# Hierarchy For All Packages

Package Hierarchies:

- org.snpeff,
- org.snpeff.align,
- org.snpeff.binseq,
- org.snpeff.binseq.coder,
- org.snpeff.binseq.comparator,
- org.snpeff.binseq.indexer,
- org.snpeff.codons,
- org.snpeff.collections,
- org.snpeff.complexity,
- org.snpeff.coverage,
- org.snpeff.fastq,
- org.snpeff.fileIterator,
- org.snpeff.fileIterator.microCosm,
- org.snpeff.fileIterator.parser,
- org.snpeff.filter,
- org.snpeff.genBank,
- org.snpeff.geneOntology,
- org.snpeff.geneSets,
- org.snpeff.geneSets.algorithm,
- org.snpeff.genotypes,
- org.snpeff.gsa,
- org.snpeff.gtex,
- org.snpeff.interval,
- org.snpeff.interval.codonChange,
- org.snpeff.interval.tree,
- org.snpeff.logStatsServer,
- org.snpeff.motif,
- org.snpeff.nextProt,
- org.snpeff.nmer,
- org.snpeff.osCmd,
- org.snpeff.outputFormatter,
- org.snpeff.overlap,
- org.snpeff.pdb,
- org.snpeff.ped,
- org.snpeff.probablility,
- org.snpeff.probablility.bootstrap,
- org.snpeff.reactome,
- org.snpeff.reactome.events,
- org.snpeff.sam,
- org.snpeff.serializer,
- org.snpeff.snpEffect,
- org.snpeff.snpEffect.commandLine,
- org.snpeff.snpEffect.factory,
- org.snpeff.spliceSites,
- org.snpeff.stats,
- org.snpeff.stats.plot,
- org.snpeff.svg,
- org.snpeff.util,
- org.snpeff.vcf

## Class Hierarchy

- java.lang.Object
  - java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    - java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      - org.snpeff.collections.AutoHashMap<K,V>
        - org.snpeff.stats.CoverageByType
      - org.snpeff.collections.MultivalueHashMap<K,V>
  - org.snpeff.spliceSites.AcgtTree
  - org.snpeff.stats.AlleleCountStats (implements org.snpeff.stats.SamplingStats<T>)
  - org.snpeff.collections.ArrayUtil
  - org.snpeff.stats.Average
  - org.snpeff.stats.AverageInt
  - org.snpeff.overlap.BasesChangeCounter
  - org.snpeff.binseq.BinarySequence (implements java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
    - org.snpeff.binseq.DnaAndQualitySequence
      - org.snpeff.binseq.DnaAndQualitySequenceWithId
    - org.snpeff.binseq.DnaSequence
      - org.snpeff.binseq.DnaNSequence
      - org.snpeff.binseq.DnaSequenceId
    - org.snpeff.binseq.DnaSequencePe
  - org.snpeff.probablility.Binomial
  - org.snpeff.fileIterator.BinSeqFileIterator<T> (implements java.lang.Iterable<T>, java.util.Iterator<E>)
    - org.snpeff.fileIterator.DnaSeqFileIterator
    - org.snpeff.fileIterator.DnaSeqIdFileIterator
    - org.snpeff.fileIterator.DnaSeqPeFileIterator
  - org.snpeff.collections.BitUtil
  - org.snpeff.fileIterator.BlastResultEntry (implements java.lang.Comparable<T>)
  - org.snpeff.stats.BooleanMutable
  - org.snpeff.interval.ChromosomeSimpleName
  - org.snpeff.gsa.ChrPosScoreList
  - org.snpeff.stats.ChrPosStats
    - org.snpeff.stats.PosStats
  - org.snpeff.interval.CircularCorrection
  - org.snpeff.probablility.CochranArmitageTest
  - org.snpeff.binseq.coder.Coder (implements java.io.Serializable)
    - org.snpeff.binseq.coder.DnaCoder
      - org.snpeff.binseq.coder.DnaQualityCoder
  - org.snpeff.interval.codonChange.CodonChange
