A B C D E F G H I J L M N O P R S T U V W Z

A

AbstractFormulator - Class in uk.ac.ebi.microarray.zooma.formulate

A simple template, designed to make adding new retrievers to existing formulators easier.

AbstractFormulator() - Constructor for class uk.ac.ebi.microarray.zooma.formulate.AbstractFormulator

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

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

AbstractTrackedHypothesis() - Constructor for class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

accept(OntologyMappingHypothesisVisitor) - Method in class uk.ac.ebi.microarray.zooma.hypothesis.NoMappingPossibleHypothesis

accept(OntologyMappingHypothesisVisitor) - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesis

Accept a visit from an OntologyMappingHypothesisVisitor.

accept(OntologyMappingHypothesisVisitor) - Method in class uk.ac.ebi.microarray.zooma.hypothesis.PossibleDuplicateMappingsHypothesis

acceptHypothesis() - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

acceptHypothesis() - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesis

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

add(OntologyMappingHypothesis) - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisSet

addAlias(String, String) - Method in interface uk.ac.ebi.microarray.zooma.service.OntologyRankingService

Adds an alias to the given ontology name.

addAll(Collection<? extends OntologyMappingHypothesis>) - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisSet

addOntologyTerm(OntologyTerm) - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

addOntologyTerm(OntologyTerm) - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesis

Adds an additional term to the collection of terms that are mapped by this hypothesis.

addRetriever(OntologyTermRetriever) - Method in class uk.ac.ebi.microarray.zooma.formulate.AbstractFormulator

addRetriever(OntologyTermRetriever) - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

Add an ontology term retriever to use to generate mapping outcomes.

aggregateContextFromEquivalentHypothesis(OntologyMappingContext) - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

AggregatedContext - Class in uk.ac.ebi.microarray.zooma.context

An ontology mapping context that is the aggregation of several contexts, normally asserting an identical mapping.

AggregatedContext(OntologyMappingContext...) - Constructor for class uk.ac.ebi.microarray.zooma.context.AggregatedContext

AjaxZoomaBean - Class in uk.ac.ebi.microarray.zooma.service.impl

An ajaxified wrapper around an ZoomaService.

AjaxZoomaBean() - Constructor for class uk.ac.ebi.microarray.zooma.service.impl.AjaxZoomaBean

apply() - Method in class uk.ac.ebi.microarray.zooma.eval.BasicZoomaOutcome

apply() - Method in class uk.ac.ebi.microarray.zooma.eval.FailureReportWriterDecorator

When applied, this outcome will write a report on itself to it's file.

apply() - Method in class uk.ac.ebi.microarray.zooma.eval.JSONProducerDecorator

apply() - Method in interface uk.ac.ebi.microarray.zooma.eval.OntologyMappingOutcome

Applies the current outcome.

apply() - Method in class uk.ac.ebi.microarray.zooma.eval.OntologyMappingOutcomeDecorator

apply() - Method in class uk.ac.ebi.microarray.zooma.eval.ReportWriterDecorator

When applied, this outcome will write a report on itself to it's file.

applyOutcome(OntologyMappingOutcome) - Method in class uk.ac.ebi.microarray.zooma.mapping.JSONOntologyMapper

applyOutcome(OntologyMappingOutcome) - Method in interface uk.ac.ebi.microarray.zooma.mapping.OntologyMapper

Assesses and applies, the given outcome.

applyOutcome(OntologyMappingOutcome) - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

B

BadOutcomeException - Exception in uk.ac.ebi.microarray.zooma.eval

An exception thrown whenever an OntologyMappingOutcome cannot be evaluated, generated or applied.

BadOutcomeException() - Constructor for exception uk.ac.ebi.microarray.zooma.eval.BadOutcomeException

BadOutcomeException(String) - Constructor for exception uk.ac.ebi.microarray.zooma.eval.BadOutcomeException

BadOutcomeException(String, Throwable) - Constructor for exception uk.ac.ebi.microarray.zooma.eval.BadOutcomeException

BadOutcomeException(Throwable) - Constructor for exception uk.ac.ebi.microarray.zooma.eval.BadOutcomeException

BasicZoomaOutcome - Class in uk.ac.ebi.microarray.zooma.eval

A default outcome implementation that simply records the set of valued hypotheses and does nothing when applied.

BasicZoomaOutcome(Value, Collection<OntologyMappingHypothesis>) - Constructor for class uk.ac.ebi.microarray.zooma.eval.BasicZoomaOutcome

BasicZoomaService - Class in uk.ac.ebi.microarray.zooma.service.impl

A basic implementation of a zooma service.

BasicZoomaService() - Constructor for class uk.ac.ebi.microarray.zooma.service.impl.BasicZoomaService

C

changed() - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

changed() - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRanking

Called whenever the ranking of hypotheses changes

changed() - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisSet

changed() - Method in interface uk.ac.ebi.microarray.zooma.track.Information

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

clear() - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisSet

clearHypotheses() - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRankingTracker

clearHypotheses() - Method in interface uk.ac.ebi.microarray.zooma.track.HypothesisTracker

Clears the current set of tracked hypotheses.

clearRetrievers() - Method in class uk.ac.ebi.microarray.zooma.formulate.AbstractFormulator

close() - Method in class uk.ac.ebi.microarray.zooma.reports.ReportWriter

Writes the header, the footer, and the content of the buffer to disk.

completed() - Method in class uk.ac.ebi.microarray.zooma.reports.ReportTimer

CompositeOntologyTermRetriever - Class in uk.ac.ebi.microarray.zooma.retrieval

An ontology term retriever that is a composite of a list of ontology term retrievers.

CompositeOntologyTermRetriever(OntologyTermRetriever...) - Constructor for class uk.ac.ebi.microarray.zooma.retrieval.CompositeOntologyTermRetriever

CompositeOntologyTermRetriever(List<OntologyTermRetriever>) - Constructor for class uk.ac.ebi.microarray.zooma.retrieval.CompositeOntologyTermRetriever

Configurator - Class in uk.ac.ebi.microarray.zooma.utils

A simple class used for conveniently loading ZOOMA configurations.

Configurator() - Constructor for class uk.ac.ebi.microarray.zooma.utils.Configurator

Constants - Class in uk.ac.ebi.microarray.zooma.utils

A convenience class for accessing properties in zooma that might need to be configurable.

Constants() - Constructor for class uk.ac.ebi.microarray.zooma.utils.Constants

containsEquivalentTerm(Collection<OntologyTerm>, OntologyTerm) - Static method in class uk.ac.ebi.microarray.zooma.utils.OntologyUtils

contentsEqual(Collection, Collection) - Static method in class uk.ac.ebi.microarray.zooma.utils.OntologyUtils

contentsEquivalent(Collection<OntologyTerm>, Collection<OntologyTerm>) - Static method in class uk.ac.ebi.microarray.zooma.utils.OntologyUtils

context - Variable in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

ContextSensitiveMappingFormulator - Class in uk.ac.ebi.microarray.zooma.formulate

An OntologyMappingFormulator that generates the most specific hypotheses possible and does basic filtering based on context.

