uk.ac.ebi.microarray.zooma.track
Class HypothesisRankingTracker

java.lang.Object
  uk.ac.ebi.microarray.zooma.track.HypothesisRankingTracker

All Implemented Interfaces:

HypothesisTracker, InformationTracker

public class HypothesisRankingTracker
extends java.lang.Object
implements HypothesisTracker

A system for scoring OntologyMappingHypothesis objects are determining which are candidates for acception, rejection, deferment or prioritisation. This system implements InformationTracker to follow the mediator pattern, describing the dependencies between objects. In this system, mapping hypotheses are the core component, but scores can be attributed to contexts and ontologies. These scores enable the system to refine the ordering of the comparison priority queue

Author:

Tony Burdett

Constructor Summary

HypothesisRankingTracker()

HypothesisRankingTracker(SourceRanker sourceRanker, OntologyRanker ontologyRanker)

Method Summary

void	clearHypotheses() Clears the current set of tracked hypotheses.
java.util.Collection<OntologyMappingHypothesis>	getBestHypotheses() Returns the collection of OntologyMappingHypothesis objects that are known to be the best possible hypotheses given the current state of assessment.
java.util.Collection<OntologyMappingHypothesis>	getCandidateAlternativeHypotheses() Returns the collection of possible alternatives to the current null hypothesis.
OntologyMappingHypothesis	getCurrentNullHypothesis() Returns the OntologyMappingHypothesis that is designated as the current null (or current accepted) hypothesis.
void	informationChanged(Information information) Called by Information objects acting as "mediator clients" whenever the information they encapsulate changes.

Methods inherited from class java.lang.Object

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

Constructor Detail

HypothesisRankingTracker

public HypothesisRankingTracker()

HypothesisRankingTracker

public HypothesisRankingTracker(SourceRanker sourceRanker,
                                OntologyRanker ontologyRanker)

Method Detail

getCurrentNullHypothesis

public OntologyMappingHypothesis getCurrentNullHypothesis()

Description copied from interface: HypothesisTracker

Returns the OntologyMappingHypothesis that is designated as the current null (or current accepted) hypothesis. This will change whenever a hypothesis different to this one is accepted.

Specified by:

getCurrentNullHypothesis in interface HypothesisTracker

Returns:

the hypothesis that is the current null

getCandidateAlternativeHypotheses

public java.util.Collection<OntologyMappingHypothesis> getCandidateAlternativeHypotheses()

Description copied from interface: HypothesisTracker

Returns the collection of possible alternatives to the current null hypothesis. Any hypotheses that have been rejected against any of the current or previous null hypotheses will not show up here. In this way, you can progressively whittle down the set of possible alternatives to derive the best possible mapping.

Specified by:

getCandidateAlternativeHypotheses in interface HypothesisTracker

Returns:

a collection of possible alternative hypotheses

getBestHypotheses

public java.util.Collection<OntologyMappingHypothesis> getBestHypotheses()

Description copied from interface: HypothesisTracker

Returns the collection of OntologyMappingHypothesis objects that are known to be the best possible hypotheses given the current state of assessment. Before any hypothesis testing has been carried out, this will be all known hypotheses: there isn't enough information to throw any away. Assuming every hypothesis has been tested at least once, this will return the set of the current null hypothesis, plus any hypotheses that have not been rejected against the current null.

Specified by:

getBestHypotheses in interface HypothesisTracker

Returns:

the set of possible hypotheses that are as good as the current null hypothesis (including the hypothesis that is the current null)

clearHypotheses

public void clearHypotheses()

Description copied from interface: HypothesisTracker

Clears the current set of tracked hypotheses. This clears the set of hypotheses that are being tracked by this tracker. Hypotheses may maintain a soft reference to this tracker, however.

Specified by:

clearHypotheses in interface HypothesisTracker

informationChanged

public void informationChanged(Information information)

Description copied from interface: InformationTracker

Called by Information objects acting as "mediator clients" whenever the information they encapsulate changes. Implementations of this interface can then define how the new information is used to update other dependent objects.

Specified by:

informationChanged in interface InformationTracker

Parameters:

information - a reference to the information object that has changed