    - org.snpeff.interval.codonChange.CodonChangeIns
    - org.snpeff.interval.codonChange.CodonChangeInterval
    - org.snpeff.interval.codonChange.CodonChangeInv
    - org.snpeff.interval.codonChange.CodonChangeMnp
      - org.snpeff.interval.codonChange.CodonChangeMixed
    - org.snpeff.interval.codonChange.CodonChangeSnp
    - org.snpeff.interval.codonChange.CodonChangeStructural
      - org.snpeff.interval.codonChange.CodonChangeDel
      - org.snpeff.interval.codonChange.CodonChangeDup
  - org.snpeff.codons.CodonTable
  - org.snpeff.codons.CodonTables (implements java.lang.Iterable<T>)
  - org.snpeff.util.CombinatorialIterator (implements java.lang.Iterable<T>, java.util.Iterator<E>)
  - org.snpeff.geneOntology.CompareByValue (implements java.util.Comparator<T>)
  - org.snpeff.geneSets.CompareByValue (implements java.util.Comparator<T>)
  - org.snpeff.snpEffect.Config (implements java.lang.Iterable<T>, java.io.Serializable)
  - org.snpeff.stats.CountByKey<T> (implements java.io.Serializable)
  - org.snpeff.stats.CountByType (implements java.io.Serializable)
  - org.snpeff.stats.Counter
  - org.snpeff.stats.CounterDouble
  - org.snpeff.coverage.CountFragments (implements java.io.Serializable)
  - org.snpeff.coverage.CountReads
  - org.snpeff.coverage.CountReadsOnMarkers
  - org.snpeff.coverage.Coverage (implements java.io.Serializable)
  - org.snpeff.coverage.CoverageChr (implements java.io.Serializable)
  - org.snpeff.nextProt.CvTerm
  - org.snpeff.interval.CytoBands
  - org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    - org.snpeff.nextProt.NextProtHandler
  - org.snpeff.util.Diff
  - org.snpeff.pdb.DistanceResult
  - org.snpeff.binseq.DnaSequenceByte
  - org.snpeff.util.Download
  - org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
    - org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
      - org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
        - org.snpeff.geneSets.algorithm.FisherPValueGreedyAlgorithm
          - org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
        - org.snpeff.geneSets.algorithm.RankSumPValueGreedyAlgorithm
    - org.snpeff.geneSets.algorithm.FisherPValueAlgorithm
    - org.snpeff.geneSets.algorithm.NoneAlgorithm
    - org.snpeff.geneSets.algorithm.RankSumPValueAlgorithm
  - org.snpeff.reactome.Entity (implements java.lang.Comparable<T>)
    - org.snpeff.reactome.Compartment
    - org.snpeff.reactome.events.Event
      - org.snpeff.reactome.events.Reaction
        - org.snpeff.reactome.events.BlackBoxEvent
        - org.snpeff.reactome.events.CatalystActivity
        - org.snpeff.reactome.events.Complex (implements java.lang.Iterable<T>)
        - org.snpeff.reactome.events.Depolymerisation
        - org.snpeff.reactome.events.Pathway (implements java.lang.Iterable<T>)
        - org.snpeff.reactome.events.Polymerisation
  - org.snpeff.interval.ExonSpliceCharacterizer
  - org.snpeff.Fastq2Fastq
  - org.snpeff.fileIterator.FastqFileIterator (implements java.lang.Iterable<T>, java.util.Iterator<E>)
