Uses of Class
network.Network

Packages that use Network

Package	Description
extractors	A group of classes responsible for calculating structural network properties.
network	A group of classes responsible for representing the network datastructure or which perform modifying operations on networks.
network.modifiers	A group of classes that performs modifying operations on networks.
network.node	A group of classes represent nodes/vertices in the network
penalties	A group of classes that represent penalty functions/cost functions
penalties.defined	A group of classes that implement a penalty
schedulers	A group of classes implementing a single re-ranking procedure.

Uses of Network in extractors

Methods in extractors that return Network

Modifier and Type	Method and Description
Network	TranscriptionFactorExtractor.getNetwork() Returns the network associated with this extractor.
Network	GraphletCounterExtractor.getNetwork() Returns the network associated with this extractor.
Network	DominatingExtractor.getNetwork() Returns the network associated with this extractor.

Methods in extractors with parameters of type Network

Modifier and Type	Method and Description
void	TranscriptionFactorExtractor.setNetwork(Network network) Sets the network associated with this extractor.
void	GraphletCounterExtractor.setNetwork(Network network) Sets the network associated with this extractor.
void	DominatingExtractor.setNetwork(Network network) Sets the network associated with this extractor.

Constructors in extractors with parameters of type Network

Constructor and Description
DominatingExtractor(Network network) Constructs a DominatingExtractor with an associated network and already calculates the metric from scratch.
GraphletCounterExtractor(Network network)
TranscriptionFactorExtractor(Network network) Constructs a Transcriptionfactor with an associated network and already calculates the metric from scratch.

Uses of Network in network

Methods in network that return Network

Modifier and Type	Method and Description
Network	NetworkFileBackedWrapper.getNetwork()
Network[]	NetworkPartition.getNetworks()
Network	NetworkPartition.getPrediction()

Methods in network that return types with arguments of type Network

Modifier and Type	Method and Description
java.util.HashMap<Network,java.lang.Double>	NetworkPartition.getNetworkCoefMap()

Methods in network with parameters of type Network

Modifier and Type	Method and Description
void	NetworkFileBackedWrapper.setNetwork(Network network)
void	NetworkPartition.setNetworks(Network[] networks)
void	NetworkPartition.setPrediction(Network prediction)

Method parameters in network with type arguments of type Network

Modifier and Type	Method and Description
void	NetworkPartition.setNetworkCoefMap(java.util.HashMap<Network,java.lang.Double> networkCoefMap)

Constructors in network with parameters of type Network

Constructor and Description
Network(Network network) Copy constructor, will return a copy of the network with new objects
NetworkPartition(Network prediction, int cutoff, int chuncks, double coefs) Constructs a new NetworkPartition object from a given ranking/original network, but first selecting the top of the ranking (defined by cutoff) and dividing it in X (defined by chuncks) parts of increasing size.

Uses of Network in network.modifiers

Methods in network.modifiers that return Network

Modifier and Type	Method and Description
Network	PredictionModifierOpt.getNetwork()
Network	NetworkModifier.getNetwork() Return the current network/ranking the modifier is working on

Methods in network.modifiers with parameters of type Network

Modifier and Type	Method and Description
void	PredictionModifierOpt.setNetwork(Network network)

Uses of Network in network.node

Methods in network.node with parameters of type Network

Modifier and Type	Method and Description
void	Node.addIncomingLink(Network net, Node node) Adds an incoming link to this node coming from another node a.
void	Node.addOutGoingLink(Network net, Node node) Adds an outgoing link to this node coming from another node a.
void	Node.clearNetwork(Network network) Removes all links of this node in a given network, use with caution as the network representation can become inconsistent.
java.util.ArrayList<Node>	Node.getBiDirectionalLinks(Network network) Returns list of nodes connected by a birectional link in a given network context
java.util.ArrayList<Node>	Node.getIncomingLinks(Network net) Returns list of nodes connected by an incoming link in a given network context
java.util.ArrayList<Node>	Node.getOutGoingLinks(Network net) Returns list of nodes connected by an outgoing link in a given network context
java.util.HashSet<Node>	Node.getUnidirectedLinks(Network net) Returns list of nodes connected by any type of link in a given network context
void	Node.removeIncomingLink(Network net, Node node) Removes an incoming link to this node coming from another node a.
void	Node.removeOutGoingLink(Network net, Node node) Removes an outgoing link to this node coming from another node a.
void	Node.resetNodeConnectivity(Network network) Similar to 'clearNetwork' this method resets a given network context.

Uses of Network in penalties

Methods in penalties with parameters of type Network

Modifier and Type	Method and Description
void	PenaltyFunction.setNetwork(Network predictionNetwork) Sets the network/ranking associated with this penalty

Uses of Network in penalties.defined

Methods in penalties.defined with parameters of type Network

Modifier and Type	Method and Description
void	TFSparsityPenalty.setNetwork(Network predictionNetwork)
void	PredictionConfidencePenalty.setNetwork(Network predictionNetwork)
void	GraphletG4Penalty.setNetwork(Network predictionNetwork)
void	AntiDominatePenalty.setNetwork(Network predictionNetwork)

Uses of Network in schedulers

Methods in schedulers that return Network

Modifier and Type	Method and Description
Network	NetworkSA.getNetwork()

Methods in schedulers with parameters of type Network

Modifier and Type	Method and Description
void	NetworkSA.setNetwork(Network network)