Hierarchy For All Packages

Package Hierarchies:

• org.monarchinitiative.exomiser.core.proto,
• org.monarchinitiative.lirical.background,
• org.monarchinitiative.lirical.background.backgroundfrequency,
• org.monarchinitiative.lirical.cli,
• org.monarchinitiative.lirical.cli.cmd,
• org.monarchinitiative.lirical.cli.cmd.experimental,
• org.monarchinitiative.lirical.cli.cmd.util,
• org.monarchinitiative.lirical.cli.yaml,
• org.monarchinitiative.lirical.configuration,
• org.monarchinitiative.lirical.configuration.impl,
• org.monarchinitiative.lirical.core,
• org.monarchinitiative.lirical.core.analysis,
• org.monarchinitiative.lirical.core.analysis.impl,
• org.monarchinitiative.lirical.core.analysis.probability,
• org.monarchinitiative.lirical.core.exception,
• org.monarchinitiative.lirical.core.io,
• org.monarchinitiative.lirical.core.likelihoodratio,
• org.monarchinitiative.lirical.core.likelihoodratio.poisson,
• org.monarchinitiative.lirical.core.model,
• org.monarchinitiative.lirical.core.output,
• org.monarchinitiative.lirical.core.sanitize,
• org.monarchinitiative.lirical.core.service,
• org.monarchinitiative.lirical.core.util,
• org.monarchinitiative.lirical.exomiser_db_adapter,
• org.monarchinitiative.lirical.exomiser_db_adapter.model,
• org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency,
• org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity,
• org.monarchinitiative.lirical.exomiser_db_adapter.serializers,
• org.monarchinitiative.lirical.io,
• org.monarchinitiative.lirical.io.analysis,
• org.monarchinitiative.lirical.io.background,
• org.monarchinitiative.lirical.io.output,
• org.monarchinitiative.lirical.io.output.svg,
• org.monarchinitiative.lirical.io.service,
• org.monarchinitiative.lirical.io.vcf

