Hierarchy For All Packages

Package Hierarchies:

• de.charite.compbio.jannovar,
• de.charite.compbio.jannovar.annotation,
• de.charite.compbio.jannovar.annotation.builders,
• de.charite.compbio.jannovar.cmd,
• de.charite.compbio.jannovar.cmd.annotate_pos,
• de.charite.compbio.jannovar.cmd.annotate_vcf,
• de.charite.compbio.jannovar.cmd.db_list,
• de.charite.compbio.jannovar.cmd.download,
• de.charite.compbio.jannovar.data,
• de.charite.compbio.jannovar.datasource,
• de.charite.compbio.jannovar.hgvs,
• de.charite.compbio.jannovar.hgvs.bridge,
• de.charite.compbio.jannovar.hgvs.legacy,
• de.charite.compbio.jannovar.hgvs.nts,
• de.charite.compbio.jannovar.hgvs.nts.change,
• de.charite.compbio.jannovar.hgvs.nts.variant,
• de.charite.compbio.jannovar.hgvs.parser,
• de.charite.compbio.jannovar.hgvs.protein,
• de.charite.compbio.jannovar.hgvs.protein.change,
• de.charite.compbio.jannovar.hgvs.protein.variant,
• de.charite.compbio.jannovar.htsjdk,
• de.charite.compbio.jannovar.impl.intervals,
• de.charite.compbio.jannovar.impl.parse,
• de.charite.compbio.jannovar.impl.parse.ensembl,
• de.charite.compbio.jannovar.impl.parse.flatbed,
• de.charite.compbio.jannovar.impl.parse.gtfgff,
• de.charite.compbio.jannovar.impl.parse.refseq,
• de.charite.compbio.jannovar.impl.parse.ucsc,
• de.charite.compbio.jannovar.impl.util,
• de.charite.compbio.jannovar.mendel,
• de.charite.compbio.jannovar.mendel.bridge,
• de.charite.compbio.jannovar.mendel.filter,
• de.charite.compbio.jannovar.mendel.impl,
• de.charite.compbio.jannovar.pedigree,
• de.charite.compbio.jannovar.pedigree.compatibilitychecker,
• de.charite.compbio.jannovar.pedigree.compatibilitychecker.ad,
• de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar,
• de.charite.compbio.jannovar.pedigree.compatibilitychecker.xd,
• de.charite.compbio.jannovar.pedigree.compatibilitychecker.xr,
• de.charite.compbio.jannovar.progress,
• de.charite.compbio.jannovar.reference,
• de.charite.compbio.jannovar.vardbs.base,
• de.charite.compbio.jannovar.vardbs.dbsnp,
• de.charite.compbio.jannovar.vardbs.exac,
• de.charite.compbio.jannovar.vardbs.facade,
• de.charite.compbio.jannovar.vardbs.uk10k

Class Hierarchy

• java.lang.Object
  • de.charite.compbio.jannovar.vardbs.base.AbstractDBAnnotationDriver<RecordType> (implements de.charite.compbio.jannovar.vardbs.base.DBAnnotationDriver)
    • de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPAnnotationDriver
    • de.charite.compbio.jannovar.vardbs.exac.ExacAnnotationDriver
    • de.charite.compbio.jannovar.vardbs.uk10k.UK10KAnnotationDriver
  • de.charite.compbio.jannovar.mendel.impl.AbstractMendelianChecker
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerAD
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerAR
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARCompoundHet
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARHom
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXD
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXR
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXRCompoundHet
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXRHom
  • de.charite.compbio.jannovar.pedigree.compatibilitychecker.AbstractVariantContextCompatibilityChecker (implements de.charite.compbio.jannovar.pedigree.compatibilitychecker.InterfaceVariantContextCompatibilityChecker)
    • de.charite.compbio.jannovar.pedigree.compatibilitychecker.ad.VariantContextCompatibilityCheckerAutosomalDominant
    • de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessive
    • de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessiveCompoundHet
    • de.charite.compbio.jannovar.pedigree.compatibilitychecker.ar.VariantContextCompatibilityCheckerAutosomalRecessiveHomozygous
    • de.charite.compbio.jannovar.pedigree.compatibilitychecker.xd.VariantContextCompatibilityCheckerXDominant
    • de.charite.compbio.jannovar.pedigree.compatibilitychecker.xr.VariantContextCompatibilityCheckerXRecessive
