Package org.monarchinitiative.lirical.core.analysis.impl

Class LiricalAnalysisRunnerImpl

java.lang.Object

org.monarchinitiative.lirical.core.analysis.impl.LiricalAnalysisRunnerImpl

All Implemented Interfaces:

Closeable, AutoCloseable, LiricalAnalysisRunner

public class LiricalAnalysisRunnerImpl
extends Object
implements LiricalAnalysisRunner

Method Summary

Modifier and Type	Method	Description
void	close()
static LiricalAnalysisRunnerImpl	of(PhenotypeService phenotypeService, BackgroundVariantFrequencyServiceFactory backgroundVariantFrequencyServiceFactory, int parallelism)
AnalysisResults	run(AnalysisData data, AnalysisOptions options)	Run analysis parametrized by analysisOptions on analysisData.

Methods inherited from class java.lang.Object

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

Method Details

of

public static LiricalAnalysisRunnerImpl of(PhenotypeService phenotypeService,
 BackgroundVariantFrequencyServiceFactory backgroundVariantFrequencyServiceFactory,
 int parallelism)

run

public AnalysisResults run(AnalysisData data,
 AnalysisOptions options)
                    throws LiricalAnalysisException

Description copied from interface: LiricalAnalysisRunner

Run analysis parametrized by analysisOptions on analysisData.

Specified by:

run in interface LiricalAnalysisRunner

Parameters:

data - data representing the analysis subject.

options - analysis parameters.

Returns:

a container with results for each evaluated disease

Throws:

LiricalAnalysisException - if the analysis cannot be run, e.g. due to missing resource, such as FunctionalVariantAnnotator for a combination of GenomeBuild and TranscriptDatabase

close

public void close()

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable