java.lang.Integer integer) Check wheather that node exists in the graph
int	getNodesCount() Returns the number of nodes in this graph.
java.lang.Integer	getNodeWithLowestDegree()
java.util.TreeSet<java.lang.Integer>	getSetOfNodes() Get all nodes of this graph as a TreeSet
boolean	haveOneCommonNeighbour(java.lang.Integer a, java.lang.Integer b) Check if a and b have one common neighbour/indirectly connected over one site a-x-b.
boolean	isConnectedTo(java.util.TreeSet<java.lang.Integer> clique, java.lang.Integer candidate) Checks wheather a vertice is fully connecte to a set of vertices
boolean	isHasIdependentSets()
boolean	isZeroNode(java.lang.String path)
void	load(java.lang.String path, int edgecountlimit, int nodecountlimit) loads a graph of the format node white space node
void	loadBipartite(java.lang.String path, int edgecountlimit, int nodecountlimit, boolean integrate)
BidirectionalGraph	loadPajek(java.lang.String path)
void	merge(java.lang.Integer toMerge, java.lang.Integer toBeMerged) merges two sites after the checking algorithm assured this operation does not violate the clique distribution.
void	printCliquesSummary() Prints a clique summary to the standard output.
void	printNetwork() Prints the network to the standard output
void	removeNode(java.lang.Integer node) Removes a node from the graph and all connections attached to it.
void	save(java.lang.String path)
void	savePajek(java.lang.String path)
void	setConnections(java.util.TreeSet<java.lang.String> connections)
void	setNetworkTreeSet(java.util.HashMap<java.lang.Integer,java.util.TreeSet<java.lang.Integer>> _networkTreeSet) sets a network
java.lang.Integer	totalCoordinationNumer(java.util.TreeSet<java.lang.Integer> partOfNetwork) Counts all coordination numbers of the network.

Methods inherited from class java.lang.Object

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

Field Detail

diameter

public int diameter

Diameter gives the distance of the most distant vertices connected by the shortest path possible. If this was not already computes diameter is -1.

edgesCount

public int edgesCount

Gives the number of edges in the graph.

Constructor Detail

BidirectionalGraph

public BidirectionalGraph()

Standard constructor

BidirectionalGraph

public BidirectionalGraph(java.util.HashMap<java.lang.Integer,java.util.TreeSet<java.lang.Integer>> localpart)

This constructor allows to instantiate an already constructed graph in a HashMap

Parameters:

localpart -

BidirectionalGraph

public BidirectionalGraph(double[][] _internalLinks)

This constructor allows to instantiate an already constructed graph from internal links of an Module.

Parameters:

_internalLinks - - internal links of an Module

BidirectionalGraph

public BidirectionalGraph(Module module)

This constructor allows to instantiate an already constructed graph from internal links of an Module.

Parameters:

module -

Method Detail

addNode

public void addNode(java.lang.Integer node)

Adds a node to the graph

Specified by:

addNode in class Graph

Parameters:

node -

removeNode

public void removeNode(java.lang.Integer node)

Removes a node from the graph and all connections attached to it.

Parameters:

node -

addNodes

public void addNodes(java.util.TreeSet<java.lang.Integer> nodes)

Adds a aet of nodes to the graph. Attention! It does not check wheather nodes are overwritten. It that case the connections are lost!

Parameters:

nodes - a set of nodes

addDirectedLink

public void addDirectedLink(java.lang.Integer nodeA,
                   java.lang.Integer nodeB)

Adds a directed Link from nodeA to nodeB. For unidirectional links use connect()

Parameters:

nodeA - node to connect from

nodeB - node to connect to

getCommonNeighbours

public java.util.TreeSet<java.lang.Integer> getCommonNeighbours(java.util.TreeSet<java.lang.Integer> Vertices,
                                                       java.lang.Integer can)

Gets common neighbours between a pool of vertices and an additional vertice.

Parameters:

Vertices - - a set of vertices

can - - a vertice

Returns:

TreeSet of vertices which are common neighbours to vertices in Vertices and can

printCliquesSummary

public void printCliquesSummary()

Prints a clique summary to the standard output.

totalCoordinationNumer

public java.lang.Integer totalCoordinationNumer(java.util.TreeSet<java.lang.Integer> partOfNetwork)

Counts all coordination numbers of the network. A coordination number of a vertice is the count of its links to other vertices. The total coordination number is the sum of the coordination numbers of every vertice

Returns:

total coordination number

connect

public void connect(java.lang.Integer nodeA,
           java.lang.Integer nodeB)

Connects two vertices in a graph in both directions from nodeA to nodeB and from nodeB to nodeA (bidirectional)

Specified by:

connect in class Graph

Parameters:

nodeA - - vertice to be connected to j

nodeB - - vertice to be connected to i

disconnect

public void disconnect(java.lang.Integer nodeA,
              java.lang.Integer nodeB)

Disconnects two vertices in a bidirectional graph in both directions from i to j and from j to i (bidirectional)

Specified by:

disconnect in class Graph

Parameters:

nodeA - - vertice to be disconnected from j

nodeB - - vertice to be disconnected from i

disconnect

public void disconnect(java.lang.Integer node)

Disconnects a vertice from a bidirectional graph in both directions

Parameters:

node - - vertice to be disconnected from graph

connectedToClique

public void connectedToClique(java.lang.Integer candidate,
                     java.util.TreeSet<java.lang.Integer> clique)

Connects a node to a node set

Parameters:

clique - a node set

candidate - a vertice to be connected to the noe set

printNetwork

public void printNetwork()

Prints the network to the standard output

merge

public void merge(java.lang.Integer toMerge,
         java.lang.Integer toBeMerged)

merges two sites after the checking algorithm assured this operation does not violate the clique distribution.