  • de.charite.compbio.jannovar.vardbs.base.AlleleMatcher
  • de.charite.compbio.jannovar.reference.AminoAcidChange
  • de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer
  • de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVariantWriter (implements java.io.Closeable)
    • de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotatedVCFWriter
  • de.charite.compbio.jannovar.vardbs.base.AnnotatingRecord<RecordType>
  • de.charite.compbio.jannovar.annotation.Annotation (implements java.lang.Comparable<T>, de.charite.compbio.jannovar.reference.VariantDescription)
  • de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderDispatcher
  • de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderOptions
  • de.charite.compbio.jannovar.annotation.AnnotationLocation
  • de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder
  • de.charite.compbio.jannovar.annotation.AnnotationTextGenerator
  • Antlr4HGVSLexer
    • de.charite.compbio.jannovar.hgvs.parser.HGVSLexer
  • de.charite.compbio.jannovar.annotation.builders.BlockSubstitutionAnnotationBuilder
  • de.charite.compbio.jannovar.reference.CDSInterval
  • de.charite.compbio.jannovar.reference.CDSPosition
  • de.charite.compbio.jannovar.data.Chromosome (implements java.io.Serializable)
  • de.charite.compbio.jannovar.mendel.filter.ConsumerProcessor (implements de.charite.compbio.jannovar.mendel.filter.VariantContextProcessor)
  • de.charite.compbio.jannovar.mendel.filter.CoordinateSortingChecker (implements de.charite.compbio.jannovar.mendel.filter.VariantContextProcessor)
  • de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommandLineParser
  • de.charite.compbio.jannovar.datasource.DataSource
    • de.charite.compbio.jannovar.datasource.FlatBEDDataSource
  • de.charite.compbio.jannovar.datasource.DataSourceFactory
  • de.charite.compbio.jannovar.datasource.DatasourceOptions
  • de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions
  • de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPGeneInfo
  • de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfo
  • de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPInfoFactory
  • de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecord
  • de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPRecordBuilder
  • de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVariantProperty
  • de.charite.compbio.jannovar.vardbs.facade.DBVariantContextAnnotator
  • de.charite.compbio.jannovar.vardbs.facade.DBVariantContextAnnotatorFactory
  • org.antlr.v4.runtime.DefaultErrorStrategy (implements org.antlr.v4.runtime.ANTLRErrorStrategy)
    • de.charite.compbio.jannovar.hgvs.parser.HGVSErrorStrategy
  • de.charite.compbio.jannovar.annotation.builders.DeletionAnnotationBuilder
  • de.charite.compbio.jannovar.impl.util.DNAUtils
  • de.charite.compbio.jannovar.cmd.download.DownloadCommandLineParser
  • de.charite.compbio.jannovar.reference.DuplicationChecker
  • de.charite.compbio.jannovar.impl.parse.ensembl.EnsemblParser (implements de.charite.compbio.jannovar.impl.parse.TranscriptParser)
  • de.charite.compbio.jannovar.vardbs.exac.ExacRecord
  • de.charite.compbio.jannovar.vardbs.exac.ExacRecordBuilder
  • de.charite.compbio.jannovar.impl.parse.FASTAParser
  • de.charite.compbio.jannovar.impl.parse.FASTARecord
  • de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord (implements java.lang.Comparable<T>)
  • de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecordParser
    • de.charite.compbio.jannovar.impl.parse.gtfgff.GFFRecordParser
    • de.charite.compbio.jannovar.impl.parse.gtfgff.GTFRecordParser
  • de.charite.compbio.jannovar.impl.parse.flatbed.FlatBEDFastaParser
  • de.charite.compbio.jannovar.impl.parse.flatbed.FlatBEDParser (implements de.charite.compbio.jannovar.impl.parse.TranscriptParser)