  - org.snpeff.fastq.FastqSplit (implements org.snpeff.snpEffect.commandLine.CommandLine)
  - org.snpeff.fastq.FastqTools
  - org.snpeff.fastq.FastqTrimmer
    - org.snpeff.fastq.FastqTrimmerMedian
      - org.snpeff.fastq.FastqTrimmerAdrian
  - org.snpeff.genBank.Feature (implements java.lang.Iterable<T>)
  - org.snpeff.genBank.FeatureCoordinates
  - org.snpeff.genBank.Features (implements java.lang.Iterable<T>)
    - org.snpeff.genBank.Embl
    - org.snpeff.genBank.GenBank
  - org.snpeff.genBank.FeaturesFile (implements java.lang.Iterable<T>, java.util.Iterator<E>)
    - org.snpeff.genBank.EmblFile
    - org.snpeff.genBank.GenBankFile
  - org.snpeff.vcf.FileIndexChrPos
  - org.snpeff.vcf.FileIndexChrPos.FileRegion
  - org.snpeff.vcf.FileIndexChrPos.LineAndPos
  - org.snpeff.fileIterator.FileIterator<T> (implements java.lang.Iterable<T>, java.util.Iterator<E>)
    - org.snpeff.fileIterator.FastaFileIterator
    - org.snpeff.fileIterator.LineClassFileIterator<T>
      - org.snpeff.fileIterator.BlastResultFileIterator
      - org.snpeff.fileIterator.MatrixEntryFileIterator
      - org.snpeff.fileIterator.microCosm.MicroCosmFileIterator
    - org.snpeff.fileIterator.LineFileIterator
      - org.snpeff.fileIterator.LineSeqFileIterator
    - org.snpeff.fileIterator.MarkerFileIterator<M>
      - org.snpeff.fileIterator.GenericMarkerFileIterator
      - org.snpeff.fileIterator.Gff3FileIterator
      - org.snpeff.fileIterator.MotifFileIterator
      - org.snpeff.fileIterator.RegulationFileIterator
        - org.snpeff.fileIterator.RegulationBedFileIterator
        - org.snpeff.fileIterator.RegulationGffFileIterator
      - org.snpeff.fileIterator.VariantFileIterator
        - org.snpeff.fileIterator.BedFileIterator
        - org.snpeff.fileIterator.BigBedFileIterator
        - org.snpeff.fileIterator.VariantTxtFileIterator
      - org.snpeff.fileIterator.VcfFileIterator (implements org.snpeff.fileIterator.parser.Parser<T>)
      - org.snpeff.fileIterator.VcfHapMapFileIterator
    - org.snpeff.ped.PedFileIterator
    - org.snpeff.fileIterator.SamFileIterator
  - org.snpeff.codons.FindRareAaIntervals
  - org.snpeff.probablility.FisherExactTest
  - org.snpeff.stats.FloatStats
  - org.snpeff.stats.GeneCountByTypeTable (implements java.lang.Iterable<T>, java.io.Serializable)
  - org.snpeff.reactome.GeneIds
  - org.snpeff.interval.Genes (implements java.lang.Iterable<T>, java.io.Serializable)
  - org.snpeff.geneSets.GeneSet (implements java.lang.Comparable<T>, java.lang.Iterable<T>, java.io.Serializable)
  - org.snpeff.geneSets.GeneSets (implements java.lang.Iterable<T>, java.io.Serializable)
    - org.snpeff.geneSets.GeneSetsRanked
  - org.snpeff.geneSets.GeneStats
  - org.snpeff.binseq.GenomicSequences (implements java.lang.Iterable<T>, java.io.Serializable)
  - org.snpeff.genotypes.Genotypes (implements java.io.Serializable)
  - org.snpeff.stats.GenotypeStats (implements org.snpeff.stats.SamplingStats<T>)
  - org.snpeff.genotypes.GenotypeVector (implements java.io.Serializable)
  - org.snpeff.stats.plot.GoogleChartVenn
