penalties

Interface PenaltyFunction

All Known Implementing Classes:

AntiDominatePenalty, GraphletG4Penalty, PredictionConfidencePenalty, TFSparsityPenalty

public interface PenaltyFunction

PenaltyFunction is an interface for all penalties, but ranking based as subnetwork based.

Since:

0.0

Version:

1.0

Author:

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

Method Summary

Modifier and Type	Method and Description
void	calculateMetricFromScratch() Calculates the metric from the current subnetwork/ranking
double	getCoef() Gets the relative weight for this penalty
double	getMetric() Returns the current penalty metric (unmapped to the cost)
java.lang.String	getPenaltyName() The penalty name, used for logging functionality
long	getPenaltyScore() Returns the current penalty score (metric mapped on cost function)
boolean	isGlobalPenalty() Indicates if this penalty works on the ranking or on (sub)network level
void	revertIncrementalPenalty() Reverts the penalty score to the previous value, discarding any changes made by the latest incremental update
void	setCoef(double coef) Sets the relative weight for this penalty
void	setNetwork(Network predictionNetwork) Sets the network/ranking associated with this penalty
void	updateIncrementalPenalty() Calculates the new penalty score in an incremental way after (small) changes have been to the network

Method Detail

calculateMetricFromScratch

void calculateMetricFromScratch()

Calculates the metric from the current subnetwork/ranking

getMetric

double getMetric()

Returns the current penalty metric (unmapped to the cost)

Returns:

the penalty metric

getPenaltyScore

long getPenaltyScore()

Returns the current penalty score (metric mapped on cost function)

Returns:

the penalty score

getPenaltyName

java.lang.String getPenaltyName()

The penalty name, used for logging functionality

Returns:

the penalty name

updateIncrementalPenalty

void updateIncrementalPenalty()

Calculates the new penalty score in an incremental way after (small) changes have been to the network

revertIncrementalPenalty

void revertIncrementalPenalty()

Reverts the penalty score to the previous value, discarding any changes made by the latest incremental update

isGlobalPenalty

boolean isGlobalPenalty()

Indicates if this penalty works on the ranking or on (sub)network level

Returns:

true if the penalty works on the ranking

setNetwork

void setNetwork(Network predictionNetwork)

Sets the network/ranking associated with this penalty

Parameters:

predictionNetwork - network or ranking associated with this penalty

getCoef

double getCoef()

Gets the relative weight for this penalty

Returns:

the relative weight

setCoef

void setCoef(double coef)

Sets the relative weight for this penalty

Parameters:

coef - the relative weight