  • de.charite.compbio.jannovar.mendel.filter.GeneWiseMendelianAnnotationProcessor (implements de.charite.compbio.jannovar.mendel.filter.VariantContextProcessor)
  • de.charite.compbio.jannovar.reference.GenomeInterval (implements java.lang.Comparable<T>, java.io.Serializable)
  • de.charite.compbio.jannovar.reference.GenomePosition (implements java.lang.Comparable<T>, java.io.Serializable)
  • de.charite.compbio.jannovar.progress.GenomeRegion
  • de.charite.compbio.jannovar.progress.GenomeRegionList
  • de.charite.compbio.jannovar.progress.GenomeRegionListFactoryFromSAMSequenceDictionary
  • de.charite.compbio.jannovar.htsjdk.GenomeRegionSequenceExtractor
  • de.charite.compbio.jannovar.reference.GenomeVariant (implements de.charite.compbio.jannovar.reference.VariantDescription)
  • de.charite.compbio.jannovar.reference.GenomeVariantNormalizer
  • de.charite.compbio.jannovar.annotation.builders.GenomicNucleotideChangeBuilder
  • de.charite.compbio.jannovar.mendel.Genotype
  • de.charite.compbio.jannovar.mendel.GenotypeBuilder
  • de.charite.compbio.jannovar.mendel.GenotypeCalls (implements java.lang.Iterable<T>)
  • de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder
  • de.charite.compbio.jannovar.pedigree.GenotypeList
  • de.charite.compbio.jannovar.pedigree.GenotypeListBuilder
  • de.charite.compbio.jannovar.vardbs.base.GenotypeMatch
  • de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser
  • de.charite.compbio.jannovar.reference.HG19RefDictBuilder
  • de.charite.compbio.jannovar.hgvs.parser.HGVSParser
  • de.charite.compbio.jannovar.hgvs.HGVSVariant (implements de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString)
    • de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideVariant
      • de.charite.compbio.jannovar.hgvs.nts.variant.MultiAlleleNucleotideVariant
      • de.charite.compbio.jannovar.hgvs.nts.variant.SingleAlleleNucleotideVariant
    • de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant
      • de.charite.compbio.jannovar.hgvs.protein.variant.MultiAlleleProteinVariant
      • de.charite.compbio.jannovar.hgvs.protein.variant.SingleAlleleProteinVariant
  • de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker
  • de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityChecker.Builder
  • de.charite.compbio.jannovar.pedigree.InheritanceVariantContextList
  • de.charite.compbio.jannovar.annotation.builders.InsertionAnnotationBuilder
  • de.charite.compbio.jannovar.impl.intervals.Interval<T> (implements java.lang.Comparable<T>, java.io.Serializable)
  • de.charite.compbio.jannovar.impl.intervals.IntervalArray<T> (implements java.io.Serializable)
  • de.charite.compbio.jannovar.impl.intervals.IntervalArray.QueryResult
  • de.charite.compbio.jannovar.Jannovar
  • de.charite.compbio.jannovar.cmd.JannovarAnnotationCommandLineParser
    • de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommandLineParser
    • de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommandLineParser
  • de.charite.compbio.jannovar.cmd.JannovarCommand
    • de.charite.compbio.jannovar.cmd.db_list.DatabaseListCommand
    • de.charite.compbio.jannovar.cmd.download.DownloadCommand
    • de.charite.compbio.jannovar.cmd.JannovarAnnotationCommand
      • de.charite.compbio.jannovar.cmd.annotate_pos.AnnotatePositionCommand
      • de.charite.compbio.jannovar.cmd.annotate_vcf.AnnotateVCFCommand
  • de.charite.compbio.jannovar.data.JannovarData (implements java.io.Serializable)
  • de.charite.compbio.jannovar.datasource.JannovarDataFactory
    • de.charite.compbio.jannovar.datasource.FlatBEDJannovarDataFactory
  • de.charite.compbio.jannovar.data.JannovarDataSerializer
  • de.charite.compbio.jannovar.JannovarOptions
  • de.charite.compbio.jannovar.hgvs.legacy.LegacyChange
    • de.charite.compbio.jannovar.hgvs.legacy.LegacyDeletion
    • de.charite.compbio.jannovar.hgvs.legacy.LegacyIndel
    • de.charite.compbio.jannovar.hgvs.legacy.LegacyInsertion