  - org.snpeff.stats.plot.GoogleGenePercentBar
  - org.snpeff.stats.plot.GoogleGeneRegionChart
    - org.snpeff.stats.plot.GoogleGeneRegionNumExonsChart
  - org.snpeff.stats.plot.GoogleLineChart
    - org.snpeff.stats.plot.GoogleBarChart
  - org.snpeff.stats.plot.GooglePlot
  - org.snpeff.stats.plot.GooglePlotInt
    - org.snpeff.stats.plot.GoogleHistogram
  - org.snpeff.geneOntology.GoTerm (implements java.lang.Comparable<T>, java.lang.Iterable<T>, java.io.Serializable)
  - org.snpeff.geneOntology.GoTerms (implements java.lang.Iterable<T>, java.io.Serializable)
  - org.snpeff.util.Gpr
  - org.snpeff.util.GprHtml
  - org.snpeff.util.GprSeq
  - org.snpeff.gtex.Gtex (implements java.lang.Iterable<T>)
  - org.snpeff.gtex.GtexExperiment
  - org.snpeff.fileIterator.GuessTableTypes
  - org.snpeff.collections.HashLongLongArray
  - org.snpeff.snpEffect.Hgvs
    - org.snpeff.snpEffect.HgvsDna
    - org.snpeff.snpEffect.HgvsProtein
  - org.snpeff.stats.HomHetStats (implements org.snpeff.stats.SamplingStats<T>)
  - org.snpeff.probablility.Hypergeometric
  - org.snpeff.binseq.IdGenerator
  - org.snpeff.gtex.IdMap
  - org.snpeff.pdb.IdMapper
  - org.snpeff.pdb.IdMapperEntry (implements java.lang.Cloneable, java.lang.Comparable<T>)
  - org.snpeff.interval.Interval (implements java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
    - org.snpeff.interval.Marker (implements org.snpeff.serializer.TxtSerializable)
      - org.snpeff.interval.Cds (implements org.snpeff.interval.MarkerWithFrame)
      - org.snpeff.interval.Chromosome
      - org.snpeff.interval.Custom (implements java.lang.Iterable<T>)
        - org.snpeff.interval.GffMarker
          - org.snpeff.interval.Gtf2Marker
      - org.snpeff.interval.Downstream
      - org.snpeff.interval.GenericMarker
      - org.snpeff.interval.Genome (implements java.lang.Iterable<T>)
      - org.snpeff.interval.Intergenic
      - org.snpeff.interval.IntergenicConserved
      - org.snpeff.interval.IntervalAndSubIntervals<T> (implements java.lang.Iterable<T>)
        - org.snpeff.interval.Gene
        - org.snpeff.interval.Transcript
      - org.snpeff.interval.Intron
      - org.snpeff.interval.IntronConserved
      - org.snpeff.interval.MarkerParentId
      - org.snpeff.interval.MarkerSeq
        - org.snpeff.interval.Exon (implements org.snpeff.interval.MarkerWithFrame)
      - org.snpeff.interval.MicroRnaBindingSite
      - org.snpeff.interval.Motif
      - org.snpeff.interval.NextProt
      - org.snpeff.interval.ProteinInteractionLocus
        - org.snpeff.interval.ProteinProteinInteractionLocus
        - org.snpeff.interval.ProteinStructuralInteractionLocus
      - org.snpeff.interval.RareAminoAcid
      - org.snpeff.interval.Regulation
      - org.snpeff.interval.SpliceSite
        - org.snpeff.interval.SpliceSiteAcceptor
        - org.snpeff.interval.SpliceSiteBranch
          - org.snpeff.interval.SpliceSiteBranchU12
        - org.snpeff.interval.SpliceSiteDonor
        - org.snpeff.interval.SpliceSiteRegion
      - org.snpeff.interval.Upstream
      - org.snpeff.interval.Utr
