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.snpEffect.testCases,
- org.snpeff.snpEffect.testCases.integration,
- org.snpeff.snpEffect.testCases.unity,
- 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.collections.AutoHashMap<K,
- java.util.HashMap<K,
- 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.binseq.DnaAndQualitySequence
- 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.binseq.coder.DnaCoder
- 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.testCases.integration.CompareEffects
- org.snpeff.snpEffect.testCases.integration.CompareToEnsembl
- org.snpeff.snpEffect.testCases.integration.CompareToVep
- 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.snpEffect.testCases.integration.CreateSpliceSiteTestCase
- 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.FisherPValueGreedyAlgorithm
- org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
- org.snpeff.geneSets.algorithm.FisherPValueAlgorithm
- org.snpeff.geneSets.algorithm.NoneAlgorithm
- org.snpeff.geneSets.algorithm.RankSumPValueAlgorithm
- org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- 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.reactome.events.Reaction
- 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.fastq.FastqTrimmerMedian
- 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.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.GffMarker
- org.snpeff.interval.Downstream
- org.snpeff.interval.GenericMarker
- org.snpeff.interval.Genome (implements java.lang.Iterable<T>, java.io.Serializable)
- org.snpeff.interval.Intergenic
- org.snpeff.interval.IntergenicConserved
- org.snpeff.interval.IntervalAndSubIntervals<T> (implements java.lang.Iterable<T>)
- org.snpeff.interval.Gene (implements java.io.Serializable)
- 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.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.Marker (implements org.snpeff.serializer.TxtSerializable)
- 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.nextProt.LocationTargetIsoform
- 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.outputFormatter.BedOutputFormatter
- 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.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.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
- java.io.BufferedReader
- 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.snpEffect.factory.SnpEffPredictorFactoryFeatures
- org.snpeff.spliceSites.SpliceTypes
- 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.snpEffect.testCases.unity.TestCasesAlign
- org.snpeff.snpEffect.testCases.unity.TestCasesBase
- org.snpeff.snpEffect.testCases.integration.TestCasesAnn
- org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse
- org.snpeff.snpEffect.testCases.unity.TestCasesBaseApply
- org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
- org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
- org.snpeff.snpEffect.testCases.unity.TestCasesApplyMixed
- org.snpeff.snpEffect.testCases.unity.TestCasesApplyMnp
- org.snpeff.snpEffect.testCases.unity.TestCasesApplySnp
- org.snpeff.snpEffect.testCases.unity.TestCasesProteinInteraction
- org.snpeff.snpEffect.testCases.unity.TestCasesBuild
- org.snpeff.snpEffect.testCases.unity.TestCasesCds
- org.snpeff.snpEffect.testCases.unity.TestCasesDels
- org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequence
- org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse
- org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse2
- org.snpeff.snpEffect.testCases.unity.TestCasesFasta
- org.snpeff.snpEffect.testCases.unity.TestCasesFileIndexChrPos
- org.snpeff.snpEffect.testCases.unity.TestCasesHgvs
- org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
- org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDupNegative
- org.snpeff.snpEffect.testCases.unity.TestCasesHgvsProtDup
- org.snpeff.snpEffect.testCases.unity.TestCasesIns
- org.snpeff.snpEffect.testCases.unity.TestCasesIntergenic
- org.snpeff.snpEffect.testCases.unity.TestCasesIntervals
- org.snpeff.snpEffect.testCases.unity.TestCasesIntervalVariant
- org.snpeff.snpEffect.testCases.unity.TestCasesIntStats
- org.snpeff.snpEffect.testCases.unity.TestCasesJaspar
- org.snpeff.snpEffect.testCases.unity.TestCasesMnps
- org.snpeff.snpEffect.testCases.unity.TestCasesSeekableReader
- org.snpeff.snpEffect.testCases.unity.TestCasesSequenceIndexer
- org.snpeff.snpEffect.testCases.unity.TestCasesSnps
- org.snpeff.snpEffect.testCases.unity.TestCasesSpliceRegion
- org.snpeff.snpEffect.testCases.unity.TestCasesSpliceSite
- org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDel
- org.snpeff.snpEffect.testCases.unity.TestCasesStructuralDup
- org.snpeff.snpEffect.testCases.unity.TestCasesStructuralInv
- org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment
- org.snpeff.snpEffect.testCases.unity.TestCasesVcf
- org.snpeff.snpEffect.testCases.unity.TestCasesZzz
- org.snpeff.snpEffect.testCases.unity.TestCasesBinomial
- org.snpeff.snpEffect.testCases.unity.TestCasesChiSquare
- org.snpeff.snpEffect.testCases.unity.TestCasesCircular
- org.snpeff.snpEffect.testCases.unity.TestCasesCochranArmitage
- org.snpeff.snpEffect.testCases.unity.TestCasesCodonTable
- org.snpeff.snpEffect.testCases.unity.TestCasesCytoBands
- org.snpeff.snpEffect.testCases.unity.TestCasesDel
- org.snpeff.snpEffect.testCases.unity.TestCasesDnaNSequence
- org.snpeff.snpEffect.testCases.unity.TestCasesDnaOverlap
- org.snpeff.snpEffect.testCases.unity.TestCasesDnaSequenceByte