Class Hierarchy

• java.lang.Object
  • com.google.protobuf.AbstractMessageLite<MessageType,BuilderType> (implements com.google.protobuf.MessageLite)
    • com.google.protobuf.AbstractMessage (implements com.google.protobuf.Message)
      • com.google.protobuf.GeneratedMessageV3 (implements java.io.Serializable)
        • org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey (implements org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKeyOrBuilder)
        • org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties (implements org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder)
        • org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar (implements org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder)
  • com.google.protobuf.AbstractMessageLite.Builder<MessageType,BuilderType> (implements com.google.protobuf.MessageLite.Builder)
    • com.google.protobuf.AbstractMessage.Builder<BuilderType> (implements com.google.protobuf.Message.Builder)
      • com.google.protobuf.GeneratedMessageV3.Builder<BuilderType>
        • org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKey.Builder (implements org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKeyOrBuilder)
        • org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleProperties.Builder (implements org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder)
        • org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.Builder (implements org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder)
  • org.monarchinitiative.lirical.core.model.Age
  • org.monarchinitiative.lirical.core.model.AlleleCount
  • org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AlleleKeyDataType (implements org.h2.mvstore.type.DataType)
  • org.monarchinitiative.lirical.exomiser_db_adapter.serializers.AllelePropertiesDataType (implements org.h2.mvstore.type.DataType)
  • org.monarchinitiative.exomiser.core.proto.AlleleProto
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.AlleleProtoAdaptor
  • org.monarchinitiative.lirical.core.analysis.AnalysisOptions.Builder
  • org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata
  • org.monarchinitiative.lirical.core.output.AnalysisResultsMetadata.Builder
  • org.monarchinitiative.lirical.background.BackgroundFrequencyCommand (implements java.util.concurrent.Callable<V>)
  • org.monarchinitiative.lirical.io.background.BackgroundVariantFrequencyParser
  • org.monarchinitiative.lirical.cli.cmd.BenchmarkCommand
  • org.monarchinitiative.lirical.core.util.BinarySearch
  • org.monarchinitiative.lirical.configuration.impl.BundledBackgroundVariantFrequencyServiceFactory (implements org.monarchinitiative.lirical.core.service.BackgroundVariantFrequencyServiceFactory)
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.CaddScore
  • org.monarchinitiative.lirical.core.model.ClinVarAlleleData
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.Builder
  • org.monarchinitiative.lirical.io.background.CustomBackgroundVariantFrequencyServiceFactory (implements org.monarchinitiative.lirical.core.service.BackgroundVariantFrequencyServiceFactory)
  • org.monarchinitiative.lirical.io.output.DifferentialDiagnosis
  • org.monarchinitiative.lirical.cli.cmd.DownloadCommand
  • org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserMvStoreMetadataServiceFactory (implements org.monarchinitiative.lirical.core.service.VariantMetadataServiceFactory)
  • org.monarchinitiative.lirical.cli.cmd.experimental.ExperimentalCommand (implements java.util.concurrent.Callable<V>)
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.Frequency
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencyData
  • org.monarchinitiative.lirical.background.backgroundfrequency.GenicIntoleranceCalculator
  • org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLikelihoodRatio
  • org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLikelihoodRatio.Options
  • org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrWithExplanation
  • org.monarchinitiative.lirical.core.service.HpoTermSanitizer
  • org.monarchinitiative.lirical.io.output.ImprobableDifferential
  • org.monarchinitiative.lirical.core.likelihoodratio.InducedDiseaseGraph
  • org.monarchinitiative.lirical.core.sanitize.InputSanitizerFactory
  • org.monarchinitiative.lirical.io.service.JannovarFunctionalVariantAnnotator (implements org.monarchinitiative.lirical.core.service.FunctionalVariantAnnotator)
  • org.monarchinitiative.lirical.io.service.JannovarFunctionalVariantAnnotatorService (implements org.monarchinitiative.lirical.core.service.FunctionalVariantAnnotatorService)
  • org.monarchinitiative.lirical.io.output.JsonAnalysisResultWriter (implements org.monarchinitiative.lirical.core.output.AnalysisResultsWriter)
  • org.monarchinitiative.lirical.core.Lirical
  • org.monarchinitiative.lirical.io.output.svg.Lirical2Svg
    • org.monarchinitiative.lirical.io.output.svg.Lr2Svg
    • org.monarchinitiative.lirical.io.output.svg.Posttest2Svg