ContextSensitiveMappingFormulator() - Constructor for class uk.ac.ebi.microarray.zooma.formulate.ContextSensitiveMappingFormulator

curate() - Method in class uk.ac.ebi.microarray.zooma.eval.CurationDecorator

CurationDecorator - Class in uk.ac.ebi.microarray.zooma.eval

An outcome of a mapping process that indicates some curation is required in order to know which of the several possible mapping hypotheses should be accepted.

CurationDecorator(OntologyMappingOutcome, CurationTracker) - Constructor for class uk.ac.ebi.microarray.zooma.eval.CurationDecorator

CurationTracker - Class in uk.ac.ebi.microarray.zooma.track

An information tracker that tracks curation operations.

CurationTracker() - Constructor for class uk.ac.ebi.microarray.zooma.track.CurationTracker

D

DefaultMappingContext - Class in uk.ac.ebi.microarray.zooma.context

A basic implementation of a mapping context that contains only core information.

DefaultMappingContext(Source) - Constructor for class uk.ac.ebi.microarray.zooma.context.DefaultMappingContext

DefaultMappingEvaluator - Class in uk.ac.ebi.microarray.zooma.eval

A basic implementation of an OntologyMappingEvaluator that utilises a mapping tracker and calculator to do incremental pairwise assessments of outcomes.

DefaultMappingEvaluator() - Constructor for class uk.ac.ebi.microarray.zooma.eval.DefaultMappingEvaluator

E

EFOOntocatRetriever - Class in uk.ac.ebi.microarray.zooma.retrieval

An ontology term retriever that utilises the ontocat API to retrieve terms from EFO.

EFOOntocatRetriever() - Constructor for class uk.ac.ebi.microarray.zooma.retrieval.EFOOntocatRetriever

endReport(int) - Method in class uk.ac.ebi.microarray.zooma.reports.ReportWriter

Finalises the report, setting the exit code of the process, sorting alphabetically and flushing to disk.

equals(Object) - Method in class uk.ac.ebi.microarray.zooma.lang.TextValue

evaluateOutcome(Value, Collection<OntologyMappingHypothesis>) - Method in class uk.ac.ebi.microarray.zooma.eval.DefaultMappingEvaluator

Incrementally performs simple pairwise comparison.

evaluateOutcome(Value, Collection<OntologyMappingHypothesis>) - Method in interface uk.ac.ebi.microarray.zooma.eval.OntologyMappingEvaluator

Evaluates the ontology mapping outcome for a collection of mapping hypotheses.

extractOntologyTermFromURI(String) - Method in class uk.ac.ebi.microarray.zooma.reports.ReportWriter

F

FailureReportWriterDecorator - Class in uk.ac.ebi.microarray.zooma.eval

Javadocs go here!

FailureReportWriterDecorator(OntologyMappingOutcome) - Constructor for class uk.ac.ebi.microarray.zooma.eval.FailureReportWriterDecorator

fetchMappingContexts(Value, OntologyTerm) - Method in class uk.ac.ebi.microarray.zooma.retrieval.CompositeOntologyTermRetriever

Returns the set of unique contexts retrieved from each retriever encapsulated by this composite retriever.

fetchMappingContexts(Value, OntologyTerm) - Method in class uk.ac.ebi.microarray.zooma.retrieval.EFOOntocatRetriever

fetchMappingContexts(Value, OntologyTerm) - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntocatRetriever

fetchMappingContexts(Value, OntologyTerm) - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntologyRetriever

fetchMappingContexts(Value, OntologyTerm) - Method in interface uk.ac.ebi.microarray.zooma.retrieval.OntologyTermRetriever

Fetch the contexts in which the given description is mapped to the given term, if any.

fetchOntologyName(OntologyTerm) - Method in class uk.ac.ebi.microarray.zooma.reports.ReportWriter

Fetches the name of the ontology for the supplied term.

fetchTerms(Value) - Method in class uk.ac.ebi.microarray.zooma.retrieval.CompositeOntologyTermRetriever

Returns a set of unique terms retrieved from each retriever encapsulated by this composite retriever.

fetchTerms(Value) - Method in class uk.ac.ebi.microarray.zooma.retrieval.EFOOntocatRetriever

fetchTerms(Value) - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntocatRetriever

fetchTerms(Value) - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntologyRetriever

Fetches terms that can be matched against EFO.

fetchTerms(Value) - Method in interface uk.ac.ebi.microarray.zooma.retrieval.OntologyTermRetriever

Fetch a collection of terms using the given description as a search parameter.

fetchTermsByAccession(String) - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntologyRetriever

Takes the given term "accession" and attempts to resolve it against the URIs for classes in the ontology.

flush() - Method in class uk.ac.ebi.microarray.zooma.reports.ReportWriter

Sorts the current buffer of report output, and flushes everything to a temporary file.

formulateHypotheses(Value) - Method in class uk.ac.ebi.microarray.zooma.formulate.ContextSensitiveMappingFormulator

formulateHypotheses(Value) - Method in class uk.ac.ebi.microarray.zooma.formulate.NoPossibleMappingFormulator

formulateHypotheses(Value) - Method in interface uk.ac.ebi.microarray.zooma.formulate.OntologyMappingFormulator

Formulate a set of hypotheses that describe the possible mappings that might be made about the given value.

G

generateAllPossibleMappings(String, String) - Method in class uk.ac.ebi.microarray.zooma.reports.TextReports

Generate a report describing possible terms, matched from a host of different ontologies, that could be used as mappings for the supplied terms.

generateHypothesis(Value, OntologyMappingContext, OntologyTerm...) - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesisFactory

Generates an ontology mapping hypothesis given a description, the term it may map to, and a context

generateHypothesis(Value, OntologyMappingContext, OntologyTerm...) - Method in class uk.ac.ebi.microarray.zooma.hypothesis.TrackedHypothesisFactory

generateJSONMappingObject(String, String) - Method in class uk.ac.ebi.microarray.zooma.service.impl.BasicZoomaService

generateJSONProducingOutcome(OntologyMappingOutcome) - Static method in class uk.ac.ebi.microarray.zooma.eval.JSONProducerDecorator

generateMappings(String) - Method in class uk.ac.ebi.microarray.zooma.service.impl.BasicZoomaService

Generates a JSON object that encapsulates any mappings generated by ZOOMA for the value specified.

generateMappings(String) - Method in interface uk.ac.ebi.microarray.zooma.service.ZoomaService

Generates a JSON object describing the mappings between the supplied value and ontology terms.

generateMappingsToSingleOntology(String, String, String) - Method in class uk.ac.ebi.microarray.zooma.reports.TextReports

Generates a report describing the mappings that match exactly against the supplied ontology.

