Uses of Interface
uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesis

Packages that use OntologyMappingHypothesis

uk.ac.ebi.microarray.zooma.calc
uk.ac.ebi.microarray.zooma.eval
uk.ac.ebi.microarray.zooma.formulate
uk.ac.ebi.microarray.zooma.hypothesis
uk.ac.ebi.microarray.zooma.track

Uses of OntologyMappingHypothesis in uk.ac.ebi.microarray.zooma.calc

Methods in uk.ac.ebi.microarray.zooma.calc with parameters of type OntologyMappingHypothesis

boolean	OntologyRanker.ontologyRanksHigher(OntologyMappingHypothesis alternativeHypothesis, OntologyMappingHypothesis nullHypothesis)
boolean	OntologyRanker.ontologyRanksLower(OntologyMappingHypothesis alternativeHypothesis, OntologyMappingHypothesis nullHypothesis)
boolean	SourceRanker.sourceRanksHigher(OntologyMappingHypothesis alternativeHypothesis, OntologyMappingHypothesis nullHypothesis)
boolean	SourceRanker.sourceRanksLower(OntologyMappingHypothesis alternativeHypothesis, OntologyMappingHypothesis nullHypothesis)
int	OntologyMappingCalculator.testHypothesis(OntologyMappingHypothesis nullHypothesis, OntologyMappingHypothesis alternativeHypothesis) Tests the alternative hypothesis against the null hypothesis.
int	RankingBasedCalculator.testHypothesis(OntologyMappingHypothesis nullHypothesis, OntologyMappingHypothesis alternativeHypothesis)

Uses of OntologyMappingHypothesis in uk.ac.ebi.microarray.zooma.eval

Methods in uk.ac.ebi.microarray.zooma.eval that return types with arguments of type OntologyMappingHypothesis

java.util.Collection<OntologyMappingHypothesis>	OntologyMappingOutcomeDecorator.getBestHypotheses()
java.util.Collection<OntologyMappingHypothesis>	BasicZoomaOutcome.getBestHypotheses()
java.util.Collection<OntologyMappingHypothesis>	OntologyMappingOutcome.getBestHypotheses() A collection of OntologyMappingHypothesis objects that describe ontology mappings.

Method parameters in uk.ac.ebi.microarray.zooma.eval with type arguments of type OntologyMappingHypothesis

OntologyMappingOutcome	OntologyMappingEvaluator.evaluateOutcome(Value value, java.util.Collection<OntologyMappingHypothesis> hypotheses) Evaluates the ontology mapping outcome for a collection of mapping hypotheses.
OntologyMappingOutcome	DefaultMappingEvaluator.evaluateOutcome(Value value, java.util.Collection<OntologyMappingHypothesis> hypotheses) Incrementally performs simple pairwise comparison.

Constructor parameters in uk.ac.ebi.microarray.zooma.eval with type arguments of type OntologyMappingHypothesis

BasicZoomaOutcome(Value value, java.util.Collection<OntologyMappingHypothesis> bestHypotheses)

Uses of OntologyMappingHypothesis in uk.ac.ebi.microarray.zooma.formulate

Methods in uk.ac.ebi.microarray.zooma.formulate that return types with arguments of type OntologyMappingHypothesis

java.util.Collection<OntologyMappingHypothesis>	NoPossibleMappingFormulator.formulateHypotheses(Value value)
java.util.Collection<OntologyMappingHypothesis>	ContextSensitiveMappingFormulator.formulateHypotheses(Value value)
java.util.Collection<OntologyMappingHypothesis>	OntologyMappingFormulator.formulateHypotheses(Value value) Formulate a set of hypotheses that describe the possible mappings that might be made about the given value.

Uses of OntologyMappingHypothesis in uk.ac.ebi.microarray.zooma.hypothesis

Classes in uk.ac.ebi.microarray.zooma.hypothesis that implement OntologyMappingHypothesis

class	AbstractTrackedHypothesis An ontology mapping hypothesis that communicates with an InformationTracker to facilitate hypothesis assessment.
class	NoMappingPossibleHypothesis An implementation of a hypothesis that can be tracked by an InformationTracker and asserts that no mapping is possible from a particular term.
class	PossibleDuplicateMappingsHypothesis A standard implementation of hypothesis that can be tracked by an InformationTracker and described a single mapping between a description and a term in a single context.

Methods in uk.ac.ebi.microarray.zooma.hypothesis that return OntologyMappingHypothesis

OntologyMappingHypothesis	TrackedHypothesisFactory.generateHypothesis(Value value, OntologyMappingContext context, uk.ac.ebi.ontocat.OntologyTerm... ontologyTerms)
OntologyMappingHypothesis	OntologyMappingHypothesisFactory.generateHypothesis(Value value, OntologyMappingContext context, uk.ac.ebi.ontocat.OntologyTerm... ontologyTerms) Generates an ontology mapping hypothesis given a description, the term it may map to, and a context

Uses of OntologyMappingHypothesis in uk.ac.ebi.microarray.zooma.track

Methods in uk.ac.ebi.microarray.zooma.track that return OntologyMappingHypothesis

OntologyMappingHypothesis	HypothesisTracker.getCurrentNullHypothesis() Returns the OntologyMappingHypothesis that is designated as the current null (or current accepted) hypothesis.
OntologyMappingHypothesis	HypothesisRankingTracker.getCurrentNullHypothesis()

Methods in uk.ac.ebi.microarray.zooma.track that return types with arguments of type OntologyMappingHypothesis

java.util.Collection<OntologyMappingHypothesis>	CurationTracker.getAcceptedHypotheses()
java.util.Collection<OntologyMappingHypothesis>	HypothesisTracker.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>	HypothesisRankingTracker.getBestHypotheses()
java.util.Collection<OntologyMappingHypothesis>	HypothesisTracker.getCandidateAlternativeHypotheses() Returns the collection of possible alternatives to the current null hypothesis.
java.util.Collection<OntologyMappingHypothesis>	HypothesisRankingTracker.getCandidateAlternativeHypotheses()
java.util.List<OntologyMappingHypothesis>	HypothesisRanking.getRankedHypotheses() Returns the list of hypotheses that have been ranked, in the order in which they rank.

Methods in uk.ac.ebi.microarray.zooma.track with parameters of type OntologyMappingHypothesis

boolean	HypothesisSet.add(OntologyMappingHypothesis hypothesis)
boolean	HypothesisRanking.rank(OntologyMappingHypothesis hypothesis) Rank, or rerank, the given hypothesis against all others
boolean	HypothesisRanking.remove(OntologyMappingHypothesis hypothesis) Removes a previously ranked hypothesis from the rankings

Method parameters in uk.ac.ebi.microarray.zooma.track with type arguments of type OntologyMappingHypothesis

boolean

HypothesisSet.addAll(java.util.Collection<? extends OntologyMappingHypothesis> c)