        - org.snpeff.interval.Utr3prime
        - org.snpeff.interval.Utr5prime
      - org.snpeff.interval.Variant
        - org.snpeff.interval.VariantBnd
        - org.snpeff.interval.VariantNonRef
        - org.snpeff.vcf.VariantVcfEntry
        - org.snpeff.interval.VariantWithScore
      - org.snpeff.vcf.VcfEntry (implements java.lang.Iterable<T>)
  - org.snpeff.interval.IntervalComparatorByEnd (implements java.util.Comparator<T>)
  - org.snpeff.interval.IntervalComparatorByStart (implements java.util.Comparator<T>)
  - org.snpeff.interval.tree.IntervalForest (implements java.lang.Iterable<T>, java.io.Serializable)
  - org.snpeff.interval.tree.IntervalNode (implements java.io.Serializable)
  - org.snpeff.interval.tree.IntervalNodeOri (implements java.lang.Iterable<T>, java.io.Serializable)
  - org.snpeff.interval.IntervalSetIterator (implements java.lang.Iterable<T>, java.util.Iterator<E>)
  - org.snpeff.interval.tree.IntervalTree (implements org.snpeff.interval.tree.Itree, java.io.Serializable)
  - org.snpeff.interval.tree.IntervalTreeArray (implements org.snpeff.interval.tree.Itree)
  - org.snpeff.interval.tree.IntervalTreeOri (implements org.snpeff.interval.tree.Itree, java.io.Serializable)
  - org.snpeff.snpEffect.IntHisto
  - org.snpeff.stats.IntStats (implements java.io.Serializable)
  - org.snpeff.util.Iterator2Iterable<T> (implements java.lang.Iterable<T>)
  - org.snpeff.util.IubString (implements java.lang.Iterable<T>, java.util.Iterator<E>)
  - org.snpeff.motif.Jaspar (implements java.lang.Iterable<T>)
  - org.snpeff.util.KeyValue<A,B> (implements java.lang.Comparable<T>)
  - org.snpeff.vcf.LineChrPos (implements java.lang.Comparable<T>)
  - org.snpeff.nextProt.Location
    - org.snpeff.nextProt.LocationTargetIsoform
      - org.snpeff.nextProt.LocationTargetIsoformInteraction
  - org.snpeff.util.Log
  - org.snpeff.snpEffect.LossOfFunction
  - org.snpeff.interval.Markers (implements java.util.Collection<E>, java.io.Serializable)
  - org.snpeff.serializer.MarkerSerializer
  - org.snpeff.coverage.MarkerTypes
  - org.snpeff.interval.MarkerUtil
  - org.snpeff.fileIterator.MatrixEntry
  - org.snpeff.fileIterator.microCosm.MicroCosmEntry
  - org.snpeff.stats.MineMarkerIntervals
  - org.snpeff.stats.MineTwoMarkerIntervals
  - org.snpeff.reactome.Monitor
  - org.snpeff.motif.MotifLogo
  - org.snpeff.align.NeedlemanWunsch
    - org.snpeff.align.SmithWaterman
    - org.snpeff.align.VcfRefAltAlign
  - org.snpeff.align.NeedlemanWunschOverlap
  - org.snpeff.nextProt.NextProtDb
  - org.snpeff.nextProt.NextProtMarkerFactory
  - org.snpeff.nextProt.NextProtSequenceConservation
  - org.snpeff.nextProt.NextProtXmlNode
    - org.snpeff.nextProt.NextProtXmlAnnotation
    - org.snpeff.nextProt.NextProtXmlEntry
    - org.snpeff.nextProt.NextProtXmlIsoform
  - org.snpeff.nmer.Nmer
  - org.snpeff.nmer.NmerCount (implements java.io.Serializable)
    - org.snpeff.nmer.NmerCountWc
  - org.snpeff.probablility.NormalDistribution
  - org.snpeff.stats.ObservedOverExpected
    - org.snpeff.stats.ObservedOverExpectedCHG
