uk.ac.ebi.microarray.zooma.calc
Class RankingBasedCalculator

java.lang.Object
  uk.ac.ebi.microarray.zooma.calc.RankingBasedCalculator

All Implemented Interfaces:

OntologyMappingCalculator

public class RankingBasedCalculator
extends java.lang.Object
implements OntologyMappingCalculator

An OntologyMappingCalculator that evaluates ontology mapping hypotheses based on a simple ranking. This ranking describes the order of sources that are preferred followed by the order of ontologies preferred.

Author:

Tony Burdett

Constructor Summary

RankingBasedCalculator()

Method Summary

protected org.slf4j.Logger	getLog()
OntologyRanker	getOntologyRanker()
SourceRanker	getSourceRanker()
void	setOntologyRanker(OntologyRanker ontologyRanker)
void	setSourceRanker(SourceRanker sourceRanker)
int	testHypothesis(OntologyMappingHypothesis nullHypothesis, OntologyMappingHypothesis alternativeHypothesis) Tests the alternative hypothesis against the null hypothesis.

Methods inherited from class java.lang.Object

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

Constructor Detail

RankingBasedCalculator

public RankingBasedCalculator()

Method Detail

getSourceRanker

public SourceRanker getSourceRanker()

setSourceRanker

public void setSourceRanker(SourceRanker sourceRanker)

getOntologyRanker

public OntologyRanker getOntologyRanker()

setOntologyRanker

public void setOntologyRanker(OntologyRanker ontologyRanker)

getLog

protected org.slf4j.Logger getLog()

testHypothesis

public int testHypothesis(OntologyMappingHypothesis nullHypothesis,
                          OntologyMappingHypothesis alternativeHypothesis)

Description copied from interface: OntologyMappingCalculator

Tests the alternative hypothesis against the null hypothesis. If the alternative hypothesis describes a mapping that is better than the null hypothesis, the alternative hypothesis is accepted and then null hypothesis rejected. If the alternative hypothesis describes a mapping that is worse, the alternative hypothesis is rejected and the null hypothesis retained.

It may not always be possible to determine absolutely whether the alternative hypothesis is better or worse than the null hypothesis. In these cases, neither the null of alternative hypothesis should be accepted or rejected, deferring the decision.

The value returned represents the outcome of this hypothesis test. A positive integer signifies that the alternative hypothesis was accepted. A negative value means it was rejected. Zero indicates that the outcome was not significantly better or worse.

Specified by:

testHypothesis in interface OntologyMappingCalculator

Parameters:

nullHypothesis - the hypothesis describing the current best mapping

alternativeHypothesis - the mapping hypothesis to test

Returns:

an integer representing the outcome of this test - positive if accepted, negative if rejected, zero if deferred