extractors

Class DominatingExtractor

java.lang.Object

extractors.DominatingExtractor

public class DominatingExtractor
extends java.lang.Object

DominatingExtractor is a class responsible for calculating and keeping track of the 'Anti-dominating' metric associated with a network. The anti-dominating penalty metric is defined as the ratio between the maximum amount of links originating from a same gene in the network and the total amount of links in the network.

Since:

0.0

Version:

1.0

Author:

Joeri Ruyssinck (joeri.ruysssinck@intec.ugent.be)

Constructor Summary

Constructors

Constructor and Description
DominatingExtractor() Constructs a DominatingExtractor without an associated network.
DominatingExtractor(Network network) Constructs a DominatingExtractor with an associated network and already calculates the metric from scratch.

Method Summary

Modifier and Type	Method and Description
double	getDominatorPercentage() Returns the current anti-dominating metric associated with the network state.
Network	getNetwork() Returns the network associated with this extractor.
void	incrementalUpdate(java.util.ArrayList<Link> nonCommittalDeleted, java.util.ArrayList<Link> nonCommitalAdded) Calculates and sets the anti-dominating metric in an incremental way given lists of links added and deleted.
void	revert() Reverts back to the current state of the network associated with this extractor.
void	setNetwork(Network network) Sets the network associated with this extractor.
void	update() Calculates the anti-dominating metric from scratch for the currently associated network

Methods inherited from class java.lang.Object

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

Constructor Detail

DominatingExtractor

public DominatingExtractor()

Constructs a DominatingExtractor without an associated network.

DominatingExtractor

public DominatingExtractor(Network network)

Constructs a DominatingExtractor with an associated network and already calculates the metric from scratch.

Parameters:

network - the associated network

Method Detail

getDominatorPercentage

public double getDominatorPercentage()

Returns the current anti-dominating metric associated with the network state.

Returns:

the anti-dominating metric

getNetwork

public Network getNetwork()

Returns the network associated with this extractor.

Returns:

the associated network

setNetwork

public void setNetwork(Network network)

Sets the network associated with this extractor.

Parameters:

network - the network which should be associated with this extractor

update

public void update()

Calculates the anti-dominating metric from scratch for the currently associated network

incrementalUpdate

public void incrementalUpdate(java.util.ArrayList<Link> nonCommittalDeleted,
                              java.util.ArrayList<Link> nonCommitalAdded)

Calculates and sets the anti-dominating metric in an incremental way given lists of links added and deleted.

Parameters:

nonCommittalDeleted - a list of links deleted from the current network

nonCommitalAdded - a list of links added to the network

revert

public void revert()

Reverts back to the current state of the network associated with this extractor. Effectively resets the metric to the current state the associated network is in. Discards any changes made by using an incremental updates.