    • org.monarchinitiative.lirical.io.output.svg.Sparkline2Svg
  • org.monarchinitiative.lirical.core.analysis.impl.LiricalAnalysisRunnerImpl (implements org.monarchinitiative.lirical.core.analysis.LiricalAnalysisRunner)
  • org.monarchinitiative.lirical.configuration.LiricalBuilder
  • org.monarchinitiative.lirical.io.LiricalDataResolver
  • org.monarchinitiative.lirical.core.LiricalOptions
  • org.monarchinitiative.lirical.io.output.LiricalTemplate
    • org.monarchinitiative.lirical.io.output.HtmlTemplate
    • org.monarchinitiative.lirical.io.output.TsvTemplate
  • org.monarchinitiative.lirical.core.output.LrThreshold
  • org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanation (implements java.lang.Comparable<T>)
  • org.monarchinitiative.lirical.core.likelihoodratio.LrWithExplanationFactory
  • org.monarchinitiative.lirical.background.Main (implements java.util.concurrent.Callable<V>)
  • org.monarchinitiative.lirical.cli.Main (implements java.util.concurrent.Callable<V>)
  • org.monarchinitiative.lirical.core.output.MinDiagnosisCount
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MpcScore
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.MutationTasterScore
  • org.monarchinitiative.lirical.exomiser_db_adapter.MvStoreUtil
  • org.monarchinitiative.lirical.core.service.NoOpVariantMetadataService (implements org.monarchinitiative.lirical.core.service.VariantMetadataService)
  • org.monarchinitiative.lirical.cli.cmd.OutputCommand
    • org.monarchinitiative.lirical.cli.cmd.PhenopacketCommand
    • org.monarchinitiative.lirical.cli.cmd.experimental.PhenopacketsCommand
    • org.monarchinitiative.lirical.cli.cmd.PrioritizeCommand
    • org.monarchinitiative.lirical.cli.cmd.YamlCommand
  • org.monarchinitiative.lirical.cli.cmd.OutputCommand.Output
  • org.monarchinitiative.lirical.core.output.OutputOptions
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityData
  • org.monarchinitiative.lirical.io.analysis.PhenopacketData (implements org.monarchinitiative.lirical.core.sanitize.SanitationInputs)
  • org.monarchinitiative.lirical.io.analysis.PhenopacketImporters
  • org.monarchinitiative.lirical.cli.cmd.PhenopacketUtil
  • org.monarchinitiative.lirical.core.likelihoodratio.PhenotypeLikelihoodRatio
  • org.monarchinitiative.lirical.core.likelihoodratio.poisson.PoissonDistribution
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PolyPhenScore
  • org.monarchinitiative.lirical.core.analysis.probability.PretestDiseaseProbabilities
  • org.monarchinitiative.lirical.core.analysis.ProgressReporter
  • java.lang.Record
    • org.monarchinitiative.lirical.core.model.FilteringStats
    • org.monarchinitiative.lirical.core.sanitize.SanityIssue
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.RemmScore
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.RsId
  • org.monarchinitiative.lirical.core.model.SampleAlleleCount
  • org.monarchinitiative.lirical.core.sanitize.SanitizedInputs
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.SiftScore
  • org.monarchinitiative.lirical.io.output.SparklinePacket
  • org.monarchinitiative.lirical.io.output.TemplateBasedAnalysisResultsWriter (implements org.monarchinitiative.lirical.core.output.AnalysisResultsWriter)
  • org.monarchinitiative.lirical.core.analysis.TestResult (implements java.lang.Comparable<T>)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.monarchinitiative.lirical.core.exception.LiricalException
        • org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResourceException
        • org.monarchinitiative.lirical.core.analysis.LiricalAnalysisException
        • org.monarchinitiative.lirical.io.LiricalDataException
        • org.monarchinitiative.lirical.core.analysis.LiricalParseException
          • org.monarchinitiative.lirical.io.analysis.PhenopacketImportException
        • org.monarchinitiative.lirical.core.exception.LiricalTermFrequencyException
      • java.lang.RuntimeException
        • org.monarchinitiative.lirical.core.exception.LiricalRuntimeException
          • org.monarchinitiative.lirical.exomiser_db_adapter.ExomiserResourceRuntimeException
            • org.monarchinitiative.lirical.exomiser_db_adapter.serializers.InvalidAlleleProtoException
  • org.monarchinitiative.lirical.io.output.TsvDifferential
  • org.monarchinitiative.lirical.cli.cmd.util.Util
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.VariantEffectPathogenicityScore
  • org.monarchinitiative.lirical.core.service.VariantPathogenicity
  • org.monarchinitiative.lirical.io.vcf.VcfGenotypedVariantParser (implements org.monarchinitiative.lirical.core.io.GenotypedVariantParser)
  • org.monarchinitiative.lirical.io.vcf.VcfVariantParserFactory (implements org.monarchinitiative.lirical.core.io.VariantParserFactory)
  • org.monarchinitiative.lirical.cli.yaml.YamlConfig (implements org.monarchinitiative.lirical.core.sanitize.SanitationInputs)
  • org.monarchinitiative.lirical.cli.yaml.YamlParser