    • de.charite.compbio.jannovar.hgvs.legacy.LegacySubstitution
  • de.charite.compbio.jannovar.hgvs.parser.LegacyChangeParser
  • de.charite.compbio.jannovar.hgvs.legacy.LegacyLocation
  • de.charite.compbio.jannovar.hgvs.legacy.LegacyVariant
  • de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker
  • de.charite.compbio.jannovar.mendel.bridge.MendelVCFHeaderExtender
  • de.charite.compbio.jannovar.impl.intervals.MutableInterval<T> (implements java.lang.Comparable<T>, java.io.Serializable)
  • de.charite.compbio.jannovar.hgvs.nts.change.NucleotideChange (implements de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString)
    • de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDeletion
    • de.charite.compbio.jannovar.hgvs.nts.change.NucleotideDuplication
    • de.charite.compbio.jannovar.hgvs.nts.change.NucleotideIndel
    • de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInsertion
    • de.charite.compbio.jannovar.hgvs.nts.change.NucleotideInversion
    • de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChange
    • de.charite.compbio.jannovar.hgvs.nts.change.NucleotideShortSequenceRepeatVariability
    • de.charite.compbio.jannovar.hgvs.nts.change.NucleotideSubstitution
  • de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele (implements de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString, java.util.List<E>)
  • de.charite.compbio.jannovar.hgvs.bridge.NucleotideChangeToGenomeVariantTranslationImplBase
  • de.charite.compbio.jannovar.hgvs.bridge.NucleotideChangeToGenomeVariantTranslator
  • de.charite.compbio.jannovar.hgvs.bridge.NucleotideLocationConverter
  • de.charite.compbio.jannovar.hgvs.nts.NucleotidePointLocation (implements de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString)
  • de.charite.compbio.jannovar.reference.NucleotidePointLocationBuilder
  • de.charite.compbio.jannovar.hgvs.nts.NucleotideRange (implements de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString)
  • de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription (implements de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString)
  • de.charite.compbio.jannovar.impl.util.PathUtil
  • de.charite.compbio.jannovar.pedigree.PedFileContents
  • de.charite.compbio.jannovar.pedigree.PedFileReader
  • de.charite.compbio.jannovar.pedigree.PedFileWriter
  • de.charite.compbio.jannovar.pedigree.Pedigree
  • de.charite.compbio.jannovar.pedigree.Pedigree.IndexedPerson
  • de.charite.compbio.jannovar.pedigree.PedigreeExtractor
  • de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator
  • de.charite.compbio.jannovar.pedigree.PedPerson
  • de.charite.compbio.jannovar.pedigree.Person
  • de.charite.compbio.jannovar.impl.util.ProgressBar
  • de.charite.compbio.jannovar.hgvs.protein.change.ProteinChange (implements de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString)
    • de.charite.compbio.jannovar.hgvs.protein.change.ProteinDeletion
    • de.charite.compbio.jannovar.hgvs.protein.change.ProteinDuplication
    • de.charite.compbio.jannovar.hgvs.protein.change.ProteinExtension
    • de.charite.compbio.jannovar.hgvs.protein.change.ProteinFrameshift
    • de.charite.compbio.jannovar.hgvs.protein.change.ProteinIndel
    • de.charite.compbio.jannovar.hgvs.protein.change.ProteinInsertion
    • de.charite.compbio.jannovar.hgvs.protein.change.ProteinMiscChange
    • de.charite.compbio.jannovar.hgvs.protein.change.ProteinShortSequenceRepeatVariability
    • de.charite.compbio.jannovar.hgvs.protein.change.ProteinSubstitution
  • de.charite.compbio.jannovar.hgvs.protein.variant.ProteinChangeAllele (implements de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString, java.util.List<E>)
  • de.charite.compbio.jannovar.hgvs.protein.ProteinPointLocation (implements de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString)
  • de.charite.compbio.jannovar.hgvs.protein.ProteinRange (implements de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString)