generateOutcome(Value) - Method in class uk.ac.ebi.microarray.zooma.mapping.JSONOntologyMapper

generateOutcome(Value) - Method in interface uk.ac.ebi.microarray.zooma.mapping.OntologyMapper

Generates an OntologyMappingOutcome given a description and a mapping context.

generateOutcome(Value) - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

generateTextFailureReportOutcome(OntologyMappingOutcome, TextReportWriter) - Static method in class uk.ac.ebi.microarray.zooma.eval.FailureReportWriterDecorator

generateTextReportOutcome(OntologyMappingOutcome, TextReportWriter) - Static method in class uk.ac.ebi.microarray.zooma.eval.ReportWriterDecorator

generateZoomaResponse(HttpSession, JSONObject) - Method in class uk.ac.ebi.microarray.zooma.service.impl.AjaxZoomaBean

Generates a JSON response to the supplied query parameter json.

getAcceptedHypotheses() - Method in class uk.ac.ebi.microarray.zooma.track.CurationTracker

getAliases(String) - Method in interface uk.ac.ebi.microarray.zooma.service.OntologyRankingService

Gets a collection of the aliases assigned to a named ontology.

getAlternativeHypothesisFormulator() - Method in class uk.ac.ebi.microarray.zooma.mapping.JSONOntologyMapper

getAlternativeHypothesisFormulator() - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

getArgDescription() - Method in interface uk.ac.ebi.microarray.zooma.utils.ZoomaMode.Argument

A short description of what this argument is for.

getArgName() - Method in interface uk.ac.ebi.microarray.zooma.utils.ZoomaMode.Argument

The full name of this argument.

getArgShortName() - Method in interface uk.ac.ebi.microarray.zooma.utils.ZoomaMode.Argument

The short name for this argument.

getArgumentsForOperation(ZoomaMode.Operation) - Method in interface uk.ac.ebi.microarray.zooma.utils.ZoomaMode

A collection of arguments that can be supplied to this operation

getBestHypotheses() - Method in class uk.ac.ebi.microarray.zooma.eval.BasicZoomaOutcome

getBestHypotheses() - Method in interface uk.ac.ebi.microarray.zooma.eval.OntologyMappingOutcome

A collection of OntologyMappingHypothesis objects that describe ontology mappings.

getBestHypotheses() - Method in class uk.ac.ebi.microarray.zooma.eval.OntologyMappingOutcomeDecorator

getBestHypotheses() - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRankingTracker

getBestHypotheses() - Method in interface uk.ac.ebi.microarray.zooma.track.HypothesisTracker

Returns the collection of OntologyMappingHypothesis objects that are known to be the best possible hypotheses given the current state of assessment.

getCandidateAlternativeHypotheses() - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRankingTracker

getCandidateAlternativeHypotheses() - Method in interface uk.ac.ebi.microarray.zooma.track.HypothesisTracker

Returns the collection of possible alternatives to the current null hypothesis.

getClassNames(OWLClass) - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntologyRetriever

Retrieve all possible names for the supplied class.

getClassRDFSLabels(OWLClass) - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntologyRetriever

Recovers all string values of the rdfs:label annotation attribute on the supplied class.

getClassSynonyms(OWLClass) - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntologyRetriever

Recovers all synonyms for the supplied owl class, based on the literal value of the efo synonym annotation.

getCompletedCount() - Method in class uk.ac.ebi.microarray.zooma.reports.ReportTimer

getContext() - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

getContext() - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesis

The context in which this mapping hypothesis should be attempted

getCurrentEstimate() - Method in class uk.ac.ebi.microarray.zooma.reports.ReportTimer

getCurrentNullHypothesis() - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRankingTracker

getCurrentNullHypothesis() - Method in interface uk.ac.ebi.microarray.zooma.track.HypothesisTracker

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

getEvaluator() - Method in class uk.ac.ebi.microarray.zooma.mapping.JSONOntologyMapper

getEvaluator() - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

getFailureReportWriter() - Method in class uk.ac.ebi.microarray.zooma.eval.FailureReportWriterDecorator

getFetchedTerms() - Method in class uk.ac.ebi.microarray.zooma.retrieval.EFOOntocatRetriever

A cached set of all terms previously fetched using this retriever

getHypothesisTracker() - Method in class uk.ac.ebi.microarray.zooma.lang.TextValue

getHypothesisTracker() - Method in interface uk.ac.ebi.microarray.zooma.lang.Value

Returns a HypothesisTracker that can be utilised to track any generated hypotheses describing mappings about this value

getInstance(String) - Static method in class uk.ac.ebi.microarray.zooma.retrieval.OntologyRetriever

Gets the singleton instance of a retriever for the named ontology.

getJSONObject() - Method in class uk.ac.ebi.microarray.zooma.eval.JSONProducerDecorator

getLog() - Method in class uk.ac.ebi.microarray.zooma.calc.OntologyRanker

getLog() - Method in class uk.ac.ebi.microarray.zooma.calc.RankingBasedCalculator

getLog() - Method in class uk.ac.ebi.microarray.zooma.calc.SourceRanker

getLog() - Method in class uk.ac.ebi.microarray.zooma.eval.DefaultMappingEvaluator

getLog() - Method in class uk.ac.ebi.microarray.zooma.formulate.AbstractFormulator

getLog() - Method in class uk.ac.ebi.microarray.zooma.formulate.NoPossibleMappingFormulator

getLog() - Method in class uk.ac.ebi.microarray.zooma.mapping.JSONOntologyMapper

getLog() - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

getLog() - Method in class uk.ac.ebi.microarray.zooma.reports.ReportWriter

getLog() - Method in class uk.ac.ebi.microarray.zooma.reports.TextReports

getLog() - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntocatRetriever

getLog() - Method in class uk.ac.ebi.microarray.zooma.service.impl.BasicZoomaService

getLog() - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRanking

getLog() - Method in class uk.ac.ebi.microarray.zooma.utils.Configurator

getMapper() - Method in class uk.ac.ebi.microarray.zooma.reports.TextReports

getMapper() - Method in class uk.ac.ebi.microarray.zooma.service.impl.BasicZoomaService

getMappingTracker() - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

getMode(String) - Method in class uk.ac.ebi.microarray.zooma.ZoomaDriver

getModeName() - Method in interface uk.ac.ebi.microarray.zooma.utils.ZoomaMode

Returns the name of this operation

getModeOptions(String) - Method in class uk.ac.ebi.microarray.zooma.ZoomaDriver

getModes() - Method in class uk.ac.ebi.microarray.zooma.ZoomaDriver

getNullHypothesisFormulator() - Method in class uk.ac.ebi.microarray.zooma.mapping.JSONOntologyMapper

getNullHypothesisFormulator() - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

getOntologiesConfig() - Method in class uk.ac.ebi.microarray.zooma.utils.Configurator

getOntologyMappingCalculator() - Method in class uk.ac.ebi.microarray.zooma.eval.DefaultMappingEvaluator

getOntologyMappingHypothesisFactory() - Method in class uk.ac.ebi.microarray.zooma.formulate.ContextSensitiveMappingFormulator

getOntologyMappingHypothesisFactory() - Method in class uk.ac.ebi.microarray.zooma.formulate.NoPossibleMappingFormulator

getOntologyRanker() - Method in class uk.ac.ebi.microarray.zooma.calc.RankingBasedCalculator

getOntologyRanker() - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRanking

getOntologyTermRetriever() - Method in class uk.ac.ebi.microarray.zooma.formulate.ContextSensitiveMappingFormulator

getOntologyTermRetrievers() - Method in class uk.ac.ebi.microarray.zooma.retrieval.CompositeOntologyTermRetriever

getOntologyTerms() - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

getOntologyTerms() - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesis

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

getOperationDescription() - Method in interface uk.ac.ebi.microarray.zooma.utils.ZoomaMode.Operation