    - org.snpeff.stats.ObservedOverExpectedCHH
    - org.snpeff.stats.ObservedOverExpectedCpG
  - org.snpeff.collections.OpenBitSet (implements java.lang.Cloneable, java.io.Serializable)
  - org.snpeff.osCmd.OsCmdQueue (implements java.lang.Iterable<T>)
  - org.snpeff.outputFormatter.OutputFormatter
    - org.snpeff.outputFormatter.BedOutputFormatter
      - org.snpeff.outputFormatter.BedAnnotationOutputFormatter
    - org.snpeff.outputFormatter.VcfOutputFormatter
  - org.snpeff.overlap.Overlap<S>
    - org.snpeff.overlap.OverlapDnaSeq
  - org.snpeff.binseq.indexer.OverlapFilterCompareAllAll (implements org.snpeff.binseq.indexer.OverlapFilter<T>)
  - org.snpeff.binseq.indexer.OverlapFilterDnaId (implements org.snpeff.binseq.indexer.OverlapFilter<T>)
  - org.snpeff.binseq.indexer.OverlapRessult<T>
  - org.snpeff.Pcingola
  - org.snpeff.pdb.PdbFile
  - org.snpeff.pdb.PdbUtil
  - org.snpeff.ped.PedGenotype
  - org.snpeff.vcf.Pedigree (implements java.lang.Iterable<T>)
  - org.snpeff.vcf.PedigreeEntry
  - org.snpeff.ped.PedPedigree (implements java.lang.Comparable<T>, java.lang.Iterable<T>)
    - org.snpeff.ped.PedFamily
  - org.snpeff.ped.PlinkMap
  - org.snpeff.PromoterSequences
  - org.snpeff.snpEffect.ProteinFastaWriter
  - org.snpeff.pdb.ProteinInteractions
  - org.snpeff.snpEffect.PurityChange
  - org.snpeff.motif.Pwm
    - org.snpeff.motif.PwmAndSeqs
  - org.snpeff.Qseq2Fastq
  - org.snpeff.probablility.RandMarker
  - org.snpeff.probablility.RankSumNoReplacementPdf
  - org.snpeff.probablility.RankSumNoReplacementSimulate
  - org.snpeff.probablility.RankSumPdf
  - org.snpeff.reactome.Reactome (implements java.lang.Iterable<T>)
  - java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    - java.io.BufferedReader
      - org.snpeff.fileIterator.SeekableBufferedReader
    - org.snpeff.fileIterator.NullReader
  - org.snpeff.stats.ReadsOnMarkersModel
  - org.snpeff.RegulationConsensusMultipleBed
  - org.snpeff.RegulationFileConsensus
  - org.snpeff.RegulationFileSplitBytType
  - org.snpeff.probablility.bootstrap.ReSampleInt
    - org.snpeff.probablility.bootstrap.ReSampleMap
    - org.snpeff.probablility.bootstrap.ReSampleMapRank
  - org.snpeff.geneSets.Result (implements java.lang.Comparable<T>)
  - org.snpeff.sam.SamEntry
  - org.snpeff.sam.SamHeader (implements java.lang.Iterable<T>)
  - org.snpeff.sam.SamHeaderRecord
    - org.snpeff.sam.SamHeaderRecordSq
  - org.snpeff.gsa.ScoreList
    - org.snpeff.gsa.PvaluesList
  - org.snpeff.complexity.SequenceComplexity
  - org.snpeff.binseq.indexer.SequenceIndexer<T> (implements java.util.Comparator<T>, java.lang.Iterable<T>)
    - org.snpeff.binseq.indexer.SuffixIndexerNmer<T>
  - org.snpeff.binseq.comparator.SequenceReference
  - org.snpeff.overlap.SequenceRotator
  - org.snpeff.SnpEff (implements org.snpeff.snpEffect.commandLine.CommandLine)
    - org.snpeff.snpEffect.commandLine.SnpEffCmdAcat
    - org.snpeff.snpEffect.commandLine.SnpEffCmdBuild
    - org.snpeff.snpEffect.commandLine.SnpEffCmdBuildNextProt
    - org.snpeff.snpEffect.commandLine.SnpEffCmdCds