Interface Hierarchy

• org.monarchinitiative.lirical.core.analysis.AnalysisData
• org.monarchinitiative.lirical.core.analysis.AnalysisOptions
• org.monarchinitiative.lirical.core.output.AnalysisResultsWriter
• org.monarchinitiative.lirical.core.output.AnalysisResultWriterFactory
• java.lang.AutoCloseable
  • java.io.Closeable
    • org.monarchinitiative.lirical.core.analysis.LiricalAnalysisRunner
  • org.monarchinitiative.lirical.core.io.VariantParser (also extends java.lang.Iterable<T>)
• org.monarchinitiative.lirical.core.service.BackgroundVariantFrequencyService
• org.monarchinitiative.lirical.core.service.BackgroundVariantFrequencyServiceFactory
• java.lang.Comparable<T>
  • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicityScore
• org.monarchinitiative.lirical.core.model.FunctionalAnnotationAware
  • org.monarchinitiative.lirical.core.model.LiricalVariant (also extends org.monarchinitiative.lirical.core.model.GenotypedVariant, org.monarchinitiative.lirical.core.model.VariantMetadata)
• org.monarchinitiative.lirical.core.service.FunctionalVariantAnnotator
• org.monarchinitiative.lirical.core.service.FunctionalVariantAnnotatorService
• org.monarchinitiative.lirical.core.model.Gene2Genotype
• org.monarchinitiative.lirical.core.model.GenotypedVariant
  • org.monarchinitiative.lirical.core.model.LiricalVariant (also extends org.monarchinitiative.lirical.core.model.FunctionalAnnotationAware, org.monarchinitiative.lirical.core.model.VariantMetadata)
• org.monarchinitiative.lirical.core.sanitize.InputSanitizer
• java.lang.Iterable<T>
  • org.monarchinitiative.lirical.core.analysis.AnalysisResults
  • org.monarchinitiative.lirical.core.model.GenesAndGenotypes
  • org.monarchinitiative.lirical.core.io.GenotypedVariantParser
  • org.monarchinitiative.lirical.core.io.VariantParser (also extends java.lang.AutoCloseable)
• com.google.protobuf.MessageLiteOrBuilder
  • com.google.protobuf.MessageOrBuilder
    • org.monarchinitiative.exomiser.core.proto.AlleleProto.AlleleKeyOrBuilder
    • org.monarchinitiative.exomiser.core.proto.AlleleProto.AllelePropertiesOrBuilder
    • org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVarOrBuilder
• org.monarchinitiative.lirical.io.analysis.PhenopacketImporter
• org.monarchinitiative.lirical.core.service.PhenotypeService
• org.monarchinitiative.lirical.core.analysis.probability.PretestDiseaseProbability
• org.monarchinitiative.lirical.core.sanitize.SanitationInputs
• org.monarchinitiative.lirical.core.sanitize.SanitationResult
• org.monarchinitiative.lirical.core.model.TranscriptAnnotation
• org.monarchinitiative.lirical.core.model.VariantMetadata
  • org.monarchinitiative.lirical.core.model.LiricalVariant (also extends org.monarchinitiative.lirical.core.model.FunctionalAnnotationAware, org.monarchinitiative.lirical.core.model.GenotypedVariant)
• org.monarchinitiative.lirical.core.service.VariantMetadataService
• org.monarchinitiative.lirical.core.service.VariantMetadataServiceFactory
• org.monarchinitiative.lirical.core.io.VariantParserFactory
• org.monarchinitiative.lirical.io.output.VisualizableVariant

Enum Class Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
    • org.monarchinitiative.exomiser.core.proto.AlleleProto.ClinVar.ClinSig (implements com.google.protobuf.ProtocolMessageEnum)
    • org.monarchinitiative.lirical.core.model.ClinvarClnSig
    • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.ClinVarData.ClinSig
    • org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
    • org.monarchinitiative.lirical.core.model.GenomeBuild
    • org.monarchinitiative.lirical.core.likelihoodratio.GenotypeLrMatchType
    • org.monarchinitiative.lirical.core.likelihoodratio.LrMatchType
    • org.monarchinitiative.lirical.core.output.OutputFormat
    • org.monarchinitiative.lirical.exomiser_db_adapter.model.pathogenicity.PathogenicitySource
    • org.monarchinitiative.lirical.core.sanitize.SanitizerType
    • org.monarchinitiative.lirical.core.sanitize.SanityLevel
    • org.monarchinitiative.lirical.core.model.Sex
    • org.monarchinitiative.lirical.core.model.TranscriptDatabase
    • org.monarchinitiative.lirical.cli.cmd.ValidationPolicy