A brief description of what this operation does.

getOperationName() - Method in interface uk.ac.ebi.microarray.zooma.utils.ZoomaMode.Operation

The name of this operation.

getOperations() - Method in interface uk.ac.ebi.microarray.zooma.utils.ZoomaMode

A collection of modes that this operation can operate in

getOperationShortName() - Method in interface uk.ac.ebi.microarray.zooma.utils.ZoomaMode.Operation

The short name for this operation.

getOriginalContexts() - Method in class uk.ac.ebi.microarray.zooma.context.AggregatedContext

getOutcome() - Method in class uk.ac.ebi.microarray.zooma.eval.OntologyMappingOutcomeDecorator

getRankedHypotheses() - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRanking

Returns the list of hypotheses that have been ranked, in the order in which they rank.

getRejectedOntologiesConfig() - Method in class uk.ac.ebi.microarray.zooma.utils.Configurator

getReportWriter() - Method in class uk.ac.ebi.microarray.zooma.eval.ReportWriterDecorator

getRetriever() - Method in class uk.ac.ebi.microarray.zooma.formulate.AbstractFormulator

getService() - Method in class uk.ac.ebi.microarray.zooma.retrieval.CompositeOntologyTermRetriever

getService() - Method in class uk.ac.ebi.microarray.zooma.retrieval.EFOOntocatRetriever

A ontocat OntologyService that can be used to retrieve EFO terms.

getSource() - Method in class uk.ac.ebi.microarray.zooma.context.AggregatedContext

getSource() - Method in class uk.ac.ebi.microarray.zooma.context.DefaultMappingContext

getSource() - Method in class uk.ac.ebi.microarray.zooma.context.NewTermContext

getSource() - Method in class uk.ac.ebi.microarray.zooma.context.OntocatContext

getSource() - Method in interface uk.ac.ebi.microarray.zooma.context.OntologyMappingContext

The "source" in which a mapping is asserted.

getSourceRanker() - Method in class uk.ac.ebi.microarray.zooma.calc.RankingBasedCalculator

getSourceRanker() - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRanking

getSourcesConfig() - Method in class uk.ac.ebi.microarray.zooma.utils.Configurator

getSupportedAnnotationTypes() - Method in class uk.ac.ebi.microarray.zooma.annotations.ZoomaProcessor

getSupportedOptions() - Method in class uk.ac.ebi.microarray.zooma.annotations.ZoomaProcessor

getText() - Method in class uk.ac.ebi.microarray.zooma.lang.TextValue

getText() - Method in interface uk.ac.ebi.microarray.zooma.lang.Value

The actual string assigned to this description.

getTotalCount() - Method in class uk.ac.ebi.microarray.zooma.reports.ReportTimer

getUnmappedValue() - Method in class uk.ac.ebi.microarray.zooma.eval.BasicZoomaOutcome

getUnmappedValue() - Method in interface uk.ac.ebi.microarray.zooma.eval.OntologyMappingOutcome

Returns that value that has been used to produce this outcome.

getUnmappedValue() - Method in class uk.ac.ebi.microarray.zooma.eval.OntologyMappingOutcomeDecorator

getValue() - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

getValue() - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesis

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

getZoomaModes() - Method in class uk.ac.ebi.microarray.zooma.utils.ZoomaInspector

getZoomaOptions() - Method in class uk.ac.ebi.microarray.zooma.ZoomaDriver

H

hashCode() - Method in class uk.ac.ebi.microarray.zooma.lang.TextValue

HypothesisFormulationException - Exception in uk.ac.ebi.microarray.zooma.hypothesis

An exception thrown whenever an attempt to formulate or generate an ontology mapping hypothesis fails.

HypothesisFormulationException() - Constructor for exception uk.ac.ebi.microarray.zooma.hypothesis.HypothesisFormulationException

HypothesisFormulationException(String) - Constructor for exception uk.ac.ebi.microarray.zooma.hypothesis.HypothesisFormulationException

HypothesisFormulationException(String, Throwable) - Constructor for exception uk.ac.ebi.microarray.zooma.hypothesis.HypothesisFormulationException

HypothesisFormulationException(Throwable) - Constructor for exception uk.ac.ebi.microarray.zooma.hypothesis.HypothesisFormulationException

HypothesisRanking - Class in uk.ac.ebi.microarray.zooma.track

An object that records ranking data for hypotheses.

HypothesisRanking(SourceRanker, OntologyRanker) - Constructor for class uk.ac.ebi.microarray.zooma.track.HypothesisRanking

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

A system for scoring OntologyMappingHypothesis objects are determining which are candidates for acception, rejection, deferment or prioritisation.

HypothesisRankingTracker() - Constructor for class uk.ac.ebi.microarray.zooma.track.HypothesisRankingTracker

HypothesisRankingTracker(SourceRanker, OntologyRanker) - Constructor for class uk.ac.ebi.microarray.zooma.track.HypothesisRankingTracker

HypothesisSet - Class in uk.ac.ebi.microarray.zooma.track

A particular type of set that records the collection of discarded OntologyMappingHypothesis.

HypothesisSet() - Constructor for class uk.ac.ebi.microarray.zooma.track.HypothesisSet

HypothesisTracker - Interface in uk.ac.ebi.microarray.zooma.track

An interface for tracking OntologyMappingHypothesis objects specifically.

I

Information - Interface in uk.ac.ebi.microarray.zooma.track

An interface encapsulating any information that can be used to assess the quality of an ontology mapping.

informationChanged(Information) - Method in class uk.ac.ebi.microarray.zooma.track.CurationTracker

informationChanged(Information) - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRankingTracker

informationChanged(Information) - Method in interface uk.ac.ebi.microarray.zooma.track.InformationTracker

Called by Information objects acting as "mediator clients" whenever the information they encapsulate changes.

