uk.ac.ebi.microarray.zooma.hypothesis
Class AbstractTrackedHypothesis

java.lang.Object
  uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

All Implemented Interfaces:

OntologyMappingHypothesis, Information

Direct Known Subclasses:

NoMappingPossibleHypothesis, PossibleDuplicateMappingsHypothesis

public abstract class AbstractTrackedHypothesis
extends java.lang.Object
implements OntologyMappingHypothesis, Information

An ontology mapping hypothesis that communicates with an InformationTracker to facilitate hypothesis assessment.

Author:

Tony Burdett

Field Summary

protected OntologyMappingContext	context
protected java.util.Collection<uk.ac.ebi.ontocat.OntologyTerm>	terms
protected Value	value

Constructor Summary

AbstractTrackedHypothesis()

Method Summary

void	acceptHypothesis() Accept this hypothesis, informing the ontology mapping mediator of this change.
void	addOntologyTerm(uk.ac.ebi.ontocat.OntologyTerm ontologyTerm) Adds an additional term to the collection of terms that are mapped by this hypothesis.
void	aggregateContextFromEquivalentHypothesis(OntologyMappingContext equivalentContext)
void	changed() Called whenever this information object is updated, this calls back to the mediator governing this information object and updates all dependent information artifacts.
OntologyMappingContext	getContext() The context in which this mapping hypothesis should be attempted
protected InformationTracker	getMappingTracker()
java.util.Collection<uk.ac.ebi.ontocat.OntologyTerm>	getOntologyTerms() Gets the collections of OntologyTerms that can hypothetically be mapped to the given value.
Value	getValue() Gets the description that is attempted to be mapped in this hypothesis.
boolean	isAccepted() Returns whether or not this hypothesis has been accepted as the best mapping hypothesis
boolean	isRejected() Returns whether or not this hypothesis has been rejected against another, better hypothesis
void	rejectHypothesis() Reject this hypothesis, informing the ontology mapping mediator of this change.
void	setOntologyMappingTracker(InformationTracker mappingTracker) Set the mediator service that this hypothesis can provide feedback to.
void	setOntologyTerms(java.util.Collection<uk.ac.ebi.ontocat.OntologyTerm> ontologyTerms) Sets the collection of OntologyTerms that can hypothetically be mapped to the value for this hypothesis.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesis

accept

Field Detail

value

protected Value value

terms

protected java.util.Collection<uk.ac.ebi.ontocat.OntologyTerm> terms

context

protected OntologyMappingContext context

Constructor Detail

AbstractTrackedHypothesis

public AbstractTrackedHypothesis()

Method Detail

getMappingTracker

protected InformationTracker getMappingTracker()

getValue

public Value getValue()

Description copied from interface: OntologyMappingHypothesis

Gets the description that is attempted to be mapped in this hypothesis.

Specified by:

getValue in interface OntologyMappingHypothesis

Returns:

the description we're trying to map

setOntologyTerms

public void setOntologyTerms(java.util.Collection<uk.ac.ebi.ontocat.OntologyTerm> ontologyTerms)

Description copied from interface: OntologyMappingHypothesis

Sets the collection of OntologyTerms that can hypothetically be mapped to the value for this hypothesis.

Specified by:

setOntologyTerms in interface OntologyMappingHypothesis

Parameters:

ontologyTerms - the collections of terms that can be mapped

getOntologyTerms

public java.util.Collection<uk.ac.ebi.ontocat.OntologyTerm> getOntologyTerms()

Description copied from interface: OntologyMappingHypothesis

Gets the collections of OntologyTerms that can hypothetically be mapped to the given value.

Specified by:

getOntologyTerms in interface OntologyMappingHypothesis

Returns:

a collection of possible ontology term mappings

addOntologyTerm

public void addOntologyTerm(uk.ac.ebi.ontocat.OntologyTerm ontologyTerm)

Description copied from interface: OntologyMappingHypothesis

Adds an additional term to the collection of terms that are mapped by this hypothesis. Implementations should define whether duplicate mappings are possible for this hypothesis.

Specified by:

addOntologyTerm in interface OntologyMappingHypothesis

Parameters:

ontologyTerm - the ontology term being added to this hypothesis

getContext

public OntologyMappingContext getContext()

Description copied from interface: OntologyMappingHypothesis

The context in which this mapping hypothesis should be attempted

Specified by:

getContext in interface OntologyMappingHypothesis

Returns:

the mapping context for this outcome

isAccepted

public boolean isAccepted()

Description copied from interface: OntologyMappingHypothesis

Returns whether or not this hypothesis has been accepted as the best mapping hypothesis

Specified by:

isAccepted in interface OntologyMappingHypothesis

Returns:

true if this hypothesis is accepted, false otherwise

isRejected

public boolean isRejected()

Description copied from interface: OntologyMappingHypothesis

Returns whether or not this hypothesis has been rejected against another, better hypothesis

Specified by:

isRejected in interface OntologyMappingHypothesis

Returns:

true if this hypothesis is rejected, false otherwise

setOntologyMappingTracker

public void setOntologyMappingTracker(InformationTracker mappingTracker)

Set the mediator service that this hypothesis can provide feedback to. Whenever a hypothesis is changed with acceptHypothesis() or rejectHypothesis() it should inform the mediator.

Parameters:

mappingTracker - the mediator to inform of changes

acceptHypothesis

public void acceptHypothesis()

Description copied from interface: OntologyMappingHypothesis

Accept this hypothesis, informing the ontology mapping mediator of this change.

Specified by:

acceptHypothesis in interface OntologyMappingHypothesis

rejectHypothesis

public void rejectHypothesis()

Description copied from interface: OntologyMappingHypothesis

Reject this hypothesis, informing the ontology mapping mediator of this change.

Specified by:

rejectHypothesis in interface OntologyMappingHypothesis

changed

public void changed()

Description copied from interface: Information

Called whenever this information object is updated, this calls back to the mediator governing this information object and updates all dependent information artifacts.

Specified by:

changed in interface Information

aggregateContextFromEquivalentHypothesis

public void aggregateContextFromEquivalentHypothesis(OntologyMappingContext equivalentContext)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object