Uses of Interface
org.monarchinitiative.lirical.core.analysis.AnalysisData

Packages that use AnalysisData

Package	Description
org.monarchinitiative.lirical.core.analysis	A high-level representation of LIRICAL analysis.
org.monarchinitiative.lirical.core.analysis.impl	Default LIRICAL analysis implementation.
org.monarchinitiative.lirical.core.output	Base data model for writing out the results of LIRICAL analysis.
org.monarchinitiative.lirical.io.output	Classes for writing out LIRICAL analysis results into HTML, TSV, and JSON files.

Uses of AnalysisData in org.monarchinitiative.lirical.core.analysis

Methods in org.monarchinitiative.lirical.core.analysis that return AnalysisData

Modifier and Type	Method	Description
static AnalysisData	AnalysisData.of(String sampleId, Age age, Sex sex, Collection<org.monarchinitiative.phenol.ontology.data.TermId> presentPhenotypeTerms, Collection<org.monarchinitiative.phenol.ontology.data.TermId> negatedPhenotypeTerms, GenesAndGenotypes genes)	Construct analysis data from the inputs.

Methods in org.monarchinitiative.lirical.core.analysis with parameters of type AnalysisData

Modifier and Type	Method	Description
AnalysisResults	LiricalAnalysisRunner.run(AnalysisData analysisData, AnalysisOptions analysisOptions)	Run analysis parametrized by analysisOptions on analysisData.

Uses of AnalysisData in org.monarchinitiative.lirical.core.analysis.impl

Methods in org.monarchinitiative.lirical.core.analysis.impl with parameters of type AnalysisData

Modifier and Type	Method	Description
AnalysisResults	LiricalAnalysisRunnerImpl.run(AnalysisData data, AnalysisOptions options)

Uses of AnalysisData in org.monarchinitiative.lirical.core.output

Methods in org.monarchinitiative.lirical.core.output with parameters of type AnalysisData

Modifier and Type	Method	Description
void	AnalysisResultsWriter.process(AnalysisData analysisData, AnalysisResults analysisResults, AnalysisResultsMetadata metadata, OutputOptions outputOptions)	Write the provided AnalysisData, AnalysisResults and AnalysisResultsMetadata into some OutputFormat as guided by OutputOptions.

Uses of AnalysisData in org.monarchinitiative.lirical.io.output

Methods in org.monarchinitiative.lirical.io.output with parameters of type AnalysisData

Modifier and Type	Method	Description
void	JsonAnalysisResultWriter.process(AnalysisData analysisData, AnalysisResults analysisResults, AnalysisResultsMetadata metadata, OutputOptions outputOptions)
void	TemplateBasedAnalysisResultsWriter.process(AnalysisData analysisData, AnalysisResults analysisResults, AnalysisResultsMetadata metadata, OutputOptions options)

Constructors in org.monarchinitiative.lirical.io.output with parameters of type AnalysisData

Modifier	Constructor	Description
protected	LiricalTemplate(org.monarchinitiative.phenol.ontology.data.MinimalOntology hpo, AnalysisData analysisData, AnalysisResultsMetadata resultsMetadata, OutputOptions outputOptions)