  • de.charite.compbio.jannovar.hgvs.protein.ProteinSeqDescription (implements de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString)
  • de.charite.compbio.jannovar.data.ReferenceDictionary (implements java.io.Serializable)
  • de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder
  • de.charite.compbio.jannovar.impl.parse.ReferenceDictParser
  • de.charite.compbio.jannovar.impl.parse.refseq.RefSeqParser (implements de.charite.compbio.jannovar.impl.parse.TranscriptParser)
  • de.charite.compbio.jannovar.annotation.builders.SNVAnnotationBuilder
  • de.charite.compbio.jannovar.impl.util.StringUtil
  • de.charite.compbio.jannovar.annotation.builders.StructuralVariantAnnotationBuilder
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • de.charite.compbio.jannovar.hgvs.bridge.CannotTranslateHGVSVariant
      • de.charite.compbio.jannovar.htsjdk.InvalidCoordinatesException
      • java.io.IOException
        • de.charite.compbio.jannovar.impl.parse.InvalidAttributeException
      • de.charite.compbio.jannovar.JannovarException
        • de.charite.compbio.jannovar.annotation.AnnotationException
          • de.charite.compbio.jannovar.annotation.InvalidGenomeVariant
        • de.charite.compbio.jannovar.mendel.bridge.CannotAnnotateMendelianInheritance
        • de.charite.compbio.jannovar.cmd.CommandLineParsingException
        • de.charite.compbio.jannovar.datasource.FileDownloadException
        • de.charite.compbio.jannovar.cmd.HelpRequestedException
        • de.charite.compbio.jannovar.mendel.IncompatiblePedigreeException
        • de.charite.compbio.jannovar.pedigree.compatibilitychecker.InheritanceCompatibilityCheckerException
        • de.charite.compbio.jannovar.reference.InvalidCodonException
        • de.charite.compbio.jannovar.datasource.InvalidDataSourceException
        • de.charite.compbio.jannovar.vardbs.base.JannovarVarDBException
        • de.charite.compbio.jannovar.pedigree.PedParseException
        • de.charite.compbio.jannovar.reference.ProjectionException
        • de.charite.compbio.jannovar.data.SerializationException
        • de.charite.compbio.jannovar.impl.parse.TranscriptParseException
      • java.lang.RuntimeException
        • de.charite.compbio.jannovar.hgvs.parser.HGVSParsingException
        • de.charite.compbio.jannovar.reference.InvalidCoordinateException
        • de.charite.compbio.jannovar.UncheckedJannovarException
          • de.charite.compbio.jannovar.mendel.filter.VariantContextFilterException
  • java.util.TimerTask (implements java.lang.Runnable)
    • de.charite.compbio.jannovar.progress.ProgressReporter
  • de.charite.compbio.jannovar.reference.TranscriptInterval
  • de.charite.compbio.jannovar.reference.TranscriptIntervalEndExtractor (implements de.charite.compbio.jannovar.impl.intervals.IntervalEndExtractor<T>)
  • de.charite.compbio.jannovar.reference.TranscriptModel (implements java.lang.Comparable<T>, java.io.Serializable)
  • de.charite.compbio.jannovar.reference.TranscriptModelBuilder
  • de.charite.compbio.jannovar.reference.TranscriptPosition
  • de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator
  • de.charite.compbio.jannovar.reference.TranscriptSequenceChangeHelper
  • de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator
  • de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator
  • de.charite.compbio.jannovar.impl.parse.TranscriptSupportLevelsSetterFromLengths
  • de.charite.compbio.jannovar.hgvs.Translator
  • de.charite.compbio.jannovar.impl.util.Translator
  • de.charite.compbio.jannovar.impl.parse.ucsc.UCSCParser (implements de.charite.compbio.jannovar.impl.parse.TranscriptParser)
  • de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecord
  • de.charite.compbio.jannovar.vardbs.uk10k.UK10KRecordBuilder
  • de.charite.compbio.jannovar.annotation.VariantAnnotations (implements de.charite.compbio.jannovar.reference.VariantDescription)