Parameters:

toMerge - a candidate to merge

toBeMerged - a candidate to merge

areNeighbours

public boolean areNeighbours(java.lang.Integer a,
                    java.lang.Integer b)

Check if a and b are neighbours/directly connected a---b

Parameters:

a - a candidate to merge

b - a candidate to merge

Returns:

true if a and b are neighbours/directly connected, false otherwise

haveOneCommonNeighbour

public boolean haveOneCommonNeighbour(java.lang.Integer a,
                             java.lang.Integer b)

Check if a and b have one common neighbour/indirectly connected over one site a-x-b. One condition must be fulfilled for this test: Sites must not neighbours

Parameters:

a - a candidate to merge

b - a candidate to merge

Returns:

true if a and b have one common neighbour/indirectly connected over one site, false otherwise

getCommonNeighbours

public java.util.TreeSet<java.lang.Integer> getCommonNeighbours(java.lang.Integer a,
                                                       java.lang.Integer b)

Gets common neighbours between two vertices.

Parameters:

a - - a set of vertices

b - - a vertice

Returns:

TreeSet of vertices which are common neighbours to vertices a and b

isConnectedTo

public boolean isConnectedTo(java.util.TreeSet<java.lang.Integer> clique,
                    java.lang.Integer candidate)

Checks wheather a vertice is fully connecte to a set of vertices

Parameters:

clique - A set of vertices which define a clique

candidate - A vertice which is to check wheather it is fully connected to the clique

getCoordinationNumber

public java.lang.Integer getCoordinationNumber(java.lang.Integer vertice)

Gets the coordination number. The coordination number is the numer of links a vertice has to another vertices.

Parameters:

vertice - - a vertice to gets its coordination number.

Returns:

count of links to vertice.

getNetworkTreeSet

public java.util.HashMap<java.lang.Integer,java.util.TreeSet<java.lang.Integer>> getNetworkTreeSet()

Get the network as a TreeSet

Returns:

network

setNetworkTreeSet

public void setNetworkTreeSet(java.util.HashMap<java.lang.Integer,java.util.TreeSet<java.lang.Integer>> _networkTreeSet)

sets a network

Parameters:

_networkTreeSet -

createLocalNetworkPart

public BidirectionalGraph createLocalNetworkPart(java.lang.Integer siteA,
                                        java.lang.Integer siteB)

Creates a local part of a this graph. The local part is cut from two sites, their neighbours and their common neighbours.

Parameters:

siteA -

siteB -

areConnected

public boolean areConnected(java.lang.Integer verticeA,
                   java.lang.Integer verticeB)

Checks wheather two vertices are connected.

Parameters:

verticeA -

verticeB -

Returns:

true if verticeAand verticeB are connected, false otherwise.

getCliqueDistribution

public java.util.HashMap<java.lang.Integer,java.lang.Integer> getCliqueDistribution()

Returns the HashMap which holds the clique distribution.

Returns:

the cliqueDistribution

getDistribution

public int[] getDistribution()

Returns the clique distribution used to construct the graph

Returns:

clique distribution

getSetOfNodes

public java.util.TreeSet<java.lang.Integer> getSetOfNodes()

Get all nodes of this graph as a TreeSet

getLinksOfNode

public java.util.TreeSet<java.lang.Integer> getLinksOfNode(java.lang.Integer vertice)

Get all connections of a vertice to neighbours as a TreeSet

Parameters:

vertice -

getNodeExists

public boolean getNodeExists(java.lang.Integer integer)

Check wheather that node exists in the graph

Parameters:

integer -

Returns:

true if node does exist, false otherwise

getNodesCount

public int getNodesCount()

Returns the number of nodes in this graph.

getConnections

public java.util.TreeSet<java.lang.String> getConnections()

setConnections

public void setConnections(java.util.TreeSet<java.lang.String> connections)

save

public void save(java.lang.String path)

Specified by:

save in class Graph

loadPajek

public BidirectionalGraph loadPajek(java.lang.String path)

savePajek

public void savePajek(java.lang.String path)

load

public void load(java.lang.String path,
        int edgecountlimit,
        int nodecountlimit)

loads a graph of the format node white space node

Parameters:

path -

edgecountlimit -

nodecountlimit -

isZeroNode

public boolean isZeroNode(java.lang.String path)

getNodeWithLowestDegree

public java.lang.Integer getNodeWithLowestDegree()

loadBipartite

public void loadBipartite(java.lang.String path,
                 int edgecountlimit,
                 int nodecountlimit,
                 boolean integrate)

existsNode

public boolean existsNode(int j)

copy

public BidirectionalGraph copy(java.util.TreeSet<java.lang.Integer> name)

detectIndependentSets

public java.util.Vector<java.util.TreeSet<java.lang.Integer>> detectIndependentSets()

isHasIdependentSets

public boolean isHasIdependentSets()