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.data,
- de.charite.compbio.jannovar.data.impl,
- de.charite.compbio.jannovar.datasource,
- de.charite.compbio.jannovar.hgnc,
- 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.impl,
- de.charite.compbio.jannovar.pedigree,
- de.charite.compbio.jannovar.reference
Class Hierarchy
- java.lang.Object
- de.charite.compbio.jannovar.mendel.impl.AbstractMendelianChecker
- de.charite.compbio.jannovar.mendel.impl.InheritanceCheckerMT
- 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.reference.Alignment (implements java.io.Serializable)
- de.charite.compbio.jannovar.reference.AminoAcidChange
- de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer
- de.charite.compbio.jannovar.reference.Anchor (implements java.io.Serializable)
- de.charite.compbio.jannovar.reference.Anchors
- 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.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.datasource.DataSource
- de.charite.compbio.jannovar.datasource.FlatBEDDataSource
- de.charite.compbio.jannovar.datasource.DataSourceFactory
- de.charite.compbio.jannovar.datasource.DatasourceOptions
- de.charite.compbio.jannovar.annotation.builders.DeletionAnnotationBuilder
- de.charite.compbio.jannovar.impl.util.DNAUtils
- 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.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.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.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.impl.parse.gtfgff.GFFParser
- de.charite.compbio.jannovar.reference.HG19RefDictBuilder
- de.charite.compbio.jannovar.hgnc.HGNCParser
- de.charite.compbio.jannovar.hgnc.HGNCRecord
- de.charite.compbio.jannovar.impl.util.IndexedFASTAReader
- 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.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.mendel.MendelianInheritanceChecker
- de.charite.compbio.jannovar.impl.intervals.MutableInterval<T> (implements java.lang.Comparable<T>, java.io.Serializable)
- de.charite.compbio.jannovar.reference.NucleotidePointLocationBuilder
- 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.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
- de.charite.compbio.jannovar.annotation.SVAnnotation (implements java.lang.Comparable<T>)
- de.charite.compbio.jannovar.annotation.builders.SVAnnotationBuilderDispatcher
- de.charite.compbio.jannovar.annotation.SVAnnotations (implements de.charite.compbio.jannovar.reference.SVDescription)
- de.charite.compbio.jannovar.annotation.SVAnnotator
- de.charite.compbio.jannovar.annotation.builders.SVBreakendAnnotationBuilder
- de.charite.compbio.jannovar.annotation.builders.SVCopyNumberVariantAnnotationBuilder
- de.charite.compbio.jannovar.annotation.builders.SVDeletionAnnotationBuilder
- de.charite.compbio.jannovar.annotation.builders.SVDuplicationAnnotationBuilder
- de.charite.compbio.jannovar.reference.SVGenomeVariant (implements de.charite.compbio.jannovar.reference.SVDescription)
- de.charite.compbio.jannovar.reference.SVBreakend
- de.charite.compbio.jannovar.reference.SVCopyNumberVariant
- de.charite.compbio.jannovar.reference.SVDeletion
- de.charite.compbio.jannovar.reference.SVDuplication
- de.charite.compbio.jannovar.reference.SVInsertion
- de.charite.compbio.jannovar.reference.SVInversion
- de.charite.compbio.jannovar.reference.SVMobileElementDeletion
- de.charite.compbio.jannovar.reference.SVMobileElementInsertion
- de.charite.compbio.jannovar.reference.SVTandemDuplication
- de.charite.compbio.jannovar.reference.SVUnknown
- de.charite.compbio.jannovar.annotation.builders.SVInsertionAnnotationBuilder
- de.charite.compbio.jannovar.annotation.builders.SVInversionAnnotationBuilder
- de.charite.compbio.jannovar.annotation.builders.SVMobileElementDeletionAnnotationBuilder
- de.charite.compbio.jannovar.annotation.builders.SVMobileElementInsertionAnnotationBuilder
- de.charite.compbio.jannovar.annotation.builders.SVTandemDuplicationAnnotationBuilder
- java.lang.Throwable (implements java.io.Serializable)
- java.lang.Exception
- 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.datasource.FileDownloadException
- de.charite.compbio.jannovar.mendel.IncompatiblePedigreeException
- de.charite.compbio.jannovar.reference.InvalidCodonException
- de.charite.compbio.jannovar.datasource.InvalidDataSourceException
- 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
- de.charite.compbio.jannovar.annotation.AnnotationException
- java.lang.RuntimeException
- de.charite.compbio.jannovar.reference.InvalidCoordinateException
- de.charite.compbio.jannovar.UncheckedJannovarException
- java.io.IOException
- java.lang.Exception
- 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.TranscriptModelBuilder.AlignmentPart
- de.charite.compbio.jannovar.datasource.TranscriptModelBuilderHGNCExtender
- 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.impl.util.Translator
- de.charite.compbio.jannovar.impl.parse.ucsc.UCSCParser (implements de.charite.compbio.jannovar.impl.parse.TranscriptParser)
- 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
- de.charite.compbio.jannovar.data.impl.VersionComparator (implements java.util.Comparator<T>)
- de.charite.compbio.jannovar.data.impl.VersionTokenizer
- de.charite.compbio.jannovar.mendel.impl.AbstractMendelianChecker
Interface Hierarchy
- de.charite.compbio.jannovar.impl.intervals.IntervalEndExtractor<T>
- de.charite.compbio.jannovar.reference.SVDescription
- de.charite.compbio.jannovar.impl.parse.TranscriptParser
- de.charite.compbio.jannovar.reference.TranscriptSupportLevels
- 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.hgnc.AltGeneIDType
- de.charite.compbio.jannovar.annotation.AnnotationLocation.RankType
- de.charite.compbio.jannovar.annotation.AnnotationMessage
- de.charite.compbio.jannovar.mendel.ChromosomeType
- de.charite.compbio.jannovar.pedigree.Disease
- de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord.Strand
- de.charite.compbio.jannovar.reference.GenomeVariantType
- de.charite.compbio.jannovar.pedigree.Genotype
- de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser.GFFVersion
- de.charite.compbio.jannovar.mendel.ModeOfInheritance
- de.charite.compbio.jannovar.annotation.OldVariantType
- de.charite.compbio.jannovar.reference.PositionType
- de.charite.compbio.jannovar.annotation.PutativeImpact
- de.charite.compbio.jannovar.impl.parse.refseq.RefSeqFastaRecordIdFormat
- de.charite.compbio.jannovar.pedigree.Sex
- de.charite.compbio.jannovar.reference.Strand
- de.charite.compbio.jannovar.mendel.SubModeOfInheritance
- de.charite.compbio.jannovar.reference.SVBreakend.Side
- de.charite.compbio.jannovar.reference.SVDescription.Type
- de.charite.compbio.jannovar.annotation.VariantEffect
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)