    - org.snpeff.snpEffect.commandLine.SnpEffCmdClosest
    - org.snpeff.snpEffect.commandLine.SnpEffCmdCount
    - org.snpeff.snpEffect.commandLine.SnpEffCmdDatabases
    - org.snpeff.snpEffect.commandLine.SnpEffCmdDownload
    - org.snpeff.snpEffect.commandLine.SnpEffCmdDump
    - org.snpeff.snpEffect.commandLine.SnpEffCmdEff (implements org.snpeff.snpEffect.VcfAnnotator)
    - org.snpeff.snpEffect.commandLine.SnpEffCmdGenes2Bed
    - org.snpeff.snpEffect.commandLine.SnpEffCmdGsa
    - org.snpeff.snpEffect.commandLine.SnpEffCmdLen
    - org.snpeff.snpEffect.commandLine.SnpEffCmdPdb
    - org.snpeff.snpEffect.commandLine.SnpEffCmdProtein
    - org.snpeff.snpEffect.commandLine.SnpEffCmdSeq
    - org.snpeff.snpEffect.commandLine.SnpEffCmdShow
    - org.snpeff.spliceSites.SnpEffCmdSpliceAnalysis
    - org.snpeff.snpEffect.commandLine.SnpEffCmdTranslocationsReport
  - org.snpeff.snpEffect.SnpEffectPredictor (implements java.io.Serializable)
  - org.snpeff.snpEffect.factory.SnpEffPredictorFactory
    - org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
      - org.snpeff.snpEffect.factory.SnpEffPredictorFactoryEmbl
      - org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenBank
    - org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenesFile
    - org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff
      - org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff2
      - org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGff3
      - org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22
      - org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRand
    - org.snpeff.snpEffect.factory.SnpEffPredictorFactoryKnownGene
    - org.snpeff.snpEffect.factory.SnpEffPredictorFactoryRefSeq
  - org.snpeff.spliceSites.SpliceTypes
  - org.snpeff.align.StringDiff
  - org.snpeff.binseq.comparator.SubsequenceComparator<T>
    - org.snpeff.binseq.comparator.DnaQualSubsequenceComparator
    - org.snpeff.binseq.comparator.DnaSubsequenceComparator<T>
  - org.snpeff.svg.Svg
    - org.snpeff.svg.SvgBnd
    - org.snpeff.svg.SvgCds
    - org.snpeff.svg.SvgExon
    - org.snpeff.svg.SvgGene
    - org.snpeff.svg.SvgIntron
    - org.snpeff.svg.SvgNextProt
    - org.snpeff.svg.SvgScale
    - org.snpeff.svg.SvgSpacer
    - org.snpeff.svg.SvgTranscript
    - org.snpeff.svg.SvgTranslocation
  - org.snpeff.fileIterator.TableFile (implements java.io.Serializable)
  - org.snpeff.ped.TfamEntry (implements java.lang.Comparable<T>)
    - org.snpeff.ped.PedEntry (implements java.lang.Iterable<T>)
  - java.lang.Thread (implements java.lang.Runnable)
    - org.snpeff.osCmd.ExecuteOsCommand (implements org.snpeff.osCmd.Progress)
    - org.snpeff.logStatsServer.LogStats
    - org.snpeff.osCmd.OsCmdRunner
    - org.snpeff.osCmd.StreamGobbler
    - org.snpeff.logStatsServer.VersionCheck
  - org.snpeff.util.Timer
  - org.snpeff.spliceSites.TranscriptSet (implements java.lang.Iterable<T>)
  - org.snpeff.stats.TranslocationReport
  - org.snpeff.stats.TsTvStats (implements org.snpeff.stats.SamplingStats<T>)