InformationTracker - Interface in uk.ac.ebi.microarray.zooma.track

A tracker that records the collection of OntologyMappingHypothesis objects that require testing.

init() - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntologyRetriever

Initializes this retriever, loading and preclassifying the ontology.

inspect() - Method in class uk.ac.ebi.microarray.zooma.utils.ZoomaInspector

Probes the set of currently loaded classes to discover all configured modes for Zooma, and binds them for use.

invokeTarget(ZoomaMode.Operation, String...) - Method in interface uk.ac.ebi.microarray.zooma.utils.ZoomaMode

Invokes the operation for the operation on this operation with the given parameters.

invokeZooma(ZoomaDriver.ZoomaTrigger) - Method in class uk.ac.ebi.microarray.zooma.ZoomaDriver

IRRELEVANT_VALUE - Static variable in interface uk.ac.ebi.microarray.zooma.context.OntologyMappingContext

A value signifying that the parameter is irrelevant for comparison purposes and should be ignored

isAccepted() - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

isAccepted() - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesis

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

isAutomaticallyAcceptable() - Method in class uk.ac.ebi.microarray.zooma.eval.BasicZoomaOutcome

isAutomaticallyAcceptable() - Method in interface uk.ac.ebi.microarray.zooma.eval.OntologyMappingOutcome

Whether or not it was possible to automatically accept a given outcome.

isAutomaticallyAcceptable() - Method in class uk.ac.ebi.microarray.zooma.eval.OntologyMappingOutcomeDecorator

isCurated() - Method in class uk.ac.ebi.microarray.zooma.track.CurationTracker

isObsolete(OWLClass) - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntologyRetriever

Returns true if this ontology term is obsolete in EFO, false otherwise.

isRejected() - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

isRejected() - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesis

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

isReportingFails() - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

isRequired() - Method in interface uk.ac.ebi.microarray.zooma.utils.ZoomaMode.Argument

Whether or not this argument is required.

isUnit(OWLClass) - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntologyRetriever

J

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

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

JSONOntologyMapper() - Constructor for class uk.ac.ebi.microarray.zooma.mapping.JSONOntologyMapper

JSONProducerDecorator - Class in uk.ac.ebi.microarray.zooma.eval

A decorator that has the ability to generate a JSON object from an outcome once applied.

JSONProducerDecorator(OntologyMappingOutcome) - Constructor for class uk.ac.ebi.microarray.zooma.eval.JSONProducerDecorator

L

loadConfiguration() - Method in class uk.ac.ebi.microarray.zooma.utils.Configurator

log - Variable in class uk.ac.ebi.microarray.zooma.service.impl.BasicZoomaService

lookupURI(String) - Static method in class uk.ac.ebi.microarray.zooma.utils.Constants

Looks up the URI value from the resource 'zooma-uris.properties', located on the classpath

lookupVersionFromMavenProperties() - Method in class uk.ac.ebi.microarray.zooma.reports.ReportWriter

Retrieves the version number of the application, by locating the version property from the automatically generated maven pom.properties file.

M

main(String[]) - Static method in class uk.ac.ebi.microarray.zooma.ZoomaDriver

matchSearchString(String) - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntologyRetriever

Searches the classes known to this retriever for any that may match the given search string.

N

NewTermContext - Class in uk.ac.ebi.microarray.zooma.context

A context representing newly submitted, text based values.

NewTermContext() - Constructor for class uk.ac.ebi.microarray.zooma.context.NewTermContext

NewTermContext(Source) - Constructor for class uk.ac.ebi.microarray.zooma.context.NewTermContext

NO_DESCRIPTION - Static variable in annotation type uk.ac.ebi.microarray.zooma.annotations.ZoomaMappingArgument

NO_DESCRIPTION - Static variable in annotation type uk.ac.ebi.microarray.zooma.annotations.ZoomaMappingOperation

NO_SHORT_NAME - Static variable in annotation type uk.ac.ebi.microarray.zooma.annotations.ZoomaMappingArgument

NO_SHORT_NAME - Static variable in annotation type uk.ac.ebi.microarray.zooma.annotations.ZoomaMappingOperation

NoMappingPossibleHypothesis - Class in uk.ac.ebi.microarray.zooma.hypothesis

An implementation of a hypothesis that can be tracked by an InformationTracker and asserts that no mapping is possible from a particular term.

NoMappingPossibleHypothesis(Value, OntologyMappingContext) - Constructor for class uk.ac.ebi.microarray.zooma.hypothesis.NoMappingPossibleHypothesis

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

A special type of OntologyMappingFormulator that generates default null hypotheses.

NoPossibleMappingFormulator() - Constructor for class uk.ac.ebi.microarray.zooma.formulate.NoPossibleMappingFormulator

normalizeSearchString(String) - Method in class uk.ac.ebi.microarray.zooma.retrieval.OntologyRetriever

"Normalizes" a string into a searchable string.

O

OntocatContext - Class in uk.ac.ebi.microarray.zooma.context

An ontology mapping context acquired from ontocat.

OntocatContext(Source) - Constructor for class uk.ac.ebi.microarray.zooma.context.OntocatContext

OntocatRetriever - Class in uk.ac.ebi.microarray.zooma.retrieval

An ontology term retriever that utilises ontocat to dispatch queries to OLS, Bioportal and EFO (using a dedicated URL).

OntocatRetriever() - Constructor for class uk.ac.ebi.microarray.zooma.retrieval.OntocatRetriever

ontologiesResource - Static variable in class uk.ac.ebi.microarray.zooma.utils.Configurator

The name of the resource containing the default ontology ranking configuration

ontologiesSuffix - Static variable in class uk.ac.ebi.microarray.zooma.utils.Configurator

The resource name suffix for ontology config files

OntologyMapper - Interface in uk.ac.ebi.microarray.zooma.mapping

A utility for performing mappings from text descriptions into a defined domain space of ontology terms.

OntologyMappingCalculator - Interface in uk.ac.ebi.microarray.zooma.calc

Calculates mappings based on an assessment of a series of hypotheses in a given context.

OntologyMappingContext - Interface in uk.ac.ebi.microarray.zooma.context

A representation of the context in which an OntologyMapper may wish to operate.

OntologyMappingEvaluator - Interface in uk.ac.ebi.microarray.zooma.eval

Evaluates ontology mapping hypotheses and produces an outcome based on assessments performed.

OntologyMappingFormulator - Interface in uk.ac.ebi.microarray.zooma.formulate

Formulates a plan by which ontology mappings can be asserted.

OntologyMappingHypothesis - Interface in uk.ac.ebi.microarray.zooma.hypothesis

A hypothesis regarding how a given description may map to a given term.

OntologyMappingHypothesisFactory - Interface in uk.ac.ebi.microarray.zooma.hypothesis

A factory for OntologyMappingHypothesis objects.

OntologyMappingHypothesisVisitor - Interface in uk.ac.ebi.microarray.zooma.hypothesis

A visitor that can visit OntologyMappingHypothesis objects and inspect the possible outcomes.

