uk.ac.ebi.microarray.zooma.formulate
Class NoPossibleMappingFormulator

java.lang.Object
  uk.ac.ebi.microarray.zooma.formulate.NoPossibleMappingFormulator

All Implemented Interfaces:

OntologyMappingFormulator

public class NoPossibleMappingFormulator
extends java.lang.Object
implements OntologyMappingFormulator

A special type of OntologyMappingFormulator that generates default null hypotheses. In this implementation, formulateHypotheses(uk.ac.ebi.microarray.zooma.lang.Value) will always generate a single hypothesis that states no mapping is possible.

Author:

Tony Burdett

Constructor Summary

NoPossibleMappingFormulator()

Method Summary

java.util.Collection<OntologyMappingHypothesis>	formulateHypotheses(Value value) Formulate a set of hypotheses that describe the possible mappings that might be made about the given value.
protected org.slf4j.Logger	getLog()
OntologyMappingHypothesisFactory	getOntologyMappingHypothesisFactory()
void	setOntologyMappingHypothesisFactory(OntologyMappingHypothesisFactory factory)

Methods inherited from class java.lang.Object

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

Constructor Detail

NoPossibleMappingFormulator

public NoPossibleMappingFormulator()

Method Detail

setOntologyMappingHypothesisFactory

public void setOntologyMappingHypothesisFactory(OntologyMappingHypothesisFactory factory)

getOntologyMappingHypothesisFactory

public OntologyMappingHypothesisFactory getOntologyMappingHypothesisFactory()

getLog

protected org.slf4j.Logger getLog()

formulateHypotheses

public java.util.Collection<OntologyMappingHypothesis> formulateHypotheses(Value value)
                                                                    throws HypothesisFormulationException

Description copied from interface: OntologyMappingFormulator

Formulate a set of hypotheses that describe the possible mappings that might be made about the given value. It is possible to use this method to formulate any hypothesis, whether this is the null or alternative hypothesis.

Implementations may use a specific strategy to fetch mappings that may, for example, spread across multiple sources. Such implementations should not usually be suitable for formulating the null hypothesis - normally the null hypothesis will prefer a mapping from a dedicated source or it will assert that no mapping is possible.

Implementations should retrieve, or construct, context information for each hypothesis formulated. Some implementations may wish to formulate hypotheses from the same source with different levels of sensitivity, for example: in some cases, species information may be required whereas in others it may be irrelevant.

Generally, formulators act as a facade over the OntologyTermRetriever and OntologyMappingHypothesisFactory interfaces to retrieve then generate hypotheses. However, most implementations will also describe some higher logic to consider only those hypotheses from relevant or interesting contexts.

Specified by:

formulateHypotheses in interface OntologyMappingFormulator

Parameters:

value - the description to hypothesise about

Returns:

the collections of mapping hypotheses that were formulated

Throws:

HypothesisFormulationException - if any hypotheses could not be generated, due to invalid data or a failure of retrieval