  - org.snpeff.util.Tuple<A,B>
  - org.snpeff.snpEffect.VariantEffect (implements java.lang.Cloneable, java.lang.Comparable<T>)
    - org.snpeff.snpEffect.VariantEffectStructural
      - org.snpeff.snpEffect.VariantEffectFusion
  - org.snpeff.filter.VariantEffectFilter (implements org.snpeff.filter.Filter<T>)
  - org.snpeff.snpEffect.VariantEffects (implements java.lang.Iterable<T>)
  - org.snpeff.stats.VariantEffectStats (implements org.snpeff.stats.SamplingStats<T>)
  - org.snpeff.align.VariantRealign
  - org.snpeff.stats.VariantStats (implements org.snpeff.stats.SamplingStats<T>)
  - org.snpeff.stats.VariantTypeStats (implements org.snpeff.stats.SamplingStats<T>)
  - org.snpeff.snpEffect.VcfAnnotatorChain (implements org.snpeff.snpEffect.VcfAnnotator)
  - org.snpeff.vcf.VcfConsequence
  - org.snpeff.vcf.VcfConsequenceHeader
  - org.snpeff.vcf.VcfEffect
  - org.snpeff.vcf.VcfGenotype
  - org.snpeff.vcf.VcfHeader (implements java.io.Serializable)
  - org.snpeff.vcf.VcfHeaderEntry (implements java.io.Serializable)
    - org.snpeff.vcf.VcfHeaderInfo
      - org.snpeff.vcf.VcfHeaderFormat
  - org.snpeff.vcf.VcfLof
    - org.snpeff.vcf.VcfNmd
  - org.snpeff.stats.VcfStats (implements org.snpeff.stats.SamplingStats<T>)
  - org.snpeff.Zzz

## Interface Hierarchy

- org.snpeff.snpEffect.commandLine.CommandLine
  - org.snpeff.snpEffect.VcfAnnotator
- org.snpeff.filter.Filter<T>
- java.lang.Iterable<T>
  - org.snpeff.interval.tree.Itree
- org.snpeff.osCmd.LineFilter
- org.snpeff.interval.MarkerWithFrame
- org.snpeff.binseq.indexer.OverlapFilter<T>
- org.snpeff.fileIterator.parser.Parser<T>
- org.snpeff.osCmd.Progress
- org.snpeff.stats.SamplingStats<T>
- org.snpeff.serializer.TxtSerializable

## Enum Class Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
    - org.snpeff.interval.BioType
    - org.snpeff.snpEffect.EffectType
    - org.snpeff.vcf.EffFormatVersion
    - org.snpeff.geneSets.algorithm.EnrichmentAlgorithm.EnrichmentAlgorithmType
    - org.snpeff.reactome.Entity.TransferFunction
    - org.snpeff.snpEffect.ErrorWarningType
    - org.snpeff.interval.Exon.ExonSpliceType
    - org.snpeff.genBank.Feature.Type
    - org.snpeff.interval.FrameType
    - org.snpeff.interval.Gene.GeneType
    - org.snpeff.interval.GffType
    - org.snpeff.util.Log.FatalErrorBehabiour
    - org.snpeff.logStatsServer.LogStats.RequestResult
    - org.snpeff.reactome.events.Reaction.RegulationType
    - org.snpeff.gsa.ScoreList.ScoreSummary
    - org.snpeff.ped.Sex
    - org.snpeff.SnpEff.GeneDatabaseFormat
    - org.snpeff.SnpEff.InputFormat
    - org.snpeff.SnpEff.OutputFormat
    - org.snpeff.snpEffect.commandLine.SnpEffCmdDump.DumpFormat
    - org.snpeff.interval.TranscriptSupportLevel
    - org.snpeff.interval.Variant.VariantType
    - org.snpeff.snpEffect.VariantEffect.Coding
    - org.snpeff.snpEffect.VariantEffect.EffectImpact
    - org.snpeff.snpEffect.VariantEffect.FunctionalClass
    - org.snpeff.vcf.VcfEntry.AlleleFrequencyType
    - org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
    - org.snpeff.vcf.VcfInfoType