OntologyMappingOutcome - Interface in uk.ac.ebi.microarray.zooma.eval

The outcome of an ontology mapping process.

OntologyMappingOutcomeDecorator - Class in uk.ac.ebi.microarray.zooma.eval

An abstract class that implements OntologyMappingOutcome and follows the decorator pattern.

OntologyMappingOutcomeDecorator(OntologyMappingOutcome) - Constructor for class uk.ac.ebi.microarray.zooma.eval.OntologyMappingOutcomeDecorator

OntologyRanker - Class in uk.ac.ebi.microarray.zooma.calc

A class containing hypothesis ranking logic, based on a configurable list of ontologies.

OntologyRanker(LinkedHashMap<String, List<String>>) - Constructor for class uk.ac.ebi.microarray.zooma.calc.OntologyRanker

OntologyRanker(LinkedHashMap<String, List<String>>, LinkedHashMap<String, List<String>>) - Constructor for class uk.ac.ebi.microarray.zooma.calc.OntologyRanker

OntologyRankingService - Interface in uk.ac.ebi.microarray.zooma.service

A service interface that can be used to rank ontologies in preference order.

ontologyRanksHigher(OntologyMappingHypothesis, OntologyMappingHypothesis) - Method in class uk.ac.ebi.microarray.zooma.calc.OntologyRanker

ontologyRanksLower(OntologyMappingHypothesis, OntologyMappingHypothesis) - Method in class uk.ac.ebi.microarray.zooma.calc.OntologyRanker

OntologyRetriever - Class in uk.ac.ebi.microarray.zooma.retrieval

Retrieves OntologyTerms from an ontology file in OWL or OBO formats.

OntologyTermRetriever - Interface in uk.ac.ebi.microarray.zooma.retrieval

A service that fetches ontology terms from some repository.

OntologyUtils - Class in uk.ac.ebi.microarray.zooma.utils

Convenience class containing static methods that are useful in comparing ontology terms etc.

OntologyUtils() - Constructor for class uk.ac.ebi.microarray.zooma.utils.OntologyUtils

OWLContext - Class in uk.ac.ebi.microarray.zooma.context

A mapping context acquired from EFO.

OWLContext() - Constructor for class uk.ac.ebi.microarray.zooma.context.OWLContext

P

PossibleDuplicateMappingsHypothesis - Class in uk.ac.ebi.microarray.zooma.hypothesis

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.

PossibleDuplicateMappingsHypothesis(Value, OntologyMappingContext, OntologyTerm...) - Constructor for class uk.ac.ebi.microarray.zooma.hypothesis.PossibleDuplicateMappingsHypothesis

process(Set<? extends TypeElement>, RoundEnvironment) - Method in class uk.ac.ebi.microarray.zooma.annotations.ZoomaProcessor

R

rank(OntologyMappingHypothesis) - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRanking

Rank, or rerank, the given hypothesis against all others

RankingBasedCalculator - Class in uk.ac.ebi.microarray.zooma.calc

An OntologyMappingCalculator that evaluates ontology mapping hypotheses based on a simple ranking.

RankingBasedCalculator() - Constructor for class uk.ac.ebi.microarray.zooma.calc.RankingBasedCalculator

rankOntologies(List<String>) - Method in interface uk.ac.ebi.microarray.zooma.service.OntologyRankingService

Ranks ontologies, by name, in preference order.

rankSources(List<String>) - Method in interface uk.ac.ebi.microarray.zooma.service.SourceRankingService

Ranks the sources in order, by name.

readOntologiesConfig(InputStream) - Method in class uk.ac.ebi.microarray.zooma.utils.Configurator

readRejectedOntologiesConfig(InputStream) - Method in class uk.ac.ebi.microarray.zooma.utils.Configurator

readSourcesConfig(InputStream) - Method in class uk.ac.ebi.microarray.zooma.utils.Configurator

recordInformation(Information) - Method in class uk.ac.ebi.microarray.zooma.track.CurationTracker

rejectedOntologiesResource - Static variable in class uk.ac.ebi.microarray.zooma.utils.Configurator

The name of the resource containing the default rejected ontology configuration

rejectedOntologiesSuffix - Static variable in class uk.ac.ebi.microarray.zooma.utils.Configurator

The resource name suffix for config files listing the ontologies to reject outright

rejectHypothesis() - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

rejectHypothesis() - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesis

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

remove(OntologyMappingHypothesis) - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRanking

Removes a previously ranked hypothesis from the rankings

remove(Object) - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisSet

removeAlias(String, String) - Method in interface uk.ac.ebi.microarray.zooma.service.OntologyRankingService

Removes the association between a given alias and the ontology named.

removeAll(Collection<?>) - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisSet

removeRetriever(OntologyTermRetriever) - Method in class uk.ac.ebi.microarray.zooma.formulate.AbstractFormulator

ReportGenerationException - Exception in uk.ac.ebi.microarray.zooma.reports

An exception that is raised whenever a report fails to generate

ReportGenerationException() - Constructor for exception uk.ac.ebi.microarray.zooma.reports.ReportGenerationException

ReportGenerationException(String) - Constructor for exception uk.ac.ebi.microarray.zooma.reports.ReportGenerationException

ReportGenerationException(String, Throwable) - Constructor for exception uk.ac.ebi.microarray.zooma.reports.ReportGenerationException

ReportGenerationException(Throwable) - Constructor for exception uk.ac.ebi.microarray.zooma.reports.ReportGenerationException

ReportTimer - Class in uk.ac.ebi.microarray.zooma.reports

Abstract class for generating Zooma reports.

ReportTimer(int) - Constructor for class uk.ac.ebi.microarray.zooma.reports.ReportTimer

ReportWriter - Class in uk.ac.ebi.microarray.zooma.reports

A writer implementation that writes all output lines supplied into a buffer, alphabetically sorts them, and flushes them to file when this writer is closed.

ReportWriter(File) - Constructor for class uk.ac.ebi.microarray.zooma.reports.ReportWriter

Creates a ReportWriter that buffers written lines, sorting them alphabetically.

ReportWriterDecorator - Class in uk.ac.ebi.microarray.zooma.eval

An outcome decorator that decorates an outcome with the ability to generate text reports whenever the outcome is applied.

