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>)
- 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.probablility.Binomial
- org.snpeff.fileIterator.BinSeqFileIterator<T> (implements java.lang.Iterable<T>, java.util.Iterator<E>)
- 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.interval.CircularCorrection
- org.snpeff.probablility.CochranArmitageTest
- org.snpeff.binseq.coder.Coder (implements java.io.Serializable)
- org.snpeff.interval.codonChange.CodonChange
- 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.util.Diff
- org.snpeff.pdb.DistanceResult
- org.snpeff.binseq.DnaSequenceByte
- org.snpeff.util.Download
- org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- org.snpeff.reactome.Entity (implements java.lang.Comparable<T>)
- 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.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.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.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.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.GoogleLineChart
- org.snpeff.stats.plot.GooglePlot
- org.snpeff.stats.plot.GooglePlotInt
- 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.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.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.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.NeedlemanWunschOverlap
- org.snpeff.nextProt.NextProtDb
- org.snpeff.nextProt.NextProtMarkerFactory
- org.snpeff.nextProt.NextProtSequenceConservation
- org.snpeff.nextProt.NextProtXmlNode
- org.snpeff.nmer.Nmer
- org.snpeff.nmer.NmerCount (implements java.io.Serializable)
- org.snpeff.probablility.NormalDistribution
- org.snpeff.stats.ObservedOverExpected
- 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.overlap.Overlap<S>
- 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.PlinkMap
- org.snpeff.PromoterSequences
- org.snpeff.snpEffect.ProteinFastaWriter
- org.snpeff.pdb.ProteinInteractions
- org.snpeff.snpEffect.PurityChange
- org.snpeff.motif.Pwm
- 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)
- org.snpeff.stats.ReadsOnMarkersModel
- org.snpeff.RegulationConsensusMultipleBed
- org.snpeff.RegulationFileConsensus
- org.snpeff.RegulationFileSplitBytType
- org.snpeff.probablility.bootstrap.ReSampleInt
- 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.gsa.ScoreList
- org.snpeff.complexity.SequenceComplexity
- org.snpeff.binseq.indexer.SequenceIndexer<T> (implements java.util.Comparator<T>, java.lang.Iterable<T>)
- org.snpeff.binseq.comparator.SequenceReference
- org.snpeff.overlap.SequenceRotator
- org.snpeff.SnpEff (implements org.snpeff.snpEffect.commandLine.CommandLine)
- org.snpeff.snpEffect.SnpEffectPredictor (implements java.io.Serializable)
- org.snpeff.snpEffect.factory.SnpEffPredictorFactory
- org.snpeff.spliceSites.SpliceTypes
- org.snpeff.align.StringDiff
- org.snpeff.binseq.comparator.SubsequenceComparator<T>
- org.snpeff.svg.Svg
- org.snpeff.fileIterator.TableFile (implements java.io.Serializable)
- org.snpeff.ped.TfamEntry (implements java.lang.Comparable<T>)
- java.lang.Thread (implements java.lang.Runnable)
- 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.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.VcfLof
- org.snpeff.stats.VcfStats (implements org.snpeff.stats.SamplingStats<T>)
- org.snpeff.Zzz