- org.snpeff.snpEffect.testCases.unity.TestCasesFisherExactTest
- org.snpeff.snpEffect.testCases.unity.TestCasesGenePvalueList
- org.snpeff.snpEffect.testCases.unity.TestCasesGenomicSequences
- org.snpeff.snpEffect.testCases.unity.TestCasesGenotypeVector
- org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
- org.snpeff.snpEffect.testCases.unity.TestCasesHgvsExon
- org.snpeff.snpEffect.testCases.unity.TestCasesHgvsIntron
- org.snpeff.snpEffect.testCases.unity.TestCasesHypergeometric
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
- org.snpeff.snpEffect.testCases.integration.IntegrationTest
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEff
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEffMultiThread
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationAlphaFold
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationApply
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBuildPdb
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCanonical
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCircularGenome
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCodingTag
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationConfig
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCovid19
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCutsomIntervals
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationDelEtc
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationDup
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEmbl
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationErrors
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationExonFrame
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationFilterTranscripts
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGenBank
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGtf22
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvs
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsDel
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsDnaDup
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsFrameShift
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsHard
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsIns
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsLarge
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsMnps
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsUpDownStream
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationInsEtc
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationInsVep
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLargeDeletion
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationLof
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMarkerSeq
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMissenseSilentRatio
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMnp
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMotif
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNextProt
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNmd
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationNoChange
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationProtein
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationProteinInteraction
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationRefSeq
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationRegulation
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSequenceOntology
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnp
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSnpEnsembl
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationSpliceRegion
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationStructural
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationTranscriptError
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVcfs
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationZzz
- org.snpeff.snpEffect.testCases.integration.IntegrationTest
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGenomicSequences
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationTranscript
- org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTree
- org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeArray
- org.snpeff.snpEffect.testCases.unity.TestCasesIntervalTreeOri
- org.snpeff.snpEffect.testCases.unity.TestCasesIubString
- org.snpeff.snpEffect.testCases.unity.TestCasesMarkerUtils
- org.snpeff.snpEffect.testCases.unity.TestCasesNextProt
- org.snpeff.snpEffect.testCases.unity.TestCasesNmers
- org.snpeff.snpEffect.testCases.unity.TestCasesOverlap
- org.snpeff.snpEffect.testCases.unity.TestCasesReactome
- org.snpeff.snpEffect.testCases.unity.TestCasesStructuralTranslocations
- org.snpeff.snpEffect.testCases.unity.TestCasesVariantDecompose
- org.snpeff.snpEffect.testCases.unity.TestGenome
- org.snpeff.snpEffect.testCases.TestSuiteIntegration
- org.snpeff.snpEffect.testCases.TestSuiteUnity
- org.snpeff.ped.TfamEntry (implements java.lang.Comparable<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.snpEffect.VariantEffectStructural
- 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
- org.snpeff.vcf.VcfHeaderEntry
- org.snpeff.vcf.VcfHeaderInfo
- org.snpeff.vcf.VcfHeaderFormat
- org.snpeff.vcf.VcfHeaderInfo
- org.snpeff.vcf.VcfLof
- org.snpeff.vcf.VcfNmd
- org.snpeff.stats.VcfStats (implements org.snpeff.stats.SamplingStats<T>)
- org.snpeff.Zzz
- java.util.AbstractMap<K,
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
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)