ReportWriterDecorator(OntologyMappingOutcome) - Constructor for class uk.ac.ebi.microarray.zooma.eval.ReportWriterDecorator

S

setAlternativeHypothesisFormulator(OntologyMappingFormulator) - Method in class uk.ac.ebi.microarray.zooma.mapping.JSONOntologyMapper

setAlternativeHypothesisFormulator(OntologyMappingFormulator) - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

setEvaluator(OntologyMappingEvaluator) - Method in class uk.ac.ebi.microarray.zooma.mapping.JSONOntologyMapper

setEvaluator(OntologyMappingEvaluator) - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

setFailureReportWriter(TextReportWriter) - Method in class uk.ac.ebi.microarray.zooma.eval.FailureReportWriterDecorator

setHypothesisRankingTracker(HypothesisRankingTracker) - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRanking

setHypothesisRankingTracker(HypothesisRankingTracker) - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisSet

setHypothesisTracker(HypothesisTracker) - Method in class uk.ac.ebi.microarray.zooma.lang.TextValue

setMapper(JSONOntologyMapper) - Method in class uk.ac.ebi.microarray.zooma.service.impl.BasicZoomaService

setNullHypothesisFormulator(OntologyMappingFormulator) - Method in class uk.ac.ebi.microarray.zooma.mapping.JSONOntologyMapper

setNullHypothesisFormulator(OntologyMappingFormulator) - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

setOntologyMappingCalculator(OntologyMappingCalculator) - Method in class uk.ac.ebi.microarray.zooma.eval.DefaultMappingEvaluator

setOntologyMappingHypothesisFactory(OntologyMappingHypothesisFactory) - Method in class uk.ac.ebi.microarray.zooma.formulate.ContextSensitiveMappingFormulator

setOntologyMappingHypothesisFactory(OntologyMappingHypothesisFactory) - Method in class uk.ac.ebi.microarray.zooma.formulate.NoPossibleMappingFormulator

setOntologyMappingTracker(InformationTracker) - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

Set the mediator service that this hypothesis can provide feedback to.

setOntologyRanker(OntologyRanker) - Method in class uk.ac.ebi.microarray.zooma.calc.RankingBasedCalculator

setOntologyRanker(OntologyRanker) - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRanking

setOntologyTermRetriever(OntologyTermRetriever) - Method in class uk.ac.ebi.microarray.zooma.formulate.ContextSensitiveMappingFormulator

setOntologyTermRetrievers(List<OntologyTermRetriever>) - Method in class uk.ac.ebi.microarray.zooma.retrieval.CompositeOntologyTermRetriever

setOntologyTerms(Collection<OntologyTerm>) - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

setOntologyTerms(Collection<OntologyTerm>) - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesis

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

setReportingFails(boolean) - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

setReportWriter(TextReportWriter) - Method in class uk.ac.ebi.microarray.zooma.eval.ReportWriterDecorator

setRetriever(OntologyTermRetriever) - Method in class uk.ac.ebi.microarray.zooma.formulate.AbstractFormulator

setSourceRanker(SourceRanker) - Method in class uk.ac.ebi.microarray.zooma.calc.RankingBasedCalculator

setSourceRanker(SourceRanker) - Method in class uk.ac.ebi.microarray.zooma.track.HypothesisRanking

setZoomaService(ZoomaService) - Method in class uk.ac.ebi.microarray.zooma.service.impl.AjaxZoomaBean

Source - Enum in uk.ac.ebi.microarray.zooma.hypothesis

An object encapsulating information about the source of a particular OntologyMappingHypothesis.

SourceRanker - Class in uk.ac.ebi.microarray.zooma.calc

A class containing hypothesis ranking logic, based on a configurable list of sources.

SourceRanker(List<Source>) - Constructor for class uk.ac.ebi.microarray.zooma.calc.SourceRanker

SourceRankingService - Interface in uk.ac.ebi.microarray.zooma.service

A service interface that can be used to rank sources in preference order.

sourceRanksHigher(OntologyMappingHypothesis, OntologyMappingHypothesis) - Method in class uk.ac.ebi.microarray.zooma.calc.SourceRanker

sourceRanksLower(OntologyMappingHypothesis, OntologyMappingHypothesis) - Method in class uk.ac.ebi.microarray.zooma.calc.SourceRanker

sourcesResource - Static variable in class uk.ac.ebi.microarray.zooma.utils.Configurator

The name of the resource containing the default source ranking configuration

sourcesSuffix - Static variable in class uk.ac.ebi.microarray.zooma.utils.Configurator

The resource name suffix for source config files

start() - Method in class uk.ac.ebi.microarray.zooma.reports.ReportTimer

startReport() - Method in class uk.ac.ebi.microarray.zooma.reports.ReportWriter

Initialises the report, setting useful information about the outcome such as start time, working directory etc.

T

terms - Variable in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

termsAreEquivalent(OntologyTerm, OntologyTerm) - Static method in class uk.ac.ebi.microarray.zooma.utils.OntologyUtils

termsAreSubset(Collection<OntologyTerm>, Collection<OntologyTerm>) - Static method in class uk.ac.ebi.microarray.zooma.utils.OntologyUtils

Returns true if collectionB contains all the terms in collectionA, plus more

termsAreSuperset(Collection<OntologyTerm>, Collection<OntologyTerm>) - Static method in class uk.ac.ebi.microarray.zooma.utils.OntologyUtils

Returns true if collectionB contains some of the terms in collectionA, and no others more

testHypothesis(OntologyMappingHypothesis, OntologyMappingHypothesis) - Method in interface uk.ac.ebi.microarray.zooma.calc.OntologyMappingCalculator

Tests the alternative hypothesis against the null hypothesis.

testHypothesis(OntologyMappingHypothesis, OntologyMappingHypothesis) - Method in class uk.ac.ebi.microarray.zooma.calc.RankingBasedCalculator

TextReportingMapper - Class in uk.ac.ebi.microarray.zooma.mapping

A mapper implementation that generates a simple tab delimited text file mapping report.

TextReportingMapper() - Constructor for class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

TextReports - Class in uk.ac.ebi.microarray.zooma.reports

A zooma mode that generates a text report in the specified directory given a list of text values to map.

TextReports() - Constructor for class uk.ac.ebi.microarray.zooma.reports.TextReports

TextReportWriter - Class in uk.ac.ebi.microarray.zooma.reports

A ReportWriter implementation that writes a simple tab delimited text report based around a simple format.

TextReportWriter(File) - Constructor for class uk.ac.ebi.microarray.zooma.reports.TextReportWriter

Creates a ReportWriter that buffers written lines, sorting them alphabetically.

TextValue - Class in uk.ac.ebi.microarray.zooma.lang

A very basic Value implementation that simply wraps a plain text string.

TextValue(String) - Constructor for class uk.ac.ebi.microarray.zooma.lang.TextValue

Generates a new TextValue with, by default, a new instance of HypothesisRankingTracker as it's tracker.

TextValue(String, HypothesisTracker) - Constructor for class uk.ac.ebi.microarray.zooma.lang.TextValue

Generates a new text value, using the supplied hypothesis tracker to track hypotheses about how this text value maps to ontology terms.

toString() - Method in class uk.ac.ebi.microarray.zooma.context.AggregatedContext

toString() - Method in class uk.ac.ebi.microarray.zooma.context.DefaultMappingContext

toString() - Method in class uk.ac.ebi.microarray.zooma.context.NewTermContext

toString() - Method in class uk.ac.ebi.microarray.zooma.context.OntocatContext

toString() - Method in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

TrackedHypothesisFactory - Class in uk.ac.ebi.microarray.zooma.hypothesis

A basic implementation of a factory for generating OntologyMappingHypothesis objects.