  • de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator
  • de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator
    • de.charite.compbio.jannovar.annotation.AllAnnotationListTextGenerator
    • de.charite.compbio.jannovar.annotation.BestAnnotationListTextGenerator
  • de.charite.compbio.jannovar.annotation.VariantAnnotator
  • htsjdk.variant.variantcontext.VariantContext (implements htsjdk.tribble.Feature, java.io.Serializable)
    • de.charite.compbio.jannovar.pedigree.InheritanceVariantContext
  • de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator
  • de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options
  • de.charite.compbio.jannovar.mendel.filter.VariantContextCounter
  • de.charite.compbio.jannovar.mendel.bridge.VariantContextMendelianAnnotator
  • de.charite.compbio.jannovar.htsjdk.VariantContextWriterConstructionHelper
  • de.charite.compbio.jannovar.vardbs.base.VariantDescription
  • de.charite.compbio.jannovar.vardbs.base.VariantNormalizer
  • de.charite.compbio.jannovar.vardbs.base.VCFHeaderExtender
    • de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVCFHeaderExtender
    • de.charite.compbio.jannovar.vardbs.exac.ExacVCFHeaderExtender
    • de.charite.compbio.jannovar.vardbs.uk10k.UK10KVCFHeaderExtender

Interface Hierarchy

• java.lang.AutoCloseable
  • java.io.Closeable
    • de.charite.compbio.jannovar.mendel.filter.VariantContextProcessor
  • de.charite.compbio.jannovar.mendel.filter.VariantContextProcessor
• de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString
• de.charite.compbio.jannovar.vardbs.base.DBAnnotationDriver
• de.charite.compbio.jannovar.pedigree.compatibilitychecker.InterfaceVariantContextCompatibilityChecker
• de.charite.compbio.jannovar.impl.intervals.IntervalEndExtractor<T>
• de.charite.compbio.jannovar.impl.parse.TranscriptParser
• de.charite.compbio.jannovar.reference.TranscriptSupportLevels
• de.charite.compbio.jannovar.vardbs.base.VariantContextToRecordConverter<RecordType>
• de.charite.compbio.jannovar.reference.VariantDescription

Annotation Type Hierarchy

• de.charite.compbio.jannovar.Immutable (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • de.charite.compbio.jannovar.hgvs.AminoAcidCode
    • de.charite.compbio.jannovar.hgvs.VariantConfiguration
    • de.charite.compbio.jannovar.hgvs.SequenceType
    • de.charite.compbio.jannovar.hgvs.nts.change.NucleotideMiscChangeType
    • de.charite.compbio.jannovar.hgvs.protein.change.ProteinMiscChangeType
    • de.charite.compbio.jannovar.hgvs.legacy.LegacyLocationType
    • de.charite.compbio.jannovar.JannovarOptions.Command
    • de.charite.compbio.jannovar.mendel.ModeOfInheritance
    • de.charite.compbio.jannovar.mendel.ChromosomeType
    • de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser.GFFVersion
    • de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord.Strand
    • de.charite.compbio.jannovar.annotation.PutativeImpact
    • de.charite.compbio.jannovar.annotation.AnnotationLocation.RankType
    • de.charite.compbio.jannovar.annotation.VariantEffect
    • de.charite.compbio.jannovar.annotation.OldVariantType
    • de.charite.compbio.jannovar.annotation.AnnotationMessage
    • de.charite.compbio.jannovar.pedigree.Sex
    • de.charite.compbio.jannovar.pedigree.Genotype
    • de.charite.compbio.jannovar.pedigree.Disease
    • de.charite.compbio.jannovar.reference.Strand
    • de.charite.compbio.jannovar.reference.GenomeVariantType
    • de.charite.compbio.jannovar.reference.PositionType
    • de.charite.compbio.jannovar.htsjdk.InfoFields
    • de.charite.compbio.jannovar.vardbs.base.DBAnnotationOptions.MultipleMatchBehaviour
    • de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVariantSuspectReasonCode
    • de.charite.compbio.jannovar.vardbs.dbsnp.DBSNPVariantAlleleOrigin
    • de.charite.compbio.jannovar.vardbs.exac.ExacPopulation