extractors

Class TranscriptionFactorExtractor

java.lang.Object

extractors.TranscriptionFactorExtractor

public class TranscriptionFactorExtractor
extends java.lang.Object

TranscriptionFactorExtractor is a class responsible for calculating and keeping track of the 'Regulatory gene function' metric associated with a network. The regulatory gene network penalty metric is defined as percentage of nodes with atleast one outgoing edge in the network. 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
TranscriptionFactorExtractor() Constructs a Transcriptionfactor with no network set.
TranscriptionFactorExtractor(Network network) Constructs a Transcriptionfactor with an associated network and already calculates the metric from scratch.

Method Summary

Modifier and Type	Method and Description
int	getAmountOfTF() Returns the amount of nodes with at least one outgoing edge in the network.
Network	getNetwork() Returns the network associated with this extractor.
int	getNodeSize() Returns the amount of nodes in the network.
void	incrementalUpdate(java.util.ArrayList<Link> nonCommittalDeleted, java.util.ArrayList<Link> nonCommitalAdded) Calculates and sets the regulatory gene function 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 regulatory gene function 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

TranscriptionFactorExtractor

public TranscriptionFactorExtractor()

Constructs a Transcriptionfactor with no network set.

TranscriptionFactorExtractor

public TranscriptionFactorExtractor(Network network)

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

Parameters:

network - the associated network

Method Detail

getAmountOfTF

public int getAmountOfTF()

Returns the amount of nodes with at least one outgoing edge in the network.

Returns:

the amount of nodes with > 0 outgoing edge

getNodeSize

public int getNodeSize()

Returns the amount of nodes in the network.

Returns:

the amount of nodes in the network

update

public void update()

Calculates the regulatory gene function metric from scratch for the currently associated network

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

incrementalUpdate

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

Calculates and sets the regulatory gene function 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.