TrackedHypothesisFactory() - Constructor for class uk.ac.ebi.microarray.zooma.hypothesis.TrackedHypothesisFactory

U

uk.ac.ebi.microarray.zooma - package uk.ac.ebi.microarray.zooma

uk.ac.ebi.microarray.zooma.annotations - package uk.ac.ebi.microarray.zooma.annotations

uk.ac.ebi.microarray.zooma.calc - package uk.ac.ebi.microarray.zooma.calc

uk.ac.ebi.microarray.zooma.context - package uk.ac.ebi.microarray.zooma.context

uk.ac.ebi.microarray.zooma.eval - package uk.ac.ebi.microarray.zooma.eval

uk.ac.ebi.microarray.zooma.formulate - package uk.ac.ebi.microarray.zooma.formulate

uk.ac.ebi.microarray.zooma.hypothesis - package uk.ac.ebi.microarray.zooma.hypothesis

uk.ac.ebi.microarray.zooma.lang - package uk.ac.ebi.microarray.zooma.lang

uk.ac.ebi.microarray.zooma.mapping - package uk.ac.ebi.microarray.zooma.mapping

uk.ac.ebi.microarray.zooma.reports - package uk.ac.ebi.microarray.zooma.reports

uk.ac.ebi.microarray.zooma.retrieval - package uk.ac.ebi.microarray.zooma.retrieval

uk.ac.ebi.microarray.zooma.service - package uk.ac.ebi.microarray.zooma.service

uk.ac.ebi.microarray.zooma.service.impl - package uk.ac.ebi.microarray.zooma.service.impl

uk.ac.ebi.microarray.zooma.track - package uk.ac.ebi.microarray.zooma.track

uk.ac.ebi.microarray.zooma.utils - package uk.ac.ebi.microarray.zooma.utils

UNKNOWN_VALUE - Static variable in interface uk.ac.ebi.microarray.zooma.context.OntologyMappingContext

An unknown value that can be used in any parameter

USER_SUBMITTED - Static variable in interface uk.ac.ebi.microarray.zooma.context.OntologyMappingContext

A value to be used whenever a none-standard parameter, supplied by the user, is required

V

value - Variable in class uk.ac.ebi.microarray.zooma.hypothesis.AbstractTrackedHypothesis

Value - Interface in uk.ac.ebi.microarray.zooma.lang

A simple text description.

valueOf(String) - Static method in enum uk.ac.ebi.microarray.zooma.hypothesis.Source

Returns the enum constant of this type with the specified name.

values() - Static method in enum uk.ac.ebi.microarray.zooma.hypothesis.Source

Returns an array containing the constants of this enum type, in the order they are declared.

visit(PossibleDuplicateMappingsHypothesis) - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesisVisitor

Visit the given PossibleDuplicateMappingsHypothesis.

visit(NoMappingPossibleHypothesis) - Method in interface uk.ac.ebi.microarray.zooma.hypothesis.OntologyMappingHypothesisVisitor

Visit the given NoMappingPossibleHypothesis

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write(char[], int, int) - Method in class uk.ac.ebi.microarray.zooma.reports.ReportWriter

write(OntologyMappingOutcome) - Method in class uk.ac.ebi.microarray.zooma.reports.TextReportWriter

writeFailureOutcomesWith(TextReportWriter) - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

writeOutcomesWith(TextReportWriter) - Method in class uk.ac.ebi.microarray.zooma.mapping.TextReportingMapper

writeReportFooter(PrintWriter) - Method in class uk.ac.ebi.microarray.zooma.reports.ReportWriter

Writes the footer of the report into the supplied print writer

writeReportHeader(PrintWriter) - Method in class uk.ac.ebi.microarray.zooma.reports.ReportWriter

Writes the header of the report into the supplied print writer.

writeReportHeader(PrintWriter) - Method in class uk.ac.ebi.microarray.zooma.reports.TextReportWriter

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ZoomaDriver - Class in uk.ac.ebi.microarray.zooma

A driver class that invokes Zooma with the command line options specified.

ZoomaException - Exception in uk.ac.ebi.microarray.zooma.lang

A generic Zooma exception.

ZoomaException() - Constructor for exception uk.ac.ebi.microarray.zooma.lang.ZoomaException

ZoomaException(String) - Constructor for exception uk.ac.ebi.microarray.zooma.lang.ZoomaException

ZoomaException(String, Throwable) - Constructor for exception uk.ac.ebi.microarray.zooma.lang.ZoomaException

ZoomaException(Throwable) - Constructor for exception uk.ac.ebi.microarray.zooma.lang.ZoomaException

ZoomaInspector - Class in uk.ac.ebi.microarray.zooma.utils

Inspects calibrated resources, to discover and bind any Zooma plugins calibrated.

ZoomaInspector() - Constructor for class uk.ac.ebi.microarray.zooma.utils.ZoomaInspector

ZoomaInvocationException - Exception in uk.ac.ebi.microarray.zooma.lang

An exception thrown whenever a zooma mode or operation is invoked programmatically or by reflection and fails.

ZoomaInvocationException(String, Throwable) - Constructor for exception uk.ac.ebi.microarray.zooma.lang.ZoomaInvocationException

ZoomaInvocationException(Throwable) - Constructor for exception uk.ac.ebi.microarray.zooma.lang.ZoomaInvocationException

ZoomaMappingArgument - Annotation Type in uk.ac.ebi.microarray.zooma.annotations

An annotation that must be applied to any parameters taken by methods annotated with ZoomaMappingOperations

ZoomaMappingGenerator - Annotation Type in uk.ac.ebi.microarray.zooma.annotations

An annotation that can be applied to classes indicating that this class contains Zooma mapping functions for a given operation.

ZoomaMappingOperation - Annotation Type in uk.ac.ebi.microarray.zooma.annotations

An annotation that can be applied to methods to indicate that this method performs a Zooma mapping operation.

ZoomaMode - Interface in uk.ac.ebi.microarray.zooma.utils

The interface for a Zooma operation, which is a mapping "endpoint".

ZoomaMode.Argument - Interface in uk.ac.ebi.microarray.zooma.utils

Defines an argument provided to modify an operation.

ZoomaMode.Operation - Interface in uk.ac.ebi.microarray.zooma.utils

Defines an operation on a operation.

ZoomaProcessor - Class in uk.ac.ebi.microarray.zooma.annotations

Processes zooma annotations to generate classpath files that can be used to inspect loaded files.

ZoomaProcessor() - Constructor for class uk.ac.ebi.microarray.zooma.annotations.ZoomaProcessor

ZoomaService - Interface in uk.ac.ebi.microarray.zooma.service

A service interface that generates ZOOMA mappings between text values and ontology terms.

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