uk.ac.ebi.microarray.zooma.mapping
Class JSONOntologyMapper

java.lang.Object
  uk.ac.ebi.microarray.zooma.mapping.JSONOntologyMapper

All Implemented Interfaces:

OntologyMapper

public class JSONOntologyMapper
extends java.lang.Object
implements OntologyMapper

An ontology mapper that generates a JSON object whenever an outcome is applied.

Author:

Tony Burdett

Constructor Summary

JSONOntologyMapper()

Method Summary

void	applyOutcome(OntologyMappingOutcome outcome) Assesses and applies, the given outcome.
OntologyMappingOutcome	generateOutcome(Value value) Generates an OntologyMappingOutcome given a description and a mapping context.
OntologyMappingFormulator	getAlternativeHypothesisFormulator()
OntologyMappingEvaluator	getEvaluator()
protected org.slf4j.Logger	getLog()
OntologyMappingFormulator	getNullHypothesisFormulator()
void	setAlternativeHypothesisFormulator(OntologyMappingFormulator alternativeHypothesisFormulator)
void	setEvaluator(OntologyMappingEvaluator evaluator)
void	setNullHypothesisFormulator(OntologyMappingFormulator nullHypothesisFormulator)

Methods inherited from class java.lang.Object

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

Constructor Detail

JSONOntologyMapper

public JSONOntologyMapper()

Method Detail

getLog

protected org.slf4j.Logger getLog()

getNullHypothesisFormulator

public OntologyMappingFormulator getNullHypothesisFormulator()

setNullHypothesisFormulator

public void setNullHypothesisFormulator(OntologyMappingFormulator nullHypothesisFormulator)

getAlternativeHypothesisFormulator

public OntologyMappingFormulator getAlternativeHypothesisFormulator()

setAlternativeHypothesisFormulator

public void setAlternativeHypothesisFormulator(OntologyMappingFormulator alternativeHypothesisFormulator)

getEvaluator

public OntologyMappingEvaluator getEvaluator()

setEvaluator

public void setEvaluator(OntologyMappingEvaluator evaluator)

generateOutcome

public OntologyMappingOutcome generateOutcome(Value value)
                                       throws BadOutcomeException

Description copied from interface: OntologyMapper

Generates an OntologyMappingOutcome given a description and a mapping context.

Specified by:

generateOutcome in interface OntologyMapper

Parameters:

value - the description requiring mapping

Returns:

the expected ontology mapping outcome for the given description in a context

Throws:

BadOutcomeException - if the outcome could not be generated due to an error

applyOutcome

public void applyOutcome(OntologyMappingOutcome outcome)
                  throws BadOutcomeException

Description copied from interface: OntologyMapper

Assesses and applies, the given outcome. Implementations are free to define the actions taken when an outcome is applied. The value and context originally being mapped from is supplied for the purposes of provenance tracking and logging

Specified by:

applyOutcome in interface OntologyMapper

Parameters:

outcome - the outcome to apply

Throws:

BadOutcomeException - if the outcome could not be applied